bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of the genetic variability of durum wheat (Triticum durum Desf.) in the face of combined stress: water and heat
Authors: Chaouachi Latifa , Marín-Sanz Miriam , Barro Francisco , Karmous Chahine 
Published: December 2023

Abstract
The devastating effects and extent of abiotic stress on cereal production continue to increase globally, affecting food security in several countries, including Tunisia. Heat waves and the scarcity of rainfall strongly affect durum wheat yields. The present study aims to screen for tolerance to combined water and heat stresses in durum wheat at the juvenile stage. Three combined treatments were tested, namely: T0 (100% field capacity (FC) at 24 °C), T1 (50% FC at 30 °C), and T2 (25% FC at 35 °C). The screening was carried out based on morphological, physiological, and biochemical criteria. The results showed that the combined stress significantly affected all the measured parameters. The relative water content (RWC) decreased by 37.6% under T1 compared to T0. Quantum yield (Fv/m) and photosynthetic efficiency (Fv/0) decreased under severe combined stress (T2) by 37.15% and 37.22%, respectively. Under T2 stress, LT increased by 63.7%. A significant increase in osmoprotective solutes was also observed, including proline, which increased by 154.6% under T2. Correlation analyses of the combination of water and heat stress confirm that the traits RWC, chlorophyll b content, Fv/m, proline content, Fv/0 and leaf temperature can be used as reliable screening criteria for the two stresses combined. The principal component analysis highlighted that Aouija tolerates the two levels of stresses studied, while the genotypes Karim and Hmira are the most sensitive. The results show that the tolerance of durum wheat to combined water and heat stress involves several adaptation mechanisms proportional to the stress intensity.
The intracellular monoamine oxidase-A inhibitory activity and the protective effect of small hairtail-related peptides in nerve cells (SH-SY5Y)
Authors: Zhang Aiyuan , Yang Xiaoxue , Su Keying , Xie Jintao , Zhang Xuewu 
Published: December 2023

ABSTRACT
This study was to investigate the inhibitory activity of small hairtail-related peptides (VFEVFW, LPNSLYQQ, LPNSLYQK, and FADAME) on intracellular monoamine oxidase-A (MAO-A) and their protective effects in a cell model. Specifically, the inhibition activity in SH-SY5Y cells indicated that VFEVFW and LPNSLYQK reduced ∼50% of MAO-A activity in cells, at 0.5 m m. The survival experiment demonstrated that the toxic effect of dexamethasone (DEX) on cells can be significantly alleviated in the presence of peptides, and these peptides can restore (&gt;20%) the mitochondrial membrane potential of SH-SY5Y cells reduced by DEX. Circular dichroism displayed that peptides affected the secondary structure of MAO-A in a concentration-dependent manner. Finally, the real-time quantitative polymerase chain reaction assay revealed that the MAO-A inhibitory activity of the peptides was associated with the upregulation of brain derived neurotrophic factor/cAMP (Cyclic adenosine monophosphate) response element binding protein)/B-cell lymphoma-2 mRNA levels.
OBMeta: a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases
Authors: Xu Cuifang , Huang Jiating , Gao Yongqiang , Zhao Weixing , Shen Yiqi , Luo Feihong , Yu Gang , Zhu Feng , Ni Yan 
Published: December 2023

Abstract

Motivation
Gut dysbiosis is closely associated with obesity and related metabolic diseases including type 2 diabetes (T2D) and nonalcoholic fatty liver disease (NAFLD). The gut microbial features and biomarkers have been increasingly investigated in many studies, which require further validation due to the limited sample size and various confounding factors that may affect microbial compositions in a single study. So far, it lacks a comprehensive bioinformatics pipeline providing automated statistical analysis and integrating multiple independent studies for cross-validation simultaneously.

Results
OBMeta aims to streamline the standard metagenomics data analysis from diversity analysis, comparative analysis, and functional analysis to co-abundance network analysis. In addition, a curated database has been established with a total of 90 public research projects, covering three different phenotypes (Obesity, T2D, and NAFLD) and more than five different intervention strategies (exercise, diet, probiotics, medication, and surgery). With OBMeta, users can not only analyze their research projects but also search and match public datasets for cross-validation. Moreover, OBMeta provides cross-phenotype and cross-intervention-based advanced validation that maximally supports preliminary findings from an individual study. To summarize, OBMeta is a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases.

Availability and implementation
OBMeta is freely available at: http://obmeta.met-bioinformatics.cn/.
MMCL-CDR: enhancing cancer drug response prediction with multi-omics and morphology images contrastive representation learning
Authors: Li Yang , Guo Zihou , Gao Xin , Wang Guohua 
Published: December 2023

AbstractMotivationCancer is a complex disease that results in a significant number of global fatalities. Treatment strategies can vary among patients, even if they have the same type of cancer. The application of precision medicine in cancer shows promise for treating different types of cancer, reducing healthcare expenses, and improving recovery rates. To achieve personalized cancer treatment, machine learning models have been developed to predict drug responses based on tumor and drug characteristics. However, current studies either focus on constructing homogeneous networks from single data source or heterogeneous networks from multiomics data. While multiomics data have shown potential in predicting drug responses in cancer cell lines, there is still a lack of research that effectively utilizes insights from different modalities. Furthermore, effectively utilizing the multimodal knowledge of cancer cell lines poses a challenge due to the heterogeneity inherent in these modalities.ResultsTo address these challenges, we introduce MMCL-CDR (Multimodal Contrastive Learning for Cancer Drug Responses), a multimodal approach for cancer drug response prediction that integrates copy number variation, gene expression, morphology images of cell lines, and chemical structure of drugs. The objective of MMCL-CDR is to align cancer cell lines across different data modalities by learning cell line representations from omic and image data, and combined with structural drug representations to enhance the prediction of cancer drug responses (CDR). We have carried out comprehensive experiments and show that our model significantly outperforms other state-of-the-art methods in CDR prediction. The experimental results also prove that the model can learn more accurate cell line representation by integrating multiomics and morphological data from cell lines, thereby improving the accuracy of CDR prediction. In addition, the ablation study and qualitative analysis also confirm the effectiveness of each part of our proposed model. Last but not least, MMCL-CDR opens up a new dimension for cancer drug response prediction through multimodal contrastive learning, pioneering a novel approach that integrates multiomics and multimodal drug and cell line modeling.Availability and implementationMMCL-CDR is available at https://github.com/catly/MMCL-CDR.
CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform
Authors: Kaya Hikmet Emre , Naidoo Kevin J 
Published: December 2023

Abstract

Motivation
Target discovery and drug evaluation for diseases with complex mechanisms call for a streamlined chemical systems analysis platform. Currently available tools lack the emphasis on reaction kinetics, access to relevant databases, and algorithms to visualize perturbations on a chemical scale providing quantitative details as well streamlined visual data analytics functionality.

Results
CytoCopasi, a Maven-based application for Cytoscape that combines the chemical systems analysis features of COPASI with the visualization and database access tools of Cytoscape and its plugin applications has been developed. The diverse functionality of CytoCopasi through ab initio model construction, model construction via pathway and parameter databases KEGG and BRENDA is presented. The comparative systems biology visualization analysis toolset is illustrated through a drug competence study on the cancerous RAF/MEK/ERK pathway.

Availability and implementation
The COPASI files, simulation data, native libraries, and the manual are available on https://github.com/scientificomputing/CytoCopasi.
Dengue virus infection and neurological manifestations: an update
Authors: Fong Si-Lei , Wong Kum-Thong , Tan Chong-Tin 
Published: December 2023

Abstract
Dengue virus is a flavivirus transmitted by the mosquitoes, Aedes aegypti and Aedes albopictus. Dengue infection by all four serotypes (DEN 1 to 4) is endemic globally in regions with tropical and subtropical climates, with an estimated 100–400 million infections annually. Among those hospitalized, the mortality is about 1%. Neurological involvement has been reported to be about 5%. The spectrum of neurological manifestations spans both the peripheral and central nervous systems. These manifestations could possibly be categorized into those directly related to dengue infection, i.e. acute and chronic encephalitis, indirect complications leading to dengue encephalopathy, and post-infectious syndrome due to immune-mediated reactions, and manifestations with uncertain mechanisms, such as acute transverse myelitis, acute cerebellitis and myositis.
The rising trend in global dengue incidence calls for attention to a more explicit definition of each neurological manifestation for more accurate epidemiological data. The actual global burden of dengue infection with neurological manifestation is essential for future planning and execution of strategies, especially in the development of effective antivirals and vaccines against the dengue virus.
In this article, we discuss the recent findings of different spectrums of neurological manifestations in dengue infection and provide an update on antiviral and vaccine development and their challenges.
Asbestos burden in lungs of mesothelioma patients with pleural plaques, lung fibrosis and/or ferruginous bodies at histology: a postmortem SEM-EDS study
Authors: Visonà S D , Bertoglio B , Capella S , Belluso E , Austoni B , Colosio C , Kurzhunbaeva Z , Ivic-Pavlicic T , Taioli E 
Published: December 2023

Abstract
The causal attribution of asbestos-related diseases to past asbestos exposures is of crucial importance in clinical and legal contexts. Often this evaluation is made based on the history of exposure, but this method presents important limitations. To assess past asbestos exposure, pleural plaques (PP), lung fibrosis and histological evidence of ferruginous bodies (FB) can be used in combination with anamnestic data. However, such markers have never been associated with a threshold value of inhaled asbestos. With this study we attempted to shed light on the dose–response relationship of PP, lung fibrosis and FBs, investigating if their prevalence in exposed individuals who died from malignant mesothelioma (MM) is related to the concentration of asbestos in lungs assessed using scanning electron microscopy equipped with energy dispersive spectroscopy. Moreover, we estimated the values of asbestos concentration in lungs associated with PP, lung fibrosis and FB. Lung fibrosis showed a significant positive relationship with asbestos lung content, whereas PP and FB did not. We identified, for the first time, critical lung concentrations of asbestos related to the presence of PP, lung fibrosis and FB at histology (respectively, 19 800, 26 400 and 27 400 fibers per gram of dry weight), that were all well-below the background levels of asbestos identified in our laboratory. Such data suggest that PP, lung fibrosis and FB at histology should be used with caution in the causal attribution of MM to past asbestos exposures, while evaluation of amphibole lung content using analytical electron microscopy should be preferred.
Do hypoallergenic skincare products contain fewer potential contact allergens?
Authors: Hiranput Siwaporn , McAllister Lucy , Hill Glenda , Yesudian Paul Devakar 
Published: December 2023

Abstract
Personal care products (PCPs) commonly cause allergic contact dermatitis (ACD). Skincare companies often market their products as ‘hypoallergenic’; however, this term is not regulated by industry standards. To determine whether PCPs marketed as hypoallergenic are truly less likely to precipitate ACD, we conducted a study of ingredients found in ‘hypoallergenic PCPs’ from two major UK retailers in 2022. Of 208 products meeting the inclusion criteria, 153 (73.6%) contained at least 1 allergen or related chemical from the British Society for Cutaneous Allergy baseline series, 21 (10.1%) had 2 potential allergens and 4 PCPs (1.9%) had 3 allergens. Cetearyl alcohol was the most common ­allergen identified in leave-on PCPs and parabens in rinse-off products; fragrance was the most frequent related chemical found in 85 PCPs (40.1%). A high prevalence of common allergens was found in hypoallergenic PCPs, suggesting that dermatologists and consumers should be cautious of product ingredients.
X-linked chronic granulomatous disease secondary to skewed X-chromosome inactivation in female patients
Authors: Zhang Yue , Shu Zhou , Li Yan , Piao Yurong , Sun Fei , Han Tongxin , Wang Tianyou , Mao Huawei 
Published: December 2023

Abstract

Background
Chronic granulomatous disease (CGD) is a heterogeneous primary immunodeficiency. X-linked (XL) CGD caused by gene defects of CYBB is the most prevalent type of CGD.

Objective
We aim to understand the clinical and molecule features of XL-CGD secondary to skewed X-chromosome inactivation (XCI) in female.

Methods
We retrospectively reviewed the medical records of a female patient diagnosed with XL-CGD. Flow cytometry was used to detect the respiratory burst function. After restriction enzyme digestion of DNA, XCI was calculated by detecting fluorescent PCR products with capillary electrophoresis. The previously published female XL-CGD cases secondary to skewed XCI was summarized.

Results
Clinical data were available for 15 female subjects. The median age of diagnosis was 16 years. Consistent with XL-CGD in males, infection was the most frequent manifestation in the female patients. Catalase-positive pathogens including Serratia marcescens and Staphylococcus aureus infections were the most common pathogens. Autoimmune/autoinflammation manifestations were observed in five patients. Dihydrorhodamine (DHR) assay showed that median %DHR+ values were 6.5% and the values varying with age were observed in 2 patients. All patients had a skewing XCI and there was no consistency between the daughter and carrier mother. Anti-infective treatment was effective in majority and there was no mortality reported in XL-CGD female patients to date.

Conclusion
XL-CGD should not be neglected in female patients manifested as CGD phenotype and it is necessary to make periodic clinical evaluation of CGD female carriers as the neutrophil oxidative function may decline with aging and increase the risk for infection.
Investigating dysregulation of TGF-β1/SMAD3 signaling in atopic dermatitis: a molecular and immunohistochemical analysis
Authors: Shafi Tabasum , Rasool Wani Roohi , Hussain Showkat , Bhat Imtiyaz A , Makhdoomi Rumana , Bashir Sheikh Adil , Hassan Iffat , Shah Zafar A 
Published: December 2023

Abstract
Atopic dermatitis (AD) is a persistent and recurring inflammatory condition affecting the skin. An expanding corpus of evidence indicates the potential participation of transforming growth factor-β1 (TGF-β1) in the modulation of inflammation and tissue remodeling in AD. The primary objective of this study was to examine the aberrant modulation of TGF-β1/small mothers against decapentaplegic homolog 3 (SMAD3) signaling through a comprehensive analysis of their molecular and protein expression profiles. The study encompassed an aggregate of 37 participants, which included 25 AD patients and 12 controls. The assessment of mRNA and protein levels of TGF-β1 and SMAD3 was conducted utilizing quantitative real-time PCR and immunohistochemistry (IHC), whereas serum IgE and vitamin D levels were estimated by ELISA and chemiluminescence, respectively. Quantitative analysis demonstrated a 2.5-fold upregulation of TGF-β1 mRNA expression in the lesional AD skin (P &lt; 0.0001). IHC also exhibited a comparable augmented pattern, characterized by moderate to strong staining intensities. In addition, TGF-β1 mRNA showed an association with vitamin D deficiency in serum (P &lt; 0.02), and its protein expression was linked with the disease severity (P &lt; 0.01) Furthermore, a significant decrease in the expression of the SMAD3 gene was observed in the affected skin (P = 0.0004). This finding was further confirmed by evaluating the protein expression and phosphorylation of SMAD3, both of which exhibited a decrease. These findings suggest that there is a dysregulation in the TGF-β1/SMAD3 signaling pathway in AD. Furthermore, the observed augmentation in mRNA and protein expression of TGF-β1, along with its correlation with the disease severity, holds considerable clinical significance and emphasizes its potential role in AD pathogenesis.
Sicilian semi- and supercentenarians: age-related Tγδ cell immunophenotype contributes to longevity trait definition
Authors: Ligotti Mattia Emanuela , Accardi Giulia , Aiello Anna , Calabrò Anna , Caruso Calogero , Corsale Anna Maria , Dieli Francesco , Di Simone Marta , Meraviglia Serena , Candore Giuseppina 
Published: December 2023

Abstract
The immune system of semi- (from ≥105 to &lt;110 years old) and supercentenarians (≥110 years old), i.e. oldest centenarians, is thought to have characteristics that allow them to reach extreme longevity in relatively healthy status. Thus, we investigated variations of the two principal subsets of Tγδ, Vδ1, and Vδ2, and their functional subsets using the markers defining Tαβ cells, i.e. CD27, CD45RA, in a cohort of 28 women and 26 men (age range 19–110 years), including 11 long-living individuals (from &gt;90 years old to&lt;105 years old), and eight oldest centenarians (≥105 years old), all of them were previously analysed for Tαβ and NK cell immunophenotypes on the same blood sample collected on recruitment day. Naïve Vδ1 and Vδ2 cells showed an inverse relationship with age, particularly significant for Vδ1 cells. Terminally differentiated T subsets (TEMRA) were significantly increased in Vδ1 but not in Vδ2, with higher values observed in the oldest centenarians, although a great heterogeneity was observed. Both naïve and TEMRA Vδ1 and CD8+ Tαβ cell values from our previous study correlated highly significantly, which was not the case for CD4+ and Vδ2. Our findings on γδ TEMRA suggest that these changes are not unfavourable for centenarians, including the oldest ones, supporting the hypothesis that immune ageing should be considered as a differential adaptation rather than a general immune alteration. The increase in TEMRA Vδ1 and CD8+, as well as in NK, would represent immune mechanisms by which the oldest centenarians successfully adapt to a history of insults and achieve longevity.
From Evidence to Effectiveness: Implications of the Randomized Trial to Prevent Vascular Events in HIV Study for People With HIV in Low- and Middle-Income Settings
Authors: Manne-Goehler Jennifer , Ali Mohammed K , Flood David , Marconi Vincent C , Venter Willem D F , Siedner Mark J 
Published: December 2023

Abstract
The Randomized Trial to Prevent Vascular Events in HIV (REPRIEVE) study found a 35% reduction in major adverse cardiovascular events for people with human immunodeficiency virus who received daily pitavastatin. However, how this evidence will change practice is far from certain. Here, we outline evidence gaps and political and healthcare delivery challenges that will need to be addressed for REPRIEVE to offer public health benefits in low- and middle-income countries.
MAESTRO-Pool Enables Highly Parallel and Specific Mutation-Enrichment Sequencing for Minimal Residual Disease Detection in Cohort Studies
Authors: Blewett Timothy , Rhoades Justin , Liu Ruolin , Xiong Kan , Sridhar Sainetra , Crnjac Andjela , Cheng Ju , Lawless Aleigha R , Frederick Dennie T , Flaherty Keith T , Makrigiorgos Gerassimos Mike , Adalsteinsson Viktor A 
Published: December 2023

Abstract

Background
Tracing patient-specific tumor mutations in cell-free DNA (cfDNA) for minimal residual disease (MRD) detection is promising but challenging. Assaying more mutations and cfDNA stands to improve MRD detection but requires highly accurate, efficient sequencing methods and proper calibration to prevent false detection with bespoke tests.

Methods
MAESTRO (Minor Allele Enriched Sequencing Through Recognition Oligonucleotides) uses mutation-specific oligonucleotide probes to enrich cfDNA libraries for tumor mutations and enable their accurate detection with minimal sequencing. A new approach, MAESTRO-Pool, which entails pooling MAESTRO probes for all patients and applying these to all samples from all patients, was used to screen for 22 333 tumor mutations from 9 melanoma patients in 98 plasma samples. This enabled quantification of MRD detection in patient-matched samples and false detection in unmatched samples from other patients. To detect MRD, a new dynamic MRD caller was used that computes a probability for MRD detection based on the number of mutations and cfDNA molecules sequenced, thereby calibrating for variations in each bespoke test.

Results
MAESTRO-Pool enabled sensitive detection of MRD down to 0.78 parts per million (ppm), reflecting a 10- to 100-fold improvement over existing tests. Of the 8 MRD positive samples with ultra-low tumor fractions &lt;10 ppm, 7 were either in upward-trend preceding recurrence or downward-trend aligning with response. Of 784 patient-unmatched tests, only one was found as MRD positive (tumor fraction = 2.7 ppm), suggesting high specificity.

Conclusions
MAESTRO-Pool enables massively parallel, tumor-informed MRD testing with concurrent benchmarking of bespoke MRD tests. Meanwhile, our new MRD caller enables more mutations and cfDNA molecules to be tested without compromising specificity. These improve the ability for detecting traces of MRD from blood.
Stealthy Backdoor Attacks On Deep Point Cloud Recognization Networks
Authors: Feng Le , Qian Zhenxing , Zhang Xinpeng , Li Sheng 
Published: December 2023

Abstract
Deep neural networks are vulnerable to backdoor attacks. Previous backdoor attacks have mainly focused on images. Unlike images composed of regular pixels, 3D point clouds are composed of irregular three-dimensional XYZ coordinates, which are widely used in areas such as autonomous driving and 3D measurement. As many deep neural networks have been developed for processing 3D point clouds, these networks also face the risk of backdoor attacks. Nevertheless, backdoor attacks on 3D point clouds have rarely been investigated. This paper proposes a stealthy backdoor attack on point clouds in the physical world, aiming to generate trainable non-rigid deformations as backdoor patterns. Instead of directly adding backdoor patterns onto the point clouds, we deform the 3D space of the point clouds to a new space, ensuring that all point clouds have the same backdoor deformation. We use point cloud alignment to overcome the inconsistency of backdoor deformation caused by shifting and scaling in the physical world. We also propose a physical transformation layer to combat the physical transformations. Additionally, we propose mask contrast learning to eliminate pseudo backdoor patterns to make the network’s backdoor property stealthier. Extensive experiments indicate that the proposed method can achieve better attack success rates and stealthiness.