bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlation between severity of knee joint osteoarthritis and alignment of patellofemoral and patellar height on radiographs
Authors: Yang Zhenlei , Shen Mingjie , Xie Deshun , Zhang Junzhe , Wei Qingjun
Published: November 2024

Background:

The correlation between the morphological structure of the patellofemoral joint (PFJ) and the severity of knee joint osteoarthritis (KOA) remains uncertain. This study aims to investigate the correlation between the severity of knee joint osteoarthritis and the alignment of patellofemoral and patellar height on radiographs.

Methods:

This multi-center, retrospective study analyzed the magnetic resonance imaging (MRI) scans and anteroposterior radiographs of 534 adult outpatients with KOA. To evaluate the radiographic severity of KOA, anteroposterior radiographs of the knee and the Kellgren-Lawrence (K-L) grade were used. Knee MRI scans were used to measure the patellar length ratio (PLR), sulcus angle (SA), lateral patellar tilt angle (LPTA), and the distance between tibial tuberosity and trochlear groove (TT-TG). We examined the association between the configuration of the PFJ, arrangement, and harshness of the KOA. Information on participants’ demographics, such as age, sex, side, height, and weight, was collected. A chi-squared test was used for the correlation of radiographic severity of KOA with sex and the affected side. Spearman correlation was used for patellofemoral alignment or morphology and the radiographic severity of lateral KOA. Multiple linear regression models were used for the association between LPTA, SA, TT-TG, and severity of KOA after accounting for demographic variables.

Results:

The study comprised of 534 patients; of these, 339 (63%) were female. A total of 586 knees were evaluated in this study. Age showed a strong positive correlation with KOA severity (r = 0.516, P <0.01), whereas LPTA showed a strong negative correlation (r = –0.662, P <0.01). Additionally, SA (r = 0.616, P <0.05), and TT-TG showed a strong positive correlation (r = 0.770, P <0.01) with tibiofemoral osteoarthritis (TFOA) severity. Multiple linear regression analysis indicated that knee osteoarthritis severity (β = –2.946, P <0.001) and side (β = –0.839, P = 0.001) was associated with LPTA; knee osteoarthritis severity (β = 5.032, P <0.001) and age (β = –0.095, P <0.001) was associated with SA; knee osteoarthritis severity (β = 2.445, P <0.001), sex (β = –0.326, P = 0.041), body mass index (β = –0.061, P = 0.017) and age (β = –0.025, P <0.001) was associated with TT-TG. The radiographic severity of KOA positively correlated with PLR, SA, and TT-TG, but negatively correlated with LPTA.

Conclusions:

Radiographic severity of KOA was positively associated with age, SA, and TT-TG but negatively associated with LPTA.
Implementation of laparoscopic colorectal surgery in a spoke hospital: Analysis of the results from a dedicated unit in a spoke center
Authors: Provenzano Daniele , Mercurio Paola , Cannistrà Marco , Mahli Sam , Vindigni Angelo , Rugiero Giovanni , Cariati Maria , Antonella Lucia , Capoano Angelo , Peta Giuseppina , Bernardi Simone , Sorrentino Tommaso , Castaldo Pasquale
Published: November 2024

Introduction:

Despite its operative benefits and oncological noninferiority, video-laparoscopic colorectal surgery is still underutilized. This study analyses the results of a program for the implementation of video-laparoscopic colorectal surgery in a spoke hospital after the COVID-19 outbreak.

Methods:

Patients were enrolled between January 2022 and May 2024 in a single center. The procedures encompassed all sections of the colon and rectum. The same team performed all the surgical treatments. The same team performed all surgeries, which were elective.

Results:

Right hemicolectomy was the most common operation performed. Intestinal continuity was restored through extracorporeal anastomosis. The laparoscopic approach was used in 98 operations (76%), while 30 operations (24%) were performed using the open technique. The conversion rate was 18.75%.

Conclusions:

Currently, 83% of colorectal surgeries in Italy use a laparoscopic technique. Our study shows an increasing trend in the minimally invasive approach (76%), which is almost in line with the national average, despite the sample coming from a spoke hospital.
Factors Influencing Preoperative Psychological Resilience in Patients With Traumatic Lower Extremity Fractures
Authors: Jiang Yiwen , Ying Dinong , Xu Shuqin , Cao Wenting , Liu Liting , Zhou Qianqian
Published: November 2024

BACKGROUND:

The psychological resilience of patients with traumatic lower extremity fractures is relevant and has been studied in the postoperative rehabilitation phase; yet, few studies have focused on the early preoperative phase.

OBJECTIVE:

This study aims to explore preoperative psychological resilience in patients with traumatic lower extremity fractures.

METHODS:

This single-center cross-sectional survey design study was conducted over 5 months from December 2022 to April 2023 in a tertiary hospital in Shanghai, China. We used a convenience sampling method to assess psychological resilience in traumatic lower extremity fracture patients electronically. We administered the online surveys using the Questionnaire Star applet prior to surgery using the following tools: (a) general information questionnaire, (b) Numerical Rating Scale, (c) Connor–Davidson Resilience Scale, and (d) General Self-Efficacy Scale.

RESULTS:

A total of N = 175 patients were studied, of which n = 166 patients fully completed the survey for a response rate of 95%. Patients with traumatic lower extremity fractures demonstrated a low degree of psychological resilience preoperatively (M = 49.28, SD = 13.64). Patients’ psychological resilience and self-efficacy showed a significant positive correlation (r = .577). Factors associated with patients’ psychological resilience in multivariate linear analyses included level of education, medical insurance, and self-efficacy (p < .05).

CONCLUSION:

We found that preoperative psychological resilience in patients with traumatic lower-extremity fractures is poor and influenced by various factors; thus, future efforts should focus on providing timely, targeted interventions.
Trauma Patient Transitional Work: A Multidisciplinary Feasibility Survey of Planned Behavior Elements
Authors: Saucier Jason A. , Dietrich Mary S. , Maxwell Cathy , Lane-Fall Meghan B. , Messing Jonathan A. , Minnick Ann
Published: November 2024

Background:

Patient transitions in critical care require coordination across provider roles and rely on the quality of providers’ actions to ensure safety. Studying the behavior of providers who transition patients in critical care may guide future interventions that ultimately improve patient safety in this setting.

Objective:

To establish the feasibility of using the Theory of Planned Behavior in a trauma environment and to describe provider behavior elements during trauma patient transfers (de-escalations) to non-critical care units.

Methods:

This cross-sectional study surveyed a convenience sample of 103 multidisciplinary providers who do the cognitive and physical work of transitioning trauma patients from critical care to another non-critical care unit at a U.S. Level I trauma center. Descriptive methods for survey development, analysis, and administration were evaluated.

Results:

A total of 72 respondents completed the survey; they included registered nurses, nurse practitioners, and medical doctors, demonstrating a 70% response rate. Statistically significant differences among ICU roles were observed in perceived control (Eta-squared = 0.09, p = .001) and in several anchors in the attitude, subjective norms, and behavioral intent theoretical domains (Cohen’s d ranging from 0.36 to 2.03, p < .05).

Conclusions:

This study demonstrated variability in theory domains, signaling an opportunity to study a representative sample. It can serve as a blueprint for future behavioral studies designed to examine the Theory of Planned Behavior elements in trauma critical care providers.
Omaha System-Based Extended Nursing Care in Hypertensive Cerebral Hemorrhage: A Randomized Study
Authors: Xiao Yamei , Wang Xiaohui
Published: November 2024

BACKGROUND:

Traditional nursing care often fails to meet the complex needs of hypertensive cerebral hemorrhage patients. Limited evidence exists on the efficacy of structured nursing frameworks such as the Omaha System in postoperative care for these patients.

OBJECTIVE:

This study aims to evaluate the efficacy of Omaha-based extended nursing care in improving patients’ outcomes.

METHODS:

This randomized controlled trial included 53 patients with hypertensive cerebral hemorrhage admitted to the neurosurgical department of a large tertiary hospital in Chengdu, China, from March to September 2023. Participants were randomly assigned to either the traditional nursing care (n = 26) or the Omaha-based nursing care in addition to the traditional nursing care (n = 27). Outcomes included self-health management abilities, anxiety and depression levels, quality-of-life, and functional independence. Data were collected before nursing care and 1- and 3-months post-nursing care.

RESULTS:

Omaha-based nursing care demonstrated improvements in self-health management abilities, with cognition scores increasing from a baseline of 31.65 (4.37) to 57.32 (5.11) at 3-months (mean difference: 25.67, 95%CI [23.45, 27.89], p = .01). Anxiety levels decreased in the Omaha-based nursing group, with SAS scores reducing from 45.71 (3.48) to 28.26 (2.74) at 3-months (mean difference: −17.45, 95% CI [−19.02, −15.88], p < .01). Quality-of-life scores improved in the Omaha-based nursing group, increasing from 6.3 (1.2) to 7.9 (0.9) at 3-months (mean difference: 1.6, 95% CI [1.12, 2.08], p = .03). Functional independence scores were also higher in the Omaha-based nursing group at 3-months (mean difference: 9.2, 95% CI [6.11, 12.29], p = .03).

CONCLUSION:

Our findings support the integration of the Omaha System into postoperative care protocols for this patient population. However, further validation is warranted by larger trials.
Prehospital Interventions to Reduce Discomfort From Spinal Immobilization in Adult Trauma Patients: A Scoping Review
Authors: Mota Mauro , Melo Filipe , Santos Eduardo , Abrantes Tito , Monteiro Mariana P. , Cunha Madalena , Santos Margarida R.
Published: November 2024

Background:

Spinal immobilization, a widely used trauma prehospital intervention, is known to cause discomfort, yet little is known about interventions to reduce this discomfort.

Objective:

This scoping review aims to evaluate prehospital interventions to reduce discomfort from spinal immobilization in adult trauma patients.

Method:

This scoping review assessed prehospital pharmacological and nonpharmacological interventions to address discomfort from spinal immobilization in adult trauma patients. We searched sources published in English, French, Spanish, and Portuguese without time restrictions. Two reviewers independently screened sources against the inclusion criteria and extracted data using a specified extraction instrument. The databases MEDLINE, CINAHL, Scopus, Embase, APA PsycINFO, International Paramedic Practice, Amber: the Home of Ambulance Service Research, JBI Evidence Synthesis, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, RCAAP, and CAPES Thesis Bank were used.

Results:

Two articles were deemed eligible, identifying two interventions. One focused on the choice of immobilization device, while the other addressed the hemodynamic implications of immobilization discomfort, considering factors such as oxygen saturation, blood pressure, and pulse.

Conclusions:

Only two interventions were found, and both only indirectly addressed spinal immobilization discomfort. More well-designed research is needed to address patient-centered concerns regarding the discomfort from spinal immobilization in trauma care.
Need for individualized counseling regarding psoriasis systemic therapy in women of childbearing age: analysis of the PsoFem study at the University Medical Center Hamburg
Authors: Stephan Brigitte , Sommer Rachel , Augustin Matthias , Ganjuur Nomun , da Silva Neuza
Published: November 2024

Background:

For patients with moderate-to-severe psoriasis and current childbearing/pregnancy, the choice of therapy is limited.

Objectives:

The present study compared the disease burden and treatment choices in women of childbearing age (WoCBA) with and without a current wish for pregnancy.

Methods:

Female patients aged 18 to 45 years, with moderate-to-severe psoriasis vulgaris, were consecutively recruited. The patients reported on sociodemographic/reproductive characteristics and quality of life impairments. The physicians assessed disease severity, comorbidities, and current treatment(s). Both patients’ and dermatologists’ perceptions of shared decision-making for the current systemic treatment were surveyed.

Results:

Participants were 145 WoCBA with psoriasis: 73 were pregnant or reported a desire to conceive (group CB+) and 72 reported no wish to have (more) children (group CB−). Patients without childbearing wishes were older and often had previous children; no significant differences in clinical features or quality of life impairments were found. A significantly higher proportion of patients in the CB+ group were prescribed tumor necrosis factor alpha blockers, particularly certolizumab pegol. This treatment option was associated with previous children and the desire to conceive, but not with disease variables. Family planning was more often discussed and considered in the clinical decision for the CB+ group, but patient-doctor agreement for shared decision-making was fair-to-moderate.

Limitations:

The small sample size prevented comparative analyses between patients planning a pregnancy in the short- vs long-term future. In addition, specific variables related to the decision-making process for the current therapy need to be assessed and examined in more detail in further research.

Conclusion:

For WoCBA with childbearing wishes, tumor necrosis factor alpha blockers were most frequently prescribed, in accordance with current guidelines/recommendations. Decision-making for continuing or changing systemic therapy during pregnancy must take into account medication specificities and the vulnerable stages in pregnancy, as well as the limited amount of pregnancy-compatible drugs.
Germline DDX41 mutations in myeloid neoplasms: the current clinical and molecular understanding
Authors: Kida Junichiro , Chlon Timothy M.
Published: November 2024

Purpose of review

DDX41 mutations are the most common cause of germline predisposition to adult-onset myeloid neoplasms. The unique mutational landscape and clinical features indicate a distinct molecular pathogenesis, but the precise mechanism by which DDX41 mutations cause disease is poorly understood, owing to the multitude of DDX41 functions. In this review, we will update DDX41's known functions, present unique clinical features and treatment considerations, and summarize the current understanding of the molecular pathogenesis of the disease.

Recent findings

Large cohort studies have revealed that germline DDX41 variants are heterozygous and predominantly loss-of-function. Acquired mutation of the contralateral DDX41 allele, typically R525H, is present in more than half of patients at disease onset, which occurs after age 50. DDX41 is essential for hematopoiesis and has versatile functions in RNA metabolism and innate immune sensing. Experimental models have suggested that innate immune activation downstream of defects in R-loop resolution and ribosome biogenesis plays a key role in the pathogenesis.

While intensive investigations unveiled a strong genotype–phenotype relationship, the optimal therapeutic approach and long-term outcome are undefined. There is an urgent need to scrutinize the patients at single cell and multiomics level and to advance experimental animal and human models to fully elucidate the molecular pathogenesis.
Sclerosing encapsulating peritonitis (Abdominal Cocoon) associated with Non-Hodgkin’s lymphoma of bowel wall: a rare case report
Authors: Khanal Kunjan , Pandey Asim , Dangol Raj B. , Sherpa Pasang L. , Jaiswal Roshan , Parajuli Samriddhi , Singh Pradeep , Shakya Sudip R.
Published: November 2024

Introduction:

Sclerosing encapsulating peritonitis (SEP) is a rare condition causing intestinal obstruction. A thick fibrous membrane envelops abdominal organs. SEP is classified into two types: abdominal cocoon syndrome (ACS), also called idiopathic or primary SEP, and secondary SEP. Symptoms range from subacute to acute intestinal blockage, and diagnosis is usually confirmed during laparotomy.

Case presentation:

The authors present a case of a 32-year-old woman who presented with intermittent per-vaginal bleeding for 1 month, abdominal distension, decreased appetite, and significant weight loss over 5 months. Examination revealed pallor and a palpable 12×12 cm mass in the right lower abdomen. Imaging revealed a lobulated mass in the mid-ileum with bowel wall thickening. She underwent laparotomy, revealing fibrous tissue, and a nodular mass on the distal ileum. Histopathology confirmed non-Hodgkin’s lymphoma.

Discussion:

Sclerosing encapsulating peritonitis is a rare chronic inflammatory condition affecting the peritoneum. Primary SEP, also known as abdominal cocoon or idiopathic SEP, lacks a definitive cause, while secondary SEP results from conditions like peritoneal dialysis, liver cirrhosis, and malignancies. It involves peritoneal irritation leading to inflammation, fibrin-like material release, and subsequent bowel encasement and fibrosis. Diagnosis is typically made during laparotomy, though contrast-enhanced CT scan aids in presumptive diagnosis.

Conclusion:

This case report highlights a rare occurrence of abdominal cocoon syndrome in a patient with non-Hodgkin B-cell lymphoma, presenting with abdominal pain, distension, and bowel obstruction. Diagnosing this condition early is crucial, especially in patients with underlying malignancies. More research is needed to improve management.
Sortilin C-terminal fragment deposition depicts tangle-related nonamyloid neuritic plaque growth in Alzheimer’s disease
Authors: Zhang Qi-Lei , Wang Yan , Coulibaly Sidiki , Sun Zhong-Ping , Cai Xiao-Lu , Tu Tian , Liu Yu , Pan Aihua , Cui Meng-Chao , Manavis Jim , Wang Jian , Zhang Yang , Wang Xiao-Pin , Yan Xiao-Xin
Published: November 2024

Sortilin C-terminal fragments (sorfra) can co-deposit in β-amyloid (Aβ) plaques in human brain. However, sorfra plaques develop in the cerebrum with a spatiotemporal trajectory as of tauopathy. Here we examined sorfra pathogenesis relative to neuritic plaque evolution in the human brains with amyloid and tau pathologies converged in the neocortex and hippocampus. Sorfra plaques occurred in correlation with pTau/tangle, but not Aβ, pathologies across cerebral regions, neighboring cortical/hippocampal areas, and along the sulcal valley to gyral hilltop transition. Sorfra plaques and neuritic plaques were matchable in location, shape and size between consecutive sections, and were colocalized in double-labeling preparations. Microscopical study and tissue clearance three-dimensional imaging revealed sorfra/Aβ colocalized as well as independent plaques. Among the former, sorfra labeling correlated negatively to Aβ/amyloid labeling and β-secretase-1 labeling in dystrophic neurites. Sorfra plaques were depleted of microtubule-associated protein 2 (MAP2) labeled neuronal somata and dendrites, whereas normal looking MAP2/sortilin co-labeled profiles occurred nearby. Sorfra deposits were seen in astrocytes but not microglia around the plaques. Taken together, sorfra plaques are anatomically matchable to silver stained neuritic plaques. They develop with tangle-related somatodendritic degeneration, presenting as nonamyloid growth of the Aβ plaques and formation of Aβ-independent neuritic plaques during Alzheimer’s disease pathogenesis.
scPrediXcan integrates advances in deep learning and single-cell data into a powerful cell-type–specific transcriptome-wide association study framework
Authors: Zhou Yichao , Adeluwa Temidayo , Zhu Lisha , Salazar Sofia , Sumner Sarah , Kim Hyunki , Gona Saideep , Nyasimi Festus , Kulkarni Rohit , Powell Joseph , Madduri Ravi , Liu Boxiang , Chen Mengjie , Im Hae Kyung
Published: November 2024

Transcriptome-wide association studies (TWAS) help identify disease causing genes, but often fail to pinpoint disease mechanisms at the cellular level because of the limited sample sizes and sparsity of cell-type-specific expression data. Here we propose scPrediXcan which integrates state-of-the-art deep learning approaches that predict epigenetic features from DNA sequences with the canonical TWAS framework. Our prediction approach, ctPred, predicts cell-type-specific expression with high accuracy and captures complex gene regulatory grammar that linear models overlook. Applied to type 2 diabetes and systemic lupus erythematosus, scPrediXcan outperformed the canonical TWAS framework by identifying more candidate causal genes, explaining more genome-wide association studies (GWAS) loci, and providing insights into the cellular specificity of TWAS hits. Overall, our results demonstrate that scPrediXcan represents a significant advance, promising to deepen our understanding of the cellular mechanisms underlying complex diseases.
The impact of FreeSurfer versions on structural neuroimaging analyses of Parkinson’s disease
Authors: Sokołowski Andrzej , Bhagwat Nikhil , Kirbizakis Dimitrios , Chatelain Yohan , Dugré Mathieu , Poline Jean-Baptiste , Sharp Madeleine , Glatard Tristan
Published: November 2024

Image processing software impacts the quantification of brain measures, playing an important role in the search for clinical biomarkers. We investigated the impact of the variability between FreeSurfer releases on the estimation of structural brain measures in Parkinson’s disease (PD). Structural brain scans from 106 controls and 209 patients were analyzed with FreeSurfer versions 5.3, 6.0.1, and 7.3.2, including longitudinal data from 125 patients. First, we measured the differences in the estimation of volume, surface area, and cortical thickness between FreeSurfer versions. Second, we focused on the relationship between MRI-derived brain measures and group differences as well as disease severity clinical outcomes, which were evaluated both cross-sectionally and longitudinally. We found high software-induced variability in the estimation of all three structural measures, which impacted clinical outcomes. There were differences between software versions in group differences between patients and healthy controls in subcortical volume and vertex-wise cortical thickness. Software variability also impacted the estimated relationship between brain structure and disease severity in patients. Hence, software variability not only relates to the estimation of structural measures, but it also impacts clinically- relevant MRI measures. Our study provides insight into the reproducibility of structural neuroimaging studies in PD populations.
Novel MRI-based Biotypes of Human Neurodevelopment associated with Impulsivity performance
Authors: Zhou Zicong , Rivas-Fernandez Miguel A. , Adise Shana , Colon-Perez Luis
Published: November 2024

Introduction

Adequate neurodevelopment is critical to the proper advancement of cognitive and emotional processing; however, variation in neurodevelopment has emerged as a potential risk factor for subsequent drug use. The Adolescent Brain Cognitive Development (ABCD) Study is an ongoing and longitudinal study to determine the developmental trajectories of the brain and how experiences impact brain development, which makes it an ideal framework study to determine proper neurodevelopmental trajectories associated with healthy executive function behavioral development and their neurobiology.

Method

Based on the availability of ABCD (Release 5.1) tabulated data, we selected 1368 subjects with neuroimaging records on multiple time points. To focus on the frontal cortex, we preprocess 20 ROIs (including ten regions with right and left cerebral hemispheres) cortical thickness measurements for SuStaIn. Once SuStaIn determined the potential control and phenotype (subtypes) group, we conducted t-tests between the control and phenotype groups on their delay discounting measurements. To overserve possible trajectories, we also investigated the correlation of the thickness measurements with delay discounting under the suggested phenotype by SuStaIn.

Results

SuStaIn identified four subtypes and one potential control group, validated by cross-validation test as the optimal solution for balancing model accuracy and complexity. Among the t-tests on delay discounting results between the control group and each subtype, subtype1 tends to show low significance on the 3-month indifference point (p=0.067), subtype 2 identifies a significant reduction in impulsivity on the 1-month indifference point (p=0.017), subtype 4 stands significant reduction at on 3-month indifference point (p=0.0092) and significance on 1-year indifference point (p=0.00418). For the correlations between each selected ROI, we identified a negative correlation (R=-0.18, p=0.0095) between the thickness of the left hemisphere caudal-anterior-cingulate and delay discounting indifference point at 3 months.

Conclusion

We successfully identified four subtypes of the ABCD, which may be putative abnormal trajectories of executive function accelerated development. Three of the four subtypes reflect impulsive behavioral phenotype, and one displays an association with cortical thinning. Overall, we present evidence that there are putative neurobiological signs of potential executive function disruption as early as nine years of age.
Multi-objective computational optimization of human 5′ UTR sequences
Authors: Yamada Keisuke , Suga Kanta , Abe Naoko , Hashimoto Koji , Tsutsumi Susumu , Inagaki Masahito , Hashiya Fumitaka , Abe Hiroshi , Hamada Michiaki
Published: November 2024

The computational design of mRNA sequences is a critical technology for both scientific research and industrial applications. Recent advances in prediction and optimization models have enabled the automatic scoring and optimization of 5′ UTR sequences, key upstream elements of mRNA. However, fully automated design of 5′ UTR sequences with more than two objective scores has not yet been explored. In this study, we present a computational pipeline that optimizes human 5′ UTR sequences in a multi-objective framework, addressing up to four distinct and conflicting objectives. Our work represents an important advancement in the multi-objective computational design of mRNA sequences, paving the way for more sophisticated mRNA engineering.
Social Anxiety Alters Theory of Mind Activation and Intersubject Neural Variability During Movie Viewing
Authors: Mangnus Margot , Koch Saskia B. J. , Devillers Robin , Hagoort Peter , Bašnáková Jana , Stolk Arjen
Published: November 2024

Social anxiety is characterized by an intense fear of judgment in social situations, yet the underlying mechanisms driving this condition remain poorly understood. One hypothesis holds that specific alterations in Theory of Mind (ToM) affect the ability to interpret others’ thoughts and emotions. Another hypothesis proposes that broader interpretive biases lead individuals to perceive social cues as overly significant, even in neutral settings. We investigated these possibilities by measuring brain activity, pupil responses, and heart rates in socially anxious individuals and matched controls as they viewed ‘Partly Cloudy’, an animated film known to engage the ToM network during specific scenes. While overall brain activity during ToM-related scenes was similar across groups, socially anxious participants exhibited reduced activation in the left posterior superior temporal sulcus (pSTS), a key area for ToM processing. Additionally, intersubject correlation analysis revealed a distinct neural response pattern in the socially anxious group, marked by uniform responses in sensory regions and heightened variability in higher-order cortical areas. This pattern persisted throughout the film and occurred without changes in heart rate or pupil responses, indicating a neural processing bias that manifests even in non-evaluative settings. These findings provide a neural basis for ToM alterations and broader interpretive biases in social anxiety, supporting cognitive-behavioral models and suggesting novel targets for intervention.
WMH-DualTasker: A Dual-Task Deep Learning Model with Self-supervised Consistency for Automated Segmentation and Visual Rating of White matter Hyperintensities - a Multicentre study
Authors: Wu Yilei , Dong Zijian , Li Hongwei Bran , Chong Yao Feng , Ji Fang , Xian Chong Joanna Su , Jie Tang Nathanael Ren , Hilal Saima , Fu Huazhu , Chen Christopher Li-Hsian , Zhou Juan Helen ,   Alzheimer’s Disease Neuroimaging Initiative
Published: November 2024

Background

White matter hyperintensities (WMH) are neuroimaging markers linked to an elevated risk of cognitive decline. WMH severity is typically assessed via visual rating scales and through volumetric segmentation. While visual rating scales are commonly used in clinical practice, they offer limited descriptive power. In contrast, supervised volumetric segmentation requires manually annotated masks, which is labor-intensive and challenging to scale for large studies. Therefore, our goal was to develop an automated deep learning model that can provide accurate and holistic quantification of WMH severity with minimal supervision.

Methods

We developed WMH-DualTasker, a deep learning model that simultaneously performs voxel-wise segmentation and visual rating score prediction. The model leverages self-supervised, transformation-invariant consistency constraints, using WMH visual ratings from clinical settings as the sole supervisory signal. Additionally, we assessed its clinical utility by applying it to identify individuals with mild cognitive impairment (MCI) and to predict dementia conversion.

Findings

The volumetric quantification performance of WMH-DualTasker was either superior to or on par with existing supervised methods, as demonstrated on the MICCAI-WMH dataset (N=60, Dice=0.602) and the SINGER dataset (N=64, Dice=0.608). Furthermore, the model exhibited strong agreement with clinical visual rating scales on an external dataset (SINGER, MAE=1.880, K=0.77). Importantly, WMH severity metrics derived from WMH-DualTasker improved predictive performance beyond conventional clinical features for MCI classification (AUC=0.718, p<0.001), MCI conversion prediction (AUC=0.652, p<0.001) using the ADNI dataset.

Interpretations

WMH-DualTasker substantially reduces the reliance on labor-intensive manual annotations, facilitating more efficient and scalable quantification of WMH severity in large-scale population studies. This innovative approach has the potential to advance preventive and precision medicine by enhancing the assessment and management of vascular cognitive impairment associated with WMH. Code and model weights are publicly available athttps://github.com/hzlab/WMH-DualTasker.
VIRALpre: Genomic Foundation Model Embedding Fused with K-mer Feature for Virus Identification
Authors: Wang Zanyi , Yu Qinze , Li Yu
Published: November 2024

Virus, a submicroscopic infectious agent, influences all life forms. Identifying viral sequences is essential to understand their biological functions and then analyze their impacts on public health, and the development of microbial communities. For its significance, tools are developed based on various mathematical methods and algorithms. However, previous methods struggle to identify viral sequences, especially short contigs accurately since the limited information and small-scale close-set dataset. Here we propose VIRALpre, a hybrid framework combined with genomic foundation model (GFM) embedding and K-mer feature of sequences to precisely recognize viral genomic fragments. VIRALpre is empowered by the generalization competencies of GFMs, which have proven their strength in various downstream tasks, thanks to newly established large-scale training databases and Attention mechanism. On the other hand, K-mer features provide additional biological information to bridge the limitation of GFMs in classification tasks. Comprehensive experimental results demonstrate that VIRALpre significantly outperforms all the previous methods on virus identification performance by 4% in accuracy. To prove that this model is qualified when facing unique contigs to training data, BLASTn-based similarity cut-off test(setting e-value as 10−5) is done and it achieves about 10% F1-score improvement. More than well-built test datasets, new zero-shot cross-dataset tests on benchmark datasets sampling from natural environments are conducted, VIRALpre performs identify almost most viral sequences while keeping a very low False Positive Rate. Based on these solid experiments, VIRALpre has the ability to manage short-contig virus identification by truly learning the distinctions of viral sequences and hopefully act as an adviser to promote virus-related research.
Seed dispersal effectiveness and plant-bird interaction networks in the Tehuacán Valley
Authors: Contreras-González Ana María , González-Montes Mónica Beatriz , Jair Ortega-Jiménez E. , Herrera-Serrano Pamela , Rivera-Ortiz Francisco Alberto , Valiente-Banuet Alfonso
Published: November 2024

The maintenance of biodiversity in communities is mediated by interactions that influence community structure, including seed dispersal. The aim of this study was to evaluate the seed dispersal effectiveness of fruit-eating bird species in the Tehuacán Valley and assess the extinction risk of both bird and plant species through interaction networks. From June 2022 to July 2024, we conducted monthly observations of bird foraging on 12 plant species in San Juan Raya and 13 plant species in Zapotitlán Salinas. We calculated the seed dispersal effectiveness and constructed quantitative and qualitative interaction networks for both locations. For both sites, we found that few birds were effective seed dispersers. The most effective dispersers in San Juan Raya wereMelanerpes hypopolius,Toxostoma curvirostre, andPhainopepla nitens, while in Zapotitlán Salinas, the main dispersers wereMimus polyglottos,T. curvirostre, andP. nitens. Through qualitative analysis of the interaction networks, we determined that plant communities in both locations are moderately fragile. Quantitative network analyses revealed that plants in Zapotitlán Salinas are particularly vulnerable, as most species could face local extinction if they lose their disperser species, potentially disrupting the community structure. In contrast, bird species exhibited a lower degree of specialization. Thus, even if certain plant species are lost, birds could continue to interact with other species or migrate to areas with a greater availability of resources. The extraction of plant species, many of which are used for firewood, could negatively impact seed dispersal, as these plants serve as facilitators for many of the species studied. This could reduce the number of available sites where birds can deposit seeds, decreasing the likelihood of seed germination and the establishment of new individuals, which, in turn, may compromise community structure.
Impacts of Structural Properties of Myosin II Filaments on Force Generation
Authors: Ding Shihang , Chou Pei-En , Deguchi Shinji , Kim Taeyoon
Published: November 2024

Cells need intracellular forces for their physiological functions, such as migration, cytokinesis, and morphogenesis. The actin cytoskeleton generates a large fraction of the forces via interactions between cytoskeletal components, such as actin filament (F-actin), myosin, and actin cross-linking proteins (ACPs). Myosin II plays the most important role in cellular force generation. Myosin II molecules self-assemble into filaments with different structures depending on myosin II isoforms and other conditions such as pH and ionic concentration. It has remained elusive how force generation in actomyosin structures is affected by the architecture of myosin II filaments. In this study, we employed an agent-based model to investigate the effects of the structural properties of myosin II filaments on force generation in disorganized actomyosin structures. We demonstrated that the magnitude of forces and the efficiency of force generation can vary over a wide range depending on the number and spatial distribution of myosin II filaments. Further, we showed that the number of myosin heads and the length of a bare zone at the center of myosin II filaments without heads highly affect the force generation process in bundles and networks. Our study provides insights into understanding the roles of the structural properties of myosin II filaments in actomyosin contractility.
Dynamic prioritisation of sensory and motor contents in working memory
Authors: Echeverria-Altuna Irene , Boettcher Sage E.P , van Ede Freek , Nobre Anna C.
Published: November 2024

Internal selective attention prioritises both sensory and motor contents in working memory to guide prospective behaviour. Prior research has shown how attention modulation of sensory contents is flexible and temporally tuned depending on access requirements, but whether the prioritisation of motor contents follows similar flexible dynamics remains elusive. Also uncharted is the degree of co-dependence of sensory and motor modulation, which gets at the nature of both working-memory representations and internal attention functions. To address these questions, we independently tracked the prioritisation of sensory and motor working-memory contents as a function of dynamically evolving temporal expectations. The design orthogonally manipulated when an item location (left vs right side) and associated prospective action (left vs right hand) would be relevant. Contralateral modulation of posterior alpha (8-12 Hz) activity in electroencephalography (EEG) tracked prioritisation of the item location, while contralateral modulation of central mu/beta (8-30 Hz) activity tracked response prioritisation. Proactive and dynamic alpha and mu/beta modulation confirmed the flexible and temporally structured prioritisation of sensory and motor contents alike. Intriguingly, the prioritisation of sensory and motor contents was temporally uncoupled, showing dissociable patterns of modulation. The findings reveal multiple modulatory functions of internal attention operating in tandem to prepare relevant aspects of internal representations for adaptive behaviour.
PrP turnover in vivo and the time to effect of prion disease therapeutics
Authors: Corridon Taylor L , O’Moore Jill , Lian Yuan , Laversenne Vanessa , Noble Briana , Kamath Nikita G , Serack Fiona E , Shaikh Abdul Basit , Erickson Brian , Braun Craig , Lenz Kenney , Howard Michael , Chan Nathan , Reidenbach Andrew G , Cabin Deborah E , Vallabh Sonia M , Grindeland Andrea , Oberbeck Nina , Zhao Hien T , Minikel Eric Vallabh
Published: November 2024

PrP lowering is effective against prion disease in animal models and is being tested clinically. Therapies in the current pipeline lower PrP production, leaving pre-existing PrP to be cleared according to its own half-life. We hypothesized that PrP’s half-life may be a rate-limiting factor for the time to effect of PrP-lowering drugs, and one reason why late treatment of prion-infected mice is not as effective as early treatment. Using isotopically labeled chow with targeted mass spectrometry, as well as antisense oligonucleotide treatment followed by timed PrP measurement, we estimate a half-life of 5-6 days for PrP in the brain. PrP turnover is not affected by over- or under-expression. Mouse PrP and human PrP have similar turnover rates measured in wild-type or humanized knock-in mice. CSF PrP appears to mirror brain PrP in real time in rats. PrP is more readily quantifiable in colon than in other peripheral organs, and appears to have a shorter half-life in colon than in brain. Our data may inform the design of both preclinical and clinical studies of PrP-lowering drugs.
Chronic inflammation drives epididymal tertiary lymphoid structure formation and autoimmune fertility disorders
Authors: Elizagaray Maia L. , Barrachina Ferran , Avenatti Maria C. , Bastepe Isinsu , Chen Angela , Odriozola Ainize , Ukairo Oluchi , Ros Vanina Da , Ottino Kiera , Subiran Nerea , Battistone Maria A.
Published: November 2024

The incomplete understanding of epididymal mucosal immunity is a significant contributing factor to the classification of many male infertility cases as idiopathic. Conditions that disrupt the immune balance in the male reproductive tract, such as vasectomy and infections, can expose sperm to the immune system, leading to increased production of anti-sperm antibodies (ASAs) and subsequent reproductive challenges. Regulatory T cells (Tregs) regulate inflammation and maintain sperm tolerance. In a murine model, we demonstrated that disrupting sperm immunotolerance induces chronic autoimmune responses characterized by antibody production targeting sperm and reproductive tissue autoantigens and unique tissue-specific immune cell signatures in the epididymis and testis. Such inflammatory features impair sperm function, contribute to epididymal damage, and drive sustained male subfertility. Tertiary lymphoid structures (TLSs) were formed within the epididymis after Treg depletion, defined by clusters of heterogenous B and T cells, fibroblasts, and endothelial cells. These ectopic structures perpetuate inflammation and lower the activation threshold for future immune threats. Similar isotypes of autoantibodies were detected in the seminal plasma of infertile patients, suggesting shared mechanistic pathways between mice and humans. Overall, we provide an in-depth understanding of the diverse B- and T-cell dynamics and TLS formation during epididymitis to develop precision-targeted therapies for infertility and chronic inflammation. Additionally, this immunological characterization of the epididymal microenvironment has the potential to identify novel targets for the development of male contraceptives.

One Sentence Summary

Understanding the epididymal immune cell landscape dynamics aids in developing targeted therapies for infertility and contraception.
Lipid polymorphism of the marginal region of plant thylakoid membranes
Authors: Böde Kinga , Dlouhý Ondřej , Javornik Uroš , Domonkos Ildikó , Zsiros Ottó , Plavec Janez , Špunda Vladimír , Garab Győző
Published: November 2024

Thylakoid membranes (TMs) of vascular plants exhibit a highly organized architecture comprising two main distinct functional domains which accommodate virtually all components of the photosynthetic machinery responsible for the light reactions: the stacked, appressed granum membranes and the unstacked stroma lamellae. A domain with distinct structural, compositional, and functional characteristics, the marginal region of grana (grana margin, GM) has also been identified, which includes the highly curved region at the periphery of the granum vesicles that is enriched in CURT1 proteins. It is also well established that plant TMs, in addition to the bilayer (or lamellar, L) phase, contain at least two isotropic (I) lipid phases and an inverted hexagonal (HII) phase. The I phases were shown to participate in membrane fusion and to be associated with the activity of the photoprotective water-soluble enzyme, the violaxanthin de-epoxidase (VDE); the HIIphase, for its trypsin sensitivity, was proposed to emerge from stroma-exposed lipid-protein assemblies. Considering the location of CURT1 in GM and that it possesses trypsin-sensitivity, it was hypothesized to participate in the formation of the HIIphase. The aim of the present study was to test this hypothesis – via fingerprinting the lipid phase behavior of GM particles isolated from spinach leaves. Our31P-NMR spectroscopy reveals that the GM fraction of TMs does not contain HIIphase signal; it exhibits an isotropic signature. This non-bilayer, isotropic lipid structure, together with CURT1 proteins, thus appear to promote the formation of the highly curved region of TMs.
Seedling recruitment after fire: Disentangling the roles of microsite conditions and seed availability
Authors: Beck Jared J. , Wagenius Stuart
Published: November 2024

Periodic fire enhances seedling recruitment for many plant species in historically fire-dependent ecosystems. Fire is expected to promote recruitment by generating environmental conditions that promote seedling emergence and survival. However, fire may also increase flowering and seed production. This makes it difficult to distinguish the effects of microsite conditions from seed availability in observational studies of seedling recruitment. Experiments that manipulate seed inputs across a representative range of conditions are needed to elucidate how seed availability versus microsite conditions influence post-fire seedling recruitment and plant demography. We experimentally manipulated time since fire across 36 patches of remnant tallgrass prairie distributed across 6400 ha in western Minnesota (USA). Over two years, we sowed 11,057Echinacea angustifolia(Asteraceae) seeds across 84 randomly placed transects and tracked 974 experimentally sown seedlings to evaluate how time since fire influenced seedling emergence and survival after experimentally controlling for variation in seed inputs. We also quantified six environmental variables and evaluated whether these covariates were associated with seedling emergence and survival. Fire influenced both seedling emergence and seedling survival. Seedlings emerged from approximately 1 percent of all seeds sown prior to experimental burns. Seeds sown one year after experimental burns emerged at 15 times the rate of seeds sown in the fall before burns, but emergence then declined as time since fire increased. Sowing seeds at high densities reduced rates of seedling emergence but increased overall recruitment. Increases in litter depth were associated with reduced emergence. Meanwhile, the probability that seedlings survived to late summer was greatest when they emerged 0-1 years after fire. The probability of seedling survival decreased with litter depth and increased with the local density of conspecific seedlings. Our findings experimentally support widespread predictions that fire enhances seedling recruitment by generating microsite conditions favorable for seedling emergence and survival – especially by increasing the light available to newly emerged seedlings. Nevertheless, recruitment also increased with seed inputs indicating that both seed availability and microsite conditions influence post-fire recruitment. Explicitly discriminating between seed-limitation and microsite-limitation is critical for understanding the demographic processes that influence plant population dynamics in historically fire-dependent ecosystems.