bluuebunny/crossref_metadata_2025 huggingface dataset:
Risk factors for urinary retention following laparoscopic total extraperitoneal inguinal hernia repair in adult males
Authors: Cheng Ting-Yao , Lin Tsu-Feng , Tsai Chia-Chi , Chen Hao-Wei , Chen Marcelo , Tseng Jen-Shu , Chiu Allen W.
Published: February 2025

Purpose:

This study aims to identify the incidence and risk factors associated with postoperative urinary retention (POUR) in patients undergoing laparoscopic total extraperitoneal (TEP) inguinal hernia repair, a common complication that significantly impacts patient recovery and health care resources.

Materials and methods:

A retrospective review was conducted of male patients who underwent laparoscopic TEP inguinal hernia repair and were observed overnight at our institution from January 2020 to December 2022. POUR was defined as the inability to void postoperatively, necessitating catheterization before discharge. Univariate and multivariate logistic regression analyses were conducted on perioperative variables to determine their association with POUR.

Results:

Of 618 analyzed patients, the incidence of POUR was 13.3% (82/618). Univariate analysis identified age ≥ 65 years, a history of benign prostatic hyperplasia (BPH), blood loss > 10 mL, operative duration > 60 minutes, intraoperative urinary catheter placement, and less surgeon experience as factors significantly associated with POUR. Multivariate logistic regression showed that age ≥ 65 years (odds ratio = 2.05, P = 0.01) and a history of BPH (odds ratio = 2.97, P < 0.001) were significant predictors of POUR.

Conclusion:

POUR is a significant postoperative complication following laparoscopic TEP inguinal hernia repair, particularly affecting male patients aged 65 years or older and those with a history of BPH. Identifying these risk factors preoperatively can help tailor perioperative care to mitigate POUR incidence and enhance recovery.
Upstroke wing clapping in bats and bat-inspired robots offers efficient lift generation
Authors: Fan Xiaozhou , Bortoni Alberto , Hao Siyang , Swartz Sharon , Breuer Kenneth
Published: February 2025

Wing articulation is critical for the efficient flight of bird- and bat-sized animals. Inspired by the flight of
Cynopterus brachyotis
, the lesser short-nosed fruit bat, we built a two-degree-of-freedom flapping wing platform with variable wing folding capability. In the late upstroke, the wings ‘clap’ and produce an air jet that significantly increases lift production, with a positive peak matched to that produced in the downstroke. Though ventral clapping has been observed in avian flight, the potential aerodynamic benefit of this behaviour is yet to be rigorously assessed. We used multiple approaches—quasi-steady modelling, direct force/power measurement and particle image velocimetry (PIV) experiments in a wind tunnel—to understand critical aspects of lift and power variation in relation to wing folding magnitude over Strouhal numbers at
St
= 0.2–0.4. While lift increases monotonically with folding amplitude in that range, power economy (ratio of lift/power) is more nuanced. At
St
= 0.2–0.3, it increases with wing folding amplitude monotonically. At
St
= 0.3–0.4, it features two maxima—one at medium folding amplitude (approx. 30°) and the other at maximum folding. These findings illuminate two strategies available to flapping wing animals and robots—symmetry-breaking lift augmentation and appendage-based jet propulsion.
On the conversion of plastic work into heat in metals
Authors: Nassar Odai
Published: February 2025

This paper provides a comprehensive review of the methodologies employed to determine the fraction of plastic work converted into heat in the deformation of metals, known as the Taylor–Quinney coefficient (TQC). This review delves into the experimental, analytical and numerical methods found in the existing literature, highlighting their respective advantages and shortcomings, and reveals a notable variation in the reported values of the TQC of metals and how these values change with strain, strain rate, loading mode and microstructure. Despite this variation, the practice of considering the TQC as a constant between 0.85 and 0.95 is still found in the literature. The review identifies critical research gaps, emphasizing the scarcity of studies investigating the TQC at extremely high strains and strain rates. In addition, the paper highlights the interchangeability of using an integral and differential TQC without clear distinctions and the absence of objective conclusions supported by statistical significance. The paper concludes with a proposed research plan to estimate the TQC of metals using
in situ
optical and thermal imaging of metal cutting to access a wide range of strains and strain rates.
Individual plasticity in response to rising sea temperatures contributes to an advancement in green turtle nesting phenology
Authors: Rickwood Mollie L. , Tucker Eve , Beton Damla , Davey Sophie , Godley Brendan J. , Snape Robin T. E. , Postma Erik , Broderick Annette C.
Published: February 2025

Phenological changes (i.e. shifts in the timing of biological events) are among the most frequently reported population-level responses to climate change and are often assumed to be adaptive and increase population viability. These may be driven by both individual-level phenotypic plasticity and population-level evolutionary and demographic changes. However, few studies have explored how individual-level versus population-level processes drive phenological trends. Using a 31-year dataset of over 600 individually marked nesting green turtles (
Chelonia mydas
), we quantify the population- and individual-level temporal trend in their first nest date. Of the latter, approximately 30% is attributable to individual phenological plasticity in response to sea surface temperature, with females advancing their nesting by 6.47 days for every degree (Celsius) increase. The remaining change is almost entirely explained by individual- and population-level changes in size and breeding experience (correlates of age), as well as the number of clutches laid per season. This is the first study of individual-level phenological change in a marine ectotherm, furthering our understanding of how this and similar species may respond to rising temperatures.
Integrated effects of neighbourhood composition and resource levels on growth of a dominant tree species in a tropical forest
Authors: Shao Xiaona , Lin Luxiang , Yao Zhiliang , Chatterjee Madhuparna , Ge Xuejun , Jin Lu , Deng Yun , Yang Xiaodong , Xia Shangwen , Liu Feng , Cao Guanghong , Swenson Nathan G.
Published: February 2025

Abiotic environments and biotic neighbourhoods interact to influence plant growth and community assembly. However, the nature of this interaction depends very much on how biotic neighbourhoods are measured, including their relatedness to focal plants. In a tropical seasonal rainforest, we examine the growth of a dominant canopy species in response to environmental factors, the densities and relatedness of conspecific and heterospecific neighbours, and their interactions. We find significant environmental effects and conspecific negative density dependence on growth. Furthermore, conspecific neighbour density has stronger negative effects on growth under high light and soil water resource levels, but weaker negative effects under low light and soil water resource levels. In addition, more closely related heterospecifics in the neighbourhood have negative effects on growth under high soil phosphorus availability, but positive effects under low soil phosphorus availability. In contrast, more closely related conspecifics in the neighbourhood have negative effects on growth under low soil potassium availability, but positive effects under high soil potassium availability. Our study emphasizes the importance of both intra- and interspecific neighbourhood composition and their interactions with resource levels for understanding tree growth. This enhances our understanding of the complex processes in community assembly and species coexistence within forest communities.
Cambrian carbonaceous protoconodonts and the early fossil record of the Chaetognatha
Authors: Slater Ben J.
Published: February 2025

Fossil remains from the early Cambrian Period suggest an ancient origin for the phylum Chaetognatha. As macrofossils, Cambrian chaetognaths are restricted to just a few Konservat-Lagerstätten sites, yet the dispersed grasping spines characteristic of this clade are relatively common as phosphatized ‘protoconodonts’. Here, an abundance of protoconodonts are described, but preserved in an entirely different manner, as ‘small carbonaceous fossils’ (SCFs) extracted from Cambrian Fortunian and Stage 4 mudrocks of Estonia and Sweden, respectively. Preservation among small carbonaceous fossils is substantial, representing an alternative but overlooked resource for tracing the origins of the chaetognath clade. Importantly, small carbonaceous fossils are abundant in normal marine siliciclastic deposits, in which conventionally studied phosphatic protoconodont fossils are scarce. Recent advances in constraining the phylogenetic position of chaetognaths suggest a relationship to the clade Gnathifera (gnathostomulids, micrognathozoans, rotifers). Newly emerging small carbonaceous fossil records, therefore, offer the chance to establish important calibration points for the divergence of deep bilaterian clades, including Protostomia, Lophotrochozoa and Gnathifera. Protoconodonts are especially valuable in this respect given their appearance close to, or prior to, the Ediacaran–Cambrian boundary. A first compilation of small carbonaceous fossil protoconodont records suggests chaetognath-like bilaterians had evolved by the latest Ediacaran (approximately 555–545 Ma), while the jaw complex possessed by the chaetognath crown-group emerged at least 520 Ma.
Metabolic rate of angiosperm seeds: effects of allometry, phylogeny and bioclimate
Authors: Dalziell Emma L. , Tomlinson Sean , Merritt David J. , Lewandrowski Wolfgang , Turner Shane R. , Withers Philip C.
Published: February 2025

Energetics is considered a fundamental ‘currency’ of ecology and the way that metabolic rate (MR)—the rate of energy expenditure on biological processes—scales relative to the size of the organism can be both an adaptive benefit and a constraint in mediating the energetic demands of ecological processes. Since few investigations have examined this relationship for angiosperm seeds, we measured standard metabolic rate (SMR) of 108 species’ seeds, spanning a broad suite of species. We used fluorescence-based closed-system respirometry at temperatures between 18°C and 30°C, based on optimal germination conditions, and Q
10
corrected to 20°C. The allometric relationship for SMR as a function of seed mass was 0.081 × M
0.780
with ordinary least squares regression and 0.057 × M
0.746
with phylogenetic generalized least squares regression. This relationship is consistent with the pervasive metabolic allometry documented for both vegetative plants and domesticated cultivars (
n
= 14) which had higher SMR residuals than wild species (seven weeds and 87 Australian native species). For native species, seed SMR was strongly related to measures of increasing environmental aridity (annual mean temperature and precipitation, and precipitation in the wettest quarter), consistent with seeds from arid environments having a high MR to supply energy needed to germinate rapidly. By comparing SMR of seeds for diverse angiosperm species, we provide insights into inter-relationships of physiology, distribution, climate and domestication on seed ecology and suggest that energetics represents a valuable addition to established functional trait libraries for seed biology.
Yokenella regensbergei : Unveiling a hidden pathogen in an immunocompetent patient: a case report
Authors: Khatri Mahima , Malhotra Shikhir , Kombade Sarika
Published: February 2025

Background : Yokenella regensburgei is Gram-negative, oxidase-negative, non-sporing, motile rod with peritrichous flagella . It is rarely isolated from human samples.
Case presentation: This a case report of a 52 year old male patient who presented to our centre with a non healing ulcer. A culture from the biopsy sample (from the ulcer) isolated Yokenella regensburgei . The patient was started on antibiotics for the same which lead to healing of the ulcer.
Conclusion : Increased discussion about such rare isolates will aid in proper identification and proper treatment of such patients especially in low income centres. To the best of our knowledge this is a first case report from India regarding Yokenella regensburgei as a cause of skin and soft tissue infection.
Genomic insights into the beneficial potential of Bifidobacterium and Enterococcus strains isolated from Cameroonian infants
Authors: Kaktcham Pierre Marie , Kujawska Magdalena , Kouam Edith Marius Foko , Piame Laverdure Tchamani , Tientcheu Michele Letitia Tchabou , Mueller Julia , Felsl Angela , Truppel Bastian-Alexander , Ngoufack François Zambou , Hall Lindsay J.
Published: February 2025

A healthy early-life gut microbiota plays an important role in maintaining immediate and long-term health. Perturbations, particularly in low- to middle-income communities, are associated with increased infection risk. Thus, a promising avenue for restoring a healthy infant microbiota is to select key beneficial bacterial candidates from underexplored microbiomes for developing new probiotic-based therapies. This study aimed to recover bifidobacteria and lactic acid bacteria from the faeces of healthy Cameroonian infants and unravel the genetic basis of their beneficial properties. Faecal samples were collected from 26 infants aged 0–5 months recruited in Dschang (Cameroon). Recovered bacterial isolates were subjected to whole-genome sequencing and in silico analysis to assess their potential for carbohydrate utilization, their antimicrobial capacities, host-adaptation capabilities and their safety. From the range of infant-associated Bifidobacterium and Enterococcus strains identified, Bifidobacterium species were found to harbour putative gene clusters implicated in human milk oligosaccharide metabolism. Genes linked to the production of antimicrobial peptides such as class IV lanthipeptides were found in Bifidobacterium pseudocatenulatum, while those implicated in biosynthesis of cytolysins, enterolysins, enterocins and propeptins, among others, were identified in enterococci. Bifidobacterial isolates did not contain genes associated with virulence; however, we detected the presence of putative tetracycline resistance genes in several strains belonging to Bifidobacterium animalis subsp. lactis and Bifidobacterium longum subsp. longum. Among the enterococci, Enterococcus mundtii PM10 did not carry any genes associated with antimicrobial resistance or virulence. The latter, together with all the Bifidobacterium strains, also encoded several putative adaptive and stress-response-related genes, suggesting robust gastroinstestinal tract colonization potential. This work provides the first genomic characterization of Bifidobacterium and Enterococcus isolates from Cameroonian infants. Several strains showed the genomic potential to confer beneficial properties. Further phenotypic and clinical investigations are needed to confirm their suitability as customized probiotics.
Morphological Variation and DUS Characterization in Bitter Gourd (Momordica charantiaL.) collections from Eastern India for Varietal Identification and Genetic Improvement
Authors: Verma Anita , Joshi Alpana
Published: February 2025

This study investigates the morphological variation and Distinctness, Uniformity, and Stability (DUS) characterization ofMomordica charantiacollections from Eastern India to facilitate varietal identification and genetic improvement. Twenty-two Bitter Gourd varieties were characterized based on morphological traits to assess genetic diversity and enhance breeding program efficiency. Significant variations were observed in fruit morphology (colour, length, surface tubercles, and ridges) and seed characteristics (Colour and margin indentation) enabling effective varietal differentiation. Notably, four accessions were classified asM. charantia var. muricatadue to their distinctly small fruit size, highlighting the presence of diverse morphological forms within the studied population. Additionally, admixture was detected in seven varieties, which underscores the necessity for purification processes to ensure the commercial viability of these accessions. This research emphasizes the rich genetic diversity of Bitter Gourd in Eastern India and identifies key traits that are essential for distinguishing between varieties. The findings provide valuable insights for breeders to develop improved cultivars with enhanced productivity and consumer-preferred traits. Moreover, this study supports ongoing plant breeding efforts to enhance crop quality and yield by identifying reliable morphological traits for varietal differentiation. Furthermore, it recommends additional research to refine DUS criteria by incorporating more traits that effectively differentiate between smooth-type Bitter Gourd varieties.
Characterizing resting-state EEG oscillatory and aperiodic activity in neurodegenerative diseases: A multicentric study
Authors: Jaramillo-Jimenez Alberto , Mantilla-Ramos Yorguin-Jose , Tovar-Rios Diego A , Lopera Francisco , Aguillón David , Ochoa-Gomez John Fredy , Paquet Claire , Gaubert Sinead , Pardini Matteo , Arnaldi Dario , Taylor John-Paul , Fladby Tormod , Brønnick Kolbjørn , Aarsland Dag , Bonanni Laura
Published: February 2025

Background

Abnormalities in resting-state electroencephalogram (rsEEG) posterior alpha rhythm are promising biomarkers of neurodegenerative diseases (NDDs), often assessed via spectral analysis, ignoring the signal’s non-rhythmic (aperiodic) component. Evidence assessing aperiodic and oscillatory rsEEG abnormalities across NDDs is scarce and often underpowered. Multicenter studies could tackle these limitations, but data pooling might introduce site-related rsEEG differences (batch effects). This study aims to characterize rsEEG oscillatory and aperiodic patterns across NDDs, minimizing potential batch effects.

Methods

RsEEGs (n = 639; 11 sites) were automatically preprocessed. Signals comprised healthy controls (HC = 153), Lewy Body Dementias (LBD = 95), Parkinson’s Disease (PD = 71), Alzheimer’s Disease (AD = 186), Frontotemporal Dementia (FTD = 23), Mild Cognitive Impairment (MCI) in positive Lewy Body pathology or PD (MCI-LBD = 34), and MCI in positive AD pathology (MCI-AD = 77). Power spectrum batch effects were harmonized using reComBat (age, sex, and diagnosis-adjusted). Harmonization was evaluated with functional and mass-univariate ANOVAs. Oscillatory and aperiodic parameters were extracted from the batch-harmonized power spectrum. NDDs-related differences were estimated with functional and mass-univariate tests, bootstrapped pairwise comparisons, and logistic regressions.

Results

Qualitative visualizations and statistical testing showed reduced batch effects after harmonization. Statistically significant findings included steeper aperiodic parameters and lower oscillatory center frequency in LBD compared to other NDDs. Additionally, oscillatory extended alpha power was lower in AD vs. LBD.

Conclusions

Batch effects in the rsEEG power spectrum can be mitigated with harmonization. Oscillatory alpha power reduction may better reflect AD abnormalities, whereas pronounced oscillatory frequency slowing and greater aperiodic activity characterize LBD.
In silico prediction of optimal multifactorial intervention in CKD
Authors: Latosinska Agnieszka , Mina Ioanna , Nguyen Nghia , Golovko Igor , Keller Felix , Mayer Gert , Rossing Peter , Staessen Jan A. , Delles Christian , Beige Joachim , Glorieux Griet , Clark Andrew L , Schanstra Joost P , vlahou antonia , Peter Karlheinz , Rychlik Ivan , Ortiz Alberto , Campbell Archie , Rupprecht Harald , Persson Frederik , Mischak Harald , Siwy Justyna
Published: February 2025

Background and Aims: Chronic kidney disease (CKD) significantly contributes to global morbidity and mortality. Early, targeted intervention offers an ideal strategy for mitigating this burden. Peptidomic changes inform on CKD onset and progression and hold insights for treatment strategies. We investigated the molecular effects of six different therapeutic interventions in silico in all possible combinations on the urine peptidome, aiming to identify the most beneficial treatment for individual patients. Method: This study predicted major adverse kidney events (MAKE), defined as a 40% decline in estimated glomerular filtration rate (eGFR) or kidney failure (median follow up time of 1.50 (95%CI 0.35, 5.0)), using the urinary peptidomic classifier CKD273 in a retrospective cohort of 935 participants. The impact of various treatments on urinary peptidomic profiles, assessed from previous studies of four different drug-based interventions (MRA, SGLT2i, GLP1-RA and ARB), one dietary intervention (olive oil) or from exercise, was applied. Treatment effects were quantified through fold changes in peptide abundance after treatment, recalibrated to align with outcomes observed in randomized controlled trials and applied to patient-specific urinary profiles, simulating intervention effects and recalculation of CKD273 scores for each individual. For combination treatments, the effects of multiple interventions were combined to model their cumulative impact. Results: Simulated interventions demonstrated a significant reduction in median CKD273 scores, from 0.57 (IQR: 0.19-0.81) before to 0.039 (IQR: -0.192-0.363) after intervention (paired Wilcoxon test, P < 0.0001), when the most beneficial treatment or combination of treatments was applied individually. The combination of all available treatments was found optimal only for 17.6% of the patients and not the most frequently predicted optimal intervention. Patients with higher baseline CKD273 scores required more complex intervention combinations to achieve the greatest reduction in scores. The findings present potential individualized treatment strategies in CKD management. Conclusion: This study supports the feasibility of in silico predicting effects of therapeutic interventions on CKD progression. By identifying the most beneficial treatment combinations for individual patients, this approach paves the way for precision medicine in CKD.
Spatial distribution of the proteome in human body and cancers
Authors: Yue Liang , Jiang Wenhao , Li Sainan , Luo Meng , Fan Ning , Zhan Xiaolu , Chen Kexin , Lu Tian , Guo Fang , Li Dongwei , Ge Weigang , Nie Zongxiang , Lyu Mengge , Jun A , Wang Yingrui , Chen Yingdan , Fu Zhenhai , Xiang Nan , Li Lu , Yu Fengchao , Teo Guo Ci , Nesvizhskii Alexey I , Wang Meng , Snyder Michael P. , Collins Ben , Aebersold Ruedi , Xu Fei , Zhu Yi , Liu Tong , Li Yan , Guo Tiannan
Published: February 2025

A comprehensive spatial distribution of the proteome in human body and cancers is fundamental for understanding human biology and diseases including cancers. Here, we present an anatomically resolved human proteome derived from 1781 benign and malignant samples from 58 major tissue types encompassing 251 specific tissues and 25 carcinomas. Based on a spectral library covering over 75% of the human protein-coding genes with 208 understudied and 82 missing proteins characterized, we quantified over 13,000 proteins in these samples using data-independent acquisition proteomics. This data resource presents the so far most comprehensive quantitative proteomic landscape of human tissues and common carcinomas. It allows systematic evaluation of tissue-specific drug responses, identification of drug candidates that may be repurposed as antineoplastics, and discovery of novel targets for anticancer therapy. This resource, available as an online knowledgebase, refines our knowledge of spatial distribution of the human proteome and tumor-specific protein modulation.
Reduced Fast Periodic Visual Stimulation Oddball Responses to Threatening Faces Associated with Anxiety
Authors: Vandenheever David , Davidson Haleigh , Kemp Jennifer , Murphy Zack , Kujawa Autumn , Shi Jingyi , Nadorff Michael R. , Bates-Brantley Kayla , Sidwell MacKenzie
Published: February 2025

Facial expression processing is crucial for social communication and survival, with anxiety disorders often linked to alterations in attentional biases toward threat-related stimuli. While previous studies using event-related potentials (ERPs) have yielded conflicting findings regarding threat sensitivity in anxiety, Fast Periodic Visual Stimulation (FPVS) offers a high signal-to-noise, implicit alternative for assessing emotion processing. This study utilized FPVS to investigate neural responses to facial expressions in individuals with anxiety compared to healthy controls. Forty-one adults participated, with 17 classified into the anxiety group based on self-reported diagnosis or PROMIS Anxiety scores. EEG responses were recorded while participants viewed sequences of neutral faces interspersed with emotional oddball expressions (angry, fearful, happy, and sad). Results revealed robust individual- and group-level neural responses, with significantly reduced summed baseline-corrected amplitudes (BCA) in central-parietal regions for angry and happy faces in the anxiety group. These findings suggest that anxious individuals exhibit attenuated discrimination of emotional expressions, particularly in higher-order processing regions, which may reflect cognitive avoidance of threat or general disengagement from emotional stimuli. The study highlights the potential of FPVS as a clinically relevant tool for objectively assessing emotion processing in anxiety and related disorders.
Genomic prediction of symbiotic interactions between twoEndozoicomonasclades and their coral host,Acropora loripes
Authors: Gotze Cecilie R , Tandon Kshitij , Philip Gayle K , Dungan Ashley M , Maire Justin , Hoj Lone , Blackall Linda L , van Oppen Madeleine JH
Published: February 2025

Background

The bacterial genusEndozoicomonasis a predominant member of the coral microbiome, widely recognised for its ubiquity and ability to form high-density aggregates within coral tissues. Hence, investigating its metabolic interplay with coral hosts offers critical insights into its ecological roles and contributions to coral health and resilience.

Results

Using long- and short-read whole-genome sequencing of 11Endozoicomonasstrains fromAcropora loripes, genome sizes were found to range between 5.8 and 7.1 Mbp. Phylogenomic analysis identified two distinct clades within the family Endozoicomonadaceae. Metabolic reconstruction uncovered clade-specific pathways, including the degradation of holobiont-derived carbon and lipids (e.g., galactose, starch, triacylglycerol, D-glucuronate), latter of suggest involvement ofEndozoicomonasin host ‘sex-type’ steroid hormone metabolism. A clade-specific type 6 Secretion System (T6SS) and predicted effector molecules were identified, potentially facilitating coral-bacterium symbiosis. Additionally, genomic analyses revealed diverse phosphorus acquisition strategies, implicatingEndozoicomonasin holobiont phosphorus cycling and stress responses.

Conclusions

This study reveals clade-specific genomic signatures ofEndozoicomonassupporting its mutualistic lifestyle within corals. Findings suggests possible roles in nutrient cycling, reproductive health, and stress resilience, offering novel insights into coral holobiont functioning and potential strategies for reef restoration.
STEAM: Spatial Transcriptomics Evaluation Algorithm and Metric for clustering performance
Authors: Reynoso Samantha , Schiebout Courtney , Krishna Revanth , Zhang Fan
Published: February 2025

Motivation

Spatial transcriptomic technologies allow researchers to explore the diversity and specificity of gene expression within their original tissue structure. Accurately identifying regions that are spatially coherent in both gene expression and physical tissue structures is an emerging topic, but challenging due to the lack of ground truth labels which renders complicating validation of clustering consistency and reproducibility. This highlights a need for a computational evaluation framework to rigorously and unbiasedly assess clustering performance.

Results

To address this gap, we propose STEAM (Spatial Transcriptomics Evaluation Algorithm and Metric), a user-friendly computational pipeline designed to evaluate the consistency and reliability of clustering results by leveraging machine learning classification and prediction methods, with the goal of maintaining the spatial proximity and gene expression patterns within clusters. We benchmarked STEAM on various public datasets, spanning multi-cell to single-cell resolution, as well as spatial transcriptomics and proteomics. The results highlighted its robustness and generalizability through comprehensive statistical evaluation metrics, such as Kappa score, F1 score, accuracy, and adjusted rand index. Notably, STEAM supports multi-sample training, enabling cross-replicate clustering consistency assessment. Moreover, STEAM provides practical guidance by comparing clustering results across multiple approaches; here, we evaluated four different methods, including spatial-aware and spatial-ignorant approaches. In summary, we believe that STEAM provides researchers a promising tool for evaluating clustering robustness and benchmarking clustering performance for spatial omics data, offering valuable insights to drive reproducible discoveries in spatial biology.

Availability and implementation

Source code and the R software tool STEAM are available fromhttps://github.com/fanzhanglab/STEAM.
Microbial metabolism of food allergens determines the severity of IgE-mediated anaphylaxis
Authors: Sánchez-Martínez Elisa , Rondeau Liam E. , Garrido-Romero Manuel , Barbosa da Luz Bruna , Haas Dominic A. , Yuen Gavin , Hall Peter , Dang Rebecca , Wang Xuan-Yu , Moreno-Serna Lucía , López-Sanz Celia , Nuñez-Borque Emilio , Garrido-Arandia Maria , Diaz-Perales Araceli , Carrasco Yolanda R. , Koenig Joshua F.E. , Walker Tina D. , Jordana Manel , Verdu Elena F. , Surette Michael G. , Ojeda Pedro , Vega Francisco , Blanco Carlos , Shreffler Wayne G. , Patil Sarita U. , Moreno F. Javier , Jiménez-Saiz Rodrigo , Caminero Alberto
Published: February 2025

Anaphylaxis is an acute, potentially life-threatening reaction, often triggered by foods and largely mediated by IgE. A critically important aspect of anaphylaxis pertains to the factors that modulate its severity. The human microbiota is known to influence oral tolerance, but the microbial mechanisms directly involved in IgE-mediated anaphylaxis remain unknown. Here, we demonstrate that human saliva harbors peanut-degrading bacteria that metabolize immunodominant allergens (Ara h 1 and Ara h 2) and alter IgE binding. Additionally, we providein vivoevidence showing that oral bacteria metabolize peanut allergens, influencing systemic allergen exposure and the severity of anaphylaxis. Finally, in a clinical study, we observe that common peanut-degrading bacteria, such asRothia,from the oral cavity, are more abundant in peanut-allergic patients who exhibit better tolerance to allergen exposure. Altogether, these results demonstrate the role of the human microbiota in modulating IgE-mediated reactions through allergen metabolism. These findings reveal a novel microbial mechanism with potential to prevent, or reduce, the severity of IgE-mediated anaphylaxis.
Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms
Authors: Zheng Hongyu , Sarkar Hirak , Raphael Benjamin J.
Published: February 2025

Spatially resolved transcriptomics (SRT) technologies measure gene expression across thousands of spatial locations within a tissue slice. Multiple SRT technologies are currently available and others are in active development with each technology having varying spatial resolution (subcellular, single-cell, or multicellular regions), gene coverage (targeted vs. whole-transcriptome), and sequencing depth per location. For example, the widely used 10x Genomics Visium platform measures whole transcriptomes from multiple-cell-sized spots, while the 10x Genomics Xenium platform measures a few hundred genes at subcellular resolution. A number of studies apply multiple SRT technologies to slices that originate from the same biological tissue. Integration of data from different SRT technologies can overcome limitations of the individual technologies enabling the imputation of expression from unmeasured genes in targeted technologies and/or the deconvolution of ad-mixed expression from technologies with lower spatial resolution. We introduce Spatial Integration for Imputation and Deconvolution (SIID), an algorithm to reconstruct a latent spatial gene expression matrix from a pair of observations from different SRT technologies. SIID leverages a spatial alignment and uses a joint non-negative factorization model to accurately impute missing gene expression and infer gene expression signatures of cell types from ad-mixed SRT data. In simulations involving paired SRT datasets from different technologies (e.g., Xenium and Visium), SIID shows superior performance in reconstructing spot-to-cell-type assignments, recovering cell-type-specific gene expression, and imputing missing data compared to contemporary tools. When applied to real-world 10x Xenium-Visium pairs from human breast and colon cancer tissues, SIID achieves highest performance in imputing holdout gene expression. A PyTorch implementation of SIID is available athttps://github.com/raphael-group/siid.
Transcriptome-proteome profiling inBurkholderia thailandensisduring the transition from exponential to stationary phase
Authors: Al-Tohamy Ahmed , Donnarumma Fabrizio , Grove Anne
Published: February 2025

Bacterial cells commonly exist in stationary phase, for instance within a host cell.Burkholderia thailandensisis closely related to, and a surrogate for highly pathogenicBurkholderiaspecies. Understanding the molecular mechanisms that characterize the transition ofB. thailandensisfrom exponential to stationary phases is critical to understanding responses to stress or nutrient limitation. We present here an integrated transcriptomic and proteomic analysis of gene and protein expression changes during entry into stationary phase. We identified 928 differentially expressed genes and 832 differentially expressed proteins. Genes encoding proteins involved in benzoate degradation and O-antigen nucleotide sugar biosynthesis were among the most highly upregulated in stationary phase, whereas processes such as translation and flagellar biosynthesis were downregulated. Proteins related to fatty acid degradation and butanoate metabolism accumulated along with proteins involved in synthesis of secondary metabolites. Markedly downregulated proteins included ribosomal proteins as well as the house-keeping iron-sulfur biogenesis proteins. An only modest correlation between transcriptome and proteome changes was seen, and the RpoS sigma factor was not significantly increased during early stationary phase; RpoS is typically abundant during stationary phase and critical for expression of stress-response genes. Our data therefore point to distinct adaptive mechanisms inB. thailandensis, including post-translational regulation.
Perceptual Decision-Making During Whisker-Guided Navigation Causally Depends on a Single Cortical Barrel Column
Authors: Armstrong Alex G. , Vlasov Yurii A.
Published: February 2025

Perceptually driven behavioral choices ae thought to develop gradually from sensation to perception in somatosensory cortex to guide decision-making in higher order cortical areas. Primary somatosensory cortex wS1 of rodents related to their mystacial whiskers has been a model system to study this information flow. However, the role of wS1 in this process is often debated based on controversial results of loss-of-function behavioral experiments that often require prolonged training and movement restraints. Here, to elucidate the role of wS1 in decision-making, we develop an ethological whisker-guided virtual reality (VR) paradigm that closely mimics natural navigation in underground burrows. Untrained mice are navigating at high speed the left and right turns by sensing VR walls with just a pair of their C2 whiskers. We inactivate less than 200 neurons in layer 4 of C2 barrel that results in loss of ability to produce turns contralateral to the lesion. Using probabilistic model of collision avoidance in the presence of noise and uncertainties we hypothesize that wS1 is involved in a feedback control loop that requires continuous updates and predictions to infer the optimal path for collision avoidance.
A curated great ape genome diversity panel
Authors: Han Sojung , Riyahi Sepand , Huang Xin , Kuhlwilm Martin
Published: February 2025

Studying the genetic diversity of non-human great apes is important for research questions in evolution as well as human diversity and disease. Genomic data of the three great ape clades (Pan, Gorilla, Pongo) has been published across multiple studies over more than one decade. However, unlike in humans, no comprehensive dataset on great ape diversity is available, due to different scopes of the original studies. Here, we present a curated dataset of 203 high coverage (≥12-fold) whole genomes, including 77 chimpanzee, 14 bonobo, 77 gorilla and 35 orangutan individuals sequenced on the Illumina platform. By integrating data from captive individuals, we contextualize them with data from wild individuals. We discuss issues with previously published data leading to removal of individuals due to low sequencing depth, missing data, or occurrence of duplicate individuals. This resource of files in CRAM and gVCF format, as well as segregating sites per clade, will allow researchers to address questions related to human and great ape evolution and diversity in a comparative manner.
Toxoplasma in a natural population of chimpanzees
Authors: Chabry Mathieu , Hobaiter Catherine , Zuberbühler Klaus , Koella Jacob C.
Published: February 2025

Toxoplasma gondiiis a unicellular parasite that can infect most warm-blooded animals. In humans, it is linked to schizophrenia and other neurological disorders. It is also responsible for congenital toxoplasmosis, which can be lethal or cause severe neurological damage in the developing foetus. More subtle behavioural effects have been observed in various species, including humans, in particular increased risk-taking, which is thought to increase the parasite’s transmission to feline predators, the definitive hosts. We investigated the prevalence ofToxoplasma gondiiin wild eastern chimpanzees (Pan troglodytes schweinfurthii) in the Budongo Forest, Uganda. We tested 45 individuals of two communities, one of which (Sonso) has a home range overlapping with human settlements. In this community, the prevalence was 22.7% (N=5 of 22), whereas in the neighbouring, but more isolated, Waibira community none of the 23 individuals tested were infected. The majority of infected Sonso individuals were adult males and/or high-ranking group members, attributes associated with increased risk-taking behaviour in chimpanzees and other animals. While further work is necessary to reveal the causal relation between infection and behaviour, our findings open new avenues of research for the neural impact of parasites on primate social behaviour.
Stand-alone mobile quantum memory system
Authors: Jutisz Martin , Erl Alexander , Wolters Janik , Gündoğan Mustafa , Krutzik Markus
Published: February 2025

We present the implementation and performance analysis of a portable rack-mounted stand-alone warm-vapor quantum memory system that also includes the laser package, control electronics, and data-processing hardware. The optical memory is based on long-lived hyperfine ground states of cesium, which are connected to an excited state via the D1 line at 895 nm in a Λ-configuration. The memory is operated with weak coherent pulses containing on average <1 photons per pulse. The long-term stability of the memory efficiency and storage fidelity is demonstrated at the single-photon level together with operation in a nonlaboratory environment.

Published by the American Physical Society
2025
Second-order nonlinear piezo-optic properties of single crystal lithium niobate thin films
Authors: Pionteck Mike N. , Roeper Matthias , Koppitz Boris , Seddon Samuel D. , Rüsing Michael , Padberg Laura , Eigner Christof , Silberhorn Christine , Sanna Simone , Eng Lukas M.
Published: February 2025

Stress plays a crucial role in thin films and layered systems, and thus significantly influences the material's electrical, mechanical and (nonlinear) optical responses. Despite lithium niobate's wide applicability as a nonlinear optical material, the impact of mechanical stress on its nonlinear optical properties is not well characterized. In this work, we systematically study both experimentally and theoretically, the nonlinear optical responses of thin film lithium niobate (TFLN) single crystals. Compressive and tensile stress is applied in our experiment using a piezodriven strain cell. We then record the second-harmonic-generated (SHG) response in back-reflection geometry, and compare these results to theoretical modeling using density functional theory (DFT). Both methods consistently reveal that uniaxial stress induces changes of the nonlinear optical susceptibility of certain tensor elements on the order of up to 1 pm/(V GPa). The exact value depends on the tensor element that is addressed in our SHG analysis, on the crystal orientation, and also whether using compressive or tensile stresses. Furthermore, a lowering of the crystal symmetry when applying stress along the x or y crystallographic axes is observed by the appearance of new nonlinear optical tensor elements within the strained crystals.

Published by the American Physical Society
2025
Robust spin-orbit coupling in semimetallic
SrIrO3
under hydrostatic pressure
Authors: Fuchs D. , Jaiswal A. K. , Wilhelm F. , Wang D. , Rogalev A. , Le Tacon M.
Published: February 2025

The semimetallic behavior of the perovskite iridate SrIrO3 shifts the end member of the strongly spin-orbit (SO) coupled Ruddlesden-Popper series Srn+1IrnO3n+1 away from the Mott insulating regime and the half-filled pseudospin Jeff=12 ground state well established in the layered iridates (n=1 and 2). To investigate the robustness of the SO coupled ground state of SrIrO3, x-ray absorption spectroscopy was carried out at the Ir L2,3 edges under hydrostatic pressure up to 50 GPa at room temperature. The effective SO coupling was deduced from the branching ratio (BR) of the Ir L2 and L3 white lines. With increasing pressure, the BR decreases, and the Ir L2,3 peak positions shift to higher energies. The number of 5d holes remains constant, indicating that the spectral weight redistribution and peak shifts arise from orbital mixing between t2g and eg related states. The expectation value of the angular part of the SO operator

〈

LS

〉

decreases by ∼15% at 50 GPa. This reduction, which is very similar to that observed in the layered iridates, is well explained by an increase of the octahedral crystal field due to the shortening of the Ir-O bond length under compression. Consistent with theoretical predictions, the orbital mixing and 〈LS〉 decrease as the crystal field increases. However, the effective SO coupling remains robust against pressure and does not indicate a covalency-driven breakdown within the investigated pressure range.

Published by the American Physical Society
2025
Baryon asymmetry from the decay and scattering of a Majorana fermion pair coupled to quarks
Authors: Gopalakrishna Shrihari , Tibrewala Rakesh
Published: February 2025

We compute the baryon asymmetry in decay and scattering processes involving the electromagnetically charge-neutral fermion χ that carries the nonzero baryon number and interacts with quarklike fermions U, D via a vector-vector dimension-six effective operator, in the theory we developed in our earlier work. Majorana masses for the χ break the baryon number and split the Dirac fermion χ into a pair of Majorana fermions Xn with an indefinite baryon number. We identify loop amplitudes for Xn decay and scattering processes that are sensitive to the baryon number violation. The phases in the Majorana mass and couplings, in conjunction with the phase from intermediate on-shell states, lead to C and CP violation in these processes. For some representative parameter choices, we numerically compute the decay and scattering baryon asymmetries between the process and its conjugate process and find that the asymmetry generated is very interesting for explaining the baryon asymmetry of the Universe.

Published by the American Physical Society
2025
More on scattering processes of dressed particles with a time-dependent mass
Authors: Yamada Yusuke
Published: February 2025

We discuss the scattering process of a scalar field having a time-dependent mass with another scalar field having a constant mass as a toy model of the scattering problems during preheating after inflation. Despite a general difficulty of analytically solving such models, in our previous work [QFT approach to dressed particle processes in preheating and non-perturbative mechanism in kinematically-forbidden regime, ], we considered an exactly calculable model of such scattering processes with a time-dependent mass of the form m2(t)⊃μ4t2 and the time-dependence never disappears formally. In this work, we discuss another exactly calculable model with a time-dependent mass that has a spike/peak but asymptotes to a constant, which effectively appears in the preheating model of Higgs inflation with a nonminimal coupling. Thanks to the localized time-dependence of the mass, the daughter particle number density behaves in a physically reasonable way contrary to the one in our previous model due to the infinite time-dependent mass in the asymptotic future. On the other hand, we find that the daughter particle experiences the kinematically forbidden process, which is a nonperturbative phenomenon found in our previous work. As in the previous model, the kinematically forbidden process produces daughter particles exponentially more than the parent particle having the time-dependent mass, which never happens for particle decay processes without time-dependent backgrounds. This result supports the existence of such a nonperturbative particle production process in general time-dependent backgrounds.

Published by the American Physical Society
2025
Generalized Haldane map from the matrix product state path integral to the critical theory of the
J1−J2
chain
Authors: Azad F. , McRoberts Adam J. , Hooley Chris , Green A. G.
Published: February 2025

We study the J1−J2 spin-1/2 chain using a path integral constructed over matrix product states (MPS). By virtue of its nontrivial entanglement structure, the MPS ansatz captures the key phases of the model even at a semiclassical, saddle-point level, and, as a variational state, is in good agreement with the field theory obtained by Abelian bosonization. Going beyond the semiclassical level, we show that the MPS ansatz facilitates a physically motivated derivation of the field theory of the critical phase: By carefully taking the continuum limit—a generalization of the Haldane map—we recover from the MPS path integral a field theory with the correct topological term and emergent SO(4) symmetry, constructively linking the microscopic states and topological field-theoretic structures. Moreover, the dimerization transition is particularly clear in the MPS formulation—an explicit dimerization potential becomes relevant, gapping out the magnetic fluctuations.

Published by the American Physical Society
2025