bluuebunny/crossref_metadata_2025_split huggingface dataset:
A revision of the NeotropicalCostaceae: results from sixty years of taxonomic struggle
Authors: Maas P.J.M. , Maas-van de Kamer H. , André T. , Skinner D. , Valderrama E. , Specht C.D. 
Published: January 2025

AbstractHere we present a taxonomic revision of all neotropicalCostaceaerepresented by 90 species, distributed in four monophyletic genera,Chamaecostus(9 spp.),Costus(76 spp.),Dimerocostus(5 spp.), andMonocostus(1 sp.). The work resulted in three new combinations, several nomenclatural changes, and four insufficiently known species are mentioned to demonstrate the need for continued and ongoing work on this charismatic yet often cryptic lineage of plants. We highlight the seventeen species ofCostusand one species ofChamaecostusthat were recently described (Maas et al. 2023) based on knowledge that emerged during this complete revisionary work, 60 years in the making. Included in this revision are details concerning the morphology, distribution, ecology, and phylogenetic relationships among the species studied. All currently recognized species are fully described, including notes on taxonomic synonymy, lectotypification, information on distribution and ecology, conservation status (either as evaluated and published in the IUCN Red List of Threatened Species or as estimated for this publication), vernacular names (when given) and short taxonomic notes. For each species, a distribution map is prepared and at least one colour photograph is included to assist in species identification. Dichotomous keys that include all species are provided, as is a list of all (c. 11.000) exsiccatae studied and an index to scientific names.
Natural Anti-NMDAR1 Autoantibodies Associate with Slowed Decline of Cognitive Functions in Alzheimer’s Diseases
Authors: Zhou Xianjin 
Published: January 2025

AbstractAnti-NMDAR1 autoantibodies can bind NMDA receptors to suppress glutamate excitotoxicity in the brain. Low titers of blood circulating natural anti-NMDAR1 autoantibodies were reported in ∼10% of the general human population. We developed a new method to more accurately quantify these low titers of natural anti-NMDAR1 autoantibodies. After quantifying natural anti-NMDAR1 autoantibodies in the plasma of 324 age– and sex-matched subjects (163 healthy controls; 161 Alzheimer’s disease (AD) patients), I found that AD patients carrying higher levels of natural anti-NMDAR1 autoantibodies have significantly (p value: 0.003) higher scores of Mini-Mental State Examination (MMSE score: 23.5) than AD patients carrying lower levels of natural anti-NMDAR1 autoantibodies (MMSE score: 21.4). No significant differences in MMSE scores were however found between healthy controls with either higher or lower levels of natural anti-NMDAR1 autoantibodies, indicating little harmful effect of the autoantibodies. Consistently, superior cognitive performances were found in AD patients carrying higher levels of natural anti-NMDAR1 autoantibodies in comparison with AD patients carrying lower levels of the autoantibodies. These data suggest that natural anti-NMDAR1 autoantibodies may have neuroprotective effects against cognitive decline in AD patients.
Hard-to-sample species are more sensitive to land-use change: implications for global biodiversity metrics
Authors: Gutiérrez-Arellano Claudia , Newbold Tim , Hodgson Jenny A. 
Published: January 2025

AbstractLand-use change drives biodiversity loss, but some species suffer more than others. Indicators of global biodiversity change must attempt to summarise these impacts representatively and meaningfully, to guide biodiversity recovery. Yet species that are hard to detect, and thus feature less in relevant databases, might possess traits that make them particularly sensitive to anthropogenic impacts. Using global data for plant, bird, and spider species, we develop a statistical approach to analyse and correct for the impact of excluding hard-to-sample species from global biodiversity indicators. Based on over 4000 species with abundance comparisons available, we found that species with fewer global occurrence records consistently decline more as land-use intensity increases, suggesting that hard-to-sample species are particularly sensitive to land-use differences. When we extrapolate this relationship to all plant, bird and spider species with valid occurrence records (0.27 M species), we obtain a more representative global indicator of overall land-use impacts for these entire taxonomic groups. Our estimates indicate a lower average abundance in anthropogenic land uses compared to results obtained when hard-to-sample species are excluded. For example, intensive agriculture only has 18% of the biodiversity level of primary vegetation, rather than the 47% estimated without extrapolation. We recommend that other existing indicators include an extrapolation solution based on ours, to incorporate the available data as effectively as possible. Using occurrence data to predict species’ sensitivity unlocks many possibilities to improve global biodiversity indicators, without demanding additional data on poorly known species.
Distinct cell types along thick ascending limb express pathways for monovalent and divalent cation transport
Authors: Demirci Hasan , Bahena-Lopez Jessica , Smorodchenko Alina , Su Xiao-Tong , Nelson Jonathan , Yang Chao-Ling , Curry Joshua , Duan Xin-Peng , Wang Wen-Hui , Sharkovska Yuliya , Liu Ruisheng , Yilmaz Duygu Elif , Quintanova Catarina , Emberly Katie , Emery Ben , Himmerkus Nina , Bleich Markus , Ellison David H. , Bachmann Sebastian 
Published: January 2025

AbstractKidney thick ascending limb cells reabsorb sodium, potassium, calcium, and magnesium and contribute to urinary concentration. These cells are typically viewed as of a single type that recycles potassium across the apical membrane and generates a lumen-positive transepithelial voltage driving calcium and magnesium reabsorption, although variability in potassium channel expression has been reported. Additionally, recent transcriptomic analyses suggest that different cell types exist along this segment, but classifications have varied and have not led to a new consensus model. We used immunolocalization, electrophysiology and enriched single nucleus RNA-Seq to identify thick ascending limb cell types in rat, mouse and human. We identified three major TAL cell types defined by expression of potassium channels and claudins. One has apical potassium channels, low basolateral potassium conductance, and is bordered by a sodium-permeable claudin. A second lacks apical potassium channels, has high basolateral potassium conductance and is bordered by calcium- and magnesium-permeable claudins. A third type also lacks apical potassium channels and has a high basolateral potassium conductance, but these cells are ringed by sodium-permeable claudins. The recognition of diverse cell types resolves longstanding questions about how solute transport can be modulated selectively and how disruption of these cells leads to human disease.
Effect of aging, endurance training, and denervation on innate immune signaling in skeletal muscle
Authors: Khemraj Priyanka , Kuznyetsova Anastasiya , Hood David A. 
Published: January 2025

AbstractSkeletal muscle function relies on mitochondria for energy and for mediating its unique adaptive plasticity. The NLRP3 inflammasome complex is an innate immune mechanism that responds to mitochondrial damage-associated molecular patterns (DAMPS), however its activity relative to mitochondrial dysfunction in muscle requires exploration. The purpose of this study was to characterize immune signaling and mitochondrial function in muscle during aging, endurance training, and disuse induced by denervation. Denervation led to decreases in muscle mass, mitochondrial content, and impaired respiration. Protein analyses revealed increases in NF-κB p65 and downstream inflammatory markers including NLRP3, caspase-1, GSDMD-N, STING and IL-1β, along with pro-apoptotic BAX and AIF. When assessing potential DAMPS, denervation led to increased ROS production but no changes in cytosolic mtDNA levels, relative to total mtDNA. Since we hypothesized that inflammasome activation would be increased with age, we studied young (6-8 months) and aged (21-22 months) mice that remained sedentary or underwent a 6-week voluntary running protocol. Aging resulted in marked increases in the expression of multiple pro-inflammatory and pro-apoptotic proteins. Remarkably, training uniformly attenuated age-related increases in BAX, NLRP3, caspase-1, STING, and GSDMD protein expression, and reduced the elevated level of cytosolic mtDNA evident in aged muscle. Training adaptations were evident also in the aged animals by the preservation of muscle mass and improvements in oxygen consumption and endurance performance and were achieved despite a lower training distance than in young animals. Our results strongly implicate endurance training as a promising therapeutic for combatting disuse and age-related inflammation in skeletal muscle.
Pretransplant targeting of TNFRSF25 and CD25 stimulates recipient Tregs in target tissues ameliorating GVHD post-HSCT
Authors: McManus Duneia , Copsel Sabrina N. , Pffeifer Brent J. , Wolf Dietlinde , Barreras Henry , Ma Symon , Khodor Ali , Komai Seitaro , Burgos da Silva Marina , Hazime Hajar , Gallardo Miguel , van den Brink Marcel RM , Abreu Maria T. , Hill Geoffrey R. , Perez Victor L. , Levy Robert B. 
Published: January 2025

AbstractThe current approach to minimize transplant-associated complications, including graft-versus-host disease (GVHD) includes long-term pharmacological immune suppression frequently accompanied by unwanted side effects. Advances in targeted immunotherapies regulating alloantigen responses in the recipient continue to reduce the need for pan-immunosuppression. Here, in vivo targeting of the TNF superfamily receptor 25 (TNFRSF25) and the high affinity IL-2 receptor with a TL1A-Ig fusion protein and low dose IL-2, respectively, was used to pretreat recipient mice prior to allogeneic-HSCT (aHSCT). Pretreatment induced Treg expansion persisting early post-aHSCT leading to diminished GVHD and improved transplant outcomes. Expansion was accompanied by an increase in frequency of stable and functionally active Tregs as evidenced byin vitroassays using cells from major GVHD target tissues including colon, liver, and eye. Importantly, pretreatment supported epithelial cell function/integrity, a diverse microbiome including reduction of pathologic bacteria overgrowth and promotion of butyrate producing bacteria, while maintaining physiologic levels of obligate/facultative anaerobes. Notably, using a sphingosine 1-phosphate receptor agonist to sequester T cells in lymphoid tissues, we found that the increased tissue Treg frequency included resident CD69+CD103+FoxP3+hepatic Tregs. In contrast to infusion of donor Treg cells, the strategy developed here resulted in the presence of immunosuppressive target tissue environments in the recipient prior to the receipt of donor allo-reactive T cells and successful perseveration of GVL responses. We posit strategies that circumvent the need of producing large numbers ofex-vivomanipulated Tregs, may be accomplished throughin vivorecipient Treg expansion, providing translational approaches to improve aHSCT outcomes.Graphical Abstract
Quantification of the volume of swallowed air in the gut finds low volumes when asleep may reduce aerobic digestion and explain why short dinner to sleep times are associated with nocturnal reflux
Authors: Hurr Thomas 
Published: January 2025

AbstractIt has been previously reported that air swallowing and breathing exercises could reduce the severity of digestive reflux by supplying oxygen directly to the gut lumen and supporting aerobic digestion, however the normal volume of air swallowed over 24 hours has not been determined. To determine the volume of air swallowed over 24 hours, the number of swallows during eating, drinking and snacks (EDS), asleep, at other times awake (OTA) and the volume of air swallowed per bolus were sought from the literature. Four models were developed to determine the volume of air swallowed per bolus, finding volumes between 0 ml and an average maximum pharyngeal volume of 40 ml were possible, with an average and range of values ≈ 11(1.7-32) ml. From a literature search, the number of swallows over 24 hours determined using a microphone, was found to be the most complete set of data to calculate the volumes of air swallowed while EDS, asleep and OTA. There was on average during EDS ≈ 31 ml air swallowed per minute, when asleep ≈ 1 ml air swallowed per minute and at OTA ≈ 4.3 ml air swallowed per minute giving a total air swallow volume of ≈ 6,400(320-47,000) ml air over 24 hours. The volume of the gases contained in swallowed air were also calculated as nitrogen ≈ 5000 ml, oxygen ≈ 1000 ml and noting swallowed air is expired air from the lungs, carbon dioxide ≈ 320 ml over 24 hours. If improved aerobic digestion reduced the probability of digestive reflux and was related to the volume of air swallowed, then digestive reflux would be least likely to occur during EDS, with the highest air swallow rate, followed by OTA and most likely to occur when asleep, when the lowest volume of air is swallowed. The volume of air swallowed over 24 hours was equivalent to only one or two minutes of breathing at ≈ 6,000 ml per minute for an adult at rest. It is still not clear whether luminal oxygen supply from air swallowing, or luminal (and systemic) oxygen supply from breathing, is the major source of oxygen supply to the gut lumen for aerobic digestion, however if air swallowing is the major source of luminal oxygen supply, then air swallowing is likely an important factor for digestive health.Graphical AbstractThe low volumes of air swallowed during sleep may reduce aerobic digestion and explain why eating, drinking and snacks less than 3 hours before sleep have been associated with an increased probability of gastric /digestive reflux.The volume of air swallowed per 24 hours is equivalent to only 1-2 minute of breathing at 6,000 ml per minute for an adult at rest.Air swallowing link to reflux diseases [8], air swallow volume per bolus [9-14], rates of swallowing per 24 hours [16] breathing air volumes [35], increased reflux less than 3 hours dinner to sleep [38].
Zero-Shot, Big-Shot, Active-Shot - How to estimate cell confluence, lazily
Authors: Joas Maximilian , Freund Daniel , Haase Robert , Rahm Erhard , Ewald Jan 
Published: January 2025

ABSTRACTMesenchymal stem cell therapy shows promising results for difficult-to-treat diseases, but standardized manufacturing requires robust quality control through automated cell confluence monitoring. While deep learning can automate confluence estimation, research on cost-effective dataset curation and the role of foundation models in this task remains limited. We systematically investigate the most effective strategies for confluence estimation, focusing on active learning-based dataset curation, goal-specific labeling, and leveraging foundation models for zero-shot inference. Here, we show that zero-shot inference with the Segment Anything Model (SAM) achieves excellent confluence estimation without any task-specific training, outperforming fine-tuned smaller models. Further, our findings demonstrate that active learning does not significantly improve model dataset curation compared to random selection in homogeneous cell datasets. We show that goal-specific, simplified labeling strategies perform comparably to precise annotations while substantially reducing annotation effort. These results challenge common assumptions about dataset curation: neither active learning nor extensive fine-tuning provided significant benefits for our specific use case. Instead, we found that leveraging SAM’s zero-shot capabilities and targeted labeling strategies offers the most cost-effective approach to automated confluence estimation. Our work provides practical guidelines for implementing automated cell monitoring in MSC manufacturing, demonstrating that extensive dataset curation may be unnecessary when foundation models can effectively handle the task out of the box.
An accessible metagenomic strategy allows for better characterization of invertebrate bulk samples
Authors: Callens Martijn , Le Berre Guillaume , Van den Bulcke Laure , Lolivier Marianne , Derycke Sofie 
Published: January 2025

ABSTRACTDNA-based techniques are a popular approach for assessing biodiversity in ecological research, especially for organisms which are difficult to detect or identify morphologically. Metabarcoding, the most established method for determining species composition and relative abundance in bulk samples, can be more sensitive and time- and cost effective than traditional morphological approaches. However, one drawback of this method is PCR bias caused by between-species variation in the amplification efficiency of a marker gene. Metagenomics, bypassing PCR amplification, has been proposed as an alternative to overcome this bias. Several studies have already shown the promising potential of metagenomics, but they all indicate the unavailability of reference genomes for most species in any ecosystem as one of the primary bottlenecks preventing its wider implementation. In this study, we present a strategy that uses unassembled reads of low-coverage whole genome sequencing to construct a genomic reference database, thus circumventing high sequencing costs and intensive bioinformatic processing. We show that this approach is superior to metabarcoding for approximating relative biomass of macrobenthos species from bulk samples. Furthermore, these results can be obtained with a sequencing effort comparable to metabarcoding. The strategy presented here can thus accelerate the implementation of metagenomics in biodiversity assessments, as it should be relatively easy to adopt by laboratories familiar with metabarcoding and can be used as an accessible alternative.
Buffer specificity of ionizable lipid nanoparticle transfection efficiency and bulk phase transition
Authors: Carucci Cristina , Philipp Julian , Müller Judith A. , Sudarsan Akhil , Kostyurina Ekaterina , Blanchet Clement E. , Schwierz Nadine , Parsons Drew F. , Salis Andrea , Rädler Joachim O. 
Published: January 2025

ABSTRACTLipid nanoparticles (LNPs) are efficient and safe carriers for mRNA vaccines based on advanced ionizable lipids. It is understood that the pH dependent structural transition of the mesoscopic LNP core phase plays a key role in mRNA transfer. However, buffer specific variations in transfection efficiency remain obscure. Here we analyze the effect of buffer type on the structure and transfection efficiency of LNPs. We find that LNPs formulated with the cationic ionizable lipid DLin-MC3-DMA (MC3) in citrate compared to phosphate and acetate buffers exhibit earlier onset and stronger mRNA-GFP expression in-vitro. Using synchrotron small angle X-ray scattering (SAXS) we determine the pH dependent mesophases of ionizable lipid MC3/cholesterol/water dialyzed against the various buffers. The results show that the phase transition with decreasing pH from inverse micellar cubic to inverse hexagonal (Fd3m-HII) is shifted by one unit to a lower transition pH for acetate and phosphate compared to citrate buffer. Based on continuum theory and ion specific adsorption obtained from all-atom MD simulations, we propose a mechanism for buffer specificity. Citrate stabilizes the inverse hexagonal phase thus shifting the formation of HIIto a higher pH. By contrast, phosphate and acetate stabilize LII. We propose that the Fd3m-to-HIItransition, which is facilitated in citrate buffer, is responsible for a sensitized pH-response of the LNP core phase. This, in turn, enhances endosomal release efficiency and accounts for the earlier onset of gene expression observed in LNPs prepared with citrate buffer.
Genome Sequencing, Molecular Marker Development and Genetic Diversity Assessment of Economically Important Vulnerable Tree SpeciesSaraca asoca (Roxb.) W.J de Wilde
Authors: Mahalakshmi P , Hegde Santhosh N , Gowda Malali , Kareem Abdul , Anbarashan M , Noorunnisa Begum S , Kukkupuni Subrahmanya Kumar , Narendran Pavithra 
Published: January 2025

AbstractSaraca asoca, is an understory tree along streams in evergreen to semi-evergreen forests up to 600 m. It is an important tree in cultural tradition and medicinally significant. It is native to India and Sri Lanka. Globally the species is found to occur in India, Sri Lanka, Myanmar, Bangladesh. It was introduced in Malaysia. Within India, it’s found in Western Ghat and Eastern Ghat. It is occasionally planted in gardens.Saraca asocais known for its extensive pharmacological properties, particularly its bark is used in treating menorrhagia, dysfunctional uterine bleeding, hemorrhagic dysentery, and other gynecological issues, it holds a prominent place in Ayurvedic medicine. This study was undertaken to sequence the whole genome ofSaraca asocausing the Illumina HiSeq2500 platform, and evaluating the genetic diversity among samples from Kolluru and other locations in southern India through Genotyping by Sequencing (GBS). Analysis of 49 samples established genetic diversity relationships using a distance matrix. Sequencing yielded 1.6 Gb, covering 76% of the estimated genome size. The genome includes 764 million bases of repetitive DNA elements. A survey of Simple Sequence Repeats (SSRs) identified 584,615 SSRs, with 236,123 sequences containing SSRs. Utilizing the KEGG database, biosynthesis pathways for catechin and epicatechin within the flavonoid synthesis pathway were identified. This comprehensive genomic analysis ofSaraca asoca(Sita Ashoka) provides critical insights for conservation efforts aimed at preserving this vulnerable species,Saraca asoca(Roxb.) Willd.
Genome wide analyses reveal the role of mutator phenotypes in the emergence of drug resistance inMycobacterium tuberculosis
Authors: Zein-Eddine R. , Le Meur A. , Skouloubris S. , Jelsbak L. , Refrégier G. , Myllykallio H. 
Published: January 2025

AbstractAntimicrobial combination therapy is widely used to combatMycobacterium tuberculosis(Mtb), yet resistance rates continue to rise. Mutator strains, with defects in DNA repair genes, are a known source of resistance in other bacterial infections, but their global role inMtbremains unclear. Here, we provide a comprehensive overview of the contribution of single nucleotide polymorphisms (SNPs) in DNA Repair, Replication, and Recombination (3R) genes to resistance inMtb. Through large-scale bioinformatics analysis of 53,589 whole-genomes, we identified 18 novel SNPs linked to genotypic drug resistance in 3R genes, covering 12.5% of clinical isolates/strains with available genome sequences. Notably, a number of the detected SNPs were positively selected duringMtbevolution. Experimental mutation frequency tests further indicated functional defects of these sequence variants in key DNA repair pathways. Our findings indicate that the role of mutability in 3R genes plays a significant role inMtbresistance at the global level.