Experience and training in field work is a critical component of undergraduate education in ecology, and many university courses incorporate field-based or experiential components into the curriculum in order to provide students hands-on experience. Due to the onset of the COVID-19 pandemic and the sudden shift to remote instruction in the spring of 2020, many instructors of such courses found themselves struggling to identify strategies for developing rigorous field activities that could be completed online, solo, and from a student’s backyard. This case study illustrates the process by which one field-based course, a UC California Naturalist certification course offered at the University of California, Davis, transitioned to fully remote instruction. The transition relied on established, publicly available, online participatory science platforms (e.g., iNaturalist) to which the students contributed data and observations remotely. Student feedback on the course and voluntary continued engagement with the participatory science platforms indicates that the student perspective of the experience was on par with previous traditional offerings of the course. This case study also includes topics and participatory science resources for consideration by other faculty facing a similar transition from group field activities to remote, individual field-based experiences.

In spring of 2012, we studied the feeding habits of snow leopard using a comprehensive approach that combines fecal genetic sampling, macro and microscopic analysis of snow leopard diets and direct observation of Naur and livestock in Kangchenjunga Conservation Area of east Nepal. Out of collected 88 putative snow leopard scat samples from 140 transects (290 km) in 27 (4*4 km2) sampling grid cells, 83% were confirmed to be from snow leopard. The genetic analysis accounted for 19 individual snow leopards (10 male and 9 female) with a mean population size estimate of 24 (95% CI: 19- 29), and an average density of 3.9 snow leopards/100 km2 within 609 km2. Total available prey biomass of Naur and Yak was estimated at 355,236 kg (505 kg yak/km2 and 78 kg Naur/km2). From the available prey biomass, we estimated snow leopards consumed 7% annually which was comprised of wild prey (49%), domestic livestock (45%), and 6% unidentified items. The estimated 47,736 kg Naur biomass gives a snow leopard-Naur ratio of 1: 59 on a weight basis. The proportion of young Naur was estimated at 17%, with an almost double predation rate at 28%. Predators such as common leopard and wolf share the same habitat and might compete with snow leopard for prey which will likely influence future predator-prey associations in KCA. Along with livestock insurance scheme improvement, there needs to be a focus on improved livestock guarding as well as engaging and educating local people to be citizen scientists on the importance of snow leopard conservation, involving them in long-term monitoring programs and promotion of ecotourism.

Dispersal abilities play a crucial role in shaping the extent of population genetic structure, with more mobile species being panmictic over large geographic ranges and less mobile ones organized in meta-populations exchanging migrants to different degrees. In turn, population structure directly influences the coalescence pattern of the sampled lineages, but the consequences on the estimated variation of the effective population size (Ne) over time obtained by means of unstructured demographic models remain poorly understood. However, this knowledge is crucial for biologically interpreting the observed Ne trajectory and further devising conservation strategies in endangered species. Here we investigated the demographic history of four shark species (Carharhinus melanopterus, Carharhinus limbatus, Carharhinus amblyrhynchos, Galeocerdo cuvier) with different degrees of endangered status and life history traits related to dispersal distributed in the Indo-Pacific and sampled off New Caledonia. We compared several evolutionary scenarios representing both structured (meta-population) and unstructured models and then inferred the Ne variation through time. By performing extensive coalescent simulations, we provided a general framework relating the underlying population structure and the observed Ne dynamics. On this basis, we concluded that the recent decline observed in three out of the four considered species when assuming unstructured demographic models can be explained by the presence of population structure. Furthermore, we also demonstrated the limits of the inferences based on the sole site frequency spectrum and warn that statistics based on linkage disequilibrium will be needed to exclude recent demographic events affecting meta-populations.

The sulfur cycle is one of the geochemical element cycles in which microorganisms play a key driving role. The microbial function of soil S cycling in response to desert degradation, however, remains largely unknown. We used metagenomics to analyze the characteristics of microbial communities and their functional genes involved in the S cycles under natural water gradients with three typical halophytes shrubs in the Ebinur Lake Basin Desert, China. Our results showed that the rhizosphere effect, water gradient, and halophyte type played a major role in shaping the S cycle. On the whole, in the rhizosphere type and low water environment, the functional genes involved in the S cycle had high abundance, and the SOX system in Alhagi sparsifolia had a high expression level. In the S cycle network structure, as the soil water content decreased, the complexity in S gene networks increased, showing the characteristics of clustering and high connectivity. Indicates the strengthening mode in microbial interactions with the water content. Interestingly, the negative correlation of the network changed with the water content, and there was more competition among communities under the low water gradient and more cooperation under the high water gradient. Through the correlation between environmental factors and the network, nitrate (NO 3 −) and soil available S (AS) constrained most S gene ecology networks. The key species involved in the S cycle were halophilic microorganisms. These results can enhance the understanding of soil S biogeochemical processes and contribute to the mitigation of desertification by improving soil conservation.

The field of medicine is witnessing an exponential growth of interest in Artificial Intelligence (AI), which enables new research questions and the analysis of larger and new types of data. Nevertheless, applications that go beyond proof of concepts and deliver clinical value remain rare, especially in the field of allergy and immunology. This narrative review provides a fundamental understanding of the core concepts of AI and critically discusses its limitations and open challenges, such as data availability and bias, along with potential directions to surmount them. We provide a conceptual framework to structure AI applications within this field and discuss forefront case examples. Most of these applications of AI and machine learning in allergy concern supervised learning and unsupervised clustering, with a strong emphasis on diagnosis and subtyping. A perspective is shared on guidelines for good AI practice to guide readers in applying it effectively and safely, along with prospects of field advancement and initiatives to increase clinical impact. We anticipate that AI can further deepen our knowledge of disease mechanisms and contribute to precision medicine in allergy.

Background: Transrectal ultrasound biopsy is the preferred method for diagnosing prostate cancer, but it can cause infectious complications as a result of fluoroquinolone resistance. We aimed to explore the potential protective effect of a second rectal enema before biopsy. Methods: Between January 2015 and December 2020, 419 patients were assessed retrospectively. Patients with a history of anticoagulant use, uncontrolled diabetes, urological surgery, prostate biopsy, or recent hospitalization or overseas travel, as well as those with previous prostatitis, were excluded from the study. The patients were subsequently divided into two groups: Group 1 (n=223) had received one enema, on the morning of the biopsy, and Group 2 (n=196) had received two, with the additional enema administered half an hour before the procedure. Results: There was no significant difference between the groups in terms of age, BMI, diabetes, prostate-specific antigen (PSA) level, and prostate size (p=0.076, p=0.489, p=0.265, p=0.193, and p=0.661, respectively) or in relation to cancer detection (p=0.428). The median hospitalization date was significantly higher in Group 1 (p=0.003) as was UTI development (p=0.004). However, there was no significant difference in terms of fever and sepsis (p=0.524 and p=0.548, respectively). Additionally, subgroup analysis demonstrated that UTI was significantly lower in patients with diabetes mellitus who had received a second enema (p=0.004), though there was no significant difference in UTI between the groups in those without diabetes mellitus (p=0.215). Multivariable analysis showed that age and diabetes were significant risk factors for the development of UTI (p=0.002andp=0.003, respectively). Furthermore, the second enema was a significant protective factor for preventing UTI (p<0.001). Conclusion: Older age and the presence of diabetes mellitus are independent risk factors for UTI after prostate biopsy. A second enema procedure before biopsy may protect patients from related infectious complications and could therefore be used as an alternative preventative method.

Accurate and testable species delimitation hypotheses are essential for measuring, surveying and managing biodiversity. Today, taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not necessarily reflect the species history. For instance, what is regarded as one single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to deep within-species mitochondrial divergences with no reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of mitochondrial DNA barcoding can only be addressed with nuclear genomic markers, which are expensive, labour intensive, poorly repeatable, and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved nuclear genetic elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation. This genomic method was assessed using six different bee species complexes suspected to harbour cryptic diversity, mitochondrial introgression, or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1860 homologous nuclear loci and provided explicit species delimitation hypotheses in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, this study provided the first conclusive evidence for both mitochondrial introgression among distinct species, and mitochondrial paraphyly within a single bee species.

Objectives: Although albuterol, the most frequently used bronchodilator, has been traditionally and generally delivered via nebulization (NEB) with compressed air/oxygen, the benefits of metered‐dose inhalers with a spacer (MDI+S) have been widely recognized as an alternative method for albuterol administration. The aim of this systematic review was to compare the response to albuterol delivered through NEB with albuterol delivered through MDI+S in pediatric patients with asthma exacerbations. Methods: We conducted an electronic search in MEDLINE/PubMed, EMBASE, Ovid and ClinicalTrials. To be included in the review, a study had to a randomized clinical trial comparing albuterol delivered via NEB versus MDI+S; and had to report the rate of hospital admission (primary outcome), or any of the following secondary outcomes: oxygen arterial saturation, heart rate (HR), respiratory rate, the pulmonary index score (PIS), adverse effects, and need for additional treatment. Results: Fifteen studies (n=2057) met inclusion criteria. No significant differences were found between the two albuterol delivery methods in terms of hospital admission (RR 0.89; 95% CI 0.55 to 1.46; I2=32%; p=0.65). There was a significant reduction in the PIS score (MD -0.63; 95% CI -0.91 to -0.35; I2=0%; p < 0.00001), and a significantly smaller increase in HR (better) (MD -6.47; 95% CI -11.69 to -1.25; I2=0%; p=0.02) when albuterol was delivered through MDI+S than when it was delivered through NEB. Conclusions: This review showed a significant reduction in the PIS and a significantly smaller increase in HR when albuterol was delivered through MDI+S than when it was delivered through NEB.

Introduction: Human atria comprise distinct epicardial layers, which can bypass endocardial layers and lead to downstream centrifugal propagation at the “epi-endo” connection. We sought to characterize anatomical substrates, electrophysiological properties, and ablation outcomes of “pseudo-focal” atrial tachycardias (ATs), defined as macroreentrant ATs mimicking focal ATs. Methods and Results: We retrospectively analyzed ATs showing centrifugal propagation with post-pacing intervals (PPIs) after entrainment pacing suggestive of a macroreentry. A total of 26 patients had pseudo-focal ATs consisting of 15 perimitral, 7 roof-dependent, and 5 cavotricuspid isthmus (CTI)-dependent flutters. A low-voltage area was consistently found at the collision site and co-localized with epicardial layers like the: (1) coronary sinus-great cardiac vein bundle (22%); (2) vein of Marshall bundle (15%); (3) Bachmann bundle (22%); (4) septopulmonary bundle (15%); (5) fossa ovalis (7%); and (6) low right atrium (19%). The mean missing tachycardia cycle length (TCL) was 67 ± 29 ms (22%) on the endocardial activation map. PPI was 9 [0-15] ms and 10 [0-20] ms longer than TCL at the breakthrough site and the opposite site, respectively. While feasible in 25 pseudo-focal ATs (93%), termination was better achieved by blocking the anatomical isthmus than ablating the breakthrough site [24/26 (92%) vs. 1/6 (17%); p < 0.001]. Conclusion: Perimitral, roof-dependent, and CTI-dependent flutters with centrifugal propagation are favored by a low-voltage area located at well-identified epicardial bundles. Comprehensive entrainment pacing maneuvers are crucial to distinguish pseudo-focal ATs from true focal ATs. Blocking the anatomical isthmus is a better therapeutic option than ablating the breakthrough site.

Viral surrogates to screen for virus inactivation (VI) can be a faster, cheaper and safer alternative to third-party testing of pathogenic BSL2 (Biosafety Level 2) model viruses. Although the bacteriophage surrogate, Ø6, has been used to assess low pH BSL2 VI, it has not been used for evaluation of detergent-mediated VI. Furthermore, Ø6 is typically assayed through host cell infectivity which introduces the risk of cross-contaminating other cell lines in the facility. To circumvent contamination, we developed an in-house RT-qPCR (reverse transcriptase quantitative polymerase chain reaction) assay for selective detection of active Ø6 from a population of live and dead phage. The RT-qPCR assay was used to evaluate Ø6 inactivation in cell culture fluid of monoclonal antibody and fusion protein. Complementary Ø6 infectivity was also conducted at a third-party testing facility. The Ø6 RT-qPCR and infectivity data was modeled against VI of three BSL2 viruses, X- MuLV, A- MuLV and HSV-1 in corresponding therapeutics. Both Ø6 methods demonstrate that any VI agent showing Ø6 clearance of ≥ 2.5 logs would demonstrate complete BSL2 VI of ≥ 4.0 logs. Compared to BSL2 virus testing, this in-house Ø6 RT-qPCR tool can screen VI agents at 5% the cost and a turnaround time of 2-3 days versus 4-7 months.

Arthritis is a common clinical feature of systemic lupus erythematosus (SLE) and is usually non-erosive as opposed to rheumatoid arthritis (RA). While RA synovial pathology has been extensively studied, little is known about the pathophysiology of lupus arthritis. Here, we aimed to explore the cytokine and cellular compartments in synovial fluids of SLE patients with arthritic manifestations. Acellular synovial fluid and paired serum samples from SLE patients (n=17) were analyzed with cytokine bead array for T helper associated cytokines. From two SLE patients, synovial fluid mononuclear cells (SFMC) were analyzed by multiparameter flow cytometry to dissect T cell, B cell, monocyte and dendritic cell phenotypes. SLE-derived SFMC were further stimulated in vitro to measure their capacity for producing IFN and IL-17A. All patients fulfilled the ACR 1982 classification criteria for SLE. Clinical records were reviewed to exclude the presence of comorbidities such as osteoarthritis or overlap with RA. IL-17A and IL-6 levels were high in SLE synovial fluid. A clear subset of the synovial CD4+ T cells expressed CCR6+, a marker associated with Th17 cells. IL-17-production was validated amongst CD4+CCR6+ T cells following in vitro stimulation. Furthermore, a strong IFN production was observed in both CD4+ and CD8+ cells. Our study shows high IL-17A and IL-6 levels in synovial fluids of patients with lupus arthritis. The Th17 pathway have been implicated in several aspects of SLE disease pathogenesis and our data points to Th17 involvement also for lupus arthritis.

Tropical montane cloud forests (TMCF) are recognized for their capacity to maintain high dry-season baseflow, and a host of other, ecosystem services. Despite their importance, they are endangered with a multidirectional array of land use changes, including conversion to pasture and crops such as coffee, while there are places where forest is being recovered. However, little is known about the effects of this complex dynamic on catchment hydrology. We investigated the effect of land use on rainfall-runoff response in five neighboring headwater micro-catchments in central Veracruz, Mexico, by comparing primary TMCF (PF), young (20 yr-old) and intermediate (40 yr-old) naturally regenerating TMCF (YF and IF, respectively), shaded coffee (SC), and an intensively grazed pasture (IP). We used a 4-year record of high-resolution rainfall and streamflow (10 min) data, collected from 2015 to 2019. These data were analyzed via hydrologic metrics and statistical tests. Results showed no statistical difference in the regulation capacity of high flows after 20 years of natural regeneration, compared to the PF. In terms of baseflow sustenance, our results suggested that PF and IF better promote this hydrological service than the other land uses, although all the catchments showed high mean annual low flows. SC exhibited a high capacity to modulate peak flows comparable to that of PF, and an intermediate capacity to sustain baseflow, suggesting that the integrated functioning of this catchment was largely preserved. Finally, we found that 40 years of pasture management can decrease the soil hydraulic properties in the area, causing a fivefold increase in the peak discharge response, and a much lower baseflow maintenance compared to PF.

In this study, the effects of solid-state fermentation (SSF), including strain (Aspergillus niger NRRL 334 and A. oryzae NRRL 5590) and fermentation time (24, 48, and 72 h) on the nutritional value of cold-pressed (CP) and hexane-extracted (HE) canola meals were examined. SSF increased the protein content of both types of meals (from ~36 to ~40%) while reducing the oil content of CP meals (from ~12 to 9%). There was a significant reduction (~80%) in the phytic acid content of both types of meals after fermentation using either fungi. Overall, fermented samples showed a decrease in the total phenolic content from 2.7-3.1 to ~1.0 mg gallic acid equivalents (GAE)/g DM (a ~65% reduction), of which specifically the HE meal fermented with A. niger sample had the greatest decrease from 3.1 to 0.6 mg GAE/g DM (~81% reduction). Seventy-two hours of fermentation decreased the in vitro protein digestibility (IVPD) of the meals. In contrast, a shorter fermentation time (24 h) increased the IVPD as compared to the controls (from ~73% to 77-81%), with the exception of the CP meal fermented with A. niger which had decreased IVPD at all fermentation times. Overall, the changes indicate that SSF using A. niger or A. oryzae can be useful to positively modify the composition of different canola meals and improve their nutritional value by significantly increasing the protein content, decreasing the levels of antinutrients, while only slightly reducing IVPD.

In this paper, we present the design and implementation of a smart irrigation system using Internet of Things (IoT) technology, which can be used for automating the irrigation process in agricultural fields. It is expected that this system would create a better opportunity for farmers to irrigate their fields efficiently, as well as eliminating the field’s under-watering, which could stress the plants. The developed system is organized into three parts: sensing side, cloud side, and user side. We used Microsoft Azure IoT Hub as an underlying infrastructure to coordinate the interaction between the three sides. The sensing side uses a Raspberry Pi 3 device, which is a low cost, credit-card sized computer device that is used to monitor in near real-time soil moisture, air temperature and relative humidity, and other weather parameters of the field of interest. Sensors readings are logged and transmitted to the cloud side. At the cloud side, the received sensing data is used by the irrigation scheduling model to determine when and for how long the water pump should be turned on based on a user-predefined threshold. The user side is developed as an Android mobile app, which is used to control the operations of the water pump with voice recognition capabilities. Finally, this system was evaluated using various performance metrics, such as latency and scalability.

Aim: This study evaluated the effect of intracavitary levobupivacaine infusion diluted with locally applied isotonic solution for pain control in cystoscopy. Methods: Included in this study are 100 patients who had previously undergone transurethral tumor resection for bladder tumor and were followed up by cystoscopy. The patients were randomized into five groups (n = 20). In the first, second, third, and fourth groups, 4, 6, 8, and 10 mL of levobupivacaine HCl (5.0 mg/mL) were mixed with 26, 24, 22, and 20 mL of isotonic solution, respectively. Hence, the total mixture was 30 mL for each group. The fifth group was the control group. In this group, the standard method commonly used in most clinics was utilized. That is, a gel containing Cathejell-2% lidocaine (25 mg lidocaine) was applied. Cystoscopic interventions were performed with a 17.5 Fr rigid cystoscope and 0°, 30°, and 70° lens. During cystoscopy and 30 min later, the pain status of patients was assessed using the Visual Analogue Scale (VAS), and patient satisfaction was questioned. Results: The mean VAS score during and after the cystoscopy procedure was significantly lower in the levobupivacaine groups compared to the lidocaine group. In addition, patient satisfaction in the levobupivacaine groups was significantly higher than in the lidocaine group. No drug-related side-effects were observed in all groups. Conclusion: Thus, levobupivacaine is a more effective drug than lidocaine alone to control pain during cystoscopy. The use of levobupivacaine is recommended to prevent possible complications of general anesthesia by eliminating the need for the aforementioned as well as its cost-saving advantage.

Predicting the range of substrates accepted by an enzyme from its amino acid sequence is challenging. Although sequence- and structure-based annotation approaches are often accurate for predicting broad categories of substrate specificity, they generally cannot predict which specific molecules will be accepted as substrates for a given enzyme, particularly within a class of closely related molecules. Combining targeted experimental activity data with structural modeling, ligand docking, and physicochemical properties of proteins and ligands with various machine learning models provides complementary information that can lead to accurate predictions of substrate scope for related enzymes. Here we describe such an approach that can predict the substrate scope of bacterial nitrilases, which catalyze the hydrolysis of nitrile compounds to the corresponding carboxylic acids and ammonia. Each of the four machine learning models (linear regression, random forest, gradient-boosted decision trees, and support vector machines) performed similarly (average ROC = 0.9, average accuracy = ~82%) for predicting substrate scope for this dataset. The approach is intended to be highly modular with respect to physicochemical property calculations and software used for docking and modeling.

Background: The rapid spread of COVID-19 has placed tremendous strain on the American healthcare system. Few prior studies have evaluated the well-being of or changes to training for American resident physicians during the COVID-19 pandemic. We aim to study predictors of trainee well-being and changes to clinical practice using an anonymous survey of American urology residents. Methods: An anonymous, voluntary, 47-question survey was sent to all ACGME-accredited urology programs in the United States. We executed a cross-sectional analysis evaluating risk factors of perception of anxiety and depression both at work and home and educational outcomes. Multiple linear regressions models were used to estimate beta coefficients and 95% confidence intervals. Results: Among approximately 1,800 urology residents in the USA, 356 (20%) responded. Among these respondents, 24 had missing data leaving a sample size of 332. Important risk factors of mental health outcomes included perception of access to PPE, local COVID-19 severity, and perception of susceptible household members. Risk factors for declination of redeployment included current redeployment, having children, and concerns regarding ability to reach case minimums. Risk factors for concern of achieving operative autonomy included cancellation of elective cases and higher level of training. Conclusions: Several potential actions, which could be taken by urology residency program directors and hospital administration, may optimize urology resident well-being, morale, and education. These include advocating for adequate access to PPE, providing support at both the residency program and institutional levels, instituting telehealth education programs, and fostering a sense of shared responsibility of COVID-19 patients.

Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus – NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter- and intra-specific level, and identified putatively adaptive SNPs using population structure outlier and genotype-environment association (GEA) analyses. At the interspecific level, we found a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation relating to differences in hibernation. At the intraspecific level, we identified 3 Evolutionarily Significant Units for NIDGS and 2 for SIDGS plus multiple Management and Adaptive Units. Elevation appears to be the main driver of adaptive differentiation in NIDGS, while neutral variation patterns match and extend that identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected the effect of natural geographic barriers, while adaptive variation reflected differences in land cover and temperature. These results clearly highlight the roles of neutral and adaptive processes for understanding species and population differentiation, which can have important conservation implications in threatened species.