bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel method for drug-target interaction prediction based on graph transformers model
Authors: Wang Hongmei , Guo Fang , Du Mengyan , Wang Guishen , Cao Chen 
Published: November 2022

AbstractBackgroundDrug-target interactions (DTIs) prediction becomes more and more important for accelerating drug research and drug repositioning. Drug-target interaction network is a typical model for DTIs prediction. As many different types of relationships exist between drug and target, drug-target interaction network can be used for modeling drug-target interaction relationship. Recent works on drug-target interaction network are mostly concentrate on drug node or target node and neglecting the relationships between drug-target.ResultsWe propose a novel prediction method for modeling the relationship between drug and target independently. Firstly, we use different level relationships of drugs and targets to construct feature of drug-target interaction. Then, we use line graph to model drug-target interaction. After that, we introduce graph transformer network to predict drug-target interaction.ConclusionsThis method introduces a line graph to model the relationship between drug and target. After transforming drug-target interactions from links to nodes, a graph transformer network is used to accomplish the task of predicting drug-target interactions.
TeaPVs: a comprehensive genomic variation database for tea plant (Camellia sinensis)
Authors: An Yanlin , Zhang Xiaoqin , Jiang Sixia , Zhao Jingjing , Zhang Feng 
Published: November 2022

AbstractGenome variation not only plays an important role in plant phenotypic modeling and adaptive evolution, but also enhances population genetic diversity and regulates gene expression. The tea tree (Camellia sinensis) has a large genome (~ 3.0 Gb), making the identification of genome-wide variants time-consuming and expensive. With the continuous publication of a large number of different types of population sequencing data, there is a lack of an open platform to integrate these data and identify variants in the tea plant genome.To integrate the genetic variation confidence in the tea plant population genome, 238 whole-genome resequencing, 213 transcriptome sequencing, and 96 hybrid F1 individuals with a total of more than 20 Tb were collected for mutation site identification. Based on these variations information, we constructed the first tea tree variation web service database TeaPVs (http://47.106.184.91:8025/ and http://liushang.top:8025/). It supports users to search all SNP, Indel, SV mutations and SSR/Polymorphic SSR sequences by location or gene ID. Furthermore, the website also provides the functions of gene expression search of different transcriptome, sequence blast, sequence extraction of CDS and mutation loci, etc.The features of the TeaPVs database make it a comprehensive tea plant genetic variation bioinformatics platform for researchers, and will also be helpful for revealing new functional mutations in the tea plant genome and molecular marker-assisted breeding.
Two-dimensional speckle tracking echocardiography demonstrates improved myocardial function after intravenous infusion of bone marrow mesenchymal stem in the X-Linked muscular dystrophy mice
Authors: Liu Xiao , Yao Shixiang , Pan Min , Cai Yingying , Shentu Weihui , Cai Wenqian , Yu Hongkui 
Published: November 2022

Abstract
Background
Bone marrow mesenchymal stem cells (BMSCs) are commonly used in regenerative medicine. However, it is not clear whether transplantation of BMSCs can improve cardiac function of the X-Linked Muscular Dystrophy Mice (mdx) and how to detect it. We aimed to investigate the role of speckle tracking echocardiography (STE) in detecting cardiac function of the BMSCs-transplanted mdx in comparison with the untreated mdx.

Methods
The experimental mice were divided into the BMSCs-transplanted mdx, untreated mdx, and control mice groups (n = 6 per group). The BMSCs were transplanted via tail vein injections into a subset of mdx at 20 weeks of age. After four weeks, the cardiac functional parameters of all the mice in the 3 groups were analyzed by echocardiography. Then, all the mice were sacrificed, and the cardiac tissues were harvested and analyzed by immunofluorescence. The serum biochemical parameters were also analyzed to determine the beneficial effects of BMSCs transplantation.

Results
Traditional echocardiography parameters did not show statistically significant differences after BMSCs transplantation for the three groups of mice. In comparison with the control group, mdx showed significantly lower left ventricular (LV) STE parameters in both the long-axis and short-axis LV images (P < 0.05). However, BMSCs-transplanted mdx showed improvements in several STE parameters including significant increases in a few STE parameters (P < 0.05). Immunofluorescence staining of the myocardium tissues showed statistically significant differences between the mdx and the control mice (P < 0.05), and the mdx transplanted with BMSCs demonstrated significantly improvement compared with the untreated mdx (P < 0.05).

Conclusion
This study demonstrated that the early reduction in the LV systolic and diastolic function in the mdx were accurately detected by STE. Furthermore, our study demonstrated that the transplantation of BMSCs significantly improved myocardial function in the mdx.
The cardiac distress inventory: A new measure of psychosocial distress associated with an acute cardiac event
Authors: Jackson Alun C , Grande Michael R Le , Rogerson Michelle C , Ski Chantal F , Amerena John , Smith Julian A , Hoover Valerie , Alvarenga Marlies E , Higgins Rosemary O , Thompson David R , Murphy Barbara M 
Published: November 2022

Abstract
Background
Many challenges are posed by the experience of a heart attack or heart surgery which can be characterised as ‘cardiac distress’. It spans multiple psychosocial domains incorporating patients’ responses to physical, affective, cognitive, behavioural and social symptoms and experiences related to their cardiac event and their recovery. Although some measures of the psychological and emotional impacts of a cardiac event exist, none provides a comprehensive assessment of cardiac distress. To address this gap, the study aimed to develop a Cardiac Distress Inventory (CDI) using best practice in instrument design.

Method
An item pool was generated through analysis of cognate measures, mostly in relation to other health conditions and through focus group and individual review by a multidisciplinary development team, cardiac patients, and end-users including cardiac rehabilitation co-ordinators. The resulting 144 items were reduced through further reviews to 74 for testing. The testing was carried out with 405 people recruited from three hospitals, through social media and by direct enrolment on the study website. A two-stage psychometric evaluation of the 74 items used exploratory factor analysis to extract the factors followed by Rasch analysis to confirm dimensionality within factors.

Results
Psychometric analysis resulted in the identification of 55 items comprising eight subscales, to form the CDI. The subscales assess fear and uncertainty, disconnection and hopelessness, changes to roles and relationships, overwhelm and depletion, cognitive challenges, physical challenges, health system challenges, and death concerns. Validation against the Kessler 6 supports the criterion validity of the CDI.

Conclusion
The CDI reflects a nuanced understanding of cardiac distress and should prove to be a useful clinical assessment tool, as well as a research instrument. Individual subscales or the complete CDI could be used to assess or monitor specific areas of distress in clinical practice. Development of a short form screening version for use in primary care, cardiac rehabilitation and counselling services is warranted.
Association between miRNA-145 and miRNA-155 expression in peripheral blood mononuclear cells of patients with multiple sclerosis: a case-control study
Authors: Ali Ashrafi Sepide , Asadi Milad , Shanehbandi Dariush , Sadigh Eteghad Saeed , Fazlollahi Asra , Nejadghaderi Seyed Aria , Shaafi Sheida 
Published: November 2022

AbstractIntroductionMicroRNAs (miR or miRNA) are short regulatory RNAs, which modulate post-transcriptional gene expression. Dysregulation of these molecules contributes to pathogenicity of autoimmune disorders, such as multiple sclerosis (MS).AimsThis study was conducted to investigate changed expression pattern of miRNA-145 and miRNA-155 in MS.MethodsWe collected blood samples of 75 patients with relapsing-remitting MS patients and 75 healthy controls. Ficoll-Hypaque density gradient method was used to isolate peripheral blood mononuclear cells. Also, total RNA was extracted and subjected to RT-PCR analysis. We used the Mann–Whitney U test to evaluate the differences in expression levels of target miRNAs between the groups.ResultsWe found that expression of miRNA-145 (P = 0.012) and miRNA-155 (P = 0.005) were partly reduced in patients with relapse-remitting MS in comparison with healthy controls. The miRNA-145 had an area under curve (AUC) of 0.621 (P = 0.01) and miRNA-155 levels had an AUC of 0.625 (P = 0.008).ConclusionDecreased expression of miRNA-145 and miRNA-155 contributes to development of relapse-remitting MS, while further large scale observational studies and meta-analyses are required.
A nomogram combining clinical factors and biomarkers for predicting the recurrence of high-risk cutaneous squamous cell carcinoma
Authors: Oh Yeongjoo , Zheng Zhenlong , Kim Ki-Yeol , Xu Xiangshu , Pei Meiling , Oh Byungho , Kim Sang Kyem , Chung Kee Yang , Roh Mi Ryung 
Published: November 2022

Abstract
Background
Although determining the recurrence of cutaneous squamous cell carcinoma (cSCC) is important, currently suggested systems and single biomarkers have limited power for predicting recurrence.

Objective
In this study, combinations of clinical factors and biomarkers were adapted into a nomogram to construct a powerful risk prediction model.

Methods
The study included 145 cSCC patients treated with Mohs micrographic surgery. Clinical factors were reviewed, and immunohistochemistry was performed using tumor tissue samples. A nomogram was constructed by combining meaningful clinical factors and protein markers.

Results
Among the various factors, four clinical factors (tumor size, organ transplantation history, poor differentiation, and invasion into subcutaneous fat) and two biomarkers (Axin2 and p53) were selected and combined into a nomogram. The concordance index (C-index) of the nomogram for predicting recurrence was 0.809, which was higher than that for the American Joint Committee on Cancer (AJCC) 7th, AJCC 8th, Brigham and Women’s Hospital, and Breuninger staging systems in the patient data set.

Conclusion
A nomogram model that included both clinical factors and biomarkers was much more powerful than previous systems for predicting cSCC recurrence.
Association between serum albumin and 60-day mortality in Chinese Hakka patients with non-APL acute myeloid leukemia: a retrospective cohort study
Authors: Xiao Zuomiao , Li Haibo , Xiao Dejun , Liu Yulan , Chen Xianchun , Luo Shi , Ji Yanhong 
Published: November 2022

Abstract
Background
Acute myeloid leukemia (AML) is the main type of adult leukemia, and 60-day mortality is a vital clinical problem that doctors have to face at the begin with treatment. Studies on the association between serum albumin and 60-day mortality from AML (non-APL) are limited.

Methods
In this retrospective cohort study, ALB was measured after admission in all patients diagnosed with primary AML from Affiliated Ganzhou Hospital of Nanchang University between January 2013 and May 2021. The outcome was all-cause, 60-day mortality. Multivariable Cox regression analyses were performed to calculate the adjusted hazard ratio (HR) and its corresponding 95% confidence interval (CI).

Results
This study included 394 primary AML patients. The overall 60-day mortality was 28.9% (114/394); it was 43.1% (56/130), 27.5% (36/131), and 16.5% (22/133) for ALB quantile1 (Q, < 34.5 g/L), quantile 2 (Q2, 34.5–38.5 g/L), and quantile 3 (Q3, ≥ 38.6 g/L), respectively (P = 0.001). After adjusting for potential confounders, we found an association between a 6% decrease in 60-day mortality rate and a 1 g/L increase in ALB level (HR = 0.94, 95% CI: 0.89–0.99, P = 0.015), which was associated with 38 and 70% decreases in 60-day mortality rates in Q2 (HR = 0.50, 95% CI: 0.30–0.86, P = 0.012) and Q3 (HR = 0.47, 95% CI: 0.2 5–0.90, P = 0.022), respectively, compared with that in Q1. Similar results were obtained after subgrouping based on an ALB level of 35 g/L (HR = 0.55, 95% CI: 0.34–0.88, P = 0.013).

Conclusions
Serum albumin was significantly associated with 60-day mortality of primary AML, which has important clinical significance. Further investigation is warranted.
Advances and limitations for the treatment of spinal muscular atrophy
Authors: Day John W. , Howell Kelly , Place Amy , Long Kimberly , Rossello Jose , Kertesz Nathalie , Nomikos George 
Published: November 2022

AbstractSpinal muscular atrophy (5q-SMA; SMA), a genetic neuromuscular condition affecting spinal motor neurons, is caused by defects in both copies of the SMN1 gene that produces survival motor neuron (SMN) protein. The highly homologous SMN2 gene primarily expresses a rapidly degraded isoform of SMN protein that causes anterior horn cell degeneration, progressive motor neuron loss, skeletal muscle atrophy and weakness. Severe cases result in limited mobility and ventilatory insufficiency. Untreated SMA is the leading genetic cause of death in young children. Recently, three therapeutics that increase SMN protein levels in patients with SMA have provided incremental improvements in motor function and developmental milestones and prevented the worsening of SMA symptoms. While the therapeutic approaches with Spinraza®, Zolgensma®, and Evrysdi® have a clinically significant impact, they are not curative. For many patients, there remains a significant disease burden. A potential combination therapy under development for SMA targets myostatin, a negative regulator of muscle mass and strength. Myostatin inhibition in animal models increases muscle mass and function. Apitegromab is an investigational, fully human, monoclonal antibody that specifically binds to proforms of myostatin, promyostatin and latent myostatin, thereby inhibiting myostatin activation. A recently completed phase 2 trial demonstrated the potential clinical benefit of apitegromab by improving or stabilizing motor function in patients with Type 2 and Type 3 SMA and providing positive proof-of-concept for myostatin inhibition as a target for managing SMA. The primary goal of this manuscript is to orient physicians to the evolving landscape of SMA treatment.
Association between preterm births and socioeconomic development: analysis of national data
Authors: Montemor Marina Sanches , Demarque Gabriella Ferreira , Rodrigues Agatha Sacramento , Francisco Rossana Pulcinelli Vieira , de Carvalho Mario Henrique Burlacchini 
Published: November 2022

Abstract
Background
The increasing prevalence of preterm birth, which is a global phenomenon, is attributable to the increased medical indications, artificial gestations, and some socioeconomic factors. This study was conducted to identify whether development and equality indices are associated with the incidence of preterm birth, specifically, spontaneous and elective preterm births.

Methods
This retrospective observational study comprised an analysis of data on live births from 2019 in Brazil and on socioeconomic indices that were derived from census information in 2017. Data were summarised using absolute and relative frequencies. Spearman’s correlation was used to determine the correlation between socioeconomic factors and the preterm birth rate. Multiple beta regression analysis was performed to determine the best model of socioeconomic covariates and preterm birth rate. The significance level was set at 5%.

Results
In 2019 in Brazil, the preterm birth rate was 11.03%, of which 58% and 42% were spontaneous and elective deliveries, respectively. For all preterm births, Spearman’s correlation varied from ρ = 0.4 for the Gini Index and ρ =  − 0.24 for illiteracy. The best fit modelled the spontaneous preterm birth fraction as a negative function of the Human Development Index (HDI). The best-fit model considered the expected elective preterm birth fraction as a positive function of the HDI and as a negative function of the Gini Index, which was used as a precision parameter.

Conclusions
We observed a reduction in the fraction of spontaneous preterm births; however, the distribution was not uniform in the territory: higher rates of spontaneous preterm birth were noticed in the north, northeast, and mid-west regions. Thus, areas with lower education levels and inequal income distribution have a higher proportion of spontaneous preterm birth. The fraction of elective preterm birth was positively associated with more advantaged indices of socioeconomic status.
Comparison of frailty in patients with nontuberculous mycobacterial lung disease and bronchiectasis: a prospective cohort study
Authors: Fujita Kohei , Ito Yutaka , Yamamoto Yuki , Kanai Osamu , Imakita Takuma , Oi Issei , Ito Takanori , Saito Zentaro , Mio Tadashi 
Published: November 2022

Abstract
Background
The incidence of nontuberculous mycobacterial lung disease (NTM-LD) peaks in middle- and old age groups, coinciding with senescence; thus, chronic infectious diseases can accelerate frailty and worsen mental health in the elderly. In this study, we aimed to compare the prevalence of physical and psychiatric frailty between patients with NTM-LD and bronchiectasis (BE).

Methods
The Kihon Checklist Questionnaire (KCQ) was used to assess physical and psychiatric frailties and identify those at risk of requiring care among patients with newly diagnosed NTM-LD and BE. Additionally, the Hospital Anxiety and Depression Scale (HADS) scores and chronic inflammatory biomarkers of the alveolar region (surfactant protein [SP]-A, SP-D, and human cationic antibacterial protein [hCAP]/LL-37) were assessed and compared between NTM-LD and BE patients.

Results
There were no significant differences in the background characteristics between the 33 NTM and 36 BE patients recruited. The KCQ revealed that the proportion of frail NTM patients at diagnosis was higher than that of frail BE patients (48.5% vs. 22.2%, p = 0.026). HADS scores were significantly higher in the NTM group than in the BE group (p < 0.01). Bronchoalveolar lavage fluid (BALF) hCAP/LL-37 and SP-D levels were significantly higher (p = 0.001), but serum hCAP/LL-37 levels were significantly lower in the NTM group than in the BE group (p = 0.023). However, there were no significant differences in the BALF and serum SP-D levels between the two groups.

Conclusions
The number of frail NTM patients at diagnosis was significantly higher than that of frail BE patients. Biomarker analysis suggested that the former had more localized lung inflammation than the latter.

Trial registration
This trial was prospectively registered in the Clinical Trials Registry (UMIN 000027652).
Attitudes of Polish physicians, nurses and pharmacists towards the ethical and legal aspects of the conscience clause
Authors: Czekajewska Justyna , Walkowiak Dariusz , Domaradzki Jan 
Published: November 2022

AbstractBackgroundWhile healthcare professionals’ right to invoke the conscience clause has been recognised as a fundamental human right, it continues to provoke a heated debate in Polish society. Although public discourse is filled with ethical and legal considerations on the conscience clause, much less is known about the attitudes of healthcare professionals regarding that matter. The aim of this study was therefore to describe the attitudes of Polish physicians, nurses and pharmacists towards the ethical and legal aspects of the conscience clause.MethodsWe analysed a group of three hundred healthcare professionals: physicians, nurses and pharmacists in Poznan, Poland, using a standard questionnaire comprising of 29 questions about various ethical and legal aspects of the conscience clause and participants’ personal experiences with the conscience clause. The study was conducted between January and March 2020.ResultsThis research shows that although most Polish healthcare workers support the right to invoke the conscience clause they differ significantly in their opinions on to whom and to what medical procedures the conscience clause should apply to. It also demonstrated that while the conscience clause is rarely invoked in Poland, most healthcare professionals declare that the current legal regulations in that sphere are unclear and inaccurate.ConclusionsWhile there is an urgent need to raise the awareness regarding the conscience clause among medical students and healthcare professionals and educate them about such issues, it is even more important to improve the legal system in regard to the CC so that it protects both HCPs’ right to the CC and safeguards patients’ rights to medical services.
Isolation and identification of the broad-spectrum high-efficiency phage vB_SalP_LDW16 and its therapeutic application in chickens
Authors: Cao Shengliang , Yang Wenwen , Zhu Xihui , Liu Cheng , Lu Jianbiao , Si Zhenshu , Pei Lanying , Zhang Leilei , Hu Wensi , Li Yanlan , Wang Zhiwei , Pang Zheyu , Xue Xijuan , Li Yubao 
Published: November 2022

Abstract
Background
Salmonella infection in livestock and poultry causes salmonellosis, and is mainly treated using antibiotics. However, the misuse use of antibiotics often triggers the emergence of multi-drug-resistant Salmonella strains. Currently, Salmonella phages is safe and effective against Salmonella, serving as the best drug of choice. This study involved 16 Salmonella bacteriophages separated and purified from the sewage and the feces of the broiler farm. A phage, vB_SalP_LDW16, was selected based on the phage host range test. The phage vB_SalP_LDW16 was characterized by the double-layer plate method and transmission electron microscopy. Furthermore, the clinical therapeutic effect of phage vB_SalP_LDW16 was verified by using the pathogenic Salmonella Enteritidis in the SPF chicken model.

Results
The phage vB_SalP_LDW16 with a wide host range was identified to the family Siphoviridae and the order Caudoviridae, possess a double-stranded DNA and can lyse 88% (22/25) of Salmonella strains stored in the laboratory. Analysis of the biological characteristics, in addition, revealed the optimal multiplicity of infection (MOI) of vB_SalP_LDW16 to be 0.01 and the phage titer to be up to 3 × 1014 PFU/mL. Meanwhile, the phage vB_SalP_LDW16 was found to have some temperature tolerance, while the titer decreases rapidly above 60 ℃, and a wide pH (i.e., 5–12) range as well as relative stability in pH tolerance. The latent period of phage was 10 min, the burst period was 60 min, and the burst size was 110 PFU/cell. Furthermore, gastric juice was also found to highly influence the activity of the phage. The clinical treatment experiments showed that phage vB_SalP_LDW16 was able to significantly reduce the bacterial load in the blood through phage treatment, thereby improving the pathological changes in the intestinal, liver, and heart damage, and promoting the growth and development of the chicken.

Conclusions
The phage vB_SalP_LDW16 is a highly lytic phage with a wide host range, which can be potentially used for preventing and treating chicken salmonellosis, as an alternative or complementary antibiotic treatment in livestock farming.