bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing insect communities within thin-soil environments
Authors: McNamara Manning Katherine , Perry Kayla I. , Bahlai Christie A. 
Published: October 2022

AbstractNatural thin-soil environments are those which have little to no soil accumulation atop hard substrates. Many of these natural thin-soil environments, such as alvars, rocky lakeshores or glades, cliffs and cliff bluffs, and barrens, are found in the Great Lakes Region of North America. Due to their ubiquity and ecosystem services they provide, characterizing insects in sensitive environments such as these is important. This study monitored insects in nine thin-soil sites, within three regions, on a 630 km latitudinal gradient in the Southeastern Great Lakes Region of North America from June - August 2019. Over 22,000 insect specimens collected were identified to order or family, and bee specimens were identified to genus or species. We found that overall insect community composition and biodiversity characteristics were similar between the three regions examined. However, the central region had higher taxonomic richness than the southern region. Although unique bee taxa were observed in each region, diversity metrics and community composition of bees were similar among sites. This study provides taxonomic information about the insect, particularly bees, and plant communities in thin-soil environments in this region, which could support conservation and management efforts.
Understanding water conservation vs. profligation traits in vegetable legumes through a physio-transcriptomic-functional approach
Authors: Fang Pingping , Sun Ting , Pandey Arun Kumar , Jiang Libo , Wu Xinyang , Hu Yannan , Cheng Shiping , Li Xiaofang , Xu Pei 
Published: October 2022

AbstractVegetable soybean and cowpea are related warm-season legumes showing contrasting leaf water use behaviors under similar root drought stresses, whose mechanisms are not well understood. Here we conducted an integrative phenomic-transcriptomic study on the two crops grown in a feedback irrigation system that enabled precise control of soil water contents. Continuous transpiration rate monitoring demonstrated that cowpea used water more conservatively under earlier soil drought stages, but tended to maintain higher transpiration under prolonged drought. Interestingly, we observed a soybean-specific transpiration rate increase accompanied by phase shift under moderate soil drought. Time-series transcriptomic analysis suggested a dehydration avoidance mechanism of cowpea at early soil drought stage, in which the VuHAI3 and VuTIP2;3 genes were suggested to be involved. Multifactorial gene clustering analysis revealed different responsiveness of genes to drought, time of day and their interactions between the two crops, which involved species-dependent regulation of the core clock genes. Gene network analysis identified two co-expression modules each associated with transpiration rate in cowpea and soybean, including a pair of negatively-correlated modules between species. Module hub genes, including the ABA-degrading gene GmCYP707A4 and the trehalose-phosphatase/synthase gene VuTPS9 were identified. Inter-modular network analysis revealed putative co-players of the hub genes. Transgenic analyses verified the role of VuTPS9 in regulating transpiration rate under osmotic stresses. These findings propose that species-specific transcriptomic reprograming in leaves of the two crops suffering similar soil drought was not only a result of the different drought resistance level, but a cause of it.
Awareness, Acceptance and Associated Factors of Human Papillomavirus Vaccine Among Parents of Daughters in Hadiya Zone, Southern Ethiopia: A Cross-Sectional Study
Authors: Larebo Yilma Markos , Elilo Legesse Tesfaye , Abame Desta Erkalo , Akiso Denebo Ersulo , Bawore Solomon Gebre , Anshebo Abebe Alemu , Gopalan Natarajan 
Published: October 2022

AbstractIntroductionHuman papillomavirus infections are the most prevalent sexually transmitted disease among women worldwide. Cervical cancer is the second most frequent disease worldwide in terms of incidence and mortality, and it is primarily responsible for fatalities in low- to middle-income nations, including Ethiopia. In the Hadiya Zone of Southern Ethiopia, the goal of this study is to determine parental knowledge about, acceptance of, and factors related to the human papillomavirus vaccine.MethodsFrom November to December 2021, a community-based cross-sectional study would be conducted in Hadiya Zone among parents with daughters in the Zone. The study respondents would be chosen using a two-stage sampling technique from parents with a 9-14-year-old daughter. An interviewer-administered questionnaire would be used to collect data. For analysis, the data were entered into Epidata version 3.1 and exported to SPSS version 25. Variables with a p-value less than 0.25 in the bivariate analysis were transferred to multivariate analysis. A logistic regression model was applied to forecast the association between the predictor and outcome variables. Statistical significance was considered at a 0.05 p-value.ResultsThe study showed that the overall acceptance of parents to vaccinate their daughter with HPV vaccination was 450 (84.9%). Parents of daughters having of male sex (AOR: 0.407; 95%CI: 0.221,0.748), having number of daughter’s one(AOR: 2.122; 95%CI: 1.221,3.685), government school type(AOR: 0.476;95%CI: 0.263,0.861), poor knowledge(AOR: 0.532;95%CI: 0.293,0.969) and negative attitude(AOR: 0.540;95%CI: 0.299,0.977) were discovered to have a strong correlation. Conclusion: This study found that there was a high level of parental acceptance; attitudes and knowledge about the HPV vaccine are significant in determining their intentions to vaccinate their daughter. Authorities in areas where cervical cancer incidence is at risk should plan and implement by providing health information regarding the human papillomavirus vaccination with an emphasis on raising community awareness.
Patient-specific Quality Assurance Failure Prediction with Deep Tabular Models
Authors: Levin R. , Aravkin A. Y. , Kim M. 
Published: October 2022

AbstractBackgroundPatient-specific quality assurance (PSQA) is part of the standard practice to ensure that a patient receives the dose from intensity-modulated radiotherapy (IMRT) beams as planned in the treatment planning system (TPS). PSQA failures can cause a delay in patient care and increase workload and stress of staff members. A large body of previous work for PSQA failure prediction focuses on non-learned plan complexity measures. Another prominent line of work uses machine learning methods, often in conjunction with feature engineering. Currently, there are no machine learning solutions which work directly with multi-leaf collimator (MLC) leaf positions, providing an opportunity to improve leaf sequencing algorithms using these techniques.PurposeTo improve patient safety and work efficiency, we develop a tabular transformer model based directly on the MLC leaf positions (without any feature engineering) to predict IMRT PSQA failure. This neural model provides an end-to-end differentiable map from MLC leaf positions to the probability of PSQA plan failure, which could be useful for regularizing gradient-based leaf sequencing optimization algorithms and generating a plan that is more likely to pass PSQA.MethodWe retrospectively collected DICOM RT PLAN files of 968 patient plans treated with volumetric arc therapy. We construct a beam-level tabular dataset with 1873 beams as samples and MLC leaf positions as features. We train an attention-based neural network FT-Transformer to predict the ArcCheck-based PSQA gamma pass rates. In addition to the regression task, we evaluate the model in the binary classification context predicting the pass or fail of PSQA. The performance was compared to the results of the two leading tree ensemble methods (CatBoost and XGBoost) and a non-learned method based on mean MLC gap.ResultsThe FT-Transformer model achieves 1.44% Mean Absolute Error (MAE) in the regression task of the gamma pass rate prediction and performs on par with XGBoost (1.53 % MAE) and CatBoost (1.40 % MAE). In the binary classification task of PSQA failure prediction, FT-Transformer achieves 0.85 ROC AUC (with CatBoost and XGBoost achieving 0.87 ROC AUC and the mean-MLC-gap complexity metric achieving 0.72 ROC AUC). Moreover, FT-Transformer, CatBoost, and XGBoost all achieve 80% true positive rate while keeping the false positive rate under 20%.ConclusionsWe demonstrate that reliable PSQA failure predictors can be successfully developed based solely on MLC leaf positions. Our FT-Transformer neural network can reduce the need for patient rescheduling due to PSQA failures by 80% while sending only 20% of plans that would not have failed the PSQA for replanning. FT-Transformer achieves comparable performance with the leading tree ensemble methods while having an additional benefit of providing an end-to-end differentiable map from MLC leaf positions to the probability of PSQA failure.
Celiac dysbiosis does not transcend geographic boundaries
Authors: Colgan John J , Burns Michael B 
Published: October 2022

ABSTRACTCeliac disease is an autoimmune disorder of the small intestine in which gluten, an energy-storage protein found in wheat and other cereals, elicits an immune response that leads to villous atrophy. Despite a strong genetic component, celiac disease arises sporadically and at any age, leading us to hypothesize that changes in the microbiome influence celiac disease development and/or progression. Here, we pooled and computationally analyzed 16S data from 3 prior international studies that examined celiac disease and the microbiome. For our analysis, we combined the dada2 and PICRUSt 2 pipelines and a variety of data transformations that control for batch effects to determine whether any taxonomic or metabolic features were consistently associated with the celiac microbiome across the globe. Our results showed the celiac microbiome displays dysbiosis without a discernable pattern, which suggests perturbations in the celiac microbiome are a result of the disease rather than a cause. Data from PICRUSt 2 supported this conclusion and revealed connections between celiac disease and the metabolome that are supported by previous research examining dysbiotic microbiomes.IMPORTANCECeliac disease is an autoimmune disorder that affects roughly 2% of the world’s population. Although the ultimate cause of celiac disease is unknown, many researchers hypothesize that changes to the intestinal microbiome play a key role in disease progression. If this is the case, it may be possible to design therapies that manipulate the microbiome to suppress celiac disease. Here, we analyzed pooled data from 3 different studies from across the globe that examined celiac disease and the microbiome to ascertain whether there exists a unique celiac microbiome that transcends geographic boundaries.
The MLL3/TP53/PIK3CA cancer driver mutations promote HIF1α-dependent recruitment and differentiation of pro-tumor ICOShiGITRhiBlimp-1+effector regulatory T cells in breast tumors
Authors: Boutet Marie , Nishitani Kenta , Erler Piril , Couturier Nicole , Zhang Zheng , Militello Anna Maria , De Miranda Marcelo Coutinho , Barbieux Emeline , Guillen Erik , Suzuki Masako , Sparano Joseph A. , Montagna Cristina , Guo Wenjun , Lauvau Gregoire 
Published: October 2022

AbstractWhile essential gatekeepers of immune homeostasis, Foxp3+regulatory T (Treg) cells infiltrating tumors acquire distinct phenotypes and become highly immunosuppressive, promoting tumor immune escape and growth. How this occurs and relates to tumor-driver mutations is largely uncharacterized. Herein, we created a mouse mammary stem cell-based tumor model using CRISPR gene editing in which we introduced known human cancer-driver mutations. These included functional loss of the MLL3 histone methyltransferase and p53, and constitutive PI3-kinase activation, recapitulating the genetic makeup of aggressive breast cancers. We show that MLL3 loss fosters tumorigenesis by promoting the rapid establishment of an immunosuppressive microenvironment through induction of HIF1α, which increases the secretion of the chemokine CCL2 by tumor cells and the recruitment of higher numbers of Foxp3+Tregcells via CCR2. Greater infiltration of Tregcells also correlates with MLL3 downregulation and mutations in human breast cancer biopsies. Interestingly, HIF1α enforces the differentiation of tumor-infiltrating Tregcells into highly immunosuppressive ICOShiGITRhiBlimp-1hieffector Tregcells that enable rapid tumor escape. Monoclonal antibody targeting of ICOS or GITR inhibits tumorigenesis in most mice even two months after the cessation of treatment as well as the growth of established tumors, suggesting possible therapeutic opportunities for MLL3-mutant breast cancers.
Prostaglandin E2 production is required for phagocyte CXCR2-mediated skin host defense in obese and hyperglycemic mice
Authors: Klopsfenstein Nathan , Hibbs Kristin , Blackman Amondrea , Serezani C. Henrique 
Published: October 2022

ABSTRACTPoorly controlled glucose observed in obese individuals with diabetes is associated with a significantly increased risk of infection, particularly in the skin and soft tissues. Staphylococcus aureus is a significant cause of skin and soft tissue infections (SSTIs) in obese and hyperglycemic individuals with growing antibiotic resistance making these infections difficult to treat. However, the events that drive dysregulated skin host defense during hyperglycemia remain to be fully elucidated. Here we examined how the prostaglandin E2 (PGE2) threshold impacts tissue injury and host defense during methicillin-resistant S. aureus (MRSA) skin infection in obese and hyperglycemic mice. Our data show that obesity and hyperglycemia are accompanied by impaired expression of prostaglandin E synthase 1 and PGE2 production in infected skin. Restoration of PGE2 levels with the PGE analog misoprostol improved infection outcomes in obese and hyperglycemic mice in a manner dependent on E prostanoid 3-mediated cAMP inhibition. Topical misoprostol restored the levels of CXC chemokines and CXCR2+ monocyte and neutrophil recruitment. Here, we are unveiling a defective signaling program that culminates in inadequate CXCR2 phagocyte migration to the infected skin of obese and hyperglycemic mice. Furthermore, these data also lead to a novel drug repurposing opportunity to treat antibiotic-resistant pathogens in hyperglycemic conditions.
The variant catalogue pipeline: A workflow to generate a background variant library from Whole Genome Sequences
Authors: Correard Solenne , Abdallah Mohammed OE , Hewitson Brittany , Wasserman Wyeth W. 
Published: October 2022

ABSTRACTToday, several projects are working toward reducing inequities and improving health care for individuals affected with rare genetic diseases from diverse populations. One route to reduce inequities is to generate variant catalogues for diverse populations. To that end, we developed the variant catalogue pipeline, an open-source pipeline implemented in the Nextflow framework. The variant catalogue pipeline includes detection of single nucleotide variants, small insertions and deletions, mitochondrial variants, structural variants, mobile element insertions, and short tandem repeats. Sample and variant quality control, allele frequency calculation (for whole and sex-stratified cohorts) and annotation steps are also included, delivering vcf files with annotated variants and their frequency in the cohort. Successful application of the variant catalogue pipeline to 100 publicly available human genomes is described. We hope that, by making this pipeline available, more under-represented populations benefit from enhanced capacity to generate high-quality variant catalogues.
“Double-Effect” strategy against Triple-Negative Breast Cancer via a synergistic therapy of Magneto-mechanical Force enhancing NIR-II Hypothermal Ablation
Authors: Du Hui , Yang Fang , Yao Chenyang , Lv Wenhao , Peng Hao , Stanciu Stefan G. , Stenmark Harald A. , Song Young Min , Jiang Bo , Wu Aiguo 
Published: October 2022

AbstractTriple-negative breast cancer (TNBC) is a form of breast cancer that is more aggressive and harder to treat than others, with a higher probability of relapse. Its highly efficient capabilities for migrating and invading other parts of the body together with the current lack of clinically established effective therapies account for a low survival rate. Thus, we propose the in-tandem use of two complementary therapeutic routes to effectively combat TNBC. Herein, a versatile magnetic-photothermal converter (MPC) is elaborately designed via integrating zinc-doped ferrite nanoparticles and polyethene glycol, synergistically enhanced through magneto-mechanical force (MMF) and near-infrared-II (NIR-II) hypothermal ablation, thereby displaying excellent therapeutic efficiency. Their combined use, which is less aggressive to the human body compared to conventional chemotherapeutic approaches, results in the splendid suppression of TNBC migration and invasion. Remotely controlling the MPCs by an external magnetic stimulus, results in cellular MMF effects that cause direct mechanical destruction to the cancer cell membrane, leading to its necrosis. Furthermore, the MMF disrupts intracellular lysosomes, thereby triggering the release of large amounts of protein hydrolases, which induce intracellular oxidative stress, and accelerate the induction of apoptosis. Complementing the therapeutic approach based on MMF, the excellent photothermal performance of the MPC in the NIR-II region (1064nm) is exploited to enable effective hypothermal ablation of the tumours, which can be achieved in deep tissue layers. The proposed multifunctional nanocomposites, together with the demonstrated “double effect” therapeutic approach, hold significant potential to pave the way for future cutting-edge weapons against the dreadful TNBC.
Nascent MSKIK peptide prevents or releases translation arrest in Escherichia coli
Authors: Ojima-Kato Teruyo , Nishikawa Yuma , Furukawa Yuki , Kojima Takaaki , Nakano Hideo 
Published: October 2022

ABSTRACTThe insertion of the sequence encoding SKIK peptide adjacent to the M start codon of a difficult-to-express protein enhances protein production in Escherichia coli. In this report, we show that the increased production of the SKIK-tagged protein is not due to codon usage of the SKIK sequence. In addition, insertion of SKX, KKX, and AKX (X = G, L, H, Y, E, and F) at the N-terminus increased protein production. Furthermore, insertion of MSKIK just before the SecM arrest peptide (FSTPVWISQAQGIRAGP), which causes translational stalling on mRNA, greatly increased the production of the protein containing the SecM arrest peptide in the E. coli reconstituted cell-free protein synthesis system (PURE system). A similar phenomenon was observed for CmlA leader whose arrest is induced by chloramphenicol. These results suggest that the nascent MSKIK peptide prevents or releases translational stalling immediately following its generation during the translation process.
Basal but not complex motor control relies on interhemispheric structural connectivity after stroke
Authors: Paul Theresa , Wiemer Valerie M. , Hensel Lukas , Cieslak Matthew , Tscherpel Caroline , Grefkes Christian , Grafton Scott T. , Fink Gereon R. , Volz Lukas J. 
Published: October 2022

AbstractObjectiveWhile ample evidence highlights that the ipsilesional corticospinal tract (CST) plays a crucial role in motor recovery after stroke, very few studies have assessed cortico-cortical motor connections with inconclusive results. Given their unique potential to serve as structural reserve enabling motor network reorganization, the question arises whether cortico-cortical connections may facilitate motor control depending on CST damage.MethodsDiffusion spectrum imaging (DSI) and a novel compartmentwise analysis approach were used to quantify structural connectivity between bilateral cortical core motor regions in chronic stroke patients. Basal and complex motor control were differentially assessed.ResultsBoth basal and complex motor performance were correlated with structural connectivity between bilateral premotor areas and ipsilesional primary motor cortex (M1) as well as interhemispheric M1-M1 connectivity. While complex motor skills depended on CST integrity, a strong association between M1-M1 connectivity and basal motor control was observed independent of CST integrity especially in patients who underwent substantial motor recovery. Harnessing the informational wealth of cortico-cortical connectivity facilitated the explanation of both basal and complex motor control.InterpretationWe demonstrate for the first time that distinct aspects of cortical structural reserve enable basal and complex motor control after stroke. In particular, recovery of basal motor control is supported via an alternative route through contralesional M1 and non-crossing fibers of the contralesional CST. Our findings help to explain previous conflicting interpretations regarding a vicarious or maladaptive role of the contralesional M1 and highlight the potential of structural connectivity of the cortical motor network as a biomarker post-stroke.
Rheo-2DIR spectroscopy reveals strain-induced hydrogen-bond redistribution in polyurethane
Authors: Giubertoni Giulia , Hilbers Michiel , Groen Hajo , Van der Weide Anne , Bonn Daniel , Woutersen Sander 
Published: October 2022

AbstractThe remarkable elastic properties of polymers are ultimately due to their molecular structure, but the relation between the macroscopic and molecular properties is often difficult to establish, in particular for (bio)polymers that contain hydrogen bonds, which can easily rearrange upon mechanical deformation. Here we show that two-dimensional infrared spectroscopy on polymer films in a miniature stress tester sheds new light on how the hydrogen-bond structure of a polymer is related to its visco-elastic response. We study thermoplastic polyurethane, a block copolymer consisting of hard segments of hydrogen-bonded urethane groups embedded in a soft matrix of polyether chains. The conventional infrared spectrum shows that upon deformation, the number of hydrogen bonds increases, a process that is largely reversible. However, the 2DIR spectrum reveals that the distribution hydrogen-bond strengths becomes slightly narrower after a deformation cycle, due to the disruption of weak hydrogen bonds, an effect that could explain the strain-cycle induced softening (Mullins effect) of polyurethane. These results show how rheo-2DIR spectroscopy can bridge the gap between the molecular structure and the macroscopic elastic properties of (bio)polymers.
Simultaneous multicolor fluorescence imaging using duplication-based PSF splitting
Authors: Eynde Robin Van den , Hertel Fabian , Abakumov Sergey , Krajnik Bartosz , Hugelier Siewert , Auer Alexander , Hellmeier Joschka , Schlichthaerle Thomas , Grattan Rachel M. , Lidke Diane S. , Jungmann Ralf , Leutenegger Marcel , Vandenberg Wim , Dedecker Peter 
Published: October 2022

AbstractWe present a way to encode more information in fluorescence imaging by splitting the emission into copies of the original point-spread function (PSF), which offers broadband operation and compatibility with other PSF engineering modalities and existing analysis tools. We demonstrate the approach using the ‘Circulator’, an add-on that encodes the fluorophore emission band into the PSF, enabling simultaneous multicolor super-resolution and single-molecule microscopy using essentially the full field of view.