bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lassa fever in pregnancy: a systematic review and meta-analysis
Authors: Kayem Nzelle D , Benson Charlotte , Aye Christina Y L , Barker Sarah , Tome Mariana , Kennedy Stephen , Ariana Proochista , Horby Peter 
Published: January 2020

Abstract
Lassa fever is a zoonotic infection endemic to West Africa and is known to have adverse effects in pregnancy. We sought to synthesize and critically appraise currently available evidence on the effects of Lassa fever in pregnancy. An exhaustive bibliographic search from dates of inception to 30 September 2019 yielded 13 studies, from which individual patient data were extracted. The absolute risk of maternal death associated with Lassa fever was estimated at 33.73% (95% CI 22.05 to 46.42%, I2=72.40%, p=0.0014). The relative risk of death in pregnant women compared with non-pregnant women was estimated at 2·86 (95% CI 1.77 to 4.63, I2=27.27%, p=0.239). The formal gap analysis shows imprecise data on the risk of Lassa-related maternal and perinatal mortality and insufficient data for other pregnancy outcomes. The currently available evidence for the use of ribavirin in pregnant patients is not conclusive. With a threefold increased risk of mortality, there is a need to prioritize pregnant women as a special subgroup of interest for Lassa research. Robust prospective studies estimating the true incidence of adverse maternal and perinatal outcomes and randomized controlled trials to evaluate the efficacy of therapeutics for maternal Lassa virus infection are urgently needed.
Predicting Alcohol Dependence from Multi-Site Brain Structural Measures
Authors: Hahn Sage , Mackey Scott , Cousijn Janna , Foxe John J. , Hester Robert , Hutchinson Kent , Korucuoglu Ozlem , London Edythe , Lorenzetti Valentina , Luijten Maartje , Momenan Reza , Orr Catherine , Paulus Martin , Schmaal Lianne , Sinha Rajita , Sjoerds Zsuzsika , Stein Dan J. , Stein Elliot , van Holst Ruth J. , Veltman Dick , Wiers Reinout W. , Yucel Murat , Thompson Paul M. , Conrod Patricia , Allgaier Nicholas , Garavan Hugh 
Published: January 2020

AbstractBackgroundThe search for neuroimaging biomarkers of alcohol use disorder (AUD) has primarily been restricted to significance testing in small datasets of low diversity. To identify neurobiological markers beyond individual differences, it may be useful to develop classification models for AUD. The ever-increasing quantity of neuroimaging data demands methods that are robust to the complexities of multi-site designs and are generalizable to data from new scanners.MethodsThis study represents a mega-analysis of previously published datasets from 2,034 AUD and comparison participants spanning 27 sites, coordinated by the ENIGMA Addiction Working Group. Data were grouped into a training set including 1,652 participants (692 AUD, 24 sites), and test set with 382 participants (146 AUD, 3 sites). A battery of machine learning classifiers was evaluated using repeated random cross-validation (CV) and leave-site-out CV. Area under the receiver operating characteristic curve (AUC) was our base metric of performance.ResultsMulti-objective evolutionary search was conducted to identify sparse, generalizable, and high performing subsets of brain measurements. Cortical thickness in the left superior frontal gyrus and right lateral orbitofrontal cortex, cortical surface area in the right transverse temporal gyrus, and left putamen volume, appeared most frequently across searches. Restricting a regularized logistic regression model to these four features yielded a test-set AUC of .768.ConclusionsDeveloping classification models on multi-site data with varied underlying class distributions poses unique challenges. Supplementing datasets with controls from new sites and performing feature selection increases generalizability. Four features identified by evolutionary search may serve as specific biomarkers for individuals with current AUD.
Accurate CNV identification from only a few cells with low GC bias in a single-molecule sequencing platform
Authors: Hu Liang , Lin Qunting , Xie Pingyuan , Zeng Lidong , Liu Lichun , Huang Mengxian , Yan Qin , Zhang Meng , Lin Ge 
Published: January 2020

ABSTRACTA technical problem of characterizing copy number variation of several cells with next-generation sequencing is the whole genome amplification induced bias. The result of CNVs and mosaicism detection is affected by the GC bias. Here, we report a rapid non-WGA sample preparation strategy for a single-molecule sequencing platform GenoCare1600. This approach, combined with a single-molecule sequencing platform that avoids the use of WGA and bridge PCR processes, can provide higher reliability with its lower GC bias. By combining our optimized Tn5-based transposon insertion approach with GenoCare, we successfully detected CNVs as small as 1.29M and mosaicism as small as 20%, which is consistent with next-generation sequencing (NGS) data. Moreover, our GenoCare-TTI protocol showed less GC bias and less Mad of Diff. These results suggest that the optimized TTI approach, together with the GenoCare1600 sequencing platform, is a promising option for CNV characterization from maybe one single cell.
ARF1 dimerization is essential for vesicle trafficking and dependent on activation by ARF-GEF dimers in Arabidopsis
Authors: Brumm Sabine , Nielsen Mads Eggert , Richter Sandra , Beckmann Hauke , Stierhof York-Dieter , Singh Manoj K. , Fischer Angela-Melanie , Sundaresan Venkatesan , Jürgens Gerd 
Published: January 2020

AbstractMembrane traffic maintains the organization of the eukaryotic cell and delivers cargo proteins to their subcellular destinations such as sites of action or degradation. Membrane vesicle formation requires ARF GTPase activation by the SEC7 domain of ARF guanine-nucleotide exchange factors (ARF-GEFs), resulting in the recruitment of coat proteins by GTP-bound ARFs.In vitroexchange assays were done with monomeric proteins, although ARF-GEFs have been shown to form dimersin vivo. This feature is conserved across the eukaryotes, however its biological significance is unknown. Here we demonstrate ARF1 dimerizationin vivoand we show that ARF-GEF dimers mediate ARF1 dimer formation. Mutational disruption of ARF1 dimers interfered with ARF1-dependent trafficking but not coat protein recruitment in Arabidopsis. Mutations disrupting simultaneous binding of two ARF1•GDPs by the two SEC7 domains of GNOM ARF-GEF dimer prevented stable interaction of ARF1 with ARF-GEF and thus, efficient ARF1 activation. Our results suggest a model of activation-dependent dimerization of membrane-inserted ARF1•GTP molecules required for coated membrane vesicle formation. Considering the evolutionary conservation of ARFs and ARF-GEFs, this initial regulatory step of membrane trafficking might well occur in eukaryotes in general.
High sensitivity (zeptomole) detection of BODIPY heparan sulfate (HS) disaccharides by ion-paired RP-HPLC and LIF detection enables analysis of HS from mosquito midguts
Authors: Maciej-Hulme Marissa L. , Leprince Anaëlle C. N. , Lavin Andre , Guimond Scott E. , Turnbull Jeremy E. , Pelletier Julien , Yates Edwin A. , Powell Andrew K. , Skidmore M. A. 
Published: January 2020

AbstractThe fine structure of heparan sulfate (HS), the glycosaminoglycan polysaccharide component of cell surface and extracellular matrix HS proteoglycans, coordinates the complex cell signalling processes that control homeostasis and drive development in multicellular animals. In addition, HS is involved in the infection of mammals by viruses, bacteria and parasites. The current detection limit for fluorescently labelled HS disaccharides that is in the low femtomole range (10-15mol), has effectively hampered investigations of HS composition from small, functionally-relevant populations of cells and tissues. Here, an ultra-high sensitivity method is described that utilises a combination of reverse-phase HPLC, with tetraoctylammonium bromide (TOAB) as the ion-pairing reagent and laser-induced fluorescence detection of BODIPY-FI-labelled disaccharides. The method provides an unparalleled increase in the sensitivity of detection by ∼ six orders of magnitude, to the zeptomolar range (∼10-21moles), enabling detection of <1000 labelled molecules. This facilitates determination of HS disaccharide compositional analysis from minute biological samples, as demonstrated by analysis of HS isolated from the midguts ofAnopheles gambiaemosquitoes that was achieved without approaching the limit of detection.
Capsaicin and its analogues impede nocifensive response ofCaenorhabditis elegansto noxious heat
Authors: Nkambeu Bruno , Salem Jennifer Ben , Beaudry Francis 
Published: January 2020

AbstractCapsaicin is the most abundant pungent molecule identified in red chili peppers, and it is widely used for food flavoring, in pepper spray for self-defense devices and recently in ointments for the relief of neuropathic pain. Capsaicin and several other related vanilloid compounds are secondary plant metabolites. Capsaicin is a selective agonist of the transient receptor potential channel, vanilloid subfamily member 1 (TRPV1). After exposition to vanilloid solution,C. eleganswild type (N2) and mutants were placed on petri dishes divided in quadrants for heat stimulation. Thermal avoidance index was used to phenotype each testedC. elegansexperimental groups. The data revealed for the first-time that capsaicin can impede nocifensive response ofC. elegansto noxious heat (32°C – 35°C) following a sustained exposition. The effect was reversed 6h post capsaicin exposition. Additionally, we identified the capsaicin target, theC. eleganstransient receptor potential channel OCR-2. Further experiments also undoubtedly revealed anti-nociceptive effect for capsaicin analogues, including ginger (Zingiber officinale) and turmeric (Curcuma longa) secondary metabolites.
Biomechanical Regulation of Breast Cancer Metastasis and Progression
Authors: Spencer Adrianne , Sligar Andrew D. , Chavarria Daniel , Lee Jason , Choksi Darshil , Patil Nikita P. , Lee HooWon , Veith Austin P. , Riley William J. , Desai Shubh , Abbaspour Ali , Singeetham Rohan , Baker Aaron B. 
Published: January 2020

AbstractPhysical activity has been consistently linked to decreased incidence of breast cancer and a substantial increase in the length of survival of patients with breast cancer. However, the understanding of how applied physical forces directly regulate breast cancer remains limited. We investigated the role of mechanical forces in altering the chemoresistance, proliferation and metastasis of breast cancer cells. We found that applied mechanical tension can dramatically alter gene expression in breast cancer cells, leading to decreased proliferation, increased resistance to chemotherapeutic treatment and enhanced adhesion to inflamed endothelial cells and collagen I under fluidic shear stress. A mechanistic analysis of the pathways involved in these effects supported a complex signaling network that included Abl1, Lck, Jak2 and PI3K to regulate pro-survival signaling and enhancement of adhesion under flow. Studies using mouse xenograft models demonstrated reduced proliferation of breast cancer cells with orthotopic implantation and increased metastasis to the skull when the cancer cells were treated with mechanical load. Using high throughput mechanobiological screens we identified pathways that could be targeted to reduce the effects of load on metastasis and found that the effects of mechanical load on bone colonization could be reduced through treatment with a PI3Kγ inhibitor.
Self-generated whisker movements drive state-dependent sensory input to developing barrel cortex
Authors: Dooley James C. , Glanz Ryan M. , Sokoloff Greta , Blumberg Mark S. 
Published: January 2020

SummaryCortical development is an activity-dependent process [1–3]. Regarding the role of activity in developing somatosensory cortex, one persistent debate concerns the importance of sensory feedback from self-generated movements. Specifically, recent studies claim that cortical activity is generated intrinsically, independent of movement [3, 4]. However, other studies claim that behavioral state moderates the relationship between movement and cortical activity [5–7]. Thus, perhaps inattention to behavioral state leads to failures to detect movement-driven activity [8]. Here, we resolve this issue by associating local field activity (i.e., spindle bursts) and unit activity in the barrel cortex of 5-day-old rats with whisker movements during wake and myoclonic twitches of the whiskers during active (REM) sleep. Barrel activity increased significantly within 500 ms of whisker movements, especially after twitches. Also, higher-amplitude movements were more likely to trigger barrel activity; when we controlled for movement amplitude, barrel activity was again greater after a twitch than a wake movement. We then inverted the analysis to assess the likelihood that increases in barrel activity were preceded within 500 ms by whisker movements: At least 55% of barrel activity was attributable to sensory feedback from whisker movements. Finally, when periods with and without movement were compared, 70–75% of barrel activity was movement-related. These results confirm the importance of sensory feedback from movements in driving activity in sensorimotor cortex and underscore the necessity of monitoring sleep-wake states to ensure accurate assessments of the contributions of the sensory periphery to activity in developing somatosensory cortex.
Arabidopsis ERF4 and MYB52 Transcription Factors Play Antagonistic Roles in Regulating Homogalacturonan De-methylesterification in Seed Coat Mucilage
Authors: Ding Anming , Tang Xianfeng , Han Linhe , Sun Jianlu , Ren Angyan , Sun Jinhao , Xu Zongchang , Hu Ruibo , Zhou Gongke , Kong Yingzhen 
Published: January 2020

ABSTRACTThe Arabidopsis (Arabidopsis thaliana) seed coat mucilage is a specialized cell wall with pectin as its major component. Pectin is synthesized in the Golgi apparatus with homogalacturonan fully methylesterified, but it must undergo de-methylesterification by pectin methylesterase (PME) after being secreted into the cell wall. This reaction is critical for pectin maturation, but the mechanisms of its transcriptional regulation remain largely unknown. Here, we show that the Arabidopsis ERF4 transcription factor positively regulates pectin de-methylesterification during seed development and directly suppresses the expression ofPME INHIBITOR13(PMEI13),14,15andSUBTILISIN-LIKE SERINE PROTEASE 1.7(SBT1.7). Theerf4mutant seeds showed repartitioning of mucilage between soluble and adherent layers as a result of decreased PME activity and increased degree of pectin methylesterification. ERF4 physically associates with and antagonizes MYB52 in activatingPMEI6,14andSBT1.7and MYB52 also antagonizes ERF4 activity in the regulation of downstream targets. Gene expression studies revealed that ERF4 and MYB52 have opposite effects on pectin de-methylesterification. Genetic analysis indicated that theerf4-2 myb52double mutant seeds show mucilage phenotype similar to wild-type. Taken together, this study demonstrates that ERF4 and MYB52 antagonize each other’s activity to maintain the appropriate degree of pectin methylesterification, expanding our understanding of how pectin de-methylesterification is fine-tuned by the ERF4-MYB52 transcriptional complex in the seed mucilage.One-sentence summaryArabidopsis ERF4 and MYB52 transcription factors interact and play antagonistic roles in regulating homogalacturonan de-methylesterification related genes in the seed coat mucilage.
STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts
Authors: Kitchen S.A. , Von Kuster G. , Vasquez Kuntz K.L. , Reich H.G. , Miller W. , Griffin S. , Fogarty Nicole D. , Baums I.B. 
Published: January 2020

AbstractStandardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral,Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two CaribbeanAcroporaspecies as well as their dominant dinoflagellate symbiont,Symbiodinium ‘fitti’.SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of the coral hybrids in Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the generaBreviolum, Cladocopium, andDurusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called theStandardTools forAcroporidGenotyping (STAG). In the workflow the user’s data is compared to the database of previously genotyped samples and generates a report of genet identification. The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning as well as be applied to downstream genomic analyses.
Geometric models for robust encoding of dynamical information into embryonic patterns
Authors: Jutras-Dubé Laurent , El-Sherif Ezzat , François Paul 
Published: January 2020

AbstractDuring development, cells gradually assume specialized fates via changes of transcriptional dynamics, sometimes even within the same developmental stage. For anterior-posterior (AP) patterning in metazoans, it has been suggested that the gradual transition from a dynamic genetic regime to a static one is encoded by different transcriptional modules. In that case, the static regime has an essential role in pattern formation in addition to its maintenance function. In this work, we introduce a geometric approach to study such transition. We exhibit two types of genetic regime transitions, respectively arising through local or global bifurcations. We find that the global bifurcation type is more generic, more robust, and better preserves dynamical information. This could parsimoniously explain common features of metazoan segmentation, such as changes of periods leading to waves of gene expressions, “speed/frequency-gradient” dynamics, and changes of wave patterns. Geometric approaches appear as possible alternatives to gene regulatory networks to understand development.
Prenylation of axonally translated proteins controls NGF-dependent axon growth
Authors: Scott-Solomon Emily , Kuruvilla Rejji 
Published: January 2020

SummaryCompartmentalized signaling is critical for cellular organization and specificity of functional outcomes in neurons. Here, we report that post-translational lipidation of newly synthesized proteins in axonal compartments allows for short-term and autonomous responses to extrinsic cues. Using conditional mutant mice, we found that protein prenylation is essential for sympathetic axon innervation of target organs. We identify a localized requirement for prenylation in sympathetic axons to promote axonal growth in response to the neurotrophin, Nerve Growth Factor (NGF). NGF triggers prenylation of proteins including the Rac1 GTPase in axons, counter to the canonical view of prenylation as constitutive, and strikingly, in a manner dependent on axonal protein synthesis. Newly prenylated proteins localize to TrkA-harboring endosomes in axons, and promote receptor trafficking necessary for axonal growth. Thus, coupling of prenylation to local protein synthesis presents a mechanism for spatially segregated cellular functions during neuronal development.
Poor hive thermoregulation produces an Allee effect and leads to colony collapse
Authors: Zeaiter Zeaiter , Myerscough Mary R. 
Published: January 2020

AbstractIn recent years the honey bee industry has bee experiencing increased loss of hives. The accumulation of multiple stressors on a hive potentially drives hive loss in various ways, including winter loss and colony collapse disorder. One of these stressors is the breakdown of thermoregulation inside the hive. For pupae to develop correctly into healthy adult bees, the temperature within the hive must be regulated by the hive bees to within a narrow range that ensures optimal development. Suboptimal development in adults affects their brain and flight muscles so bees becomes inefficient foragers with shorter life spans. We model the effect of thermoregulation on hive health using a system of delay differential equations that gives insights into how varying hive temperatures have an effect on the survival of the colony. We show that thermoregulatory stress has the capacity to drive colony loss in the model via a saddle-node bifurcation with an associated Allee effect.
Nipponbare and wild rice species as unexpected tolerance and susceptibility sources againstSchizotetranychus oryzae(Acari: Tetranychidae) mite infestation
Authors: Bufon Giseli , dos Reis Blasi Édina Aparecida , Lamb Thainá Inês , Adamski Janete Mariza , Schwambach Joséli , Ricachenevsky Felipe Klein , Bertolazi Amanda , Silveira Vanildo , Barbosa Lopes Mara Cristina , Sperotto Raul Antonio 
Published: January 2020

AbstractCultivated rice (Oryza sativaL.) is frequently exposed to multiple stresses, includingSchizotetranychus oryzaemite infestation. Rice domestication has narrowed the genetic diversity of the species, reducing the stress resistance and leading to a wide susceptibility. Therefore, wild rice species present an alternative to search for this lost variability. Aiming to observe the response of two wild rice species (Oryza barthiiandOryza glaberrima) and twoOryza sativagenotypes (cv. Nipponbare andO. sativaf.spontanea) toS. oryzaeinfestation, we used agronomic, physiological and molecular analyses. Surprisingly, analyses of leaf damage, histochemistry, chlorophyll concentration and chlorophyll fluorescence showed that the wild species present higher level of leaf damage, increased accumulation of H2O2and lower photosynthetic capacity when compared toO. sativagenotypes under infested conditions. Infestation did not affect plant height, but decreased tiller number, except in cv. Nipponbare, whose development was not affected. Infestation also caused the death of wild plants during the reproductive stage, unlikeO. sativagenotypes, which were able to tolerate stress and produce seeds. While infestation did not affect the weight of 1,000 grains in bothO. sativagenotypes, the number of panicles per plant was affected only inO. sativaf.spontanea, and the percentage of full seeds per panicle and seed length were increased only in cv. Nipponbare. Proteomic analysis allowed us to identify 195 differentially abundant proteins when comparing susceptible (O. barthii) and tolerant (O. sativacv. Nipponbare) genotypes under control and infested conditions. We found thatO. barthiihas a less abundant antioxidant arsenal. In addition, it is unable to modulate proteins involved with general metabolism and energy production under infested condition. In Nipponbare we found high abundance of detoxification-related proteins, general metabolic processes and energy production, which allows us to suggest that, under infested condition, the primary metabolism is maintained more active compared toO. barthii. Also, Nipponbare presents a greater abundance of defense-related proteins, such as osmotin, ricin B-like lectin, and protease inhibitors of the Bowman Birk trypsin inhibitor family, as well as higher levels of the compatible osmolyte Proline under infested condition. Identification of these differentially abundant proteins can be used as an important biotechnological tool in breeding programs that aim increased tolerance to phytophagous mite infestation.