bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies
Authors: Cormier Michael J. , Pedersen Brent S. , Bayrak-Toydemir Pinar , Quinlan Aaron R. 
Published: March 2022

AbstractBackgroundDespite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is identifying variants that cause deleterious alternative splicing at intronic or exonic loci outside of canonical donor or acceptor splice sites.ResultsSeveral existing tools predict the likelihood that a genetic variant causes alternative splicing. We sought to extend such methods by developing a new metric that aids in discerning whether a genetic variant leads to deleterious alternative splicing. Our metric combines genetic variation in the Genome Aggregate Database with alternative splicing predictions from SpliceAI to compare observed and expected levels of splice-altering genetic variation. We infer genic regions with significantly less splice-altering variation than expected to be constrained. The resulting model of regional splicing constraint captures differential splicing constraint across gene and exon categories, and the most constrained genic regions are enriched for pathogenic splice-altering variants. Building from this model, we developed ConSpliceML. This ensemble machine learning approach combines regional splicing constraint with multiple per-nucleotide alternative splicing scores to guide the prediction of deleterious splicing variants in protein-coding genes. ConSpliceML more accurately distinguishes deleterious and benign splicing variants than state-of-the-art splicing prediction methods, especially in “cryptic” splicing regions beyond canonical donor or acceptor splice sites.ConclusionIntegrating a model of genetic constraint with annotations from existing alternative splicing tools allows ConSpliceML to prioritize potentially deleterious splice-altering variants in studies of rare human diseases.
Metabolome and transcriptome analysis reveals components regulating triterpenoid saponin biosynthesis of soapberry
Authors: Xu Yuanyuan , Zhao Guochun , Ji Xiangqin , Liu Jiming , Zhao Tianyun , Gao Yuan , Gao Shilun , Hao Yingying , Gao Yuhan , Wang Lixian , Weng Xuehuang , Chen Zhong , Jia Liming 
Published: March 2022

AbstractSoapberry (Sapindus mukorossi Gaertn.) pericarps are rich in valuable bioactive triterpenoid saponins. However, the saponin content dynamics and the molecular regulatory network of saponin biosynthesis in soapberry pericarps remain largely unclear. Here, we performed combined metabolite profiling and transcriptome analysis to identify saponin accumulation kinetic patterns, investigate gene networks, and characterize key candidate genes and transcription factors involved in saponin biosynthesis in soapberry pericarps. A total of 54 saponins were tentatively identified, including 25 that were differentially accumulated. Furthermore, 49 genes putatively involved in sapogenin backbone biosynthesis and some candidate genes assumed to be responsible for the backbone modification, including 41 cytochrome P450s and 45 glycosyltransferases, were identified. Saponin-specific clusters/modules were identified by Mfuzz clustering and weighted gene co-expression network analysis, and one TF–gene regulatory network underlying saponin biosynthesis was proposed. The results of yeast one-hybrid assay and electrophoretic mobility shift assay suggested that SmbHLH2, SmTCP4, and SmWRKY27 may play important roles in the triterpenoid saponin biosynthesis by directly regulating the transcription of SmCYP71D-3 in soapberry pericarp. Overall, these findings provide valuable information for understanding the molecular regulatory mechanism of saponin biosynthesis, enriching the gene resources, and guiding further research on triterpenoid saponin accumulation in soapberry pericarps.One–sentence summaryCombining metabolome and transcriptome analysis to identify saponin kinetic patterns, gene networks, and key candidate genes and transcription factors involved in saponin biosynthesis of soapberry.
RK-33, a small molecule inhibitor of host RNA helicase DDX3, suppresses multiple variants of SARS-CoV-2
Authors: Vesuna Farhad , Akhrymuk Ivan , Smith Amy , Winnard Paul T. , Lin Shih-Chao , Scharpf Robert , Kehn-Hall Kylene , Raman Venu 
Published: March 2022

AbstractSARS-CoV-2, the virus behind the deadly COVID-19 pandemic, continues to spread globally even as vaccine strategies are proving effective in preventing hospitalizations and deaths. However, evolving variants of the virus appear to be more transmissive and vaccine efficacy towards them is waning. As a result, SARS-CoV-2 will continue to have a deadly impact on public health into the foreseeable future. One strategy to bypass the continuing problem of newer variants is to target host proteins required for viral replication. We have used this host-targeted antiviral (HTA) strategy that targets DDX3, a host DEAD-box RNA helicase that is usurped by SARS-CoV-2 for virus production. We demonstrated that targeting DDX3 with RK-33, a small molecule inhibitor, reduced the viral load in four isolates of SARS-CoV-2 (Lineage A, and Lineage B Alpha, Beta, and Delta variants) by one to three log orders in Calu-3 cells. Furthermore, proteomics and RNA-seq analyses indicated that most SARS-CoV-2 genes were downregulated by RK-33 treatment. Also, we show that the use of RK-33 decreases TMPRSS2 expression, which may be due to DDX3s ability to unwind G-quadraplex structures present in the TMPRSS2 promoter. The data presented supports the use of RK-33 as an HTA strategy to control SARS-CoV-2 infection, irrespective of its mutational status, in humans.
Temporal and environmental factors interact with rootstock genotype to shape leaf elemental composition in grafted grapevines
Authors: Harris Zachary N , Pratt Julia E , Bhakta Niyati , Frawley Emma , Klein Laura L. , Kwasniewski Misha T , Migicovsky Zoë , Miller Allison J 
Published: March 2022

AbstractPlants take up elements through their roots and transport them to their shoot systems for use in numerous biochemical, physiological, and structural functions. Elemental composition of above-ground plant tissues, such as leaves, reflects both above- and below-ground activities of the plant genotype, as well the local environment. Perennial, grafted plants, where the root system of one individual is fused to the shoot system of a genetically distinct individual, offer a powerful experimental system in which to study the role of the root system in the elemental composition of the shoot system. We measured elemental composition of over 7000 leaves in the grapevine cultivar ‘Chambourcin’ growing ungrafted and grafted to three rootstock genotypes. Leaves were collected over multiple years and phenological stages (across the season) and along a developmental time series. Temporal components of this study had the largest effect on leaf elemental composition; and rootstock genotype interacted with year, phenological stage, and leaf age to differentially modulate leaf elemental composition. Further, the local, above-ground environment affected leaf elemental composition, an effect influenced by rootstock genotype. This work highlights the dynamic nature by which root systems interact with shoot systems to respond to temporal and environmental variation.
A BALB/c IGHV Reference Set, defined by haplotype analysis of long-read VDJ-C sequences from F1 (BALB/c / C57BL/6) mice
Authors: Jackson Katherine JL , Kos Justin T , Lees William , Gibson William S , Smith Melissa Laird , Peres Ayelet , Yaari Gur , Corcoran Martin , Busse Christian E. , Ohlin Mats , Watson Corey T , Collins Andrew M 
Published: March 2022

AbstractThe immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/c x C57BL/6) hybrid animals. Previously unreported strain variations were identified in theIghmandIghg2bgenes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is highly expressed in the BALB/cJ substrain. Only four of the BALB/c alleles were also observed in the C57BL/6 haplotype. The full set of inferred BALB/c sequences has been used to establish a BALB/c IGHV reference set, hosted athttps://ogrdb.airr-community.org. We assessed whether assemblies from the Mouse Genome Project (MGP) are suitable for the determination of the genes of the IGH loci. Only 37 (43.5%) of the 85 confirmed IMGT-named BALB/c IGHV and 33 (42.9%) of the 77 confirmed non-IMGT IGHV were found in a search of the MGP BALB/cJ genome assembly. This suggests that Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data, but not currently-available genome assemblies, are suited to the documentation of germline IGHV genes.
ATM modulates nuclear mechanics by regulating lamin A levels
Authors: Shah Pragya , McGuigan Connor W. , Cheng Svea , Vanpouille-Box Claire , Demaria Sandra , Weiss Robert S. , Lammerding Jan 
Published: March 2022

AbstractAtaxia-telangiectasia mutated (ATM) is one of the three main apical kinases at the crux of DNA damage response and repair in mammalian cells. ATM activates a cascade of downstream effector proteins to regulate DNA repair and cell cycle checkpoints in response to DNA double-strand breaks. While ATM is predominantly known for its role in DNA damage response and repair, new roles of ATM have recently begun to emerge, such as in regulating oxidative stress or metabolic pathways. Here, we report the surprising discovery that ATM inhibition and deletion lead to reduced expression of the nuclear envelope protein lamin A. Lamins are nuclear intermediate filaments that modulate nuclear shape, structure, and stiffness. Accordingly, inhibition or deletion of ATM resulted in increased nuclear deformability and enhanced cell migration through confined spaces, which requires substantial nuclear deformation. These findings point to a novel connection between ATM and lamin A and may have broad implications for cells with ATM mutations—as found in patients suffering from Ataxia Telangiectasia and many human cancers—which could lead to enhanced cell migration and increased metastatic potential.
Novel QTLs for cucumber resistance to two Colletotrichum orbiculare strains of different pathogenic races
Authors: Matsuo Hiroki , Isobe Sachiko , Shirasawa Kenta , Yoshioka Yosuke 
Published: March 2022

AbstractColletotrichum orbiculare is a hemibiotrophic fungal pathogen that causes anthracnose disease in cucumber (Cucumis sativus L.) and other cucurbit crops. The cucumber accession Ban Kyuri (G100) has a high level of resistance to anthracnose and is considered to be promising breeding material. Here, we report genetic mapping of loci from this cultivar that confer resistance to 104-T and CcM-1 of C. orbiculare that belong to pathogenic races 0 and 1, respectively. Quantitative trait locus (QTL) analysis based on phenotypic data from 196 F2:3 families detected one major QTL, An5, and one minor QTL, An6.2, for resistance to race 0, and one major QTL, An2, and three minor QTLs (An1.1, An1.2 and An6.1) for resistance to race 1. We identified lysM domain receptor-like kinase 3 (CsaV3_5G036150) and wall-associated receptor kinase-like (CsaV3_6G048820) as candidate genes for An5 and An6.2, respectively. Multiple genes encoding pattern recognition receptors were located in the regions of the QTLs conferring resistance to race 1. Thus, we identified potential sources of genetic resistance to different pathogenic races of C. orbiculare in the Ban Kyuri cultivar of cucumber.Key messageQuantitative trait locus analysis identified independent novel loci in cucumber responsible for resistance to races 0 and 1 of the anthracnose fungal pathogen Colletotrichum orbiculare.
Isolation of a potently neutralizing and protective human monoclonal antibody targeting yellow fever virus
Authors: Doyle Michael P. , Genualdi Joseph R. , Bailey Adam L. , Kose Nurgun , Gainza Christopher , Rodriguez Jessica , Reeder Kristen M. , Nelson Christopher A. , Jethva Prashant N. , Sutton Rachel E. , Bombardi Robin G. , Gross Michael L. , Julander Justin G. , Fremont Daved H. , Diamond Michael S. , Crowe James E. 
Published: March 2022

AbstractYellow fever virus (YFV) causes sporadic outbreaks of infection in South America and sub-Saharan Africa. While live-attenuated yellow fever virus vaccines based on three substrains of 17D are considered some of the most effective vaccines in use, problems with production and distribution have created large populations of unvaccinated, vulnerable individuals in endemic areas. To date, specific antiviral therapeutics have not been licensed for human use against YFV or any other related flavivirus. Recent advances in monoclonal antibody (mAb) technology have allowed for identification of numerous candidate therapeutics targeting highly pathogenic viruses, including many flaviviruses. Here, we sought to identify a highly neutralizing antibody targeting YFV envelope (E) protein as a therapeutic candidate. We used human B cell hybridoma technology to isolate mAbs from the circulating memory B cells from human YFV vaccine recipients. These antibodies bound to recombinant YFV E protein and recognized at least five major antigenic sites on E. Two mAbs (designated YFV-136 and YFV-121) recognized a shared antigenic site and neutralized the YFV 17D vaccine strainin vitro. YFV-136 also potently inhibited infection by multiple wild-type YFV strains, in part, at a post-attachment step in the virus replication cycle. YFV-136 showed therapeutic protection in two animal models of YFV challenge including hamsters and immunocompromised mice engrafted with human hepatocytes. These studies define features of the antigenic landscape on YFV E protein recognized by the human B cell response and identify a therapeutic antibody candidate that inhibits infection and disease caused by highly virulent strains of YFV.
Assessing the transportability of clinical prediction models for cognitive impairment using causal models
Authors: Fehr Jana , Piccininni Marco , Kurth Tobias , Konigorski Stefan ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: March 2022

AbstractBackgroundMachine learning models promise to support diagnostic predictions, but may not perform well in new settings. Selecting the best model for a new setting without available data is challenging. We aimed to investigate the transportability by calibration and discrimination of prediction models for cognitive impairment in simulated external settings with different distributions of demographic and clinical characteristics.MethodsWe mapped and quantified relationships between variables associated with cognitive impairment using causal graphs, structural equation models, and data from the ADNI study. These estimates were then used to generate datasets and evaluate prediction models with different sets of predictors. We measured transportability to external settings under guided interventions on age, APOE ε4, and tau-protein, using differences between internal and external settings measured by calibration metrics and area under the receiver operating curve (AUC).ResultsCalibration differences indicated that models predicting with causes of the outcome were more transportable than those predicting with consequences. AUC differences indicated inconsistent trends of transportability between the different external settings. Models predicting with consequences tended to show higher AUC in the external settings compared to internal settings, while models with parents or all variables showed similar AUC.ConclusionsWe demonstrated with a practical prediction task example that predicting with causes of the outcome results in better transportability compared to anti-causal predictions measured by calibration differences. We conclude that calibration differences are more suitable than AUC differences to assess model transportability to external settings.
In vitro Characterization of SARS-CoV-2 Protein Translated from the Moderna mRNA-1273 Vaccine
Authors: Veenstra Timothy D. , Pauley Brad , Injeti Elisha , Rotello Rocco J. 
Published: March 2022

ABSTRACTExtensive research around mRNA vaccines and their proposed utility during the current COVID-19 pandemic resulted in many publications concerning the SARS-Cov-2 spike protein and angiotensin converting enzyme-2 receptor-binding domain of the virus, but none describe the characteristics of the full-length protein obtained from the modified/synthetic mRNA that is part of the Moderna and Pfizer-BioNTech vaccines. In this paper, we provide the first data characterizing the actual proteins produced by mouse and human cells in culture that had been incubated up to 30 minutes with the commercial vaccine produced by Moderna (i.e., Spikevax). The mRNA vaccine continues to produce proteins up to 12-14 days after introduction to the cells. The molecular weight of the SARS-CoV-2 encoded protein ranges from 135-200 kilodaltons depending on the extent of glycosylation.
Fine-scale variation in the effect of national border on COVID-19 spread: A case study of the Saxon-Czech border region
Authors: Mertel Adam , Vyskočil Jiří , Schüler Lennart , Schlechte-Wełnicz Weronika , Calabrese Justin M. 
Published: March 2022

AbstractThe global extent and temporally asynchronous pattern of COVID-19 spread have repeatedly highlighted the role of international borders in the fight against the pandemic. Additionally, the deluge of high resolution, spatially referenced epidemiological data generated by the pandemic provides new opportunities to study disease transmission at heretofore inaccessible scales. Existing studies of cross-border infection fluxes, for both COVID-19 and other diseases, have largely focused on characterizing overall border effects. Here, we couple fine-scale incidence data with localized regression models to quantify spatial variation in the inhibitory effect of an international border. We take as a case study the border region between the German state of Saxony and the neighboring regions in northwestern Czechia, where municipality-level COVID-19 incidence data are available on both sides of the border. Consistent with past studies, we find an overall inhibitory effect of the border, but with a clear asymmetry, where the inhibitory effect is stronger from Saxony to Czechia than vice versa. Furthermore, we identify marked spatial variation along the border in the degree to which disease spread was inhibited. In particular, the area around Löbau in Saxony appears to have been a hotspot for cross-border disease transmission. The ability to identify infection flux hotspots along international borders may help to tailor monitoring programs and response measures to more effectively limit disease spread.
Dual Guidance in Regional Anesthesia – Influence of Needle Electrode Configuration on Stimulation Success at Sciatic Nerve; A Randomized, Controlled Pilot Trial
Authors: Wegner Julia , Ertmer Martin , Tafelski Sascha , Klotz Edda , Birnbaum Jürgen 
Published: March 2022

ABSTRACTIntroductionIn contrast to ultrasound technology (US), peripheral nerve stimulation (PNS) for regional anesthesia was little improved in recent years. When using the combination of both techniques, PNS can give additional information for nerve localization to improve safety and success of regional anesthesia. There are influencing factors on the success rate of stimulation in PNS remaining uninvestigated in a clinical setting to date. This randomized controlled pilot trial evaluates the impact of shape and size of stimulation needles electrodes under dual guidance conditions.MethodsIn a randomized controlled clinical trial 35 participants undergoing lower limb surgery received a preoperative proximal sciatic nerve block in dual guidance technique. Use of facet needles with point shaped electrodes (N=19, facet group) were compared with tuohy needles with large electroconductive tips (N=16, touhy group). Stimulation success at minimal distance between needle tip and nerve was recorded. Block success and complications of regional anesthesia were assessed.ResultsIn 87% of successful stimulation (20 of 23) an ultrasound-proven contact of needle tip and sciatic nerve was necessary to elicit a motor response. More successful stimulations could performed using facet needles (84%, 16/19) compared to tuohy needles (44%, 7/16, p=0.03). If stimulation was successful the number of successful sensory blockades was increased (78%, 18/23, p=0.02). No serious complications of regional anesthesia were recorded.DiscussionThis pilot trial suggests that stimulation needles with small electrodes may be more reliable in indicating a contact of needle and nerve, which may improve safety and success of proximal sciatic nerve blocks.
No impact of sex on surgical site infections in abdominal surgery: A multi-center study
Authors: Zwicky Simone Nora , Gloor Severin , Tschan Franziska , Candinas Daniel , Demartines Nicolas , Weber Markus , Beldi Guido 
Published: March 2022

AbstractObjectiveMale sex is controversially discussed as a risk factor for surgical site infections (SSI). The aim of the present study was to evaluate the impact of sex on SSI in abdominal surgery under elimination of relevant confounders.MethodsClinicopathological data of 6603 patients undergoing abdominal surgery from a multi-center prospective database of four Swiss hospitals including patients between 2015 and 2018 were assessed. Patients were stratified according to postoperative SSI and risk factors for SSI were assessed using univariate and multivariate analysis.ResultsIn 649 of 6603 patients SSI was reported (9.8%). SSI was significantly associated with reoperation (22.7% vs. 3.4%, p <0.001), higher mortality rate (4.6% vs. 0.9%, p <0.001) and higher rate of length of hospital stay over the 75th percentile (57.0 % vs. 17.9 %, p <0.001). In univariate analysis male sex was a significant risk factor for SSI (p = 0.01). In multivariate analysis including multiple confounders ‘ such as comorbidities and perioperative factors there was no association between male sex and risk of SSI (odds ratio (OR) 1.1 [CI 0.8 – 1.4]). Independent risk factors for SSI in multivariate analysis were BMI ≥ 30 kg/m2 (OR 1.8 [CI 1.3 - 2.3]), duration of surgery > 75th percentile (OR 2.3 [1.8 - 2.9]), high contamination level (OR 1.3 [1.0 – 1.6]), laparotomy (OR 1.3 [1.0 – 1.7]), pervious laparotomy (OR 1.4 [1.1 – 1.7]), blood transfusion (OR 1.7 [1.2 – 2.4]), cancer (OR 1.3 [1.0-1.8], malnutrition (OR 2.5 [1.8 – 3.4]).ConclusionUnder elimination of relevant confounders there is no significant correlation between sex and risk of SSI after abdominal surgery.