bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimizing Reference Bias with an Impute-First Approach
Authors: Vaddadi Kavya , Mun Taher , Langmead Ben 
Published: December 2023

AbstractPangenome indexes reduce reference bias in sequencing data analysis. However, bias can be reduced further by using a personalized reference, e.g. a diploid human reference constructed to match a donor individual’s alleles. We present a novel impute-first alignment framework that combines elements of genotype imputation and pangenome alignment. It begins by genotyping the individual using only a subsample of the input reads. It next uses a reference panel and efficient imputation algorithm to impute a personalized diploid reference. Finally, it indexes the personalized reference and applies a read aligner, which could be a linear or graph aligner, to align the full read set to the personalized reference. This framework achieves higher variant-calling recall (99.54% vs. 99.37%), precision (99.36% vs. 99.18%), and F1 (99.45% vs. 99.28%) compared to a graph pangenome aligner. The personalized reference is also smaller and faster to query compared to a pangenome index, making it an overall advantageous choice for whole-genome DNA sequencing experiments.
Human naïve stem cell models reveal the role of FGF in hypoblast specification in the human embryo
Authors: Dattani Anish , Corujo-Simon Elena , Radley Arthur , Heydari Tiam , Taheriabkenar Yasaman , Carlisle Francesca , Lin Simeng , Mill Jonathan , Zandstra Peter , Nichols Jennifer , Guo Ge 
Published: December 2023

SUMMARYThe hypoblast is an essential extra-embryonic tissue set aside within the inner cell mass early in mammalian embryo development, in the blastocyst. Research with human embryos is challenging. Thus, stem cell models that reproduce hypoblast differentiation provide valuable alternatives. We show here that human naïve PSC to hypoblast differentiation proceeds via reversion to a transitional ICM-like state, from which hypoblast emerges in concordance with the trajectory in human blastocysts. We identified a window when fibroblast growth factor (FGF) signalling is critical for hypoblast specification. Revisiting FGF signalling in human embryos revealed that inhibition in the early blastocyst suppresses hypoblast formation.In vitro, the induction of hypoblast is synergistically enhanced by limiting trophectoderm and epiblast fates. This finding revises previous reports and establishes a conservation in lineage specification between mouse and human. Overall, this study demonstrates the utility of human naïve PSC-based models in elucidating mechanistic features of early human embryogenesis.
Plasmacytoid dendritic cells (pDCs) display surface but not membrane-bound IgE across a broad range of total serum IgE levels
Authors: Chen Jonathan H. , MacGlashan Donald W. , McCormack Amanda , Schroeder John T. , Tversky Jody R. 
Published: December 2023

AbstractIntroductionPlasmacytoid dendritic cells (pDCs) are unique antigen presenting cells that may be implicated in allergic disease because they bind IgE on their surface and modulate important Th1/Th2 cytokine responses. While conducting in vitro experiments using excess omalizumab to capture IgE, we discovered that this immunoglobulin is not readily removed from pDC to the same extent observed for basophils suggesting that a portion of the IgE on pDC is membrane bound.MethodsBasophils and pDC were prepared from leukopacks using established protocols. In order to isolate PBMCs, blood was also drawn from consenting donors with a wide range in total serum IgE levels. B cells and pDCs were identified by flow cytometry by gating on CD19/CD27 and BDCA2/CD123, respectively. Quilizumab, a mouse anti-human monoclonal IgG1 antibody with specificity only for membrane-bound IgE, was used to detect this molecule in both cell types.ResultsWhen used in vitro at 1.5 mg/ml, omalizumab removed ∼80-90% of the IgE expressed by basophils. In contrast, IgE expression decreased only 30-40% on pDC treated likewise. Upon analyzing pDC for membrane-bound IgE, there was no significant difference in number of target-bound cells and mean fluorescence between the mouse isotype control and quilizumab among pDCs (P= 0.125, 0.165). However, the ratio of the proportion of target-bound CD19+27+B cells compared to other cells was 32:1 for isotype (P< 0.001) and 54:1 for quilizumab (P= 0.015).ConclusionOverall, this study demonstrates that while pDCs express significant levels of FcεRI that binds IgE to the surface, there is no appreciable amount of membrane-bound IgE noted. The reason for omalizumab’s poor ability to remove IgE from pDCs remains unknown.
PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS
Authors: Clasen Milan Avila , Ruwolt Max , Kurt Louise U. , Gozzo Fabio C , Wang Shuai , Chen Tao , Carvalho Paulo C , Lima Diogo Borges , Liu Fan 
Published: December 2023

AbstractAdvancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here, we develop wellcontrolled XL-MS standards comprising hundreds of recombinant proteins that are systematically mixed for cross-linking. We use one standard dataset to guide the development of Scout, a search engine for XL-MS with MS-cleavable cross-linkers. Using other, independent datasets from our standards as well as published datasets, we benchmark the performance of Scout and existing XL-MS software. This demonstrates that Scout offers the best combination of speed, sensitivity, and false-discovery rate control. These results illustrate how our large recombinant standards can support the development of XL-MS analysis tools and evaluation of XL-MS results.
Unraveling Unbreakable Hairpins: Characterizing RNA secondary structures that are persistent after dinucleotide shuffling
Authors: Pratt Alyssa A , Hendrix David A 
Published: December 2023

AbstractThe sequence of nucleotides that make up an RNA determines its structure, which determines its function. The RNA hairpin, also known as a stem-loop, is a ubiquitous and fundamental feature of RNA secondary structure. A common method of randomizing an RNA sequence is dinucleotide shuffling with the Altschul-Erickson algorithm, which preserves the dinucleotide content of the sequence. This algorithm generates randomized sequences by sampling Eulerian paths through the de Bruijn graph representation of the original sequence. We identified a subset of RNA hairpins in the bpRNA-1m meta-database that always form hairpins after repeated application of dinucleotide shuffling. We investigated these “unbreakable hairpins” and found several common properties. First, we found that unbreakable hairpins had on average similar folding energies compared to other hairpins of similar lengths, although they frequently contained ultra-stable hairpin loops. We found that they tend to be split by purines and pyrimidines on opposite strands of the stem. Furthermore, we found that this specific sequence feature restricts the number of distinct Eulerian paths through their de Bruijn graph representation, resulting in a small number of distinguishable dinucleotide-shuffled sequences. Beyond this algorithmic means of identification, these distinct sequences may have biological significance because we found that a significant percentage occur in a specific location of 16S ribosomal RNAs. Finally, we present a formula to calculate the number of possible unique dinucleotide shuffled sequences for an input RNA sequence, which has utility for the general application of the Altschul-Erickson algorithm.
Complex ecosystems lose stability when resource consumption is out of niche
Authors: Liu Yizhou , Hu Jiliang , Lee Hyunseok , Gore Jeff 
Published: December 2023

AbstractNatural communities exhibit diverse dynamics, encompassing global stability, multi-stability, periodic oscillations, and chaotic fluctuations in species abundances. Resource-consumer interactions provide a lens for mechanistic understanding of community behaviors, yet only a globally stable equilibrium can exist in the original MacArthur resource-consumer model. Here we find that diverse dynamics emerges when species consume resources that contribute little to their own growth. Key to understanding these results is comparison of niche range (difference between growth-promoting resources of similar species) and consumption range (difference between growth-promoting resources and the resources that are actually consumed). If the consumption range is small, we observe global stability as in the MacArthur model. But when consumption range increases to about the niche range, stability is lost, giving rise to emergent alternative stable states, globally stable states but with species extinction, and slightly later, persistent fluctuations. Given its importance in dictating stability, we define the ratio between consumption and niche ranges as encroachment, and find that it predicts key community properties like diversity and attractor basins even after the instability transition. In particular, after the loss of stability (encroachment greater than one), species extinction increases approximately linearly with encroachment. Since encroachment relies only on intrinsic species properties, community stability is resilient to environmental changes such as resource supply and mortality rate. Encroachment provides a framework for capturing resource competition due to growth-consumption inconsistency in complex communities as well as a robust quantitative characterization of the resulting emergent dynamics.
CTCF-mediated 3D chromatin predetermines the gene expression program in the male germline
Authors: Kitamura Yuka , Takahashi Kazuki , Maezawa So , Munakata Yasuhisa , Sakashita Akihiko , Kaplan Noam , Namekawa Satoshi H. 
Published: December 2023

AbstractSpermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution 3D chromatin architecture of male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin predetermines the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin contacts on autosomes pre-establish meiosis-specific super-enhancers (SE). These meiotic SE recruit the master transcription factor A-MYB in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 resolves chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB establish the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization enforces epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.
Preference and Perception of Indian Caregivers Towards Formal Long–Term Supportive Services – A Mixed–Methods Study
Authors: Ghosh Subharati , Mathur Arvind 
Published: December 2023

AbstractPurpose of the StudyIn India, the rate of population aging, the greater burden of chronic disease-related care, and smaller families question the sustainability of traditional family based, home long term support and services (LTSS). However, little is still known about Indians’ perception of formal LTSS.Design and MethodsA mixed-methods design of family caregivers for older adults from Jodhpur, Rajasthan (n=30 in-depth interviews; n=100 quantitative survey). Inductive qualitative data analysis identified emergent themes about perceptions of either informal or formal LTSS. Caregivers self-reported which common LTSS they needed in a quantitative survey. Multivariable Poisson and logistic regression models were used to estimate the average total number of LTSS and probabilities of self reporting wanting individual LTSS, respectively.ResultsThe central theme was a negative perception of formal LTSS, especially the idea of paid helpers. A second theme served as the rationale for the first theme: caregivers reported a “duty” to provide care to one’s family that “others” and those “doing it for money” could not meet. Caregivers reported on average 2.8 LTSS needs of 10 options. Formal LTSS, like home-health care assistance with instrumental activities of daily living, were least frequently reported; caregiver education and self-care activities were the most reported.ImplicationsDespite providing intensive amounts of informal LTSS and care for their family members, Indian caregivers consistently reported disinterest in using formal LTSS alternatives in qualitative and quantitative data. Caregivers reported a stronger desire for services that support their ability to carry out their caregiving roles.
Leveraging DNA Methylation to Predict Treatment Response in Major Depressive Disorder: A Critical Review
Authors: Dahrendorff Jan , Currier Glenn , Uddin Monica 
Published: December 2023

AbstractBackgroundMajor depressive disorder (MDD) is a debilitating and prevalent mental disorder with a high disease burden. Despite a wide array of different treatment options, many patients do not respond to initial treatment attempts. Selection of the most appropriate treatment remains a significant clinical challenge in psychiatry, highlighting the need for the development of biomarkers with predictive utility. Recently, the epigenetic modification DNA methylation (DNAm) has emerged to be of great interest as a potential predictor of MDD treatment outcomes. Here we review efforts to date that seek to identify DNAm signatures associated with treatment response in individuals with MDD.MethodsSearches were conducted in the databases PubMed, Scopus, and Web of Science with the concepts and keywords major depressive disorder, DNA methylation, antidepressants, psychotherapy, cognitive behavior therapy, electroconvulsive therapy, transcranial magnetic stimulation, and brain stimulation therapies.ResultsWe identified 31 studies implicating DNAm patterns associated with MDD treatment outcomes. The majority of studies (N=25) are focused on selected target genes exploring treatment outcomes in pharmacological treatments (N=22) with a few studies assessing treatment response to electroconvulsive therapy (N=3). Additionally, there are few genome-scale efforts (N=6) to characterize DNAm patterns associated with treatment outcomes.LimitationsThere is a relative dearth of studies investigating DNAm patterns in relation to psychotherapy, electroconvulsive therapy, or transcranial magnetic stimulation; importantly, most existing studies have limited sample sizes.ConclusionsGiven the heterogeneity in both methods and results of studies to date, there is a need for additional studies before existing findings can inform clinical decisions.
Donor-Specific Antibody Testing is an Effective Surveillance Strategy for High-Risk Antibody Mediated Rejection in Heart Transplant Patients in the Contemporary Era
Authors: Cusi Vincenzo , Cardenas Ashley , Tada Yuko , Vaida Florin , Wettersten Nicholas , Chak Jennifer , Pretorius Victor , Urey Marcus Anthony , Morris Gerald P. , Lin Grace , Kim Paul J. 
Published: December 2023

AbstractBackground:Pathologic antibody mediated rejection (pAMR) evaluation and donor specific antibody (DSA) testing are recommended in the first year after heart transplantation (HTx) in adult patients. Whether DSA testing adds prognostic information to contemporary pAMR surveillance has not been fully studied.Methods:This was a single center study of consecutive endomyocardial biopsies (EMB) performed between November 2010 and February 2023 in adult HTx patients. The primary objective was to evaluate whether DSA testing contributes additional information to pAMR surveillance to better predict overall survival. Secondary endpoints included cardiac allograft dysfunction and loss.Results:A total of 6,033 EMBs from 544 HTx patients were reviewed for the study. The pAMR+/DSA+ group had significantly lower overall survival versus the pAMR-/DSA-group (hazard ratio [HR] = 2.63; 95% confidence interval [CI], 1.35-5.11; pc= 0.013). In the pAMR+/DSA+ group, patients with cardiac allograft dysfunction, compared to those without allograft dysfunction, had significantly lower overall and cardiac survival (pc< 0.001 for both). In contrast, pAMR+/DSA+ and pAMR-/DSA-patients without cardiac allograft dysfunction showed no difference in overall and cardiac survival. Primary graft dysfunction (PGD) was a novel risk factor for development ofde novoDSAs (dnDSA) three weeks post-HTx (p = 0.007).Conclusions:DSA testing as the primary surveillance method can identify high-risk pAMR+/DSA+ patients. Surveillance pAMR testing in the contemporary era may need to be reevaluated. Earlier DSA testing at 10-14 days post-HTx should be considered in PGD patients.
Multiscale Bayesian Simulations Reveal Functional Chromatin Condensation of Gene Loci
Authors: Brandani Giovanni B , Gu Chenyang , Gopi Soundhararajan , Takada Shoji 
Published: December 2023

AbstractChromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in orchestrating various genomic functions. To aid our understanding of the principles underlying chromatin organization, we introduce Hi-C metainference, a Bayesian approach that integrates Hi-C contact frequencies into multiscale prior models of chromatin. This approach combines both bottom-up (the physics-based prior) and top-down (the data-driven posterior) strategies to characterize the 3D organization of a target genomic locus. We first demonstrate the capability of this method to accurately reconstruct the structural ensemble and the dynamics of a system from contact information. We then apply the approach to investigate the Sox2, Pou5f1, and Nanog loci of mouse embryonic stem cells using a bottom-up chromatin model at 1kb resolution. We observe that the studied loci are conformationally heterogeneous and organized as crumpled globules, favoring contacts between distant enhancers and promoters. Using nucleosome-resolution simulations, we then reveal how the Nanog gene is functionally organized across the multiple scales of chromatin. At the local level, diverse chromatin folding motifs correlate with epigenetics, with open chromatin predominantly observed at cis-regulatory elements and compact tetranucleosomes in between. At the larger scale, we find that enhancer-promoter contacts are driven by the transient condensation of chromatin into compact domains stabilized by extensive inter-nucleosome interactions. Overall, this work highlights the condensed, but dynamic nature of chromatinin vivo, contributing to a deeper understanding of gene structure-function relationships.
Immediate impact of the 2021 harmful algal bloom in southeast Hokkaido on the rocky intertidal community and its spatial variation
Authors: Yao Yuan , Noda Takashi 
Published: December 2023

AbstractThere has been a limited number of studies on the effects of harmful algal blooms (HABs) on natural rocky intertidal ecosystems. From mid-September to early November 2021, an unprecedented HAB caused byKarenia selliformishit the Pacific coast of southeast Hokkaido, Japan, for the first time, causing massive mortalities among marine organisms. To clarify the immediate impacts of the HAB on abundance of 10 rocky intertidal species in four functional groups (macroalgae, sessile invertebrates, molluscan grazers, and molluscan carnivores), we focused on two questions. 1) How did the HAB affect the abundance of each species differently at the regional scale? 2) How did the impacts of the HAB on the abundance of each functional groups vary spatially, and was the spatial variation of the HAB impacts related to the spatial distribution of cell density of HAB species? To study these issues, we compared census data for 17 years before the HAB and within one month after it for five shores on the southeast coast of Hokkaido. Results showed that two macroalgae species and all three molluscan grazer species declined significantly after the HAB. Moreover, the decrease of molluscan grazers was significantly correlated with cell density. These results suggest that the impacts of the HAB in southeast Hokkaido on abundance of rocky intertidal organisms are highly variable depending on species and locality, presumably because of differences in species-specific tolerances to HAB toxins and spatial variation in the density of the HAB organisms.
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes
Authors: da Silva Rafael Peres , Suphavilai Chayaporn , Nagarajan Niranjan 
Published: December 2023

AbstractBackgroundWith the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic classification by using alignment-based approaches to reduce the impact of higher sequencing error rates. While alignment-based methods are generally slower, k-mer-based taxonomic classifiers can overcome this limitation, potentially at the expense of lower sensitivity for strains and species that are not in the database.ResultsWe present MetageNN, a memory-efficient long-read taxonomic classifier that is robust to sequencing errors and missing genomes. MetageNN is a neural network model that uses short k-mer profiles of sequences to reduce the impact of distribution shifts on error-prone long reads. Benchmarking MetageNN against other machine learning approaches for taxonomic classification (GeNet) showed substantial improvements with long-read data (20% improvement in F1 score). By utilizing nanopore sequencing data, MetageNN exhibits improved sensitivity in situations where the reference database is incomplete. It surpasses the alignment-based MetaMaps and MEGAN-LR, as well as the k-mer-based Kraken2 tools, with improvements of 100%, 36%, and 23% respectively at the read-level analysis. Notably, at the community level, MetageNN consistently demonstrated higher sensitivities than the previously mentioned tools. Furthermore, MetageNN requires < 1/4thof the database storage used by Kraken2, MEGAN-LR and MMseqs2 and is >7x faster than MetaMaps and GeNet and >2x faster than MEGAN-LR and MMseqs2.ConclusionThis proof of concept work demonstrates the utility of machine-learning-based methods for taxonomic classification using long reads. MetageNN can be used on sequences not classified by conventional methods and offers an alternative approach for memory-efficient classifiers that can be optimized further.