bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional clustering of splice-altering variants in whole genome sequencing data reveals hidden heritability in rare variant disorder
Authors: Wang Yan , van Dijk Charlotte , Timpanaro Ilia , Hop Paul , Kenna Brendan , Kooyman Maarten , Aronica Eleonora , Pasterkamp R. Jeroen , van den Berg Leonard , Cooper-Knock Johnathan ,   Project MinE ALS sequencing consortium,   NYGC ALS consortium, Veldink Jan , Kenna Kevin 
Published: May 2023

AbstractExplaining missing heritability in rare disorders requires effective methods to interpret genetic variants. Sequence-to-function models such as SpliceAI support discovery of splice altering variants but filtering their output to identify pathogenic mutations remains challenging. We developed SpliPath to address 2 unmet needs in this process. First, SpliPath links the output of SpliceAI with reference transcriptomics data. This allows users to identify genetic variants that induce unannotated splice isoforms selectively expressed in disease models or patient tissue. Second, SpliPath aggregates variants with similar functional consequences into collapsed splicing quantitative trait loci (csQTLs) for more powerful genetic association analyses. We first used SpliPath to annotate whole genome sequencing (WGS) of 9,467 ALS patients and controls using RNAseq data from an iPSC model of TDP-43 dysfunction. Through this, SpliPath identified 53 variants predicted to enhance cryptic exon (CE) retention events associated with a core ALS pathomechanism. We then applied SpliPath to 294 ALS patients where both WGS and RNAseq were available and discovered missing genetic risk in the known ALS geneKIF5A. This revealed a first of kind intronic mutation hotspot that was validated using minigene reporter assays. Finally, using the same RNAseq data we then predicted 754 candidate csQTL for an independent WGS cohort of 6,625 ALS patients and 2,472 controls. Unbiased genomewide csQTL association testing successfully recoveredKIF5Aand nominatedEPG5as a potential pathogenic gene. These effects were undetectable using simplistic SpliceAI gene burden tests. Collectively, our study demonstrates the utility of SpliPath for uncovering missing heritability in rare disorders.
Prevalence of Erythromycin Resistantemm92-type Invasive Group A Streptococcal Infections in West Virginia, United States, 2021-2023
Authors: Powell Lillie M. , Choi Soo Jeon , Haught Breanna L. , Demkowicz Ryan , LaSala P. Rocco , Lukomski Slawomir 
Published: May 2023

BackgroundIncreasing incidence of invasive group AStreptococcus(iGAS) disease has been reported in Europe and United States over the past several years. Coupled with this are observations of higher rates of resistance to non-beta lactam antimicrobials.ObjectivesThe aim of this study was to characterize iGAS and pharyngitis isolates from West Virginia (WV), a region outside of the US national active bacteria core surveillance purview, where risk factors associated with iGAS infections are prevalent.MethodsSeventy-seven invasive group AStreptococcusisolates were collected from sixty-seven unique patients at the J.W. Ruby Memorial Hospital Clinical Microbiology Laboratory in WV from 2021-23. Invasive isolates and twenty unique pharyngitis isolates were tested for clindamycin and erythromycin susceptibilities in the clinical laboratory. Patient demographic and clinical information was retrieved from patient electronic health records. Isolates were further characterized based onemm-type and detection of MLSBresistance determinants.ResultsTwenty-six (39%) isolates were of a singleemm-type,emm92. Allemm92isolates were uniformly erythromycin/clindamycin resistant with inducible or constitutive MLSBresistance imparted by the plasmid-borneerm(T) gene. The majority ofemm92infections were associated with adult patients who reported intravenous drug use, whereas no pharyngitis infections were caused by anemm92strain. Overall, fifty-one (76%) of the sixty-seven iGAS isolates were determined to carry MLSBresistance.ConclusionsIsolates ofemm-type 92 predominated in this collection, were uniformly erythromycin/clindamycin resistant, and were associated with adult intravenous drug use but not with pediatric pharyngitis.
Striatal dopamine regulates sleep states and narcolepsy-cataplexy
Authors: Toth Brandon A. , Chang Katie S. , Burgess Christian R. 
Published: May 2023

AbstractDisruptions to sleep can be debilitating and have a severe effect on daily life. Patients with the sleep disorder narcolepsy suffer from excessive daytime sleepiness, disrupted nighttime sleep, and cataplexy - the abrupt loss of postural muscle tone (atonia) during wakefulness, often triggered by strong emotion. The dopamine (DA) system is implicated in both sleep-wake states and cataplexy, but little is known about the function of DA release in the striatum - a major output region of midbrain DA neurons - and sleep disorders. To better characterize the function and pattern of DA release in sleepiness and cataplexy, we combined optogenetics, fiber photometry, and sleep recordings in a murine model of narcolepsy (orexin−/−; OX KO) and in wildtype mice. Recording DA release in the ventral striatum revealed OX-independent changes across sleep-wake states as well as striking increases in DA release in the ventral, but not dorsal, striatum prior to cataplexy onset. Tonic low frequency stimulation of ventral tegmental efferents in the ventral striatum suppressed both cataplexy and REM sleep, while phasic high frequency stimulation increased cataplexy propensity and decreased the latency to rapid eye movement (REM) sleep. Together, our findings demonstrate a functional role of DA release in the striatum in regulating cataplexy and REM sleep.
Radip light-induced phosphorylation changes in microtubule related proteins in arabidopsis
Authors: Arico Denise Soledad , Wengier Diego Leonardo , Burachik Natalia B. , Mazzella María Agustina 
Published: May 2023

SummaryRapid hypocotyl elongation allows buried seedlings to reach the surface, where light triggers de-etiolation and inhibits hypocotyl growth mainly by phytochromes A, B and cryptochromes 1, 2. Dynamic phosphorylation/dephosphorylation events provide a mechanism to rapidly transduce light signals. Only recently we have begun to uncover the earliest phospho-signaling responders to light.Here, we report a large-scale phosphoproteomic analysis and identify 20 proteins that change their phosphorylation pattern after 20 min of white light pulse compared to darkness. Microtubule-associated proteins (MAPs) were highly overrepresented in this group. Among them, we studied CIP7 (COP1-INTERACTING-PROTEIN-7), which presented microtubule (MT) localization, in contrast to what was previously described. Phosphorylated isoform in Serine 915 (Sp915) of CIP7 was detected in etiolated seedlings but undetectable after a light pulse in the presence of photoreceptors, while its expression decays with long light exposure.The short hypocotyl phenotype and rearrangement of MTs in etiolatedcip7mutants are complemented by CIP7-YFP and the phospho-mimetic CIP7S915D-YFP, but not the phospho-null CIP7S915A-YFP suggesting that Sp915CIP7 is the active isoform that promotes hypocotyl elongation thorough MT reorganisation in darkness.Our results reveal that the small repertory of proteins that changes the phosphorylation status after a rapid light signal is tightly focused on MAPs; suggesting that phospho-regulation of microtubule-base processes are early targets during de-etiolation. The evidence on Sp915CIP7 supports this idea.
Wnt binding to Coatomer proteins directs secretion on exosomes independently of palmitoylation
Authors: Gurriaran-Rodriguez Uxia , Datzkiw David , Radusky Leandro G. , Esper Marie , Xiao Fan , Ming Hong , Fisher Solomon , Rojas Marina A. , De Repentigny Yves , Kothary Rashmi , Rojas Adriana L. , Serrano Luis , Hierro Aitor , Rudnicki Michael A. 
Published: May 2023

SummaryWnt proteins are secreted hydrophobic glycoproteins that act over long distances through poorly understood mechanisms. We discovered that Wnt7a is secreted on extracellular vesicles (EVs) following muscle injury. Structural analysis identified the motif responsible for Wnt7a secretion on EVs that we term the Exosome Binding Peptide (EBP). Addition of the EBP to an unrelated protein directed secretion on EVs. Disruption of palmitoylation, knockdown of WLS, or deletion of the N-terminal signal peptide did not affect Wnt7a secretion on purified EVs. Bio-ID analysis identified Coatomer proteins as candidates responsible for loading Wnt7a onto EVs. The crystal structure of EBP bound to the COPB2 coatomer subunit, the binding thermodynamics, and mutagenesis experiments, together demonstrate that a dilysine motif in the EBP mediates binding to COPB2. Other Wnts contain functionally analogous structural motifs. Mutation of the EBP results in a significant impairment in the ability of Wnt7a to stimulate regeneration, indicating that secretion of Wnt7a on exosomes is critical for normal regenerationin vivo. Our studies have defined the structural mechanism that mediates binding of Wnt7a to exosomes and elucidated the singularity of long-range Wnt signalling.
The Arabidopsis SWEET1 and SWEET2 uniporters recognize similar substrates despite differences in subcellular localization
Authors: Gwon Sojeong , Park Jihyun , Huque AKM Mahmudul , Cheung Lily S. 
Published: May 2023

AbstractSugars Will Eventually be Exported Transporters (SWEETs) are central for sugar allocation in plants. The SWEET family is vast, with approximately 20 homologs in most plant genomes. Despite extensive research on their structures and molecular functions, it is still unclear how diverse SWEETs recognize their substrates. Previous work using SweetTrac1, a biosensor constructed by the intramolecular fusion of a conformation-sensitive fluorescent protein in the plasma membrane transporter SWEET1 fromArabidopsis thaliana, identified common features in the transporter’s substrates. Here, we report SweetTrac2, a new biosensor based on the Arabidopsis vacuole membrane transporter SWEET2 and use it to explore the substrate specificity of this second protein. Our results show that SWEET1 and SWEET2 recognize similar substrates but some with different affinities. Sequence comparison and mutagenesis analysis support the conclusion that the differences in affinity depend on non-specific interactions involving key residues in the binding pocket. Furthermore, SweetTrac2 can be an effective tool for monitoring sugar transport at vacuolar membranes that would be otherwise challenging to study.
N-glycans show distinct spatial distribution in mouse brain
Authors: Noel Maxence , Cummings Richard D. , Mealer Robert G. 
Published: May 2023

ABSTRACTProtein N-linked glycosylation is a ubiquitous modification in the secretory pathway that plays a critical role in the development and function of the brain. N-glycans have a distinct composition and undergo tight regulation in the brain, but the spatial distribution of these structures remains relatively unexplored. Here, we systematically employed carbohydrate binding lectins with differing specificities to various classes of N-glycans and appropriate controls to identify multiple regions of the mouse brain. Lectins binding high-mannose-type N-glycans, the most abundant class of brain N-glycans, showed diffuse staining with some punctate structures observed on high magnification. Lectins binding specific motifs of complex N-glycans, including fucose and bisecting GlcNAc, showed more partitioned labeling, including to the synapse-rich molecular layer of the cerebellum. Understanding the distribution of N-glycans across the brain will aid future studies of these critical protein modifications in development and disease of the brain.
Citrate cross-feeding betweenPseudomonas aerguinosagenotypes supportslasRmutant fitness
Authors: Mould Dallas L. , Finger Carson E. , Botelho Nico , Stuut Stacie E. , Hogan Deborah A. 
Published: May 2023

ABSTRACTAcross the tree of life, clonal populations—from cancer to chronic bacterial infections — frequently give rise to subpopulations with different metabolic phenotypes. Metabolic exchange or cross-feeding between subpopulations can have profound effects on both cell phenotypes and population-level behavior. InPseudomonas aeruginosa, subpopulations with loss-of-function mutations in thelasRgene are common. Though LasR is often described for its role in density-dependent virulence factor expression, interactions between genotypes suggest potential metabolic differences. The specific metabolic pathways and regulatory genetics enabling such interactions were previously undescribed. Here, we performed an unbiased metabolomics analysis that revealed broad differences in intracellular metabolomes, including higher levels of intracellular citrate in LasR- strains. We found that while both strains secreted citrate, only LasR- strains, consumed citrate in rich media. Elevated activity of the CbrAB two component system which relieves carbon catabolite repression enabled citrate uptake. Within mixed genotype communities, we found that the citrate responsive two component system TctED and its gene targets OpdH (porin) and TctABC (transporter) required for citrate uptake were induced and required for enhanced RhlR signalling and virulence factor expression in LasR- strains. Enhanced citrate uptake by LasR- strains eliminates differences in RhlR activity between LasR+ and LasR- strains thereby circum-venting the sensitivity of LasR- strains to quorum sensing controlled exoproducts. Citrate cross feeding also induces pyocyanin production in LasR- strains co-cultured withStaphylococcus aureus, another species known to secrete biologically-active concentrations of citrate. Metabolite cross feeding may play unrecognized roles in competitive fitness and virulence outcomes when different cell types are together.IMPORTANCECross-feeding can change community composition, structure and function. Though cross-feeding has predominantly focused on interactions between species, here we unravel a cross-feeding mechanism between frequently co-observed isolate genotypes ofPseudomonas aeruginosa. Here we illustrate an example of how such clonally-derived metabolic diversity enables intraspecies cross-feeding. Citrate, a metabolite released by many cells includingP. aeruginosa, was differentially consumed between genotypes, and this cross-feeding induced virulence factor expression and fitness in genotypes associated with worse disease.
Single-cell RNA sequencing reveals microenvironment context-specific routes for epithelial-mesenchymal transition in pancreas cancer cells
Authors: Brown Brooke A. , Lazzara Matthew J. 
Published: May 2023

ABSTRACTIn the PDAC tumor microenvironment, multiple factors initiate the epithelial-mesenchymal transition (EMT) that occurs heterogeneously among transformed ductal cells, but it is unclear if different drivers promote EMT through common or distinct signaling pathways. Here, we use single-cell RNA sequencing (scRNA-seq) to identify the transcriptional basis for EMT in pancreas cancer cells in response to hypoxia or EMT-inducing growth factors. Using clustering and gene set enrichment analysis, we find EMT gene expression patterns that are unique to the hypoxia or growth factor conditions or that are common between them. Among the inferences from the analysis, we find that the FAT1 cell adhesion protein is enriched in epithelial cells and suppresses EMT. Further, the receptor tyrosine kinase AXL is preferentially expressed in hypoxic mesenchymal cells in a manner correlating with YAP nuclear localization, which is suppressed by FAT1 expression. AXL inhibition prevents EMT in response to hypoxia but not growth factors. Relationships between FAT1 or AXL expression with EMT were confirmed through analysis of patient tumor scRNA-seq data. Further exploration of inferences from this unique dataset will reveal additional microenvironment context-specific signaling pathways for EMT that may represent novel drug targets for PDAC combination therapies.
The Nβ motif of NaTrxh directs secretion as an endoplasmic reticulum transit peptide and variations might result in different cellular targeting
Authors: Zaragoza-Gómez Andre , García-Caffarel Emilio , Cruz-Zamora Yuridia , González James , Anaya-Muñoz Víctor H. , Cruz-García Felipe , Juárez-Díaz Javier Andrés 
Published: May 2023

AbstractSoluble secretory proteins with a signal peptide reach the extracellular space through the endoplasmic reticulum-Golgi conventional pathway. During translation, the signal peptide is recognised by the secretory recognition particle and results in a co-translational translocation to the endoplasmic reticulum to continue the secretory pathway. However, soluble secretory proteins lacking a signal peptide are also abundant, and several unconventional (endoplasmic reticulum/Golgi independent) pathways have been proposed and some demonstrated. This work describes new features of the secretion signal called Nβ, originally identified in NaTrxh, a plant extracellular thioredoxin, that does not possess an orthodox signal peptide. We provide evidence that other proteins, including thioredoxins typeh, with similar sequences are also signal peptide-lacking secretory proteins. To be a secretion signal, positions 5, 8 and 9 must contain neutral residues –a negative residue in position 9 in animal proteins– to maintain the Nβ motif negatively charged and a hydrophilic profile. Moreover, our results suggest that the NaTrxh translocation to the endoplasmic reticulum occurs as a post-translational event. Finally, the Nβ motif sequence at the N- or C-terminus could be a feature that may help to predict protein localisation, mainly in plant and animal proteins.
LQR and LQG control of the helicopter during landing on the ship deck
Authors: Topczewski Sebastian , Bibik Przemyslaw 
Published: May 2023

Purpose
The purpose of this study is to test the performance of the designed automatic control system based on the Linear Quadratic Regulator (LQR) and Linear Quadratic Gaussian (LQG) algorithms during landing of the helicopter on the ship deck. This paper is a further development of the series based on Topczewski et al. (2020).

Design/methodology/approach
The system consists of two automatic control algorithms based on LQR and the LQG. It is integrated with the ship motion prediction system based on autoregressive algorithm with parameters calculated using Burg’s method. It is assumed that the source of necessary navigation data is integrated Inertial Navigation System with Global Positioning System. Landing of the helicopter on the ship deck is performed in automatic way, based on the preselected procedure. Performance of the control system is analyzed when all necessary navigation data is available for the system and in case when one of the parameters is unavailable during performing the procedure.

Findings
In this paper, description of the designed control system developed for performing the approach and landing of the helicopter using selected procedure is presented. Helicopter dynamic model is validated using the manufacturer data and by test pilots, overview is presented. Necessary information about ship motion model is also included. Tests showing mission performance while using LQR and LQG algorithms applied to the control system are presented and analyzed, taking into account both situations when full navigation data is available/unavailable for the control system.

Practical implications
Results of the system performance analyses can be used for selection of the proper control methodology for prospective helicopters autopilots. Furthermore, the system can be used to analyze the mission safety when information about one of the navigation parameters is identified by the navigation system as unavailable or incorrect and therefore unavailable during landing on the ship deck.

Originality/value
In this paper, control system dedicated for the automatic landing of the helicopter on the ship deck, based on two different control algorithms is presented. Influence of lack of information about one of the navigation parameters on the mission performance is analyzed.
Analysis of longitudinal dynamic stability of tandem wing aircraft
Authors: Figat Marcin , Kwiek Agnieszka 
Published: May 2023

Purpose
Tandem wing aircrafts belong to an unconventional configurations group, and this type of design is characterised by a strong aerodynamic coupling, which results in lower induced drag. The purpose of this paper is to determine whether a certain trend in the wingspan impact on aircraft dynamic stability can be identified. The secondary goal was to compare the response to control of flaps placed on a front and rear wing.

Design/methodology/approach
The aerodynamic data and control derivatives were obtained from the computational fluid dynamics computations performed by the MGAERO software. The equations of aircraft longitudinal motion in a state space form were used. The equations were built based on the aerodynamic coefficients, stability and control derivatives. The analysis of the dynamic stability was done in the MATLAB by solving the eigenvalue problem. The response to control was computed by the step response method using MATLAB.

Findings
The results of this study showed that because of a strong aerodynamic coupling, a nonlinear relation between the wing size and aircraft dynamic stability proprieties was observed. In the case of the flap deflection, stronger oscillation was observed for the front flap.

Originality/value
Results of dynamic stability of aircraft in the tandem wing configuration can be found in the literature, but those studies show outcomes of a single configuration, while this paper presents a comprehensive investigation into the impact of wingspan on aircraft dynamic stability. The results reveal that because of a strong aerodynamic coupling, the relation between the span factor and dynamic stability is nonlinear. Also, it has been demonstrated that the configuration of two wings with the same span is not the optimal one from the aerodynamic point of view.
Risk-adjusted farm returns and farm size
Authors: Noumir Ashraf M. , Langemeier Michael R. , Mallory Mindy L. 
Published: May 2023

PurposeThe average U.S. farm size has risen dramatically over the last three decades. Motives for this trend are the subject of a large body of literature. This study incorporates farm size risk and return analysis into this research stream. In this paper, cross-sectional and temporal relations between farm size and returns are examined and characterized.Design/methodology/approachRelying on farm level panel data from Kansas Farm Management Association (KFMA) for 140 farms from 1996 to 2018, this article examines the relationship between farm size and returns and investigates whether farm size is related to risk. Two measures of farm returns are used: excess return on equity and risk-adjusted return on equity. Value of farm production and total farm acres are used as measures of farm size.FindingsFindings suggest a significant and positive relationship between farm size and excess return on equity as well as farm size and risk-adjusted return on equity. However, this return premium associated with farm size is not associated with additional risk. Stated differently, farm size can be viewed as a farm characteristic that is associated with higher return without additional risk.Practical implicationsThese findings provide further support for ongoing farm consolidation.Originality/valueThe results suggest the trend towards consolidation in production agriculture is likely to continue. Larger farms bear less risk.