bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ak-mer-based maximum likelihood method for estimating distances of reads to genomes enables genome-wide phylogenetic placement
Authors: Şapcı Ali Osman Berk , Mirarab Siavash 
Published: January 2025

AbstractConsider comparing a sequencing read of unknown origin to a set of reference genomes. This problem underlines many applications, including metagenomic analyses. The exact genome generating the read is not in the reference set, but may be evolutionarily related to some references. Ideally, we need not just the identity of the closest references to the read but also their distance to the read. The distances can help us identify the read at the right taxonomic level and, more ambitiously, place it on a reference phylogeny. Aligning reads to reference genomes, the only available approach for computing such distances, becomes impractical for very large reference sets. It is also not effective at higher distances when used with efficient indexes (e.g., Bowtie2). Whilek-mers can create scalable indexes, existingk-mer-based methods are incapable of distance calculation. Thus, estimating distances between short reads and large, diverse reference sets remains challenging and seldom used. We introduce a method called krepp that combines four ideas to solve this challenge and to further enable placing reads on a reference phylogeny. We usei) locality-sensitive hashing to find inexactk-mer matches,ii) a phylogeny-guided coloredk-mer index to map eachk-mer to all references containing it,iii) a maximum likelihood framework to estimate read-genome distances usingk-mer matches, andiv) an extension of distances to clades of the reference tree, which enables placement using a likelihood ratio test. We show that krepp matches true distances using a fraction of time compared to alignment, extends to higher distances, and accurately places short reads coming from any part of the genome (not just marker genes) on the reference phylogeny. We demonstrate that krepp easily extends to databases with tens of thousands of reference genomes and performs well in characterizing real microbial samples.AvailabilityThe tool is available atgithub.com/bo1929/krepp. All results, auxiliary data, and scripts used in the analyses can be found atgithub.com/bo1929/shared.krepp.
Combined expression of FOXO and Tribbles proteins predicts survival of glioma patients
Authors: Santos Bruno F. , Maia Ana-Teresa , Ferreira Bibiana I. , Link Wolfgang 
Published: January 2025

1.AbstractGlioma, a primary tumor of the central nervous system originating from glial cells, continues to pose significant therapeutic challenges, particularly in its high-grade variants. Genetic analyses have revealed that the majority of gliomas exhibit significant alterations in the RTK/RAS/PI3K/AKT signaling cascade. Forkhead box protein O (FOXO) transcription factors and their upstream regulator protein family Tribbles have been characterized as important components of the downstream effector network of this pathway. Here, we investigated the role of the FOXO and Tribbles family members mRNA levels in the clinical outcomes of patients with gliomas. We show that while high expression of FOXO1 and low expression of FOXO3 and FOXO4 is associated with worse survival of glioma patients, low expression of TRIB1, TRIB2, and TRIB3 improves prognosis. We also found that FOXO3 and FOXO4 levels are downregulated in patients with grade 4 gliomas, compared to those with lower tumor grades, while FOXO1 and all three Tribbles isoforms are overexpressed in the same patients. We also show that transcriptional profiles of FOXO and Tribbles can predict the clinical outcome of glioma patients better than MGMT status, one of the most important biomarkers currently used in glioblastoma treatment. These findings highlight the potential of FOXO and Tribbles mRNA as predictive biomarkers and their proteins as therapeutic targets, paving the way for more personalized and effective glioma treatments.
ProtRAP-LM: Fast and accurate protein relative accessibility prediction and membrane protein screening through protein language model embeddings
Authors: Wang Lei , Kang Kai , Song Chen 
Published: January 2025

AbstractMembrane proteins play pivotal roles in cellular signaling and transport, making them prime targets for therapeutic intervention. Therefore, expeditious screening and accurate property prediction of these proteins is crucial. Recently, we proposed a new metric, the membrane contact probability (MCP), to characterize the membrane-contacting features of membrane proteins and further refine the prediction of the relative accessibility of proteins (ProtRAP). However, these models relied on evolutionary information in the form of multiple sequence alignments (MSAs), which hindered rapid predictions. In this study, we present a novel transformer-based model, ProtRAP-LM, utilizing language model (LM) embeddings as input features, to quickly and accurately predict MCP and relative accessibility for each residue of a given protein sequence. ProtRAP-LM can achieve accurate predictions for entire proteomes within hours, demonstrating superior performance compared to previous MSA-based models, with a speedup of over 300 times. This empowers us to furnish more thorough annotations of membrane protein sequences on a proteome-wide scale, particularly for single-pass transmembrane proteins, membrane-anchored proteins, and β-sheet-containing membrane proteins, which have long been a challenge in the field. In the end, we provide a comprehensive list of membrane proteins for 48 living organisms, offering a rich resource for investigating the structure and function of these essential biomolecules in the future.
Benchmarking and optimizing Perturb-seq in differentiating human pluripotent stem cells
Authors: Sivakumar Sushama , Wang Yihan , Goetsch Sean C , Pandit Vrushali , Wang Lei , Zhao Huan , Sundarrajan Anjana , Armendariz Daniel , Takeuchi Chikara , Nzima Mpathi , Chen Wei-Chen , Dederich Ashley E , El Hayek Lauretta , Gao Taosha , Ghazawi Renad , Gogate Ashlesha , Kaur Kiran , Kim Hyung Bum , McCoy Melissa K , Niederstrasser Hanspeter , Oura Seiya , Pinzon-Arteaga Carolos A , Sanghvi Menaka , Schmitz Daniel A , Yu Leqian , Zhang Yanfeng , Zhou Qinbo , Kraus W. Lee , Xu Lin , Wu Jun , Posner Bruce A , Chahrour Maria H , Hon Gary C , Munshi Nikhil V 
Published: January 2025

ABSTRACTPerturb-seq is a powerful approach to systematically assess how genes and enhancers impact the molecular and cellular pathways of development and disease. However, technical challenges have limited its application in stem cell-based systems. Here, we benchmarked Perturb-seq across multiple CRISPRi modalities, on diverse genomic targets, in multiple human pluripotent stem cells, during directed differentiation to multiple lineages, and across multiple sgRNA delivery systems. To ensure cost-effective production of large-scale Perturb-seq datasets as part of the Impact of Genomic Variants on Function (IGVF) consortium, our optimized protocol dynamically assesses experiment quality across the weeks-long procedure. Our analysis of 1,996,260 sequenced cells across benchmarking datasets reveals shared regulatory networks linking disease-associated enhancers and genes with downstream targets during cardiomyocyte differentiation. This study establishes open tools and resources for interrogating genome function during stem cell differentiation.
Optimization of crossing strategy based on the usefulness criterion in inter-population crosses considering different genetic effects among populations
Authors: Kinoshita Sei , Sakurai Kengo , Hamazaki Kosuke , Tsusaka Takahiro , Sakurai Miki , Shirasawa Kenta , Isobe Sachiko , Iwata Hiroyoshi 
Published: January 2025

AbstractIn the breeding programs of self-pollinated plants, achieving genetic improvement in multiple traits can be challenging when relying solely on a single biparental population. Interpopulation crosses are employed to integrate favorable alleles from multiple biparental populations to overcome this limitation. In this context, it is crucial to consider the distinct genetic effects in different populations. In this study, we utilized a selection method based on the usefulness criterion (UC) to identify cross pairs suitable for interpopulation crosses. We expanded this approach to enhance breeding programs accounting for varying genetic backgrounds within the genomic selection framework. Using the medicinal plant red perilla as the study material, we conducted simulations to compare the efficacy of selection based on estimated genomic breeding values with that based on UC. Our findings demonstrate that the proposed method is effective in facilitating the simultaneous improvement of multiple traits, particularly by considerably increasing genetic gains among the top-performing individuals in the population. Furthermore, we provide guidelines for implementing interpopulation crosses, including recommendations for the optimal generation for crossing and the appropriate reference generation for calculating the UC. The results obtained in this study offer valuable insights for small-scale breeding programs aimed at simultaneously enhancing multiple traits through inter-population crosses and are applicable to a wide range of crops, including neglected and underutilized species.Key MessageHerein, a method has been proposed for selecting optimal cross pairs based on the genetic potential of progeny in inter-population crosses, considering different genetic effects among populations.
Sex Hormone Binding Globulin Controls Gender Specific Lipolytic Activity in Human Abdominal Subcutaneous Adipocytes
Authors: Abildgaard Julie , Palani Nagendra , Henriksen Tora Ida , Aleliunaite Aiste , Horváth-Rudigier Carla , Svenstrup Victor , Frederiksen Hanne , Juul Anders , Scheele Camilla Charlotte , Pedersen Bente Klarlund , Nielsen Søren 
Published: January 2025

ABSTRACTRegulation of lipid metabolism is fundamental for metabolic health, and adipose tissue is a central component in this process. Adipose tissue differs dramatically between women and men with a higher subcutaneous capacity for storage and healthy metabolism in women. Sex hormone-binding globulin (SHBG) contributes to the regulation of circulating sex hormone bioavailability and has been shown to predict risk of metabolic dysfunction. We here investigate the sex-specific relationship of SHBG with metabolic status and adipocyte-dependent lipolysis. We measured serum concentrations of sex hormones, SHBG, fasting glucose and insulin in a cohort of 63 women and 27 men from which adipose biopsies were collected and mature adipocytes were isolated. We found that, in women, high serum SHBG concentrations were strongly associated with low HOMA-IR in vivo, and lower baseline lipolysis but higher responsiveness to isopropanol-induced lipolysis ex vivo. In contrast, no effect of SHBG on the above-mentioned parameters were observed in men. In vitro, cultured adipocytes also increased lipolytic capacity in response to SHBG, but only in the absence of testosterone, suggesting that testosterone inhibits the catecholmine-induced lipolysis of SHBG in adipose tissue. In conclusion, we here define a novel role for SHBG in adipocyte lipolysis. At the same time, our data emphasize sex-dependent differences in adipocyte lipid metabolism, and we propose testosterone binding to SHBG as a driving factor mediating these differences.
Metrics Matter: Why We Need to Stop Using Silhouette in Single-Cell Benchmarking
Authors: Rautenstrauch Pia , Ohler Uwe 
Published: January 2025

AbstractCurrent-day single-cell studies comprise complex data sets affected by nested batch effects caused by technical and biological factors, relying on advanced integration methods. Silhouette is an established metric for assessing clustering results, comparing within-cluster cohesion to between-cluster separation, and adaptations of it have emerged as the dominant choice to evaluate the success of these integration methods. However, silhouette’s assumptions are often violated in single-cell data integration scenarios. We demonstrate that silhouette-based metrics can neither reliably assess batch effect removal nor biological signal conservation and are thus inherently unsuitable for data with (nested) batch effects. We propose alternative, robust evaluation strategies that enable accurate integration method assessment and call to update benchmarking practices.
Disrupted Sphingosine-1-Phosphate Homeostasis Drives Nephrotoxicity in Sphingosine-1-Phosphate Lyase Insufficiency Syndrome (SPLIS)
Authors: Majcher Adam , Buder Kathrin , Khan Ranjha , Saba Julie D. , Hornemann Thorsten 
Published: January 2025

AbstractSphingosine-1-phosphate lyase insufficiency syndrome (SPLIS), also known as nephrotic syndrome type 14 (NPHS14), is an autosomal recessive disorder characterized by renal, neurological, dermatological, endocrine, and immunological symptoms. This condition is caused by loss-of-function mutations in theSGPL1gene, which encodes sphingosine-1-phosphate lyase (SGPL1p/SPL), the enzyme responsible for the terminal degradation of sphingosine-1-phosphate (S1P) in sphingolipid catabolism.We investigated a novel case of SPLIS associated with a recently reportedSGPL1mutation (c.1084T>A; p.Ser362Thr). Using stable isotope flux analyses, we demonstrated in patient-derived fibroblasts andHEK293TSGPL1 knockout models that SGPL1p deficiency does not consistently result in pathological S1P accumulation.Instead, SPL-deficient cells are able to maintain steady-state S1P levels through two compensatory mechanisms:Regulation of de novo sphingolipid synthesis via the ORMDL-ceramide axis.Increased conversion of excess ceramides into glycosphingolipids.However, when steady-state conditions are disrupted—either by external sphingolipid supplementation or by impairing homeostatic control—a pathological increase in intracellular S1P occurs in SPL-deficient cells.In vivo,Sgpl1-/-mice exhibited significant urinary excretion of S1P and marked S1P enrichment in the kidneys. This pathological accumulation of S1P dysregulates cytoskeletal homeostasis, impairing renal epithelial formation. Based on these findings, we hypothesize that the reabsorption of urinary S1P contributes to toxic renal accumulation, providing an explanation for the nephrotoxicity observed in SPLIS and its association with nephrotic syndrome.Importantly, we found that the cytoskeletal disruptions could be mitigated by inhibiting the Rho-ROCK signaling pathway using the clinically approved inhibitor Fasudil. These findings illuminate the pathophysiological basis of SPLIS nephrotoxicity and propose a promising pharmacological intervention strategy.Graphical abstract
Tunable fluorogenic DNA probes drive fast and high-resolution single-molecule fluorescence imaging
Authors: Kümmerlin Mirjam , Zhao Qing , Hazra Jagadish , Hepp Christof , Farrar Alison , Turner Piers , Kapanidis Achillefs N. 
Published: January 2025

AbstractA main limitation of single-molecule fluorescence (SMF) measurements is the “high concentration barrier”, describing the maximum concentration of fluorescent species tolerable for sufficient signal-to-noise ratio (SNR). To address this barrier in several SMF applications, we design fluorogenic probes based on short ssDNAs, fluorescing only upon hybridising to their complementary target sequence. We engineer the quenching efficiency and fluorescence enhancement upon duplex formation through screening several fluorophore-quencher combinations, label lengths, and sequence motifs, which we utilise as tuning screws to adapt our labels to different experimental designs. Using these fluorogenic probes, we can perform SMF experiments at concentrations of 10 µM fluorescent labels; this concentration is 100-fold higher than the operational limit for standard TIRF experiments. We demonstrate the ease of implementing these probes into existing protocols by performing super-resolution imaging with DNA-PAINT, employing a fluorogenic 6 nt-long imager; through the faster acquisition of binding events, the imaging of viral genome segments could be sped up significantly to achieve extraction of 20-nm structural features with only ∼150 s of imaging. The exceptional tunability of our probe design will overcome concentration barriers in SMF experiments and unlock new possibilities in super-resolution imaging, molecular tracking, and smFRET.Abstract Figure
Distinct Colitis-Associated Macrophages Drive NOD2-Dependent Bacterial Sensing and Gut Homeostasis
Authors: Katkar Gajanan D. , Anandachar Mahitha Shree , Ibeawuchi Stella-Rita , Espinoza Celia R. , Coates Jane , Malhotra Yashaswat S. , Mullick Madhubanti , Castillo Vanessa , Vo Daniella T. , Sahoo Debashis , Sinha Saptarshi , Ghosh Pradipta 
Published: January 2025

ABSTRACTSingle-cell studies have revealed that intestinal macrophages maintain gut homeostasis through the balanced actions of reactive (inflammatory “accelerators”) and tolerant (non-inflammatory “brakes”) subpopulations. How these populations function in inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), remains unresolved. Using multi-omics data and computational tools, here we define colon-specific macrophage states and reveal the critical role ofnon-inflammatorycolon-associatedmacrophages (ni-ColAMs) in IBD recovery. Through trans-scale analyses—integrating computational transcriptomics, proteomics, andin vivointerventional studies—we pinpointed GIV (CCDC88A), a heterotrimeric G-protein modulator, as a key regulator of ni-ColAMs. Notably, GIV emerged as the top-ranked gene in ni-ColAMs that physically and functionally interacts with nucleotide-binding oligomerization domain-containing protein 2 (NOD2), an innate immune sensor implicated in both CD and UC. Myeloid-specific depletion of GIV exacerbates infectious colitis, prolongs disease course, and abolishes the protective effects of muramyl dipeptide (MDP) in chemical colitis and sepsis models. GIV is required for NOD2 to dampen inflammation and efficiently clear microbes. GIV binds directly to NOD2’s terminal leucine-rich repeat (LRR#10) via its C-terminus. This interaction is disrupted in the CD-associated1007fsNOD2 variant, which lacks LRR#10, leading to impaired bacterial sensing and clearance. Findings illuminate how GIV and NOD2 collaborate to maintain gut homeostasis and reveal how derailment of such collaboration may drive dysbiosis and inflammation in IBD.
High-speed mapping of whole-mouse peripheral nerves at subcellular resolution
Authors: Shi Mei-Yu , Yao Yuchen , Wang Miao , Yang Qi , Ding Lufeng , Li Rui , Li Yuanyuan , Huang Haimeng , Yang Chao-Yu , Zhou Zhao , Zhu Zhenxiang , Wen Pengjie , Dai Fangling , Zeng Xiaohui , Zhang Ke-Ming , Guo Yuhong , Sun Zi-An , Xia Huanhuan , Ren Zhenhua , Cakmak Yusuf Ozgur , Zhang Ming , Xu Fuqiang , Qu Lei , Zhu Qingyuan , Lau Pak-Ming , Xu Cheng , Bi Guo-Qiang 
Published: January 2025

AbstractIn contrast to the rapid advancements in mesoscale connectomic mapping of the mammalian brain, similar mapping the peripheral nervous system has remained challenging due to the body’s size and complexity. Here, we present a high-speed blockface volumetric imaging system with an optimized workflow of whole-body clearing, capable of imaging the entire adult mouse at micrometer resolution within 40 hours. Three-dimensional reconstruction of individual spinal fibers in Thy1-EGFP mice reveals distinct morphological features of sensory and motor projections along the ventral and dorsal rami. Immunostaining facilitates body-wide mapping of sympathetic nerves and their branches, highlighting their perivascular patterns in limb muscles, bones, and most visceral organs. Viral tracing elucidates the fine architecture of vagus nerves and individual vagal fibers, revealing unexpected projection routes to various organs. Our approach offers an effective means to achieve a holistic understanding of cellular-level interactions among different systems that underlie body physiology and disease.HighlightsImaging of whole adult mouse at uniform subcellular resolution within 40 hoursReconstruction of 191 thoracic spinal neuron projections for Thy1-EGFP miceMapping of immunolabeled sympathetic projections and their perivascular patternsResolving virus-labeled architecture of vagus nerves and complex single-fiber routes
Bioaugmentation in anaerobic digesters: A systematic review
Authors: Alipoursarbani Mozhdeh , Tideman Jeroen , López Mitzy , Abendroth Christian 
Published: January 2025

AbstractBioaugmentation, the intentional introduction of specific microorganisms into anaerobic digestion (AD) systems, has shown promise in enhancing methane production and in mitigating stressful conditions, particularly in systems operating below optimal performance. This review presents a systematic literature review (SLR) and meta-analysis to evaluate the efficacy of bioaugmentation strategies in AD. This review identified and analyzed studies meeting predefined eligibility criteria through a structured methodology involving research protocol, search, appraisal, synthesis, analysis, and reporting. A notable innovation of this review is its comprehensive critical comparison of different controls used in bioaugmentation studies, which has been inadequately addressed in previous literature. To facilitate the functional understanding, strains for bioaugmentation were grouped into the four phases of anaerobic digestion (hydrolysis, acidogenesis, acetogenesis and methanogenesis). A highly diverse set of microbes has been described for bioaugmentation, especially from the familiesClostridiaceae,PseudomonadaceaeandSyntrophomonadaceae. Most works are related to hydrolysis. The few works that address acidogenesis are mostly related to dark fermentation. Several studies used methanogenic archaea as well as syntrophic acetate oxidising bacteria, despite the difficulties in culturing them. On the other hand, studies applying strains for acetogenesis were largely underrepresented. Especially works on syntrophic propionate and butyrate oxidation (SPO and SBO) were missing.
Early-life paternal relationships predict adult female survival in wild baboons
Authors: Jansen David A.W.A.M. , Kinyua Warutere J. , Tung Jenny , Alberts Susan C. , Archie Elizabeth A. 
Published: January 2025

ABSTRACTParent-offspring relationships can have profound effects on offspring behavior, health, and fitness in adulthood. These effects are strong when parents make heavy investments in offspring care. However, in some mammals, including several species of carnivores, rodents, and primates, fathers live and socialize with offspring, but paternal careper seis subtle or indirect. Do these limited father-offspring relationships also affect later-life outcomes for offspring? Working in a well-studied baboon population where males contribute little direct offspring care, we found that juvenile female baboons who had stronger paternal relationships, or who co-resided longer with their fathers, led adult lives that were 2-4 years longer than females with weak or short paternal relationships. This pattern did not differ between females who experienced high versus low levels of early-life adversity; hence, paternal relationships were not especially protective against harsh early environments. Males’ relationships were strongest with juvenile females they were most likely to have sired and when males had few current mating opportunities. Hence, father-daughter relationships may be constrained by male mating effort. Because survival predicts female fitness, fathers and their daughters may experience selection to engage socially and stay close in daughters’ early lives.