bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fustin suppressed melanoma cell growth via cAMP/PKA-dependent mechanism
Authors: Kumazoe Motofumi , Fujimura Yoshinori , Shimada Yu , Onda Hiroaki , Hatakeyama Yui , Tachibana Hirofumi 
Published: June 2024

ABSTRACT
Melanoma, a cancer arising from melanocytes, requires a novel treatment strategy because of the ineffectiveness of conventional therapies in certain patients. Fustin is a flavanonol found in young fustic (Cotinus coggygria). However, little is known about its antimelanoma effects. Our study demonstrates that fustin suppresses the growth of B16 melanoma cells. Phalloidin staining of cytoskeletal actin revealed that fustin induced a conformational change in the actin structure of melanoma cells, accompanied by suppressed phosphorylation of myosin regulatory light chain 2 (MLC2), a regulator of actin structure. Furthermore, the protein kinase A (cAMP-dependent protein kinase) inhibitor H89 completely attenuated fustin-induced downregulation of phosphorylated myosin phosphatase targeting subunit 1, which is involved in dephosphorylation of MLC2. In a mouse model, administration of fustin suppressed tumor growth in B16 melanoma cells without adverse effects. In conclusion, our findings suggest that fustin effectively suppresses melanoma cell growth both in vitro and in vivo.
OM2Seq: learning retrieval embeddings for optical genome mapping
Authors: Nogin Yevgeni , Sapir Danielle , Zur Tahir Detinis , Weinberger Nir , Belinkov Yonatan , Ebenstein Yuval , Shechtman Yoav 
Published: June 2024

Abstract

Motivation
Genomics-based diagnostic methods that are quick, precise, and economical are essential for the advancement of precision medicine, with applications spanning the diagnosis of infectious diseases, cancer, and rare diseases. One technology that holds potential in this field is optical genome mapping (OGM), which is capable of detecting structural variations, epigenomic profiling, and microbial species identification. It is based on imaging of linearized DNA molecules that are stained with fluorescent labels, that are then aligned to a reference genome. However, the computational methods currently available for OGM fall short in terms of accuracy and computational speed.

Results
This work introduces OM2Seq, a new approach for the rapid and accurate mapping of DNA fragment images to a reference genome. Based on a Transformer-encoder architecture, OM2Seq is trained on acquired OGM data to efficiently encode DNA fragment images and reference genome segments to a common embedding space, which can be indexed and efficiently queried using a vector database. We show that OM2Seq significantly outperforms the baseline methods in both computational speed (by 2 orders of magnitude) and accuracy.

Availability and implementation
https://github.com/yevgenin/om2seq.
Improving the performance and interpretability on medical datasets using graphical ensemble feature selection
Authors: Battistella Enzo , Ghiassian Dina , Barabási Albert-László 
Published: June 2024

AbstractMotivationA major hindrance towards using Machine Learning (ML) on medical datasets is the discrepancy between a large number of variables and small sample sizes. While multiple feature selection techniques have been proposed to avoid the resulting overfitting, overall ensemble techniques offer the best selection robustness. Yet, current methods designed to combine different algorithms generally fail to leverage the dependencies identified by their components. Here, we propose Graphical Ensembling (GE), a graph-theory-based ensemble feature selection technique designed to improve the stability and relevance of the selected features.ResultsRelying on four datasets, we show that GE increases classification performance with fewer selected features. For example, on rheumatoid arthritis patient stratification, GE outperforms the baseline methods by 9% Balanced Accuracy while relying on fewer features. We use data on sub-cellular networks to show that the selected features (proteins) are closer to the known disease genes, and the uncovered biological mechanisms are more diversified. By successfully tackling the complex correlations between biological variables, we anticipate that GE will improve the medical applications of ML.Availability and implementationhttps://github.com/ebattistella/auto_machine_learning.
HE2Gene: image-to-RNA translation via multi-task learning for spatial transcriptomics data
Authors: Chen Xingjian , Lin Jiecong , Wang Yuchen , Zhang Weitong , Xie Weidun , Zheng Zetian , Wong Ka-Chun 
Published: June 2024

Abstract

Motivation
Tissue context and molecular profiling are commonly used measures in understanding normal development and disease pathology. In recent years, the development of spatial molecular profiling technologies (e.g. spatial resolved transcriptomics) has enabled the exploration of quantitative links between tissue morphology and gene expression. However, these technologies remain expensive and time-consuming, with subsequent analyses necessitating high-throughput pathological annotations. On the other hand, existing computational tools are limited to predicting only a few dozen to several hundred genes, and the majority of the methods are designed for bulk RNA-seq.

Results
In this context, we propose HE2Gene, the first multi-task learning-based method capable of predicting tens of thousands of spot-level gene expressions along with pathological annotations from H&E-stained images. Experimental results demonstrate that HE2Gene is comparable to state-of-the-art methods and generalizes well on an external dataset without the need for re-training. Moreover, HE2Gene preserves the annotated spatial domains and has the potential to identify biomarkers. This capability facilitates cancer diagnosis and broadens its applicability to investigate gene-disease associations.

Availability and implementation
The source code and data information has been deposited at https://github.com/Microbiods/HE2Gene.
Effect of parasite infection and invasion history on feeding, growth, and energy allocation of cane toads
Authors: Crane Hailey R , Rollins Lee A , Shine Richard , Brown Gregory P 
Published: June 2024

Abstract
The energy allocation decisions that organisms make can differ between sexes and populations and can be influenced by factors such as age and parasite infection. We conducted experimental parasite infections on common-garden reared cane toads originating from sites across the species’ invasive range in Australia to assess how sex, parasite infection, and invasion history affected the toad’s food intake, growth rate, and organ weights. Female toads had larger fat stores, larger livers, and larger gonads than did males, reflecting increased investment into gametes. Growth rate did not differ between the sexes. Lungworm infection increased feeding by male but not female toads and increased fat storage in all toads. Fat body, liver, gonad sizes, and feeding rates all differed among toads from different locations within the toad’s invasion transect across Australia, even though our measurements were made under standardized conditions on captive animals. Toads from populations close to the invasion front ate more, had heavier fat bodies, and had larger livers than did toads from long-colonized areas, but they had smaller gonads. This pattern reflects the evolution of a more dispersive phenotype among invasive populations, whereby the rate of dispersal is enhanced by increased energy intake and storage, and delayed reproduction.
Prevalence, incidence and treatment patterns of prurigo nodularis in England: a retrospective database analysis
Authors: Bahloul Donia , Hudson Richard , Balogh Orsolya , Mathias Elgan , Heywood Ben , Hubbuck Ellen , Diribe Onyinye , McDonald Robert , Bewley Anthony 
Published: June 2024

Abstract

Background
Prurigo nodularis (PN) is a pruritic skin disease characterized by multiple intensely itchy skin nodules in symmetrically distributed areas of the extremities. There are limited studies on the epidemiology and treatment pathways of PN, especially moderate-to-severe PN, from England.

Objectives
To assess the epidemiology and treatment pathways of mild and moderate-to-severe PN in England.

Methods
This retrospective cohort study used data from the Clinical Practice Research Datalink and Hospital Episode Statistics in England. Adult patients (aged ≥ 18 years) with a PN-specific diagnosis code allocated any time between 1 April 2007 and 1 March 2019 (patient identification period) were selected. Patients were included if their first PN diagnostic code (index diagnosis date; IDD) was recorded during the identification period, with data available 6 months before and ≥ 12 months after the IDD. Patients were classified as having moderate-to-severe PN (MSPN) or mild PN (MiPN), based on the presence or absence of a prescription record, post-IDD, for either a systemic immunosuppressant or a gabapentinoid. Patients with MSPN and MiPN were matched 1 : 1 according to age, sex and IDD. Prevalence and incidence were calculated for each year from 2007 to 2019. Drugs prescribed post-IDD were analysed.

Results
A total of 8933 patients (MSPN, n = 2498; MiPN, n = 6435) were included in the study; 2462 patients with MiPN and 2462 with MSPN were included for the comparative analysis. The presence of atopic dermatitis, asthma and eosinophilic oesophagitis were significantly higher (all P &lt; 0.001) in patients with MSPN compared with those with MiPN. The overall prevalence of cases of PN increased during the study period. The incidence rate also showed a similar trend. The rates of prescription of potent and super-potent topical corticosteroids (TCS), topical calcineurin inhibitors, first- and second-generation antihistamines, oral and injectable systemic corticosteroids, methotrexate, antidepressants and tacrolimus were significantly higher (all P &lt; 0.001) in patients with MSPN compared with those with MiPN.

Conclusions
The epidemiology of PN was consistent with that found in other European studies. Patients with MSPN received a significantly higher number of prescriptions for potent TCS and systemic drugs compared with patients with MiPN.
Survival after live donor versus deceased donor liver transplantation: propensity score–matched study
Authors: Kaltenmeier Christof , Liu Hao , Zhang Xingyu , Ganoza Armando , Crane Andrew , Powers Colin , Gunabushanam Vikraman , Behari Jaideep , Molinari Michele 
Published: June 2024

Abstract

Background
For individuals with advanced liver disease, equipoise in outcomes between live donor liver transplant (LDLT) and deceased donor liver transplant (DDLT) is uncertain.

Methods
A retrospective cohort study was performed using data extracted from the Scientific Registry of Transplant Recipients. Adults who underwent first-time DDLT or LTDL in the United States between 2002 and 2020 were paired using propensity-score matching with 1:10 ratio without replacement. Patient and graft survival were compared using the model for end-stage liver disease (MELD) score for stratification.

Results
After propensity-score matching, 31 522 DDLT and 3854 LDLT recipients were included. For recipients with MELD scores ≤15, LDLT was associated with superior patient survival (HR = 0.92; 95% c.i. 0.76 to 0.96; P = 0.013). No significant differences in patient survival were observed for MELD scores between 16 and 30. Conversely, for patients with MELD scores &gt;30, LDLT was associated with higher mortality (HR 2.57; 95% c.i. 1.35 to 4.62; P = 0.003). Graft survival was comparable between the two groups for MELD ≤15 and for MELD between 21 and 30. However, for MELD between 16 and 20 (HR = 1.15; 95% c.i. 1.00 to 1.33; P = 0.04) and MELD &gt; 30 (HR = 2.85; 95% c.i. 1.65 to 4.91; P = 0.001), graft survival was considerably shorter after LDLT. Regardless of MELD scores, re-transplantation rate within the first year was significantly higher after LDLT.

Conclusions
In this large propensity score–matched study using national data, comparable patient survival was found between LDLT and DDLT in recipients with MELD scores between 16 and 30. Conversely, for patients with MELD &gt; 30, LDLT was associated with worse outcomes. These findings underscore the importance of transplant selection for patients with high MELD scores.
TRIM71 mutations cause a neurodevelopmental syndrome featuring ventriculomegaly and hydrocephalus
Authors: Duy Phan Q , Jux Bettina , Zhao Shujuan , Mekbib Kedous Y , Dennis Evan , Dong Weilai , Nelson-Williams Carol , Mehta Neel H , Shohfi John P , Juusola Jane , Allington Garrett , Smith Hannah , Marlin Sandrine , Belhous Kahina , Monteleone Berrin , Schaefer G Bradley , Pisarska Margareta D , Vásquez Jaime , Estrada-Veras Juvianee I , Keren Boris , Mignot Cyril , Flore Leigh A , Palafoll Irene V , Alper Seth L , Lifton Richard P , Haider Shozeb , Moreno-De-Luca Andres , Jin Sheng Chih , Kolanus Waldemar , Kahle Kristopher T 
Published: June 2024

Abstract
Congenital hydrocephalus, characterized by cerebral ventriculomegaly, is one of the most common reasons for paediatric brain surgery. Recent studies have implicated lin-41 (lineage variant 41)/TRIM71 (tripartite motif 71) as a candidate congenital hydrocephalus risk gene; however, TRIM71 variants have not been systematically examined in a large patient cohort or conclusively linked with an OMIM syndrome.
Through cross-sectional analysis of the largest assembled cohort of patients with cerebral ventriculomegaly, including neurosurgically-treated congenital hydrocephalus (totalling 2697 parent-proband trios and 8091 total exomes), we identified 13 protein-altering de novo variants (DNVs) in TRIM71 in unrelated children exhibiting variable ventriculomegaly, congenital hydrocephalus, developmental delay, dysmorphic features and other structural brain defects, including corpus callosum dysgenesis and white matter hypoplasia.
Eight unrelated patients were found to harbour arginine variants, including two recurrent missense DNVs, at homologous positions in RPXGV motifs of different NHL domains. Seven patients with rare, damaging, unphased or transmitted variants of uncertain significance were also identified. NHL-domain variants of TRIM71 exhibited impaired binding to the canonical TRIM71 target CDKN1A; other variants failed to direct the subcellular localization of TRIM71 to processing bodies. Single-cell transcriptomic analysis of human embryos revealed expression of TRIM71 in early first-trimester neural stem cells of the brain.
These data show TRIM71 is essential for human brain morphogenesis and that TRIM71 mutations cause a novel neurodevelopmental syndrome that we term ‘TRIM71-associated developmental disorders (TADD)’, featuring variable ventriculomegaly, congenital hydrocephalus and other structural brain defects.
Neuroanatomy of cerebellar mutism syndrome: the role of lesion location
Authors: Skye Jax , Bruss Joel , Toescu Sebastian , Aquilina Kristian , Grafft Amanda , Bardi Lola Gino , Boes Aaron D 
Published: June 2024

Abstract
Approximately 25% of paediatric patients who undergo cerebellar tumour resection develop cerebellar mutism syndrome. Our group recently showed that damage to the cerebellar deep nuclei and superior cerebellar peduncles, which we refer to as the cerebellar outflow pathway, is associated with an increased risk of cerebellar mutism syndrome. Here, we tested whether these findings replicate in an independent cohort. We evaluated the relationship between lesion location and the development of cerebellar mutism syndrome in an observational study of 56 paediatric patients ranging from five months to 14 years of age who underwent cerebellar tumour resection. We hypothesized that individuals who developed cerebellar mutism syndrome after surgery, relative to those who did not, would have lesions that preferentially intersect with: (i) the cerebellar outflow pathway and (ii) a previously generated ‘lesion-symptom map’ of cerebellar mutism syndrome. Analyses were conducted in accordance with pre-registered hypotheses and analytic methods (https://osf.io/r8yjv/). We found supporting evidence for both hypotheses. Compared to patients who did not develop cerebellar mutism syndrome, patients with cerebellar mutism syndrome (n = 10) had lesions with greater overlap with the cerebellar outflow pathway (Cohen’s d = 0.73, P = 0.05), and the cerebellar mutism syndrome lesion-symptom map (Cohen’s d = 1.1, P = 0.004). These results strengthen the association of lesion location with the risk of developing cerebellar mutism syndrome and demonstrate generalizability across cohorts. These findings may help to inform the optimal surgical approach to paediatric cerebellar tumours.
Overview of coals as carbon anode materials for sodium-ion batteries
Authors: Kong Junli , Su Zhijiang , Dong Chunwei , Chen Quanbin , Pan Guanghong 
Published: June 2024

Abstract
Energy storage is an important technology in achieving carbon-neutrality goals. Compared with lithium-ion batteries, the raw materials of sodium-ion batteries are abundant, low-cost, and highly safe. Furthermore, their costs are expected to be further reduced as large-scale applications take off, making them viable for energy storage applications. The primary anode material for sodium-ion batteries is hard carbon, which has a high sodium-ion storage capacity but is relatively expensive, limiting its applications in energy storage. In order to widen the applications of sodium-ion batteries in energy storage and other fields, it is particularly important to develop anode materials that have both high performance and low cost. Coals, with abundant reserves and worldwide availability, can serve as low-cost carbon sources for anode materials. Additionally, coals of different grades of metamorphism have different structural characteristics that can be tailored for the structural characteristics of coal-based anode materials for sodium-ion batteries. Recent research on tailoring coals as the anode materials for sodium-ion batteries is summarized and the recent progress made towards mitigating the existing issues is analysed in this review. Specifically, the impacts of different grades of metamorphism on the sodium-ion storage performance of coal-based anode materials prepared using direct carbonization are discussed in detail. Studies on improving the electrochemical performances of coal-based anode materials through pore and microcrystalline structure controls and surface as well as interface modifications are presented. Finally, the advantages and disadvantages of different preparation methods are identified. To make the industrial applications of coal-based anode materials for sodium-ion batteries more viable, the importance of the de-ashing process is introduced.
The large-scale organization of shape processing in the ventral and dorsal pathways is dissociable from attention
Authors: Goldstein-Marcusohn Yael , Asaad Rahaf , Asaad Leen , Freud Erez 
Published: June 2024

Abstract
The two visual pathways model posits that visual information is processed through two distinct cortical systems: The ventral pathway promotes visual recognition, while the dorsal pathway supports visuomotor control. Recent evidence suggests the dorsal pathway is also involved in shape processing and may contribute to object perception, but it remains unclear whether this sensitivity is independent of attentional mechanisms that were localized to overlapping cortical regions. To address this question, we conducted two fMRI experiments that utilized different parametric scrambling manipulations in which human participants viewed novel objects in different levels of scrambling and were instructed to attend to either the object or to another aspect of the image (e.g. color of the background). Univariate and multivariate analyses revealed that the large-scale organization of shape selectivity along the dorsal and ventral pathways was preserved regardless of the focus of attention. Attention did modulate shape sensitivity, but these effects were similar across the two pathways. These findings support the idea that shape processing is at least partially dissociable from attentional processes and relies on a distributed set of cortical regions across the visual pathways.
Reaction path search for propane dehydrogenation and metathesis on titanium hydride
Authors: Miyakage Takumi , Yasumura Shunsaku , Huang Mengwen , Toyao Takashi , Maeno Zen , Shimizu Ken-ichi 
Published: June 2024

Abstract
The reaction mechanisms of C3H8 dehydrogenation and subsequent metathesis on a TiH2 surface were investigated using an automated reaction path search method. The predicted pathway suggests that dehydrogenation could occur at the H vacancies present on the TiH2 surface. The propylidene species formed by the initial dehydrogenation reaction are crucial intermediates in butane formation; this compound is in turn required by the subsequent metathesis reaction on the surface of the metal hydrides.
Overall survival after definitive chemoradiotherapy for patients with esophageal cancer: a retrospective cohort study
Authors: van der Zijden Charlène J , Bouwman Anna , Mostert Bianca , Nuyttens Joost J M E , van der Sluis Pieter C , Spaander Manon C W , Mens Jan Willem M , Homs Marjolein Y V , van Doorn Leni , Wijnhoven Bas P L , Lagarde Sjoerd M 
Published: June 2024

Summary
Definitive chemoradiotherapy (dCRT) is a potentially curative therapy for esophageal cancer. As indications for dCRT differ widely, it is challenging to draw conclusions on outcomes and survival. The aim of this study was to evaluate overall survival (OS) and recurrence patterns according to indications for treatment. Patients who underwent dCRT (50.4 Gy concomitant with carboplatin/paclitaxel) for esophageal cancer between 2012 and 2022 were identified. Indications for dCRT were: cervical tumor, irresectable disease, unfit for surgery, and patient and/or physician preference. The primary endpoint was OS calculated with the Kaplan–Meier method. Secondary endpoints included the proportion of patients that completed the dCRT regimen, 30- and 90-day mortality, and disease recurrence. One hundred and fifty-seven patients were included (72.6% esophageal squamous cell carcinoma) with a median follow-up of 20 months (IQR 10.0–43.9). The full dCRT regimen was completed by 116 patients (73.9%). Thirty- and 90-day mortality were 2.5% and 8.3%, respectively. Median and 5-year OS for all patients were 22.9 months (95% CI 18.0–27.9) and 31.4%, respectively. The median OS per indication was 23.7 months (95% CI 6.5–40.8) for patients with cervical tumors, 10.9 months (95% 0.0–23.2) for irresectable disease, 28.2 months (95% CI 12.3–44.0) for unfit patients, and 22.9 months (95% CI 15.4–30.5) for patients’ preference for dCRT (P = 0.11). Disease recurrence was observed in 74 patients (46%), located locoregionally (46%), distant (19%), or combined (35%). Patients who underwent dCRT had a 5-year OS of 31.4%, but OS differed according to indications for treatment with patients who had irresectable disease having the worst prognosis.