bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure-Aware Annotation of Leucine-rich Repeat Domains
Authors: Xu Boyan , Cerbu Alois , Lim Daven , Tralie Christopher J , Krasileva Ksenia 
Published: November 2023

AbstractProtein domain annotation is typically done by predictive models such as HMMs trained on sequence motifs. However, sequence-based annotation methods are prone to error, particularly in calling domain boundaries and motifs within them. These methods are limited by a lack of structural information accessible to the model. With the advent of deep learning-based protein structure prediction, existing sequenced-based domain annotation methods can be improved by taking into account the geometry of protein structures. We develop dimensionality reduction methods to annotate repeat units of the Leucine Rich Repeat solenoid domain. The methods are able to correct mistakes made by existing machine learning-based annotation tools and enable the automated detection of hairpin loops and structural anomalies in the solenoid. The methods are applied to 127 predicted structures of LRR-containing intracellular innate immune proteins in the model plantArabidopsis thalianaand validated against a benchmark dataset of 172 manually-annotated LRR domains.Author summaryIn immune receptors across various organisms, repeating protein structures play a crucial role in recognizing and responding to pathogen threats. These structures resemble the coils of a slinky toy, allowing these receptors to adapt and change over time. One particularly vital but challenging structure to study is the Leucine Rich Repeat (LRR). Traditional methods that rely just on analyzing the sequence of these proteins can miss subtle changes due to rapid evolution. With the introduction of protein structure prediction tools like AlphaFold 2, annotation methods can study the coarser geometric properties of the structure. In this study, we visualize LRR proteins in three dimensions and use a mathematical approach to ‘flatten’ them into two dimensions, so that the coils form circles. We then used a mathematical concept called winding number to determine the number of repeats and where they are in a protein sequence. This process helps reveal their repeating patterns with enhanced clarity. When we applied this method to immune receptors from a model plant organism, we found that our approach could accurately identify coiling patterns. Furthermore, we detected errors made by previous methods and highlighted unique structural variations. Our research offers a fresh perspective on understanding immune receptors, potentially influencing studies on their evolution and function.
Structural basis of epitope recognition by anti-alpha synuclein antibodies MJFR14-6-4-2
Authors: Liekniņa Ilva , Panteļejevs Teodors , Lends Alons , Reimer Lasse , Jaudzems Kristaps , El-Turabi Aadil , Gram Hjalte , Jensen Poul Henning , Tārs Kaspars 
Published: November 2023

AbstractIntraneuronal α-synuclein inclusions in the brain are hallmarks of so-called Lewy body diseases - Parkinson’s disease and Dementia with Lewy bodies. Lewy bodies are cytoplasmic inclusions, containing mainly aggregated α-synuclein together with some other proteins including ubiquitin, neurofilament protein, and alpha B crystallin. In its monomeric form, α-synuclein is predominantly localized in nerve terminals, regulating neuronal transmission and synaptic vesicle trafficking. Monomeric α-synuclein lacks a well-defined three-dimensional structure and is considered an intrinsically disordered protein. However, in diseased cells α-synuclein aggregates into oligomeric and fibrillar amyloid species, which can be detected using aggregate-specific antibodies. Here we investigate the aggregate specificity of rabbit monoclonal MJFR14-6-4-2 antibodies, preferentially recognizing aggregated α-synuclein species. We conclude that partial masking of epitope in unstructured monomer in combination with a high local concentration of epitopes instead of distinct epitope conformation is the main reason for apparent selectivity towards various aggregates, including oligomers, fibrils, and artificial virus-like particle constructs bearing multiple copies of the MJFR14-6-4-2 epitope. Based on the structural insight, we were able to express mutant α-synuclein that when fibrillated are unable to bind MJFR14-6-4-2. Using these “stealth” fibrils as a tool for seeding cellular α-synuclein aggregation, provides superior signal/noise ratio for detection of cellular α-synuclein aggregates by MJFR14-6-4-2 immunocytochemistry. Our data provide a molecular level understanding of specific recognition of toxic amyloid oligomers, which is critical for the development of inhibitors against synucleinopathies.
A multilocus perspective on the evolutionary dynamics of multistrain pathogens
Authors: McLeod David V. , Bank Claudia , Gandon Sylvain 
Published: November 2023

AbstractMany human pathogens, including malaria, dengue, influenza,Streptococcus pneumoniae, and cytomegalovirus, coexist as multiple genetically distinct strains. Understanding how these multistrain pathogens evolve is of critical importance for forecasting epidemics and predicting the consequences of vaccination. One factor believed to play an important role is naturally acquired immunity. Consequently, a large body of research has sought to predict how acquired immunity molds the genomics of pathogen populations (i.e., what shapes pathogen strain structure). The diversity of existing models has resulted in conflicting evolutionary predictions, and has sparked an ongoing debate about which predictions are most broadly applicable. Here, we adopt a multilocus population genetics perspective that unifies the predictions of existing models. We identify three key factors that determine the role of naturally acquired immunity in the evolution of pathogen strain structure: (i) the strength and specificity of immune protections, (ii) the dynamic immunological landscape, and (iii) the number of loci coding for the antigens of the pathogen. Isolating and discussing these three factors clarifies the relationship among previous models of multistrain dynamics, and establishes a solid theoretical foundation for the study of the evolutionary epidemiology of multistrain pathogens.
The actin-associated protein Kaptin modulates F-actin barbed-end dynamics
Authors: Dutta Priyanka , Maiti Ipshita , Ghose Aurnab , Chauhan Radha , Maiti Sankar 
Published: November 2023

AbstractLiving cells require a dynamic and precisely regulated actin cytoskeleton to carry out normal cellular functions. In addition to well-established actin cytoskeleton regulators, such as nucleators, capping proteins, and bundlers, cells likely have uncharacterized modulators that regulate cytoskeleton dynamics, the detailed functions of which are not yet fully understood. In this study, we conducted biochemical exploration to identify the actin-regulatory activity of Kaptin (KPTN), a protein known to co-localize with actin-rich structures at the cell’s periphery. Using single-molecule assays, we demonstrated that KPTN inhibits actin nucleation. Our results revealed that KPTN possesses a novel barbed-end capping activity, which stabilizes and bundles actin filaments. Structural modeling, based on AlphaFold, suggests that KPTN is a member of the WD-repeat-containing protein family. Furthermore, we identified a crucial cationic residue in the putative N-terminal beta-propeller region of KPTN that plays a critical role in modulating actin dynamics. In summary, our data unveil the mechanistic underpinning functions of KPTN and establish its novel role as a regulator of the actin cytoskeleton.
Galectin-9 regulates dendritic cell polarity and uropod contraction by modulating RhoA activity
Authors: Franken Guus , Cuenca-Escalona Jorge , Stehle Isabel , van Reijmersdal Vince , Rodgers Furones Andrea , Gokhale Rohit , Classens René , Di Blasio Stefania , Dolen Yusuf , van Spriel Annemiek B. , Querol Cano Laia 
Published: November 2023

AbstractAdaptive immunity relies on dendritic cell (DC) migration to transport antigens from tissues to lymph nodes. Galectins, a family of β-galactoside-binding proteins, control cell membrane organisation, exerting crucial roles in multiple physiological processes.Here, we report a novel mechanism underlying cell polarity and uropod retraction. We demonstrate that galectin-9 regulates chemokine-driven and basal DC migration both in humans and mice, indicating a conserved function for this lectin. We identified the underlying mechanism, namely a deficiency in cell rear contractility mediated by galectin-9 interaction with CD44 that in turn regulates RhoA activity. Analysis of DC motility in the 3D tumour-microenvironment revealed galectin-9 is also required for DC infiltration. Moreover, exogenous galectin-9 rescued the motility of tumour-immunocompromised human blood DCs, validating the physiological relevance of galectin-9 in DC migration and underscoring its implications for DC-based immunotherapies.Our results identify galectin-9 as a necessary mechanistic component for DC motility and highlight a novel role for the lectin in regulating cell polarity and contractility.
Allele-specific digital PCR enhances precision and sensitivity in the detection and quantification of copy number alterations in heterogeneous DNA samples: anin silicoandin vitrovalidation study
Authors: Nell Rogier J. , Versluis Mieke , Zoutman Willem H. , Luyten Gregorius P.M. , Jager Martine J. , van der Velden Pieter A. 
Published: November 2023

AbstractThe analysis of genetic variation is of crucial importance in cancer care. Measuring copy number alterations, however, remains challenging in heterogenous DNA samples, such as (liquid) biopsies. Using digital PCR, these alterations are classically studied by comparing the abundances of the target of interest to a stable genomic reference. Alternatively, copy numbers may be quantified based on the allelic (im)balance of a heterozygous common single-nucleotide polymorphism (SNP). In this study, the accuracy, practicability, precision and sensitivity of both approaches are evaluatedin silicousing a newly introduced R library ‘digitalPCRsimulations’, andin vitroby analysing control samples and uveal melanoma specimens in duplex and multiplex experimental setups.Our analyses show that both methodologies are equally effective, as long as a stable reference is identified (classic approach) and the allelic imbalance is caused by the loss or gain/amplification of only one of both alleles (SNP-based approach). Though, heterogeneous copy number alterations can be measured with more precision and sensitivity using the SNP-based approach. In DNA from formalin-fixed and paraffin-embedded samples, the latter approach can also overcome technical artefacts causing inconsistencies between DNA amplicons.In conclusion, the limits of detecting copy number alterations in heterogeneous DNA can be improved using the SNP-based approach. Consequently, an increasing number of clinical samples may be successfully analysed, providing novel potential for the identification, prognostication and management of cancer.
Body mass index and all-cause mortality in HUNT and UK Biobank studies: revised non-linear Mendelian randomization analyses
Authors: Burgess Stephen , Sun Yi-Qian , Zhou Ang , Buck Christopher , Mason Amy M , Mai Xiao-Mei 
Published: November 2023

ABSTRACTObjectivesTo estimate the shape of the causal relationship between body mass index (BMI) and mortality risk in a Mendelian randomization framework.DesignMendelian randomization analyses of two prospective population-based cohorts.SettingIndividuals of European ancestries living in Norway or the United Kingdom.Participants56,150 participants from the Trøndelag Health Study (HUNT) in Norway and 366,385 participants from UK Biobank recruited by postal invitation.OutcomesAll-cause mortality and cause-specific mortality (cardiovascular, cancer, non-cardiovascular non-cancer).ResultsA previously published non-linear Mendelian randomization analysis of these data using the residual stratification method suggested a J-shaped association between genetically-predicted BMI and mortality outcomes with the lowest mortality risk at a BMI of around 25 kg/m2. However, the “constant genetic effect” assumption required by this method is violated. The re-analysis of these data using the more reliable doubly-ranked stratification method still indicated a J-shaped relationship, but with less precision in estimates at the lower end of the BMI distribution. Evidence for a harmful effect of reducing BMI at low BMI levels was only present in some analyses, and where present, only below 20 kg/m2. A harmful effect of increasing BMI for all-cause mortality was evident above 25 kg/m2, for cardiovascular mortality above 24 kg/m2, for non-cardiovascular non-cancer mortality above 26 kg/m2, and for cancer mortality above 30 kg/m2. In UK Biobank, the association between genetically-predicted BMI and mortality at high BMI levels was stronger in women than in men.ConclusionThis research challenges findings from previous conventional observational epidemiology and Mendelian randomization investigations that the lowest level of mortality risk is at a BMI level of around 25 kg/m2. Our results provide evidence that reductions in BMI will only increase mortality risk for a small proportion of the population, and increases in BMI will increase mortality risk for those with BMI above 25 kg/m2.Strengths and limitations of the studyMendelian randomization design minimizes bias due to confounding and reverse causationLarge sample sizes enable powerful analyses even in low BMI individualsValidity of the genetic variants as instrumental variables cannot be verifiedBias due to selection could be non-negligible and could vary across strataAll estimates are averaged across a stratum of the population; individual effects of raising or lowering BMI may vary between individuals
Biomarkers of neurodegeneration in schizophrenia: Systematic Review and Meta-Analysis
Authors: Wilson Jack C. , Liu Kathy Y. , Jones Katherine , Mahmood Jansher , Arya Utkarsh , Howard Robert 
Published: November 2023

AbstractQuestionDoes neurodegenerative disease underlie the increased rate of dementia observed in older people with schizophrenia? Several studies have reported a higher prevalence of dementia in people with schizophrenia compared to the general population. This may reflect higher risk of developing neurodegenerative diseases such as vascular dementia or Alzheimer’s disease (AD). Alternatively, this may reflect nonpathological, age-related cognitive decline in a population with low cognitive reserve. We reviewed the literature on neurodegeneration markers in older people with schizophrenia and dementia or cognitive impairment to establish whether neurodegenerative disease underlies the increased rate of dementia observed.Study Selection and AnalysisWe reviewed papers that compared post-mortem findings, hippocampal volume, or CSF markers of AD, in schizophrenia patients with evidence of cognitive impairment (age ≥45 years) with controls. Most studies investigated AD neuropathology. We subsequently performed a meta-analysis of post-mortem studies that compared amyloid-β plaques (APs) or neurofibrillary tangles (NFTs) in cognitively impaired schizophrenia patients to either controls or an AD group.FindingsNo studies found significant increase of amyloid-β plaques (APs) or neurofibrillary tangles (NFTs) in cognitively impaired schizophrenia patients compared to controls. All postmortem studies that compared APs or NFTs in schizophrenia patients to an AD group found significantly more APs or NFTs in AD. No studies found significant differences in CSF total tau or phosphorylated tau between schizophrenia patients and controls. Two studies found significantly decreased CSF Aβ42 in schizophrenia compared to patients. Findings for hippocampal volume were mixed.ConclusionsStudies have not found higher rates of AD-related pathology in cognitively impaired schizophrenia individuals compared to controls. Higher rates of dementia identified in population studies may reflect lack of specificity in clinical diagnostic tools used to diagnose dementia.
Pilot study of a multifaceted nurse-led antimicrobial stewardship intervention in residential aged care
Authors: Jokanovic Natali , Lee Sue J , Haines Terry , Hilmer Sarah N , Jeon Yun-Hee , Travis Laura , Ayton Darshini , Watson Eliza , Tsindos Tess , Stewardson Andrew J , Stuart Rhonda L , Cheng Allen C , Peel Trisha N , Peleg Anton Y 
Published: November 2023

AbstractObjectiveTo evaluate the feasibility of a nurse-led antimicrobial stewardship (AMS) program in two Australian residential aged care homes (RACHs) to inform a stepped-wedged, cluster randomised controlled trial (SW-cRCT).MethodsA mixed-methods pilot study of a nurse-led AMS program was performed in two RACHs in Victoria, Australia between July and December 2019. The AMS program comprised education, infection assessment and management guidelines, and documentation to support appropriate antimicrobial use in urinary, lower respiratory and skin/soft tissue infections. The program was implemented over three phases over five months: 1) pre-implementation education and integration (1-month); 2) implementation of the intervention (3-months); 3) post-intervention evaluation (1-month). Baseline RACH and resident data and weekly infection and antimicrobial usage was collected. Feedback on intervention resources and implementation barriers were identified from semi-structured interviews, online staff questionnaire and researcher field notes.ResultsSix key barriers to implementation of the intervention were identified and used to refine the intervention; aged care staffing and capacity, access to education, resistance to practice change, role of staff in AMS, leadership and ownership of the intervention at the RACH and organisation-level, and expectations from family. A total 61 antimicrobials were prescribed for 40 residents over the 3-month intervention period. Overall, 48% of antibiotics did not meet the minimum criteria for appropriate initiation (respiratory 73%; urinary: 54%; skin/soft tissue: 0%).ConclusionsSeveral barriers and opportunities to improve the implementation of AMS in RACHs were identified. Findings were used to inform a revised intervention to be evaluated in a larger SW-cRCT.
Improving imputation quality in Samoans through the integration of population-specific sequences into existing reference panels
Authors: Carlson Jenna C. , Krishnan Mohanraj , Liu Shuwei , Anderson Kevin J. , Zhang Jerry Z. , Yapp Toni-Ann J. , Chiyka Elizabeth A. , Dikec Devin A. , Cheng Hong , Naseri Take , Reupena Muagututi‘a Sefuiva , Viali Satupa‘itea , Deka Ranjan , Hawley Nicola L. , McGarvey Stephen T. , Weeks Daniel E. , Minster Ryan L. 
Published: November 2023

AbstractGenotype imputation is fundamental to association studies, and yet even gold standard panels like TOPMed are limited in the populations for which they yield good imputation. Specifically, Pacific Islanders are poorly represented in extant panels. To address this, we constructed an imputation reference panel using 1,285 Samoan individuals with whole-genome sequencing, combined with 1000 Genomes (1000G) samples, to create a reference panel that better represents Pacific Islander, specifically Samoan, genetic variation. We compared this panel to 1000G and TOPMed panels based on imputed variants using genotyping array data for 1,834 Samoan participants who were not part of the panels. The 1000G + 1285 Samoan panel yielded up to 2.25-2.76 times more well-imputed (r2≥ 0.80) variants than TOPMed and 1000G. There was improved imputation accuracy across the minor allele frequency (MAF) spectrum, although it was more pronounced for variants with 0.01 ≤ MAF ≤ 0.05. Imputation accuracy (r2) was greater for population-specific variants (high fixation index, FST) and those from larger haplotypes (high LD score). The gain in imputation accuracy over TOPMed was largest for small haplotypes (low LD score), reflecting the Samoan panel’s ability to capture population-specific variation not well tagged by other panels. We also augmented the 1000G reference panel with varying numbers of Samoan samples and found that panels with 48 or more Samoans included outperformed TOPMed for all variants with MAF ≥ 0.001. This study identifies variants with improved imputation using population-specific reference panels and provides a framework for constructing other population-specific reference panels.
How do clinical researchers generate data-driven scientific hypotheses? Cognitive events using think-aloud protocol
Authors: Jing Xia , Draghi Brooke N. , Ernst Mytchell A. , Patel Vimla L. , Cimino James J. , Shubrook Jay H. , Zhou Yuchun , Liu Chang , De Lacalle Sonsoles 
Published: November 2023

AbstractObjectivesThis study aims to identify the cognitive events related to information use (e.g., “Analyze data”, “Seek connection”) during hypothesis generation among clinical researchers. Specifically, we describe hypothesis generation using cognitive event counts and compare them between groups.MethodsThe participants used the same datasets, followed the same scripts, used VIADS (avisual interactiveanalysis tool for filtering and summarizing largedatasets coded with hierarchical terminologies) or other analytical tools (as control) to analyze the datasets, and came up with hypotheses while following the think-aloud protocol. Their screen activities and audio were recorded and then transcribed and coded for cognitive events.ResultsThe VIADS group exhibited the lowest mean number of cognitive events per hypothesis and the smallest standard deviation. The experienced clinical researchers had approximately 10% more valid hypotheses than the inexperienced group. The VIADS users among the inexperienced clinical researchers exhibit a similar trend as the experienced clinical researchers in terms of the number of cognitive events and their respective percentages out of all the cognitive events. The highest percentages of cognitive events in hypothesis generation were “Using analysis results” (30%) and “Seeking connections” (23%).ConclusionVIADS helped inexperienced clinical researchers use fewer cognitive events to generate hypotheses than the control group. This suggests that VIADS may guide participants to be more structured during hypothesis generation compared with the control group. The results provide evidence to explain the shorter average time needed by the VIADS group in generating each hypothesis.What is already known on this topichow hypotheses were generated when solving a puzzle or a medical case and the reasoning differences between experienced and inexperienced physicians.What this study addsOur study facilitates our understanding of how clinical researchers generate hypotheses with secondary data analytical tools and datasets, the cognitive events used during hypothesis generation in an open discovery context.How this study might affect research, practice, or policyOur work suggests secondary data analytical tools and visualization may facilitate hypothesis generation among inexperienced clinical researchers regarding the number of hypotheses, average time, and the cognitive events needed per hypothesis.