Retroviral gene delivery is widely used in T cell therapies for hematological cancers. However, viral vectors are expensive to manufacture, they integrate genes in semi-random patterns, and their transduction efficiency is highly variable. In this study, several non-viral gene delivery vehicles, promoters, and additional variables were compared to optimize non-viral transgene delivery and expression in both Jurkat and primary T cells. Overall, transfecting Jurkat cells in X-VIVOTM 15 media with Lipofectamine LTX provided a high transfection efficiency (63.0±10.9% EGFP+). However, the same method yielded a much lower transfection efficiency in primary T cells (8.1±0.8% EGFP+). Subsequent confocal microscopy revealed that a majority of the lipoplexes did not enter the primary T cells, which might be due to relatively low expression levels of heparan sulfate proteoglycans (HSPGs) detected via mRNA-sequencing. PYHIN DNA sensors (e.g., AIM2, IFI16) were also expressed at high levels in Primary T cells, which can induce apoptosis when bound to cytoplasmic DNA. Therefore, transfection of primary T cells appears to be limited at the level of cellular uptake and/or DNA sensing in the cytoplasm, so both of these factors should be considered in the development of future viral and non-viral T cell gene delivery methods.

Data for visual acuity (VA) after treatment of neurofibromatosis type 1-associated optic pathway gliomas (NF1-OPGs) is limited. We retrospectively collected VA, converted to logMAR, before and after targeted therapy with everolimus for NF1-OPG, and compared to radiologic outcomes (14/18 with NF1-OPG, 25 eyes [3 without quantifiable vision]). Upon completion of treatment, VA was stable in 19 eyes, improved in 4 eyes, and worse in 2 eyes; visual and radiologic outcome were discordant. In summary, the majority of children with NF1-OPG exhibited stabilization of their VA after everolimus treatment. A larger, prospective study will help delineate visual outcomes after targeted therapy.

NTRK gene-fusions are rare but can occur in diverse cancers. The NTRK inhibitor larotrectinib is newly approved by the FDA. This paper reports the first case of a man with a NTRK-rearranged soft tissue sarcoma treated with larotrectinib in the neoadjuvant setting, in Belgium, to avoid limb amputation.

Objective Studies restricted to live births may underestimate severe teratogenic effects. We address the limitation by including data from both prenatal and postnatal diagnoses of cardiac malformations. Design Register-based study. Setting Denmark. Population 364,012 singleton pregnancies from 2007 to 2014. Methods We used data from five nationwide registries. Exposure to antidepressants was measured using redeemed prescriptions. Main Outcome Measures Pregnancies with cardiac malformations that end in miscarriage, termination, stillbirth, postnatal death or cardiac surgery <1 year of birth were classified as severe cardiac malformations (SCM). Propensity scores with adjusted prevalence ratios (PRs) were calculated. Results SCM were reported in 972 / 364 012 pregnancies overall and in 16 / 4105 exposed. PRs for SCM were 1.09 (95%CI: 0.52-2.30) for selective serotonin reuptake inhibitors (SSRIs) and 2.13 (95%CI: 0.89-5.13) for venlafaxine. Among the venlafaxine-exposed pregnancies, there was a cluster of hypoplastic left heart syndromes (HLHS) (crude PR 17.4 (95%CI: 6.41-47.2)) of which none ended in a live birth. For HLHS, the absolute risk increase was 4.4 per 1000, the number needed to harm (NNH) was 225. PRs for cardiac malformations not classified as SCM were 1.38 (95%CI: 1.00-1.92) for SSRIs, and 1.73 (95%CI: 1.08-2.77) for venlafaxine. Conclusions Pregnancy exposure to venlafaxine, but not SSRIs, is associated with an increased risk of SCM but with a low absolute risk. Potential mechanisms include direct effects or confounding by indication. Venlafaxine exposure is a marker for risk pregnancies for which fetal echocardiography may be considered. Keywords pregnancy, antidepressants, SSRI, venlafaxine, prenatal ultrasound, selection bias

Characterization of microbial assemblages via environmental DNA metabarcoding is increasingly being used in routine monitoring programs due to its sensitivity and cost-effectiveness. Several programs have been developed recently which infer functional profiles from 16S rRNA gene data using hidden-state prediction (HSP) algorithms. These might offer an economic and scalable alter-native to shotgun metagenomics. To date, HSP-based methods have seen limited use for benthic marine surveys and their performance in these environments remains unevaluated. In this study, 16S rRNA metabarcoding was applied to sediment samples collected at 0 and ≥ 1200 m from Norwegian salmon farms, and three metabolic inference approaches (PAPRICA, PICRUSt2 and TAX4FUN2) evaluated against metagenomics and environmental data. While metabarcoding and metagenomics recovered a comparable functional diversity, the taxonomic composition differed be-tween approaches, with genera richness up to 20× higher for metabarcoding. Comparisons between the sensitivity (highest true positive rates) and specificity (lowest true negative rates) of HSP-based programs in detecting functions found in metagenomics data ranged, respectively, from 0.52 and 0.60 to 0.76 and 0.79. However, little correlation was observed between the relative abundance of their specific functions. Functional beta-diversity of HSP-based data was strongly associated with that of metagenomics (r ≥ 0.86 for PAPRICA and TAX4FUN2) and responded similarly to the impact of fish farm activities. Our results demonstrate that although HSP-based metabarcoding approaches provide a slightly different functional profile than metagenomics, partly due to recovering a distinct community, they represent a cost-effective and valuable tool for characterizing and assessing the effects of fish farming on benthic ecosystems.

The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. Omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth, and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer n-3 LC-PUFA distributions among major ecosystems, between habitats, and among species within habitats. We highlight some of the key nutritional contrasts that can shape behavioral and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal, and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers’ metabolic networks, and review the evolutionary genetic mechanisms underpinning consumer adaptation to n-3 LC-PUFA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.

Plant growth depends on the diurnal regulation of cellular processes, but it is not well understood if and how transcriptional regulation controls diurnal fluctuations at the protein-level. Here we report a high-resolution Arabidopsis thaliana (Arabidopsis) leaf rosette proteome acquired over a 12 h light : 12 h dark diurnal cycle and the phosphoproteome immediately before and after the light-to-dark and dark-to-light transitions. We quantified nearly 5000 proteins and 800 phosphoproteins, of which 288 fluctuated in their abundance and 226 fluctuated in their phosphorylation status. Of the phosphoproteins, 60% were quantified for changes in protein abundance. This revealed six proteins involved in nitrogen and hormone metabolism that had concurrent changes in both protein abundance and phosphorylation status. The diurnal proteome and phosphoproteome changes involve proteins in key cellular processes, including protein translation, light perception, photosynthesis, metabolism and transport. The phosphoproteome at the light-dark transitions revealed the dynamics at phosphorylation sites in either anticipation of or response to a change in light regime. Phosphorylation site motif analyses implicate casein kinase II and calcium/calmodulin dependent kinases among the primary light-dark transition kinases. The comparative analysis of the diurnal proteome and diurnal and circadian transcriptome established how mRNA and protein accumulation intersect in leaves during the diurnal cycle of the plant.

Size and shape profoundly influence an organism’s ecophysiological performance and evolutionary fitness, suggesting a link between morphology and diversity. However, not much is known about how body shape is related to taxonomic richness, in particular in the microbial realm. Here we analyse global datasets of unicellular phytoplankton, a major photosynthetic group with an exceptional diversity of cell sizes and shapes. Using two measures of cell shape elongation, we quantify taxonomic diversity as a function of cell size and shape. We find that cells of intermediate volume have the greatest shape variation, from oblate to extremely elongated forms, while small and large cells are mostly compact (e.g., spherical or cubic). Taxonomic diversity is strongly related with cell elongation and cell volume, with both traits, in combination, explaining up to 92% of total variance. Diversity decays exponentially with cell elongation and displays a log-normal dependence on cell volume, peaking for compact, intermediate-volume cells. These previously unreported broad patterns in phytoplankton diversity reveal selective pressures and ecophysiological constraints on the geometry of phytoplankton cells which may improve our understanding of marine ecology and the evolutionary rules of life.

Autoimmune neutropenia (AIN) in childhood is characterized by chronic neutropenia and positivity for antineutrophil antibodies, resulting in the excessive destruction of neutrophils. In this study, we investigated the involvement of regulatory T cells (Tregs) in the pathogenesis of AIN in childhood. Tregs have been classified into three subpopulations based on the expressions of CD45RA and FOXP3: resting Tregs, activated Tregs, and non-suppressive Tregs. The frequency of activated Tregs (CD4+CD25+FOXP3highCD45RA− T cells) as well as that of total Tregs (CD4+CD25+FOXP3+ T cells) in peripheral blood was significantly decreased in patients with AIN. Analysis of the T cell receptor (TCR)-Vβ repertoire of CD4+ T cells revealed skewed usages in patients with AIN compared with that observed in age-matched control subjects. Regarding T cell subsets, the use of four of 24 TCR-Vβ families in Tregs and one in conventional T cells were increased in patients with AIN. The number of patients with AIN who showed skewed usages of TCR-Vβ family in conventional and Tregs was significantly higher than that reported in control subjects. When the preference between Tregs and conventional T cells in each TCR-Vβ family was individually compared, different use was prominently observed in the TCR-Vβ 9 family in patients with AIN. These results suggest that the quantitative abnormalities of Tregs and the skew of the TCR-Vβ repertoire in CD4+ T cells, including Tregs and conventional T cells, may be related to autoantibody production through a human neutrophil antigen-reactive T cell clone.

Objective: To report on the effectiveness of a standardized core Maternity Waiting Home (MWH) model to increase facility deliveries and access to reproductive health services among women living farthest from a health facility (>10km) using facility-based data. Design: Quasi-experimental design. Setting: Seven rural districts in Zambia. Population: Women delivering at 40 health facilities between June 2016 to August 2018. Methods: 20 intervention sites and 20 comparison sites were used to test if MWHs increased access to reproductive health services for women living in rural Zambia. The difference-in-differences (DID) methodology was used to examine the effectiveness of the core MWH model on our primary outcomes. Main Outcome Measures: Differences in the change from baseline to endline in the percentage of women who: 1) traveled greater than 10 km for delivery, (2) attended a postnatal visit at 6 days postpartum, and (3) were referred to a higher-level health facility between intervention and comparison group. Results: We detected a significant difference for the percentage of deliveries at intervention facilities with the core MWH model for all women living >10km away (p=0.03), adolescent women (<18 years) living >10km away (p=0.002), and primigravida women living >10km away (p=0.01). There were no significant differences for women attending a postnatal care visit at 6 days postpartum (p=0.07) or for women referred to the next level of care (p=0.29). Conclusion: The core MWH model was successful in reaching women with historically low rates of facility delivery, those living >10km from a healthcare facility, including adolescent women and primigravidas.

The stability analysis of dynamic continuous structural system (DCSS) has often been investigated by discretizing it into several low-dimensional elements. The integrated results of all elements are employed to describe the whole dynamic behavior of DCSS. In this paper, DCSS is regarded as the complex dynamic network with the discretized elements as the dynamic nodes and the time-varying stiffness as the dynamic link relations between them, by which the DCSS can be regarded to be the large-scale system composed of the node subsystem (NS) and link subsystem (LS). Therefore, the dynamic model of DCSS is proposed as the combination of dynamic equations of NS and LS, in which their state variables are coupled mutually. By using the model, this paper investigates the stability of DCSS. The research results show that the state variables of NS and LS are uniformly ultimately bounded (UUB) associated with the synthesized coupling terms in LS. Finally, the simulation example is utilized to demonstrate the validity of method in this paper.

By the Lagrangian multiplier and constraint variational derivative, a relationship between conserved quantities and multi-Hamiltonian structures is built. Making using the relation a method is founded to prove the infinite-dimensional Liouville integrability of evolution equations with continuous variables. As the application, the conservation laws of the Kundu equation are firstly obtained. Its conserved quantities are deduced for comparing by Fokas' method different from the method used in the existed literature. The integrability of the equation is proved through taking the conservation laws as a starting point.

Very recently one has started to study Bergman and Szeg\“o kernels in the setting of octonionic monogenic functions. In particular, explicit formulas for the Bergman kernel for the octonionic unit ball and for the octonionic right half-space as well as a formula for the Szeg\”o kernel for the octonionic unit ball have been established. In this paper we extend this line of investigation by developing explicit formulas for the Szeg\“o kernel of strip domains of the form ${\cal{S}} := \{z \in \mathbb{O} \mid 0 < \Re(z) < d\}$ from which we derive by a limit argument considering $d \to \infty$ the Szeg\”o kernel of the octonionic right half-space. Additionally, we set up formulas for the Bergman kernel of such strip domains and relate both kernels with each other. In fact, these kernel functions can be expressed in terms of one-fold periodic octonionic monogenic generalizations of the cosecant function and the cotangent function, respectively.

Introduction: The 2017-2018 National Survey of Children’s Health estimates that 30 million (42%) US children have experienced at least one adverse childhood experience (ACE), including abuse, neglect, and household dysfunction. ACEs negatively impact long-term health, and there has been no study of ACEs in cystic fibrosis (CF). We assessed willingness to disclose ACEs experienced by children with CF by surveying their parents and adults with CF. Methods: We anonymously surveyed parents of children with CF and adults with CF at the Northwestern University/ Lurie Children’s CF Center to determine their willingness to disclose ACEs. Results: The survey was completed by 46/157 (29%) parents and 36/105 (34%) adults with CF. Few parents (22%) and adults (17%) were willing to discuss most or all specific ACEs, more were willing to disclose the number of ACEs experienced in a category (57% parents, 47% adults), and the majority were willing to participate in anonymous research about ACEs (76% parents, 67% adults). Most parents (63%) and adults (50%) would prefer to have ACEs screened separately from their CF appointment, and most parents (63%) and adults (56%) wanted to learn more about ACEs from a member of their care team. Conclusions: Participants preferred to disclose the number of categorical ACEs rather than specific ACEs and most were open to participating in anonymous ACEs research. More research is needed before widespread adoption of ACE screening in CF.

The existing methods of flexibility index are mainly based on mixed-integer linear or nonlinear programming methods, making it difficult to readily deal with complex mathematical models. In this article, a novel solution strategy is proposed for finding a reliable upper bound of the flexibility index where the process model is implemented in a black box that can be directly executed by a commercial simulator, and also avoiding the need for calculating derivatives. Then, the flexibility index problem is formulated as a sequence of univariate derivative-free optimization (DFO) models. An external DFO solver based on trust-region methods can be called to solve this model. Finally, after calculating the critical point of the model parameters, the vertex enumeration method and two gradient approximation methods are proposed to evaluate the impact of process parameters and to evaluate the flexibility index. A reaction model is studied to show the efficiency of the proposed algorithm.

Introduction: Patients with chronic obstructive pulmonary disease (COPD) have impaired balance and hence fall more frequently. Easy application of balance evaluation tests can prevent the loss of time in the outpatient clinic for patients with COPD. Therefore, we compared the effectiveness of the Berg Balance Scale (BBS) test, a relatively more recommended but time-consuming test, with easy-to-perform tests such as the Single Leg Stance (SLS), Five Repetition Sit to Stand (5STS), Four Step Square (FSS), and Timed Up and Go (TUG) tests. Methods: A total of 71 patients with COPD and 70 control subjects with matching demographic characteristics were included in the study. All patients undertook pulmonary function tests and their scores of 6-min walk-test (6MWT), modified Medical Research Council (mMRC) dyspnea scale, COPD assessment questionnaire (CAT), and body mass index (B) were recorded. In addition, the severity of airway obstruction (O), the dyspnea severity (D), and exercise capacity (E) (BODE) index scores were measured. All patients with COPD were classified into 4 groups, A to D, based on the GOLD 2017 criteria. All subjects undertook the BBS, SLS, 5STS, Four Step Square Test, and TUG tests. Results: Balance tests revealed increased balance impairment in patients with COPD in comparison with the control subjects (P < 0.05). The BBS, SLS, Four Step Square Test (FSST), and TUG examinations suggested that balance impairment was frequent in Groups C and D patients with COPD (P < 0.05). TUG and FSST had the highest correlation with BBS (r = −0.812 and −0.842 and P <0.001 and <0.001, respectively). The results of TUG and FSST were the closest to those of BBS test. Conclusions: TUG and FSST tests can be applied for the assessment of bodily balance status among patients with COPD in outpatient clinics.

Objectives To investigate the operation time (OT) and the ureteral access sheath (UAS) usage with the infection rates and to determine a cut-off value for OT Methods We retrospectively analyzed the data of the patients who underwent FURS for renal stones larger than 20 mm between 2010 and 2019. The investigated parameters were OT, UAS using, and infection status. The data were analyzed by forming two groups according to whether the OT was less than 60 minutes and more, whether the UAS was used and whether an infection occurred. In addition, independent risk factors that may affect postoperative urinary infection development were also investigated by logistic regression analysis. And, a ROC curve analysis was applied to determine a cut-off value in OT terms, where infection rates increase more. Results A total of 575 patients were enrolled in the study. The rates of the usage UAS and infection were greater statistically in the group for longer than 60 minutes. OT was longer statistically in the infection group than in the group without infection ( 94.1±14.2 and 68.01±23.1, for groups 1 and 2, respectively, p<0.05, Table 2). OT was statistically longer in the UAS group than unused one ( 79.3±24.4 and 66.7±22.4, for groups 1 and 2, respectively, p<0.05, Table 3). ROC analyses revealed a cut-off point of 87.5min for OT in terms of infection rate Conclusion While the infection risk increases when OT exceeds 60 minutes, FURS can be safely performed up to 87.5 minutes with 89% sensitivity and 69% specificity infection risk.

Background: EBUS-TBNA is a frequently used diagnostic method for mediastinal/hilar lymphadenopathies and masses. This procedure is performed with intravenous sedation (IVS). During IVS, patients often develop hypoxemia and nasal oxygen delivery is insufficient in some patients. The aim of this study was to investigate the effect of oxygen application with nCPAP on hypoxemia during EBUS-TBNA. Methods: Patients with EBUS-TBNA indication who did not have any serious heart-lung disease were randomly divided into two groups. One group received only oxygen and the other group received nCPAP+oxygen. Patient characteristics, arterial oxygen saturations, anesthetic agents, CPAP pressures, oxygen concentrations and processing times were recorded during the procedure. Practitioner satisfaction was evaluated at the end. Results: 29 nCPAP+oxygen, 31 oxygen patients were included in the study. There were no significant differences in terms of age, sex, smoking history and presence of additional diseases in two groups. Neck circumference, BMI and STOP BANG questionnaire values were similar. Desaturation time was significantly longer in oxygen group than nCPAP+oxygen group (316±390 sec, 12±118 sec, respectively, p=0,019). Snoring was detected during the procedure in 22 patients in the oxygen group and in 11 patients in the nCPAP group (p=0,01). There were no serious complications in both groups. Practitioner satisfaction was higher in the nCPAP group but this was not statistically significant (p=0,052). Conclusions: Oxygen application by nCPAP during EBUS-TBNA under IVS, significantly reduces desaturation time. Oxygen delivery with nCPAP seems to be a better choice especially for the patients with high Mallampati index.