bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using zebrafish to understand reciprocal interactions between the nervous and immune systems and the microbial world
Authors: Levraud Jean-Pierre , Rawls John F. , Clatworthy Anne E. 
Published: June 2022

AbstractAnimals rely heavily on their nervous and immune systems to perceive and survive within their environment. Despite the traditional view of the brain as an immunologically privileged organ, these two systems interact with major consequences. Furthermore, microorganisms within their environment are major sources of stimuli and can establish relationships with animal hosts that range from pathogenic to mutualistic. Research from a variety of human and experimental animal systems are revealing that reciprocal interactions between microbiota and the nervous and immune systems contribute significantly to normal development, homeostasis, and disease. The zebrafish has emerged as an outstanding model within which to interrogate these interactions due to facile genetic and microbial manipulation and optical transparency facilitating in vivo imaging. This review summarizes recent studies that have used the zebrafish for analysis of bidirectional control between the immune and nervous systems, the nervous system and the microbiota, and the microbiota and immune system in zebrafish during development that promotes homeostasis between these systems. We also describe how the zebrafish have contributed to our understanding of the interconnections between these systems during infection in fish and how perturbations may result in pathology.
Sparse logistic regression revealed the associations between HBV PreS quasispecies and hepatocellular carcinoma
Authors: Jia Jian-an , Zhang Shuqin , Bai Xin , Fang Meng , Chen Shipeng , Liang Xiaotao , Zhu Shanfeng , Wong Danny Ka-Ho , Zhang Anye , Feng Jianfeng , Sun Fengzhu , Gao Chunfang 
Published: June 2022

Abstract
Background
Chronic infection with hepatitis B virus (HBV) has been proved highly associated with the development of hepatocellular carcinoma (HCC).

Aims
The purpose of the study is to investigate the association between HBV preS region quasispecies and HCC development, as well as to develop HCC diagnosis model using HBV preS region quasispecies.

Methods
A total of 104 chronic hepatitis B (CHB) patients and 117 HBV-related HCC patients were enrolled. HBV preS region was sequenced using next generation sequencing (NGS) and the nucleotide entropy was calculated for quasispecies evaluation. Sparse logistic regression (SLR) was used to predict HCC development and prediction performances were evaluated using receiver operating characteristic curves.

Results
Entropy of HBV preS1, preS2 regions and several nucleotide points showed significant divergence between CHB and HCC patients. Using SLR, the classification of HCC/CHB groups achieved a mean area under the receiver operating characteristic curve (AUC) of 0.883 in the training data and 0.795 in the test data. The prediction model was also validated by a completely independent dataset from Hong Kong. The 10 selected nucleotide positions showed significantly different entropy between CHB and HCC patients. The HBV quasispecies also classified three clinical parameters, including HBeAg, HBVDNA, and Alkaline phosphatase (ALP) with the AUC value greater than 0.6 in the test data.

Conclusions
Using NGS and SLR, the association between HBV preS region nucleotide entropy and HCC development was validated in our study and this could promote the understanding of HCC progression mechanism.
Migrant experiences of sexual and gender based violence: a critical interpretative synthesis
Authors: Tan Sze Eng , Kuschminder Katie 
Published: June 2022

Abstract
Background
Gender based violence (GBV) is a critical issue and migrants are at higher risk of experiencing and being victimized by GBV. This critical interpretative synthesis (CIS) examines migrants experiences of GBV with a focus on different migrant groups and experiences at different stages of the migrant journey.

Method
The guiding question of this review is: “how do migrants experience gender-based violence?” A total of 84 studies were included in the CIS, of which 67 peer-reviewed academic articles were selected from 2356 studies found on WebofScience, MedLINE, and ProQuest, and 17 relevant studies from the grey literature were selected from the time period 2011 to 2020. All final studies were reviewed and synthesized using a critical inductive approach to formulate the key results.

Results
The results demonstrate a high prevalence of GBV amongst migrants, and in particular among vulnerable migrant groups such as forced migrants and irregular migrants, with an emerging focus on male victims. Findings of the CIS revealed three key themes: 1) Most GBV occurrences are rooted in unequal power dynamics; 2) Victims often live with long-lasting consequences that are worsened by their fear of disclosure and stigmatization; 3) There are differential understandings of victimhood across organizations, communities, and victims themselves. In order to support access, sampling, and methodological challenges in this field of research, this article also reports its findings on common risk-factors identified, consequences and coping mechanisms reported, protection policies targeting GBV, and finally, available databases and data collection methods.

Conclusion
Further directions for research should be encouraged to move beyond prevalence reporting into identifying risk-factors and possible prevention in both sexes. In addition, more research on GBV experiences throughout migrants’ journeys, and coping mechanisms should be encouraged.
Pelvic U-Net: multi-label semantic segmentation of pelvic organs at risk for radiation therapy anal cancer patients using a deeply supervised shuffle attention convolutional neural network
Authors: Lempart Michael , Nilsson Martin P. , Scherman Jonas , Gustafsson Christian Jamtheim , Nilsson Mikael , Alkner Sara , Engleson Jens , Adrian Gabriel , Munck af Rosenschöld Per , Olsson Lars E. 
Published: June 2022

Abstract
Background
Delineation of organs at risk (OAR) for anal cancer radiation therapy treatment planning is a manual and time-consuming process. Deep learning-based methods can accelerate and partially automate this task. The aim of this study was to develop and evaluate a deep learning model for automated and improved segmentations of OAR in the pelvic region.

Methods
A 3D, deeply supervised U-Net architecture with shuffle attention, referred to as Pelvic U-Net, was trained on 143 computed tomography (CT) volumes, to segment OAR in the pelvic region, such as total bone marrow, rectum, bladder, and bowel structures. Model predictions were evaluated on an independent test dataset (n = 15) using the Dice similarity coefficient (DSC), the 95th percentile of the Hausdorff distance (HD95), and the mean surface distance (MSD). In addition, three experienced radiation oncologists rated model predictions on a scale between 1–4 (excellent, good, acceptable, not acceptable). Model performance was also evaluated with respect to segmentation time, by comparing complete manual delineation time against model prediction time without and with manual correction of the predictions. Furthermore, dosimetric implications to treatment plans were evaluated using different dose-volume histogram (DVH) indices.

Results
Without any manual corrections, mean DSC values of 97%, 87% and 94% were found for total bone marrow, rectum, and bladder. Mean DSC values for bowel cavity, all bowel, small bowel, and large bowel were 95%, 91%, 87% and 81%, respectively. Total bone marrow, bladder, and bowel cavity segmentations derived from our model were rated excellent (89%, 93%, 42%), good (9%, 5%, 42%), or acceptable (2%, 2%, 16%) on average. For almost all the evaluated DVH indices, no significant difference between model predictions and manual delineations was found. Delineation time per patient could be reduced from 40 to 12 min, including manual corrections of model predictions, and to 4 min without corrections.

Conclusions
Our Pelvic U-Net led to credible and clinically applicable OAR segmentations and showed improved performance compared to previous studies. Even though manual adjustments were needed for some predicted structures, segmentation time could be reduced by 70% on average. This allows for an accelerated radiation therapy treatment planning workflow for anal cancer patients.
The potential role of herbal extract Wedelolactone for treating particle-induced osteolysis: an in vivo study
Authors: Lu Yung-Chang , Chang Ting-Kuo , Lin Tzu-Chiao , Yeh Shu-Ting , Fang Hsu-Wei , Huang Chun-Hsiung , Huang Chang-Hung 
Published: June 2022

Abstract
Background
Osteolysis is one of the most prevalent clinical complications affecting people who undergo total joint replacement (TJR). Wedelolactone (WDL) is a coumestan compound derived from the Wedelia chinensis plant and has been demonstrated to exhibit anti-inflammatory properties. This study aimed to investigate the oral administration of WDL as a potential treatment for particle-induced osteolysis using a well-established mice calvarial disease model.

Methods
Thirty-two C57BL/6 J mice were randomized into four groups: Sham, vehicle, osteolysis group with oral WDL treatment for 4 weeks (WDL 4w), and osteolysis group treated for 8 weeks (WDL 8w). Micro-CT was used to quantitatively analyze the bone mineral density (BMD), bone volume/tissue volume (BV/TV) and trabecular bone thickness (Tb.Th). Osteoclast numbers were also measured from histological slides by two investigators who were blind to the treatment used.

Results
The results from micro-CT observation showed that BMD in the WDL 8w group improved significantly over the vehicle group (p < 0.05), but there was no significant difference between WDL 4w and 8w for BV/TV and Tb.Th. Osteoclast numbers in the WDL 4w group were also lower than the vehicle group (p < 0.05), but the difference between WDL 8w and 4w groups was not significant.

Conclusions
Particle-induced osteolysis is an inevitable long-term complication after TJR. The results of this animal study indicate that an oral administration of WDL can help reduce the severity of osteolysis without adverse effects.
Patient-reported outcomes in a Chinese cohort of osteogenesis imperfecta unveil psycho-physical stratifications associated with clinical manifestations
Authors: Chen Peikai , Tan Zhijia , Qiu Anmei , Yin Shijie , Zhou Yapeng , Dong Zhongxin , Qiu Yan , Xu Jichun , Li Kangsen , Dong Lina , Shek Hiu Tung , Liu Jingwen , Yeung Eric H. K. , Gao Bo , Cheung Kenneth Man Chee , To Michael Kai-Tsun 
Published: June 2022

AbstractBackgroundOsteogenesis imperfecta (OI) is a rare congenital disorder of the skeletal system, inflicting debilitating physical and psychological distress on patients and caregivers. Over the decades, much effort has been channeled towards understanding molecular mechanisms and developing new treatments. It has recently become more apparent that patient-reported outcome measurements (PROM) during treatment, healing and rehabilitation are helpful in facilitating smoother communication, refining intervention strategies and achieving higher quality of life. To date, systematic analyses of PROM in OI patients remain scarce.ResultsHere, utilizing a PROM Information System, we report a cross-sectional and longitudinal study in a southern Chinese cohort of 90 OI patients, covering both the child and adult age-groups. In the child group where both self and parental surveys were obtained, we identified two clusters of comparable sizes showing different outlooks in physical mobility and emotional experiences. One cluster (Cluster 1) is more negative about themselves than the other (Cluster 2). A concordance of 84.7% between self and parental assessments was recorded, suggesting the stability and validity of PROM-based stratification. Clinical subtyping, deformity, leg length discrepancy, and limited joint mobility were significantly associated with this stratification, with Cluster 1 showing higher percentages of severe phenotypes than Cluster 2. Since OI is a genetic disorder, we performed genetic testing on 72 of the 90 patients, but found no obvious association between genotypes and the PROM stratification. Analyses of longitudinal data suggested that patients tended to stay in the same psychological state, in both clusters. Adult patients also showed a continuous spectrum of self-evaluation that matches their clinical manifestations.ConclusionBy systematically analyzing patient-reported outcomes, our study demonstrated the link between the sociopsychological wellbeing of OI patients, and their clinical manifestations, which may serve as the basis for evaluating clinical interventions and help achieve better patient-centric medical practices. The lack of genotype-PROM association may be due to the diverse mutational spectrum in OI, which warrants further investigation when a larger sample size is available.
Effectiveness of relaxation techniques ‘as an active ingredient of psychological interventions’ to reduce distress, anxiety and depression in adolescents: a systematic review and meta-analysis
Authors: Hamdani Syed Usman , Zill-e-Huma  , Zafar Syeda Wajeeha , Suleman Nadia , Um-ul-Baneen  , Waqas Ahmed , Rahman Atif 
Published: June 2022

AbstractBackgroundAdolescent depression and anxiety are among the leading contributors to health burden worldwide. ‘Relaxation Techniques (RTs)’ are a “set of strategies to improve physiological response to stress” and are frequently cited as an active ingredient of trans-diagnostic, psychosocial interventions for scaling-up care for preventing and treating these conditions in adolescents. However, there is a little evidence on the effectiveness of ‘relaxation techniques’ for this age group.AimAs a part of the Wellcome Trust’s Active Ingredients commission, we did a systematic review and meta-analysis to evaluate the effectiveness of RTs to reduce the symptoms of distress, anxiety and depression in young people, aged 14 to 24 years old, globally.MethodsWe searched 10 academic databases to include 65 Randomized Controlled Trials (RCTs) of relaxation-based interventions for young people with the symptoms of anxiety and depression. Primary outcomes were reduction in symptoms of distress, anxiety and/or depression. We employed the Cochrane risk of bias tool and GRADE (Grading of Recommendations, Assessment, Development and Evaluations) guidelines to assess certainty of outcomes pertaining to anxiety, depression and distress. Standardized mean difference was estimated using effect size.ResultsThe analysis of 65 RCTs with 8009 young people showed that RTs were highly effective in treating anxiety (pooled effect size of (Standardized Mean Difference-SMD) − 0.54 (95%CI− 0.69 to − 0.40); moderately effective in reducing distress (SMD = − 0.48, 95%CI− 0.71 to − 0.24) and had only a weak effect on improving depression in young people (SMD = − 0.28 (95%CI− 0.40% to − 0.15). Face-to-face delivered relaxation techniques yielded higher effect size (SMD = − 0.47, 95% CI − 0.64 to − 0.30) compared to online delivery (SMD = − 0.22, 95% CI − 0.48 to 0.04) for anxiety.ConclusionMost of the included studies were from High Income Countries (HICs) and had a high risk of bias. Further high-quality studies with low risk of bias, especially from low resource settings are needed to evaluate the evidence for effectiveness of RTs as an active ingredient of psychological interventions to reduce the symptoms of distress, anxiety and depression in young people.
Fusobacterium nucleatum promotes the development of acute liver failure by inhibiting the NAD+ salvage metabolic pathway
Authors: Cao Pan , Chen Qian , Shi Chunxia , Wang Luwen , Gong Zuojiong 
Published: June 2022

Abstract
Background
Acute liver failure (ALF) patients are often accompanied by severe energy metabolism abnormalities and intestinal microecological imbalance. The intestinal mucosal barrier is severely damaged. Intestinal endotoxin can induce intestinal endotoxemia through the "Gut-Liver axis". More and more evidence shows that members of the gut microbiota, especially Fusobacterium nucleatum (F. nucleatum), are related to inflammatory bowel disease, but whether F. nucleatum is involved in the development of ALF and whether it affects the liver energy metabolism is unclear.

Methods
This study first detected the abundance of F. nucleatum and its effect on ALF disease, and explored whether F. nucleatum aggravated liver inflammation in vitro and in vivo.

Results
Our data showed that liver tissues of ALF patients contained different abundances of F. nucleatum, which were related to the degree of liver inflammation. In addition, we found that F. nucleatum infection affected the energy metabolism of the liver during the development of ALF, inhibited the synthesis pathway of nicotinamide adenine dinucleotide (NAD+)'s salvage metabolism, and promoted inflammatory damage in the liver. In terms of mechanism, F. nucleatum inhibited NAD+ and the NAD+-dependent SIRT1/AMPK signaling pathway, and promoted liver damage of ALF.

Conclusions
Fusobacterium nucleatum coordinates a molecular network including NAD+ and SIRT1 to control the progress of ALF. Detection and targeting of F. nucleatum and its related pathways may provide valuable insights for the treatment of ALF.
Metabolic profiling in periparturient dairy cows and its relation with metabolic diseases
Authors: Kabir Mojahidul , Hasan Md. Mehedi , Tanni Nobonita Sarker , Parvin Mst. Sonia , Asaduzzaman Md. , Ehsan Md. Amimul , Islam Md. Taohidul 
Published: June 2022

Abstract
Objective
Periparturient period is associated with multiple changes including serum concentration of macro minerals and drop in feed intake. Therefore, it is essential to know the actual concentrations of major macro minerals, glucose and ketone bodies in blood during the periparturient period. The objectives of the study were to study the dynamics of calcium, magnesium, phosphorus, and glucose in serum and ketone bodies in the urine of periparturient cows and to estimate the incidence of subclinical metabolic diseases.

Results
Results showed that all the urine samples were negative for ketone bodies. Incidence of subclinical form of hypocalcaemia, hypomagnesaemia, hypophosphatemia, and hypoglycemia in periparturient cows was 31.03%, 48.28%, 17.24% and 55.17%, respectively. Older cows with high BCS and milk yield were mostly affected with a subclinical form of hypocalcaemia and hypoglycemia. No significant differences were observed in serum level of macro minerals and glucose at different time points of periparturient period of cows fed with a balanced ration, and between two groups of cows those were given IV injection of calcium and magnesium on the day of parturition and those were not given. Age, parity, and milk yield had no significant effect on the concentration of calcium, magnesium, phosphorus, and glucose.
Aberrant DNA hydroxymethylation reshapes transcription factor binding in myeloid neoplasms
Authors: Li Jia , Hong Tingting , Wei Yue , Guo Lei , Lee Minjung , Yang Hui , Class Caleb , Yang Yaling , Wang Xiaoqiong , He Hua , Siwko Stefan , You M. James , Zhou Yubin , Garcia-Manero Guillermo , Huang Yun 
Published: June 2022

AbstractEpigenetic abnormalities in DNA hydroxymethylation (5hmC) have been detected in patients with myeloid neoplasms, suggesting that 5hmC might act as a valuable epigenetic mark to reflect the disease status of myeloid neoplasms. Here, we report systematic genome-wide mapping of the DNA hydroxymethylomes in over 70 patients with myeloid neoplasms. Our integrative analysis leads to the identification of distinct 5hmC signatures that can sensitively discriminate patients from healthy individuals. At the molecular level, we unveiled dynamic 5hmC changes within key transcription factor (e.g., the CEBP family) binding motifs that are essential for hematopoiesis and myeloid lineage specification. 5hmC redistribution was found to alter the genome-wide binding of CEBP-α, thereby reprogramming transcriptional outputs to affect leukemia cell survival and stemness. Taken together, we provide a comprehensive 5hmC atlas representative of myeloid neoplasms, which sets the stage for future exploration on the epigenetic etiology of hematological malignancies. Mechanistically, our study further furnishes important insights into how abnormal 5hmC distribution in patients directly interrupts the binding of transcription factors to reshape transcriptional landscapes and aggravate leukemogenesis.
Mesenchymal stromal cell treatment improves outcomes in children with pneumonia post-hematopoietic stem cell transplantation: a retrospective cohort study
Authors: Qu Yuhua , Yang Xu , Zhang Xiaohong , Liu Shanshan , Liu Xiaoping , Liu Xiaodan , Luo Ailing , Cai Mansi , Yan Yaping , Xu Ling , Jiang Hua 
Published: June 2022

Abstract
Background
Hematopoietic stem cell transplantation (HSCT) is a standard therapy strategy for most malignant disorders in children. However, transplant-related pneumonia remains a major therapy challenge and mesenchymal stromal cells (MSCs) are rarely reported in HSCT-related pneumonia. The aim of our study was to assess the efficacy of MSC for HSCT-related pneumonia in children.

Methods
We retrospectively retrieved HSCT-related (severe and non-severe) pneumonia cases (aged < 18 years), which underwent MSC treatment (MSC group) or non-MSC treatment (non-MSC group) in Guangzhou Women and Children’s Medical Center, from December 2017 to December 2019. We investigated outcomes of the two different treatments among severe cases and non-severe cases, respectively. The primary endpoints were differences in overall cure rate and time to cure between MSC and non-MSC groups. The secondary endpoints were 180-day overall survival and cumulative cure rate.

Results
Finally, 31 severe pneumonia cases (16 in MSC group, 15 in non-MSC group) and 76 non-severe cases (31 in MSC group, 45 in non-MSC group) were enrolled in this study. Among severe pneumonia cases, overall cure rate in MSC group was significant higher than that in non-MSC group (12[75.0%] vs. 5[33.3%]; OR = 6.00, 95% CI [1.26–28.5]; p = 0.020); the time (days) to cure in MSC group was dramatically reduced compared with that in non-MSC group (36 [19–52] vs. 62 [42–81]; OR = 0.32, 95% CI [0.12–0.88]; p = 0.009); the 180-day overall survival in MSC group was better than that in non-MSC group (74.5% [45.4–89.6] vs. 33.3% [12.2–56.4]; p = 0.013). Among non-severe pneumonia cases, the time (days) to cure in MSC group was notably decreased compared with that in non-MSC group (28 [24–31] vs. 33 [26–39]; OR = 0.31, 95% CI [0.18–0.56]; p = 0.003). Compared with non-MSC group, MSC-treated patients achieved significant improvements of cumulative cure rate not only in severe pneumonia cases (p = 0.027), but also in non-severe cases (p < 0.001).

Conclusions
This study revealed that MSC treatment could contribute to improving outcomes in children with pneumonia post-HSCT, especially in severe cases. These findings suggest MSC treatment as a promising therapy for HSCT-related pneumonia in children.