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A classical model of a particle passing double slits
Peifeng Wang

Peifeng Wang

May 05, 2019
A classical model is presented that, due to electric field, when a particle is passing double slits, a self induced force can arise so that the particle is impacted by both slits simultaneously to form concentration varying patterns. While this model may not precisely account for the interference fringes, it raises a question on the origin of the diffraction patterns and imposes restrictions on wave-particle duality.
Hyperexcitable pyramidal neurons embedded in an inhibition-dominated network in the s...

Ellen Brennan

and 3 more

May 02, 2019
AUTHORS:Ellen K.W. Brennan1,2*, Shyam Kumar Sudhakar1*, Izabela Jedrasiak-Cape1 &Omar J. Ahmed1,2,3,4,5
The Neural Circuitry Supporting Successful Spatial Navigation Despite Variable Moveme...
William Sheeran
Omar Ahmed

William Sheeran

and 1 more

May 02, 2019
AUTHORS:William M. Sheeran1,6,7 and Omar J. Ahmed1,2,3,4,5 1Department of Psychology,2Department of Biomedical Engineering,3Neuroscience Graduate Program,4Kresge Hearing Research Institute,5Michigan Center for Integrative Research in Critical Care,6Department of Molecular, Cellular & Developmental Biology,University of Michigan, Ann Arbor, MI 481057Medical Scientist Training Program, University of Colorado School of Medicine, Aurora, CO 80045CORRESPONDENCE: Omar J. Ahmed 4040 East Hall, 530 Church Street, Ann Arbor, MI 48109 ojahmed@umich.edu
Unnamed Article
Marcelo Lisboa Mota

Marcelo Lisboa Mota

May 01, 2019
MODELAGEM DO CAMPO GRAVITACIONAL DE UM CORPO COM DISTRIBUIÇÃO DE MASSA IRREGULAR Marcelo Lisboa Mota \({}^{1}\), Evandro Marconi Rocco\({}^{2}\)\({}^{1}\)Instituto Federal de Educação\({}^{2}\)Instituto Nacional de Pesquisas EspaciaisO objetivo deste trabalho é estabelecer um modelo analítico que reproduza com maior precisão o campo gravitacional em torno de um corpo não esférico, com densidade constante, pois, em razão da irregularidade de sua distribuição de massa, seu potencial apresenta uma perturbação em relação ao campo central. A partir de sua decomposição em elementos tetraédricos e utilizando o método da expansão do potencial em série, obtém-se seu potencial total aproximado, somando os potenciais relativos a cada tetraedro gerado. Tendo em vista verificar a validade desse procedimento, modelou-se o campo gravitacional de um cubo homogêneo unitário utilizando esse método, confrontando os resultados obtidos, com aqueles apresentados pelo modelo exato desse hexaedro, além de compará-los, também, com os resultados obtidos pelo modelo das concentrações de massa. Dessa maneira, comprovou-se a consistência do modelo concebido pelo método da expansão do potencial em série, o qual apresenta a vantagem de expressar o potencial gravitacional por meio de uma função polinomial homogênea, e, portanto, contínua e de fácil manipulação algébrica. De fato, o estudo apresentado aqui, possibilita aplicar esta técnica em corpos com distribuições de massas irregulares, tais como, os asteroides, fornecendo subsídios às análises mais complexas, tais como o estudo de órbitas periódicas ao redor de corpos celestes não esféricos, verificações de suas estabilidades, assim como na trajetória de pouso suave de um veículo espacial.
Locking away toxic metals into tiny holes    
Aaron J. Celestian

Aaron J. Celestian

May 03, 2019
Toxic and radioactive metals left over from the nuclear fuel cycle are of primary concern to the health of humans and the environment.  Why?  Because as the uranium from the reactor core 'burns', it decays to other elements, and leaving a pile of toxic material.  Most of these remaining elements are still radioactive, and of particular concern are cesium (Cs) and strontium (Sr), which have the highest level of radioactivity in the waste.  Check out this HBO show by John Oliver, in a hilariously disturbing portrayal of America's nuclear waste problem, he accurately points out many issues that never seem to go away.  I am deeply concerned by the nation's nuclear waste problem, and I spent a great deal of my career finding ways to safely separate highly radioactive elements, and securely store them for as long as thousands of years.  A recent paper I published looks into how the mineral gaidonnayite (pronounced: gay-don-NAY-ite), a hydrated sodium zirconium silicate, is surprisingly good at absorbing those toxic metals.
Article template makes your main claim in its brief title
Myles Axton

Myles Axton

June 19, 2022
To use the actual template to write an Article, please use this link: https://authorea.com/templates/article_template_for_genetics_genomics_nextSubmissions should be made via the online manuscript tracking system.  For technical help with the submission system, please contact the journal. Initial submission does not need to be formatted to this journal's style  For ease of evaluation and submission, the journal recommends an editable Word .docx or Authorea text document and a single merged PDF that includes all parts of main text and high-resolution figures embedded into the file.  A suitable PDF will be constructed by uploading text and figures using the online manuscript tracking system.  This journal does not impose word count and figure limits.  Table 1 contains the journal’s suggestions so that the manuscript is respectful of reader time and are readable by specialist and generalist alike.AcknowledgementsAuthors should list all funding sources here, please check Open Funder Registry. Contributions and material support from anyone not listed as an author should be acknowledged here, with permission from the contributor. Thanks to anonymous reviewers are not allowed.Conflict of Interest StatementAll authors are required to declare if they have potential conflicts of interest related to the submission, or none. This declaration shall be published. Submitting authors shall confirm all co-authors agree with the final statement.AbstractWhat is known in the field, for a general readership. Define the area and knowledge for a specialist.Explain the motivation and need for the research defined by the gap in existing knowledge.State your main claim or finding . Support that with evidence, statistics and detail, mentioning essential methods and analytical techniques that provided the evidence.State the meaning and significance of your new results for research in the field.End by suggesting realistic immediate implications and uses of your findings in your field and more broadly.IntroductionGive credit to and cite all the primary research publications that lay the background to this work including those to be discussed in the Discussion. Give context as to whether these are essential methods and analytic strategies or experimental findings. Ensure that causation, correlation and conjectureResults Make the main claims in logical order, supported by display items and methodsDiscussion Summarize and evaluate the robustness and meaning of the main findings in light of existing publications. Be skeptical and discuss any limitations of the study and conditions where the results may or may not be applicableMaterials and MethodsMethods and materials transparencyOffer methods used in the analysis, and materials used to conduct the research to any researcher for purposes of reproducing the results or replicating the procedure.  Indicate any restrictions on analytic methods including software, and tools and study materials available to other researchers. Specify how, where and when that material will be available.  If an existing method or tool is used in the research, the authors are responsible for checking the license and state confirmation of permission.To obtain Research Resource Identifiers (RRIDs): Use the Resource Identification Portal .Design and analysis transparencyAuthors are encouraged to review standards for disclosing key aspects of the research design and data analysis at http://www.equator-network.org/ and use those that are relevant for their research. Research reporting standards are widely adopted in our field, and exceeding their evolving requirements is essential to sustain the impact of genetics and genomics for research and for society.  Here is the current list of reporting standards, vocabularies, models, schemas and databases that we recommend we recommend at FAIRsharing.org.Human studies and research participantsIdentify the ethics committee that approved the human study, and that the study conforms to recognized standards, for example: Declaration of Helsinki; US Federal Policy for the Protection of Human Subjects; or European Medicines Agency Guidelines for Good Clinical Practice. If no formal ethics committee is available, state that the research was carried out in accordance with recognized standards (e.g. the Declaration of Helsinki, as revised in 2013).Images and information from individual participants, including participants from patient registries and databases, will only be published where the authors have obtained the individual's free prior informed consent. Authors do not need to provide a copy of consent forms to the publisher but, in signing the author license to publish, authors are required to confirm that specific informed consent to publish the image has been obtained. Wiley has a standard patient consent form available for authors to use if required. This requirement to obtained informed consent applies whether or not patients are identifiable from the information presented in the submission.Animal studiesFor submissions involving animal studies, state the protocol and procedures employed were ethically reviewed and approved, and the name of the organization giving approval. State whether experiments were performed in accordance with relevant institutional and national guidelines and regulations for the care and use of laboratory animals:US authors should cite compliance with the US National Research Council's Guide for the Care and Use of Laboratory Animals, the US Public Health Service's Policy on Humane Care and Use of Laboratory Animals, and Guide for the Care and Use of Laboratory Animals.UK authors should conform to UK legislation under the Animals (Scientific Procedures) Act 1986 Amendment Regulations (SI 2012/3039).EU authors should conform to Directive 2010/63/EU.Cell line authentication Declare where the cells were obtained, whether the cell lines have been tested and authenticated and the method by which the cells were tested. If cells were obtained directly from a cell bank that performs cell line characterizations and passaged in the user’s laboratory for fewer than 6 months after receipt or resuscitation, re-authentication is not required. Data Availability StatementPlease choose text from Table 3 and provide a citation to available data in the References list. These sequence data have been submitted to the DDBJ/EMBL/GenBank databases under accession number XXXXX  Gene expression data (derived from microarrays or sequencing) has been deposited to a MIAME- or MINSEQE-compliant public repository like the Gene Expression Omnibus (GEO) with accession XXXXXProtein Sequence Data should be submitted to UniProt with accession XXXXXReferences [terms in brackets will be removed before publication]1. [article] Wood WG, Eckert GP, Igbavboa U, Muller WE. Statins and neuroprotection: a prescription to move the field forward. Ann N Y Acad Sci 2010; 1199:69-76. 2. [book] Hoppert, M. Microscopic techniques in biotechnology. Weinheim: Wiley-VCH; 2003.3. [dataset]Authors; Year; Dataset title; Data repository or archive; Version (if any); Persistent identifier (e.g. DOI)4. [URI, GWAS summary statistics] Savage, J.E. et al. Genome-wide association meta-analysis in 269,867      individuals identifies new genetic and functional links to intelligence      https://www.ebi.ac.uk/gwas/studies/GCST006250 (2018)5. [supplementary data] Jagadeesan, A. et al. MDS/PCA plots within West Africa    https://doi.org/10.6084/m9.figshare.5640931 (2017)Tables (each table complete with title and footnotes)      
                  Phytochemical  Composition of Various Parts of Moringa oleifera Tre...
YOONSUNG JUNG

YOONSUNG JUNG

April 29, 2019
Moringa oleifera (Fam. - Moringaceae), commonly known as Drumstick in English, is a tree that grows widely in the tropics and subtropics of Asia, Africa and Caribbean. This plant is known to have tremendous benefits not only to improve health, but also for the treatment and/or prevention of many diseases including diabetes, heart disease, arthritis, liver disease, and digestive disorder. The objective of this study is to determine the phytochemical composition of leaves, stems, seeds, pods and roots of Moringa oleifera grown in Texas. Approximately, 70-80 mg plant samples were analyzed for CHNS concentration using vario MACRO cube. One gram of Moringa oleifera leaves were extracted using Accelerated Liquid Extractor (ASE 350) with hexane and nitric acid solvent. Then extracted samples were used to analyze volatile components of Moringa oleifera using GCMS and cations/metals using ICP. Moringa oleifera was found to contain a lot of phytochemicals such as Heptacosane, Nonacosane, Tetracosane and some more.
Neural circuits linking sleep and addiction: animal models to understand why select i...
Allison Ahrens
Omar Ahmed

Allison M. Ahrens

and 1 more

April 24, 2019
Authors:Allison M. Ahrens1 & Omar J. Ahmed1,2,3,4,5
Ensuring You’re Healthy While Working At Your Desk
Andy Morton

Andy Morton

April 24, 2019
As an office worker, you are likely to spend extended periods at your desk, staring at a computer screen. For those of us who have been in the game for a long time, this way of working might stretch all the way back to university and beyond. Unsurprisingly, research has shown that sedentary working habits can have an adverse effect on our health in the long term. In a number of white-collar industries, many of us are expected to work an 80-hour week mainly at our desks. If you want to ensure you stay healthy while working an office job, here are a few tips to help you on your way.Cycle or Walk to WorkHealthy work habits can begin with your commute. One of the best ways to keep yourself fit and save money/the environment in the long term is to cycle to work where possible. Many cities are evolving to become more cycle-friendly, and the government’s cycle to work scheme can help you to get a bike through work at a discounted rate. While not all of us will live close enough for this to be a viable option, you could even look at taking public transport part of the way there, keeping you and your bank balance healthy. Keep a Healthy Office DietIn the UK, we have problems with eating properly at lunchtime. There is a work culture across many places that frowns upon people taking extended breaks, and it expects people to work through their lunch, at their desk. This often means a quick lunch consisting of a pre-made sandwich or some other kind of fast food. Take the time to make yourself a nutritious lunch and stay away from the pre-made stuff that is often an unhealthy option. Many offices now offer staff free fruit, so make sure you’re taking full advantage of this and staying away from the chocolate and crisps in the vending machine.Sit Properly At Your DeskIn recent years, a great deal of research has been undertaken into the physical effects of working at a desk in the long term. In terms of proper posture and desk height, you should make sure you always sit upright at your computer and have your computer monitors right in your eye line. There are useful guides on preventing back pain that can help you to set up your desk properly. Spending long periods working at a computer can also hurt your eyesight. If your monitors are poorly adjusted or your office is dark, you can be doing yourself real damage in the long term without knowing it. Have a read up on the recommended settings to ensure you aren’t doing yourself any harm. We are increasingly finding ourselves in jobs that require us to be sedentary for extended periods of time. As humans, we are not built to work this way day-in-day-out, so it is vital that we take steps to remain healthy in our jobs. Sometimes doing something as simple as getting up from your desk once an hour for a wander around the office will do you a world of good. Making these little habits part of your routine will help you to maintain a healthy lifestyle in the long-term.
Expression and purification of the Green Fluorescent Protein via immobilized metal io...
Olga Dagmara Sieluzycka

Olga Dagmara Sieluzycka

April 23, 2019
Expression and purification of the Green Fluorescent Protein via immobilized metal ion affinity.Olga D. SieluzyckaSchool of Biological and Chemical Sciences (Fogg Building)Queen Mary University of London Mile End RoadLondon E14NS UKABSTRACT: The aim of the experiment is to express and purify recombinant His-tagged Green Fluorescent Protein (GFP) protein inEscherichia coli (E.coli) using metal affinity chromatography. GFP is an excellent trafficking tool in modern biochemistry. The protein was expressed in E.Coli and introduced to the required organism by a plasmid transformation. Plasmid containing the GFP was controlled by the T7 promoter had ampicillin resistance and had an N-terminal His6 tag fusion to facilitate the process of purification in the later stages of experiment. The expression of proteins was confirmed by the SDS gel by comparing the bands widths. The goal of experiment was not fully met.Introduction: The main objective of the experiment is to express and purify recombinant His tagged, Green Fluorescent Protein (GFP). GFP is a protein native to a jellyfish, Aequorea Victoriaand due to its remarkable fluorescence it has a vast amount of applications in modern biochemistry such as in vivo labelling and visualization of cells structures. Since the GFPs fluorescence disturbed by unfavorable conditions can recover in the correct pH and temperature it is incredibly useful in molecular biology and its ability to track “real time” changes in cells with a “naked eye” captured the attention of various researchers. (Wu et al., 2008) Another big advantage of using GFP over other molecular trackers is that it does not require any substrates or cofactors has a low toxicity towards examined cells and does not alter the localization of its fusion partner. (Kumar et al., 2016)
IKEA's Challenges and Opportunities In Asia
Benjamin Etukudoh
Esther Joe - Daniel Joe

Benjamin Etukudoh

and 1 more

April 22, 2019
Introduction.Large organizations like IKEA would equally face challenges like those faced by smaller market players especially when attempting to penetrate new markets. More so when the language, culture and legal requirements are very different from where she comes from or origin. The opportunities and challenges in the new country determine managerial and marketing strategies that must be employed by any company on the growth journey.In the sections that follow, first, an attempt is made to analyze the opportunities and challenges for IKEA in their market operations in China, an emerging market as well as Japan which was a more advanced economy. The entry strategies are also being analyzed, key considerations and strategies for market entries are presented. IKEA’s product, pricing, marketing communication and distribution decisions and how the selected options addressed the identified challenges is discussed.Finally, my opinion on what would be IKEA’s marketing strategy in future in order to gain and sustain market shares thereby increasing shareholder value is presented.
Visualizing the Ergosphere from Supermassive Black Hole M87 shadow image taken by Ev...
Alan Gómez

Alan Gómez

August 18, 2019
Using a free image editing software, GIMP, by applying edge filters we show a possible real shape of the nearly region of the event horizon, what could actually be in contact with the ergosphere of M87 Supermassive Black Hole; images  are in high quality from Event Horizon Telescope Collaboration on april 11th 2019 papers.
Editor's review: “CoRR — The Cloud of Reproducible Records”
Lorena A. Barba

Lorena A. Barba

April 13, 2019
SummaryThis is the editor’s review of manuscript CiSESI-2018-02-0016: “CoRR — The Cloud of Reproducible Records,” submitted to Computing in Science and Engineering Reproducible Research (RR) Track. We requested via email to the corresponding author that a preprint be made available on arXiv or an equivalent service, but did not receive a reply. It is policy of the RR Track to require a preprint; see our launch editorial \citep*{Barba_2017}.
Aged Tissues Bear the Hallmarks of Chronic Inflammation
Alison Liu

Alison Liu

April 11, 2019
Chronic inflammation has been associated with numerous diseases, and many old people suffer from chronic inflammatory illnesses; however, the connections between age and inflammation are still obscure.Aging is marked by an overall decline of tissue and cellular functions. At the cellular level, it is accompanied with damages to DNA, RNA, and impairments of protein functions. Organisms can detect these damages and elicit innate immune responses to remove aged, dying or dead cells, and cell debris from tissues. However, as the cells of innate immunity age, their reduced energy production may hinder the clearance processes, which require energy, thus, the persistence of this debris in tissues, resulting in subsequent inflammatory responses. Cytokines accumulated during inflammation could further deteriorate local tissues and accelerate the aging process.Benayoun et al. \cite{Benayoun_2019} used machine learning that is capable of data-training, self-improvement, and prediction to investigate epigenomic (three histone marks) and transcriptomic landscapes in mice during the aging process and generated by far the largest datasets, using multiple tissues such as heart, liver, cerebellum, olfactory bulb, and primary culture of neural stem cells from young, middle-aged, and old mice. The researchers determined epigenomic states that could predict transcriptional changes at specific genomic loci during aging. They found that, in all examined tissues, the interferon response pathway was robustly activated, perhaps to detect DNA damages and the expression of retrovirus-like transposons, and that multiple innate immune pathways were also upregulated significantly. These results strongly supported the conclusion that inflammation is a commonly shared hallmark for vertebrate aging tissues.If we can reduce or prevent the inflammation process, aged tissues may be rejuvenated and prolonged for their normal functions. These transcription factors provide potential targets for pharmaceutical development and therapeutic strategies for healthy aging.Author ORCiDAlison Liu https://orcid.org/0000-0003-0171-6441
Single-Cell Sequencing of Mitochondrial Mutations Traces Human Cell Lineages
Alison Liu

Alison Liu

April 11, 2019
A new method  \cite{Ludwig_2019} traces the cellular relationship and hierarchies (the “pedigrees”) of human cells within the body by reading the DNA sequences of hundreds to thousands of mitochondria extracted from single cells.Various genetic labeling techniques have been developed for lineage tracing in other model organisms. However, the above techniques are not applicable in intact humans. Cell lineage tracing is the most direct way to understand the development of complex cell types and their relationships in an organism, and an important method to trace abnormal cells over time to monitor developmental mosaicism, as demonstrated in C. elegans . In mammals, cell lineage tracing is particularly important for tracing cancer cells and their migration because cancers present special difficulties due to fast-paced proliferation and sequential genetic mutations. Lineage tracing can also determine if transplantation is successful and transplanted cells or tissues are on the correct site.The researchers showed that single-cell RNA sequencing (RNA-seq) and transposase accessible chromatin sequencing (ATAC-seq) methods could be used in combination to trace the inheritance of mitochondrial mutations, chromosomal states, and gene expressions at the same time, in multiple human cell colonies obtained from cultured cells, multiple human tissues, tumor cells, and transplanted cells.  ATAC-seq detects the regions of chromosomes that are not wrapped into nucleosomes by histone proteins, thus defining cellular or chromosomal states.  Using this method, they identified large numbers of mitochondrial DNA mutations and heteroplasmy (the presence of different types of mitochondrial genomes) that were associated with specific cell populations, tissues, or individuals. These experiments led to an important conclusion that mitochondrial mutations were inherited in the cellular colonies with extensive divisions stably and without being affected by cellular or chromosomal state, and the high mutation rate in mitochondrial DNA allows cellular sub-colonies to be traced with high resolution.Thus, the single-cell sequencing of mitochondrial DNA mutations provides a method that is much more accurate, stable, and affordable than a single-cell genome sequencing method to study clonal architecture in human health and diseases.Author ORCiDAlison Liu https://orcid.org/0000-0003-0171-6441
Reading and writing genomes
Myles Axton
Alison Liu

Myles Axton

and 1 more

April 11, 2019
Research in genetics provides the basis for understanding the function and evolution of all living things. The disciplines of reading and writing genomes translate into sustainable economic development with the rational global goals of food security, maternal and child health, precision medicine, education and access to informatics technologies. We believe that many publications in our field are motivated by these goals and contain reusable modular elements that can be recombined both in research and in its translation, to attain them. Open research entails sharing not only the conclusions of science, but its materials, provenance and gestation for the widest reuse by human and computational users. This means that we and our readers deplore any hiding or obscuring datasets or methods, and regret datasets in formally public repositories that have very slow accession or transfer rates. However, we will endeavor to work with all data producers who make contributions in good faith to genetics and genomics research.Genetics & Genomics Next (GGN ) is an Open Research journal from Wiley, published online using the CC-BY 4.0 open attribution license to encourage maximum credit and rapid creative reuse of all scholarly work. We are delighted to receive original research Articles, Resources, Analysis, Technical Reports and Perspectives in the areas of human, animal, plant and microbial genetics, genomics and epigenomics, selecting those reports for peer review that we judge editorially to have the highest research utility, ethical standards and societal impact. As professional, full-time editors at Wiley, we take responsibility for all manuscript decisions and peer reviewer assignment. Our Advisory Board Members have a complementary role to guide GGN’s mission as they see fit, anticipating the evolution of research and standards in our field, and, with us, providing leadership in promoting excellence in open research. Unlike Editorial Board members at some journals, GGN advisors are our mentors, not manuscript editors. We welcome their commitment to the journal for as long as they wish, and advisors may leave or rejoin the board at will.Since we offer an online journal, we are happy to consider reports in any format for peer review, provided they would not burden referees with their unusual length or complexity. We also welcome pre-submission enquiries via our online database (https://mc.manuscriptcentral.com/ggn). Author and dataset contributions and consortium roles can be described via the CRediT contributor taxonomy (https://www.casrai.org/credit.html). We support a range of community standards and databases and the FAIRSharing \cite{Sansone_2019} community standards site (https://fairsharing.org) for best practices and semantic precision. The journal endorses the FAIR \cite{Wilkinson_2016} data principles  (https://www.go-fair.org/fair-principles/) and we recommend database submission of datasets and workflows to replace most of the prior use cases for Supplementary Information.Research Articles should offer a new and substantial conceptual advance based on original experimental research and data, whereas Technical Reports need only detail a useful new method. Perspectives are literature reviews that set standards or propose future strategies in our field. Analysis articles offer opportunity to generate and test new hypotheses by interoperating or reusing existing datasets with new workflows. Resources provide provenance and curation of new datasets that will be of use to the community. If submissions are outside the scope of the journal or if editors consider them premature with respect to their field, we will make customized recommendation for appropriate Wiley journals that would peer review the work or suggest revisions that would typically qualify the work for peer review.Enabling the market for genomics-based ideas needs generosity with rich metadata and careful attention to semantic precision, as well as a sensitive understanding of the legal, ethical and economic underpinning of resources based in the code and the families of living people. For an editor, this means having patience in the face of the many exceptions to the ideal of publicly funded, universal research access to all human, animal and plant genomes and their associated traits and measurements. The resource-benefit balance is ever-present, and legal and ethics frameworks of genetic research evolve slowly in the legacy of past abuses of concepts of heredity. It is therefore essential that we recognize those data license conditions that aim to preserve participation of research subjects, build local resources and capacity and return benefits to the societies that initiated the studies. So, when genetics advances only on the terms of a commercial animal breeder or a security-conscious government, the conclusions and resources offered in the publication need to be maximized for reuse without derailing the sustainable long-term commitment of those producers to make their results available. Even in the sphere of publicly funded data resources in developed countries, it may be networks of excellence (consortia) spanning continents, institutions and generations of diverse funding sources that are the guarantors of the security of the research subjects’ data and the translational success of the research. Publishers looking for a highly cited paper - or data reusers looking to test their new algorithm - need to see where they fit in, and lobby for greater FAIRness from well-funded data generators. Proof of the reuse and interoperability of open research rests with the data users, so data providers need to enable and encourage their work.Author ORCiDsMyles Axton https://orcid.org/0000-0002-8042-4131Alison Liu https://orcid.org/0000-0003-0171-6441
INFORME FINAL DE PROYECTO DE INVESTIGACIÓN: POBREZA Y DESIGUALDAD DEL MACRO-ENTORNO E...
Liz Pérez-Castillo
fernando ivan rojas gamez

Liz Pérez-Castillo

and 2 more

August 28, 2020
Agradecimientos Este trabajo pudo ser realizado gracias al impulso recibido por parte de nuestros padres:Antonio Pérez Fuentes, Sofía Castillo López y Adolfo Flores Horta, Maribel López Delgado y Juan Rojas Silva, Ana Maria Gamez Salazar, para lograr superarnos y tener un futuro mejor.Así como el apoyo constante del maestro Fernando Favela Rosales, recibiendo de su parte críticas constructivas acerca de nuestro proyecto para mejorarlo. Agradecemos sus aportaciones e instrucciones para realizar encuestas adecuadamente, obteniendo resultados precisos.Para nuestros compañeros de clase del 6to semestre, que junto con el maestro, nos brindaron su punto de vista y de esta manera el proyecto tuviera mejor apariencia, mejor estructura, mayor comprensión y una buena redacción.Por último pero no menos importante, agradecemos la participación del maestro Andrew Ayala  por haber  revisado nuestro proyecto e indicarnos errores, ventajas y desventajas, brindando su conocimiento para poder dar una mejor forma.Resumen En este trabajo se exponen algunas reflexiones teóricas básicas que relacionan el crecimiento económico con cambios en la desigualdad en el ingreso de la población, se revisan las investigaciones realizadas previamente a la población y se analiza el comportamiento de esas variables en la cabecera municipal mediante datos representativos en gráficas e imágenes; asimismo se concluye con una breve explicación de propuestas relacionadas con mecanismos dirigidos a la población más pobre.Introducción“Cualquiera que haya luchado con la pobreza sabe lo extremadamente caro que es ser pobre”-          James A. Baldwin.La desigualdad y la pobreza son dos de los más graves problemas sociales que, en general, resultan de las relaciones históricas que se establecen entre las esferas de la sociedad, el Ingreso Salarial y los servicios básicos. Esos fenómenos se observan a escala mundial entre regiones y países, y al interior de cada uno de éstos como el municipio de Sombrerete Zacatecas. En una línea de investigación se los ha relacionado con algunas dimensiones como el crecimiento económico, la distribución del ingreso, el comportamiento del gasto público y las condiciones sociales analizadas mediante diferentes variables e indicadores. En este trabajo se revisan algunos análisis empíricos asociados a los planteamientos formulados.
Genome-wide association studies of intelligence: a review of the literature
Jinkinson Smith

Jinkinson Smith

June 13, 2019
AbstractThere has long been controversy concerning whether genes influence human intelligence, and if so, which genes influence it, and to what extent. Many genome-wide association studies (GWASs) have attempted to find single nucleotide polymorphisms (SNPs) that are significantly associated with intelligence to shed light on this issue. My aim is to examine whether these studies have generated replicable findings concerning associations between one or more SNPs and variation in intelligence as it has generally been defined. Data on 17 published intelligence GWASs (3 of which reported no associations whatsoever) were downloaded from the GWAS Catalog and analyzed in the current study. Results show a generally low rate of replication: over 87% of the 2,335 included SNPs were reported only once, and only 4 of the 17 studies included follow-up testing in a replication sample. Of these 4, none found any replicable genome-wide significant hits. The literature was also found to be severely lacking in diversity: all study samples in which ancestry was described were of European and/or British ancestry. Additionally, evidence of a "winner's curse" was found: among the minority of SNPs reported more than once, the associated p-value tended to be higher in subsequent studies than in the study in which it was originally reported, corresponding to weaker SNP-intelligence associations in later studies.IntroductionMany studies have previously reported evidence that the trait of human intelligence is under significant genetic influence. Specifically, it has long been estimated that intelligence has a high heritability (i.e. proportion of variation associated with genetic variation), with twin and family studies typically reporting narrow-sense heritability estimates of between 50% and 80%.\cite{Hill_2018} This conclusion, combined with the prevailing interpretation of heritability estimates as reflecting a genetic basis for a given trait, implies that between 50 and 80% of variation in intelligence is due to additive genetic factors specifically. This is because narrow-sense heritability estimates only include additive genetic effects.\cite{Hill_2018}\cite{Plomin_2014}However, genome-wide association studies (GWASs) have generally failed to reveal genes that account for all, or even most, of the reported heritability of intelligence. Instead, genetic variants reported to be associated with intelligence in GWASs invariably have very small effects, typically explaining no more than 1% of trait variance individually.\cite{Plomin_2014} Even when taken together, only about 20% of the heritability of intelligence can be accounted for by known DNA differences.\cite{Plomin_2018} There are two schools of thought to why the heritability of intelligence remains "missing", that is, unable to be accounted for by even the combination of all SNPs known to be associated with intelligence. The first is that the heritability of this trait, like that of most complex traits, is due to many genes of very small effect (e.g. \cite{Chabris_2015}, \cite{Plomin_2012}). The second is that the original estimates of heritability have been inaccurate, thereby misleading researchers into searching for genes to explain the heritability of IQ, when in fact such heritability estimates may be fatally confounded by environmental factors.\cite{Feldman2018} Distinguishing between these possibilities is difficult, but if the first explanation is true, then we should see a relatively high rate of replication of associations, especially with such higher-powered studies as are needed to detect the expected small effects.\cite{Chabris_2015}In this paper I aim to comprehensively assess whether GWASs of intelligence have generated replicable findings. In doing so, I hope to shed light on the extent to which genetic associations with intelligence reported in GWASs are false positives, as is known to be the case with many candidate gene studies,\cite{Chabris_2012} or whether the identified SNPs in GWASs actually contribute to differences in human intelligence. I will also examine other patterns in the GWAS literature on intelligence, such as whether these studies are done on populations of diverse ancestries, and whether there is a "winner's curse" in this literature with earlier studies reporting stronger associations than later ones.\cite{Xiao2009}MethodsOn April 7, 2019, I downloaded all data on the GWAS Catalog\cite{Buniello2019} for the trait of "intelligence" (URL: https://www.ebi.ac.uk/gwas/efotraits/EFO_0004337). This was done simply by clicking the button on the page linked in the previous sentence labeled "Download Catalog Data". I then assessed whether these associations had been replicable across different studies, as well as whether there was significant ancestral diversity in the populations on which the studies were conducted.Functional annotationConveniently, the GWAS Catalog database, and data downloaded from it, includes information about the functional status of each SNP (in the "CONTEXT" column). Specifically, it categorizes each SNP (with exceptions detailed in the "inconsistent reporting" section below) into exactly one of the following categories:
Paving the Way to Open Data    
Yan WU
Elizabeth C Moylan

Yan Wu

and 3 more

March 20, 2019
It  is easy to argue that open data is critical to enabling faster and more effective research discovery. In this article we describe the approach we have taken at Wiley to support open data and FAIR (Findable, Accessible, Interoperable and Reusable) data with the implementation of four data policies: “Encourages”, “Expects”, “Mandates” and “Mandates and Peer Reviews Data.” We describe the rationale for these policies and levels of adoption so far. In the coming months we plan to measure and monitor the implementation of these policies via the publication of data availability statements and data citations. With this information, we’ll be able to celebrate adoption of data-sharing practices by the research communities we work with and serve, and we hope to showcase researchers from those communities leading in open research.
Non-Hermitian quantum physics in cerebral dynamics: Preliminary results

test

and 1 more

June 24, 2019
We propose that cerebral dynamics can be considered as a non-Hermitian quantum system which during a short interval of the cardiac cycle has real eigenvalues. We show that driving the system into PT symmetry is only possible with the help of the active matter changing from a laminar flow into a Ceilidh dance-like flow. During this change, the flow experiences  a transition from broken to unbroken PT symmetries which results in a topological phase. The topological phase is then imparted onto the topological defects which are an essential part of this Ceilidh dance flow. This so-called topological braid could be the basis of topological computing in the brain. Our recent experimental findings in conscious humans have shown that the predicted PT symmetry changes may exist. This is important because it is also related to consciousness underpinning  the computational aspect of the phenomenon. 
Glucose imaging is not just [18F]FDG!            
SRSTT Radiopharmaconnect

SRSTT Radiopharmaconnect

August 06, 2020
by Benjamin RotsteinImaging glucose utilization is a mainstay and the most well-known application of positron emission tomography (PET) imaging. If one had to choose a single tracer that headlines the technology, surely many would select [18F]2-deoxy-2-fluoro-d-glucose ([18F]FDG). But imaging with [18F]FDG does not reflect the total picture of glucose distribution and metabolism in vivo; it mostly tells us about the facilitated glucose transporters GLUTs, and especially GLUT1, which provides basal glucose supply to almost all tissues. Over the last several years, a group out of University of California Los Angeles (UCLA) has been developing radiotracers for the sodium-glucose linked transporters (SGLTs). Methyl [18F]4-deoxy-4-fluoro-α-D-glucosepyranoside ([18F]Me-4FDG) is also a glucose derivative, but is a poor substrate for the GLUTs and has greater affinity for SGLT1 and SGLT2. Similar to [18F]FDG, [18F]Me-4FDG is effectively trapped intracellularly as it is not a substrate for further downstream metabolism and due to low rate of exit through SGLTs.
BU NeuroPreprint JC review of Taxidis et al., 2019 "Emergence of stable sensory and d...
BU NeuroPreprint Journal Club

BU NeuroPreprint Journal Club

March 04, 2019
Emergence of stable sensory and dynamic temporal representations in the hippocampus during working memory Jiannis Taxidis, Eftychios Pnevmatikakis, Apoorva L Mylavarapu, Jagmeet S Arora, Kian D Samadian, Emily A Hoffberg, Peyman Golshani  Posted on Biorxiv,  November 20, 2018 https://doi.org/10.1101/474510 Note: Below is our review of the Biorxiv preprint article by Taxidis and colleagues, "Emergence of stable sensory and dynamic temporal representations in the hippocampus during working memory." There has recently been an interesting discussion about best practices in open peer review. Accordingly, we decided to reach out to the authors with our review prior to posting online. The authors were extremely receptive and engaged and responded to our review. Below our comments are in plain text and author responses are in bold. We are grateful to the Golshani lab, and in particular Jiannis Taxidis, for engaging in open dialogue. Summary In this manuscript, Taxidis et al. recorded sequential activity in CA1 during a delayed olfactory non-match-to-sample task in mice over multiple days. They describe two populations of cells active during the task. One population, termed “odor-cells”, are active during odor delivery and another, termed “time-cells” are active at specific time intervals in the intervening delay between two odor presentations. They showed that classifiers trained on these cells can reliably decode the presented odor and also the time interval on the delay, suggesting that items might be held in working memory by these cells. They also found that odor cells generally are reactivated more across days than time cells, and that temporal and odor information can be reliably extracted (by Bayesian classifiers) up to 5 days later. In additional experiments, the delay was elongated and the authors found that odor cells generally retained their firing field whereas time cells shifted their fields. Over behavioral training, the number of time cells increased as well as odor decoding and temporal interval decoding fidelity, which all correlated to behavioral performance. On the other hand, the number of odor cells stayed relatively constant. Lastly, mice exposed to a passive version of this task with no memory demand showed far fewer time cells and no change in these metrics over days.  The manuscript is a technical tour de force involving complex behavior, learning data, and sophisticated analyses. The results add valuable knowledge to how the hippocampus produces and maintains neural sequences. Particularly interesting is how these sequences evolve while the mice learn the task. Overall, we are excited about this impressive body of data and believe that it would greatly enhance our understanding of encoding mechanisms in the hippocampus. We have several suggestions, though some may have been addressed in the supplemental figures, which we were unable access through the preprint servers.
The effects of forest edge and nest height on nest predation in a U.K. deciduous fore...
Noah Atkin

Noah Atkin

February 28, 2019
It has been previously hypothesised that nest predation is higher at forest edges. This has important conservation implications for the increasingly fragmented U.K. climax community. I aimed to test the generality of this edge effect in a mixed deciduous forest fragment which borders open grassland. Artificial nests containing a combination of quail and plasticine eggs were used, at ground and arboreal levels. I found an overall edge effect on nest predation rates, however this effect was not specifically seen in ground nests. Ground nests experienced significantly higher levels of predation than arboreal nests. I suggest this edge effect is due in part to the steep productivity gradient over the ecotone.
Diversity and Inclusion: Creating an Equitable Future
EarthRates RCN
Katie Kirakosian

EarthRates RCN

and 1 more

March 18, 2020
Myrbo, A. Yacobucci, P. Lundgren, L., Loeffler, S., and Kirakosian, K. (2018) Diversity and Inclusion: Creating an Equitable Future. EarthRates, Minneapolis, MN. https://drive.google.com/file/d/1xW041p44MoXSPmvNLcaBw1UtW4SkIi55/view 
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