bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling group heteroscedasticity in single-cell RNA-seq pseudo-bulk data
Authors: You Yue , Dong Xueyi , Wee Yong Kiat , Maxwell Mhairi J. , Alhamdoosh Monther , Smyth Gordon K. , Hickey Peter F. , Ritchie Matthew E. , Law Charity W. 
Published: May 2023

AbstractGroup heteroscedasticity is commonly observed in pseudo-bulk single-cell RNA-seq datasets and its presence can hamper the detection of differentially expressed genes. Since most bulk RNA-seq methods assume equal group variances, we introduce two new approaches that account for heteroscedastic groups, namely voomByGroup and voomWithQualityWeights using a blocked design (voomQWB). Compared to current gold-standard methods that do not account for group heteroscedasticity, we show results from simulations and various experiments that demonstrate the superior performance of voomByGroup and voomQWB in terms of error control and power when group variances in pseudo-bulk single-cell RNA-seq data are unequal.
DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis
Authors: Lee Seungchul , Choi Jaemyung , Park Jihwan , Hong Chang Pyo , Choi Daeseok , Han Soeun , Choi Kyuha , Roh Tae-Young , Hwang Daehee , Hwang Ildoo 
Published: May 2023

AbstractBackgroundPlants memorize previous pathogen attacks and are “primed” to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and gene bodies are reported to be frequently methylated. Demethylation of transposons can affect disease resistance by regulating the transcription of nearby genes during defense response, but the role of gene body methylation (GBM) in defense responses remains unclear.ResultsHere, we find that loss of the chromatin remodeler decrease in DNA methylation 1 (ddm1) synergistically enhances resistance to a biotrophic pathogen under mild chemical priming. DDM1 mediates gene body methylation at a subset of stress-responsive genes with distinct chromatin properties from conventional gene body methylated genes. Decreased gene body methylation in loss ofddm1mutant is associated with hyperactivation of these gene body methylated genes. Knockout of glyoxysomal protein kinase 1 (gpk1), a hypomethylated gene inddm1loss-of-function mutant, impairs priming of defense response to pathogen infection inArabidopsis. We also find that DDM1-mediated gene body methylation is prone to epigenetic variation among naturalArabidopsispopulations, andGPK1expression is hyperactivated in natural variants with demethylatedGPK1.ConclusionsBased on our collective results, we propose that DDM1-mediated GBM provides a possible regulatory axis for plants to modulate the inducibility of the immune response.
Totally laparoscopic associating simultaneous bile duct and portal vein ligation for planned hepatectomy for primary liver cancer: a case report
Authors: Jinghan Wang , Jianyang Ao , Wencong Ma , Chen Liu 
Published: May 2023

Abstract
Background
Some patients with liver cancer lose the chance to have surgical treatment due to insufficient future remnant liver. To address this problem, individual or occlusion of both the portal vein and the bile duct was used to achieve quick hypertrophy. This is the first study reported in which simultaneous ligation of the portal vein and the bile duct was applied as the first step of planned hepatectomy of primary liver cancer.

Case presentation
Here we report a case of a 38-year-old Asian male patient with hepatocellular carcinoma with tumor thrombus in the right anterior branch of the portal vein. Right hemihepatectomy can be curative, but patients face a high risk of liver failure because of the small volume of the remaining left liver lobe. Hence we developed a two-step liver resection strategy in which the patient underwent laparoscopic simultaneous bile duct and portal vein ligation of the right hepatic lobe prior to right hemihepatectomy under laparoscopy. Using this procedure, we achieved fast hypertrophy of the left liver lobe and successfully reversed the primary unresectability.

Conclusion
This case report demonstrates that simultaneous bile duct and portal vein ligation may be a feasible option for those patients with liver cancer who cannot get surgical treatment due to insufficient future remnant liver.
Global prevalence of self-harm during the COVID-19 pandemic: a systematic review and meta-analysis
Authors: Cheng Huan , Wang Di , Wang Lu , Zou Haiou , Qu Yanhua 
Published: May 2023

Abstract
Background
COVID-19 and its transmission mitigation measures have caused widespread mental health problems. Previous studies have suggested that psychological, economic, behavioral, and psychosocial problems associated with the COVID-19 pandemic may lead to a rise in self-harm. However, little is known about the prevalence of self-harm worldwide during COVID-19. Therefore, a quantitative synthesis is needed to reach an overall conclusion regarding the prevalence of self-harm during the pandemic.

Methods
By using permutations of COVID-19, self-harm or relevant search terms, we searched the following electronic databases from November 2019 to January 2022: Web of Science, PubMed, MEDLINE, Embase, PsycINFO, Cochrane Database of Systematic Reviews, China National Knowledge Infrastructure (CNKI), Wanfang Database and systematically reviewed the evidence according to MOOSE guidelines. We employed Cochran’s chi-squared test (Cochran’s Q), I2test and subgroup analysis to assess and address the heterogeneity. Sensitivity analysis was conducted by eliminating each included study individually and then combining the effects.

Results
Sixteen studies that met the inclusion and exclusion criteria were identified, with sample sizes ranging from 228 to 49,227. The methodological quality of the included studies was mostly at the medium level. By using a random effect model, the pooled prevalence of self-harm was 15.8% (95% CI 13.3–18.3). Based on subgroup analysis, the following characteristics of the included studies were more likely to have a higher prevalence of self-harm: studies conducted in Asia or prior to July 2020, cross-sectional studies, samples recruited in hospitals or schools, adolescents, females, the purpose of self-harm (NSSI), mental symptoms and restriction experiences.

Conclusions
We provided the first meta-analytic estimated prevalence of self-harm based on a large sample from different countries and populations. The prevalence of self-harm during COVID-19 was not encouraging and requires attention and intervention. Further high-quality and prospective research are needed in order to determine the prevalence of self-harm with greater accuracy because to the clear heterogeneity across the included studies. In addition, this study also provides new directions for future research, including the identification of high-risk groups for self-harm, the formulation and implementation of prevention and intervention programs, and the long-term impact of COVID-19 on self-harm.
Propofol inhibits myocardial injury induced by microvesicles derived from hypoxia-reoxygenated endothelial cells via lncCCT4-2/CCT4 signaling
Authors: Zhang Xiaojun , Wang Changsen , Xu Hao , Cai Shuyun , Liu Keyu , Li Simeng , Chen Linming , Shen Siman , Gu Xiaoxia , Tang Jing , Xia Zhengyuan , Hu Zhe , Ma Xiaotang , Zhang Liangqing 
Published: May 2023

Abstract
Background
Ischemia-reperfusion (IR) induces increased release of extracellular vesicles in the heart and exacerbates myocardial IR injury. We have previously shown that propofol attenuates hypoxia/reoxygenation (HR)-induced injury in human umbilical vein endothelial cells (HUVECs) and that microvesicles derived from propofol-treated HUVECs inhibit oxidative stress in endothelial cells. However, the role of microvesicles derived from propofol post-treated HUVECs ((HR + P)-EMVs) in IR-injured cardiomyocytes is unclear. In this study, we aimed to investigate the role of (HR + P)-EMVs in cardiac IR injury compared to microvesicles derived from hypoxic/reoxygenated HUVECs (HR-EMVs) and to elucidate the underlying mechanisms.

Methods
Hypoxia/reoxygenation (HR) models of HUVECs and AC16 cells and a mouse cardiac IR model were established. Microvesicles from HR-injured HUVECs, DMSO post-treated HUVECs and propofol post-treated HUVECs were extracted by ultra-high speed centrifugation, respectively. The above EMVs were co-cultured with HR-injured AC16 cells or injected intracardially into IR mice. Flow cytometry and immunofluorescence were used to determine the levels of oxidative stress and apoptosis in cardiomyocytes. Apoptosis related proteins were detected by Western blot. Echocardiography for cardiac function and Evans blue-TTC staining for myocardial infarct size. Expression of lncCCT4-2 in EMVs and AC16 cells was analysed by whole transcriptome sequencing of EMVs and RT-qPCR. The molecular mechanism of inhibition of myocardial injury by (HR + P)-EMVs was elucidated by lentiviral knockdown of lncCCT4-2, plasmid overexpression or knockdown of CCT4, and actinomycin D assay.

Results
In vitro and in vivo experiments confirmed that HR-EMVs exacerbated oxidative stress and apoptosis in IR-injured cardiomyocytes, leading to increased infarct size and worsened cardiac function. Notably, (HR + P)-EMVs induced significantly less oxidative stress and apoptosis in IR-injured cardiomyocytes compared to HR-EMVs. Mechanistically, RNA sequencing of EMVs and RT-qPCR showed that lncCCT4-2 was significantly upregulated in (HR + P)-EMVs and cardiomyocytes co-cultured with (HR + P)-EMVs. Reduction of lncCCT4-2 in (HR + P)-EMVs enhanced oxidative stress and apoptosis in IR-injured cardiomyocytes. Furthermore, the anti-apoptotic activity of lncCCT4-2 from (HR + P)-EMVs was achieved by increasing the stability of CCT4 mRNA and promoting the expression of CCT4 protein in cardiomyocytes.

Conclusions
Our study showed that (HR + P)-EMVs uptake by IR-injured cardiomyocytes upregulated lncCCT4-2 in cardiomyocytes and promoted CCT4 expression, thereby inhibiting HR-EMVs induced oxidative stress and apoptosis.
Financial decision-making behaviors of Ethnic Tibetan Households based on mental accounting
Authors: Zang DunGang , Paudel Krishna P. , Liu Yan , Liu Dan , He Yating 
Published: May 2023

AbstractEthnic Tibetans (ETs) typically reside in the remote plateaus of China and possess strong cultural and spiritual values. Their financial decision-making is influenced by economic and physical factors, unique culture, social norms, and psychological motivators. We conducted an in-person survey of 480 randomly selected ET households across four provinces in rural China. The survey data was analyzed using three different econometric models—probit, ordered probit, and ranked ordered logit—to examine the choice of borrowing from formal or informal credit sources, the number of sources borrowed from, and repayment priority. Our findings indicate that mental accounting plays a significant role in the financial decision-making process of ET households. Additionally, we find that the informal credit source is strongly associated with the financial decisions of ET households. The majority of loans from formal financial institutions are used to meet daily needs, as opposed to purchasing productive inputs. Our results also suggest that strong social relationships and religious beliefs prevent households from defaulting, and that loans from formal financial sources receive repayment priority. China would benefit from promoting inclusive finance and encouraging the adoption of improved agricultural practices to support the prosperity of ET and other minority communities.
Inflammatory biomarkers in overweight and obese Iranian women are associated with polyphenol intake
Authors: Shiraseb Farideh , Hosseininasab Dorsa , Noori Sahar , Ebrahimi Sara , Asjodi Foad , Ghaffarian-Ensaf Rasool , Carnauba Renata A. , Mirzaei Khadijeh 
Published: May 2023

AbstractBackgroundThe evidence shows that obesity is associated with chronic inflammation in obese subjects. Polyphenols are a complex group of plant secondary metabolites that may play a role in reducing the risk of obesity and obesity-related diseases. Given the scarcity of evidence on the association between inflammatory markers and dietary polyphenols intake in overweight/obese Iranian women, the current study aims to investigate this link.MethodThe present cross-sectional study was conducted on 391 overweight and obese Iranian women aged 18–48 years (body mass index (BMI) ≥ 25 kg/m2). A 147-item food frequency questionnaire (FFQ) was used to assess dietary intake, as well as anthropometric indices including weight, height, waist circumference (WC), and hip circumference (HC) and biochemistry parameters including triglyceride (TG), total cholesterol (Chole), low-density lipoprotein cholesterol (LDL-c), high-density lipoprotein cholesterol (HDL-c), serum glutamic pyruvic transaminase (SGPT), serum glutamic-oxaloacetic transaminase (SGOT), galactin-3 (Gal-3), monocyte chemoattractant protein-1 (MCP-1), transforming growth factor beta (TGF-β), interleukin-1 beta (IL_1β), plasminogen activator inhibitor-1 (PA-I), serum leptin concentrations, and C-reactive protein of high sensitivity (hs-CRP) in all participants. The inflammatory markers were assessed using the enzyme-linked immunosorbent assay (ELISA).ResultThe findings revealed a significant negative association between flavonoids intake and MCP-1 (P = 0.024), lignans intake and MCP-1 (P = 0.017), and Gal-3 (P = 0.032). These significant associations were observed between other polyphenols intake and IL_1β (P = 0.014). There was also a significant positive association between other polyphenol intake and TGF-β (P = 0.008) and between phenolic acid intake and TGF-β (P = 0.014).ConclusionOur findings suggest that a high polyphenol intake may help individuals to reduce systemic inflammation. Further large studies involving participants of different ages and genders are highly warranted.
Comparative study of postmortem computed tomography (PMCT) against traditional forensic autopsy findings in fatal road traffic accidents — a pilot analysis
Authors: K. Karthi Vignesh Raj , Khan Anam , Yadav Abhishek , Jana Manisha , Gupta Sudhir K. , A. Varun Chandran , D. Balaji , Simon Alex Eldo , Chauhan Aditya Pratap Singh 
Published: May 2023

Abstract

Background
Virtopsy is “a virtual alternative to the traditional autopsy, conducted with scanning and imaging technology,” mainly with the use of postmortem computed tomography (PMCT). It is still in the budding stage in India. The Department of Forensic Medicine and Toxicology, All India Institute of Medical Science, New Delhi, is the first center in the country that has established a facility for virtual autopsy. This facility aims to supplement the traditional autopsy findings and also to replace/curtail internal dissection in autopsy in the future, for which there has always been an aversion in relatives of the deceased due to emotional and religious reasons. The PMCT being a noninvasive, preservative, and objective procedure would be preferred by relatives than traditional autopsy. So, in this regard, this pilot study was conducted with the objective for comparison of PMCT vs traditional autopsy findings in fatal road traffic accidents to analyze its advantages and limitations in order to replace/augment the traditional autopsy with PMCT in the near future in road traffic accident cases.

Results
The authors evaluated 10 cases of road traffic accident victims. In each case, an autopsy was preceded by a PMCT examination using a 16-slice Multi-Slice CT spiral scanner. The fractures of the skull, facial bones, clavicle, scapula, and vertebra were located more precisely as compared to traditional autopsy. Interpretation of the ventricular hemorrhages of the brain is much better in PMCT. PMCT should be the investigation of choice for pneumothorax, pneumoperitoneum, pneumocephalus, and hemosiuns, while it needs further exploration to detect injuries of soft tissues as out of 14 injuries only 2 were identified by PMCT.

Conclusions
The procedure of whole-body PMCT followed by region-wise CT can be studied for a better PMCT acquisition to detect soft tissue injury findings more precisely. However, the PMCT in this study was able to conclude the cause of death in a more scientific way than the traditional autopsy.
Intelligent safety assessment method for demolition construction of closure segment of long-span continuous rigid frame bridges
Authors: Wang Qiusheng , Xian Jianping , Xiao Jun , Wang Xing 
Published: May 2023

AbstractIn order to clarify the risk of demolition construction of large-span continuous rigid structure bridge and put forward an intelligent safety assessment method to ensure the safety of demolition construction of the closure segment. Taking a concrete continuous rigid bridge as an example, this paper uses the combination of finite element analysis, theoretical calculation and actual measurement verification to study the influencing parameters and construction safety assessment methods of the long-span continuous rigid bridge in the demolition construction stage of the closure segment. The results show that the parameters that have a great influence on the stress state of box girder and pier during the demolition stage of the closure segment are mainly the self-weight of the structure, tendon prestress state and construction temperature difference. Through the influence envelope analysis of each parameter, it is clear that the ultimate failure mode caused by the most unfavorable parameter combination in the demolition stage of the closure segment is the crushing of the bottom plate of the box girder in the middle span, and the cracking of the piers on the side span at the top and the variable section. In order to further accurately evaluate the construction safety in the demolition stage of the closure segment, based on the long-term down-warping state inversion analysis of the box girder, the identification method of cross-section damage and prestress loss of the box girder and the calculation results of engineering examples are given. Finally, a safety assessment method of the most unfavorable section based on the principle of influence matrix is proposed. Through the analysis of an example, the safety of the closure segment demolition construction is clarified, and the correctness of the analysis is verified by intelligent monitoring means.
DMM Outstanding Paper Prize 2022 winners: Tamihiro Kamata, Jennifer K. Sargent and Mark A. Warner
Authors: Hackett Rachel 
Published: May 2023

Abstract
Disease Models & Mechanisms (DMM) is delighted to announce that the winners of the DMM Outstanding Paper Prize 2022 are Tamihiro Kamata for their Research Article (titled ‘ Statins mediate anti- and pro-tumourigenic functions by remodelling the tumour microenvironment’), and Jennifer K. Sargent and Mark A. Warner for their Resource Article (titled ‘ Genetically diverse mouse platform to xenograft cancer cells’). The two prizes of £1000 are awarded to the first author(s) of the papers that are judged by the journal's Editors to be the most outstanding contribution to the journal that year.
Wheel Running Exacerbates Joint Damage after Meniscal Injury in Mice, but Does Not Alter Gait or Physical Activity Levels
Authors: CHAN KIARA M. , GRIFFITH JACOB L. , PACHECO YAN CARLOS , ALLEN KYLE D. 
Published: May 2023

ABSTRACT

Purpose
Exercise and physical activity are recommended to reduce pain and improve joint function in patients with knee osteoarthritis (OA). However, exercise has dose effects, with excessive exercise accelerating OA development and sedentary behaviors also promoting OA development. Prior work evaluating exercise in preclinical models has typically used prescribed exercise regimens; however, in-cage voluntary wheel running creates opportunities to evaluate how OA progression affects self-selected physical activity levels. This study aimed to evaluate how voluntary wheel running after a surgically induced meniscal injury affects gait characteristics and joint remodeling in C57Bl/6 mice. We hypothesize that injured mice will reduce physical activity levels as OA develops after meniscal injury and will engage in wheel running to a lesser extent than the uninjured animals.

Methods
Seventy-two C57Bl/6 mice were divided into experimental groups based on sex, lifestyle (physically active vs sedentary), and surgery (meniscal injury or sham control). Voluntary wheel running data were continuously collected throughout the study, and gait data were collected at 3, 7, 11, and 15 wk after surgery. At end point, joints were processed for histology to assess cartilage damage.

Results
After meniscal injury, physically active mice showed more severe joint damage relative to sedentary mice. Nevertheless, injured mice engaged in voluntary wheel running at the same rates and distances as mice with sham surgery. In addition, physically active mice and sedentary mice both developed a limp as meniscal injury progressed, yet exercise did not further exacerbate gait changes in the physically active mice, despite worsened joint damage.

Conclusions
Taken together, these data indicate a discordance between structural joint damage and joint function. Although wheel running after meniscal injury did worsen OA-related joint damage, physical activity did not necessarily inhibit or worsen OA-related joint dysfunction or pain in mice.
A 2-Year Randomized Controlled Trial on Creatine Supplementation during Exercise for Postmenopausal Bone Health
Authors: Chilibeck Philip D. , Candow Darren G. , Gordon Julianne J. , Duff Whitney R.D. , Mason Riley , Shaw Keely , Taylor-Gjevre Regina , Nair Bindu , Zello Gordon A. 
Published: May 2023

ABSTRACT

Purpose
Our purpose was to examine the effects of 2 years of creatine monohydrate supplementation and exercise on bone health in postmenopausal women.

Methods
237 postmenopausal women (mean age 59y) were randomized to receive creatine (0.14 g·kg -1·day -1) or placebo during a resistance training (3d/wk) and walking (6d/wk) program for 2 years. Our primary outcome was femoral neck bone mineral density (BMD), with lumbar spine BMD, and proximal femur geometric properties as secondary outcomes.

Results
Compared to placebo, creatine supplementation had no effect on BMD of the femoral neck (creatine: 0.725 ± 0.110 to 0.712 ± 0.100; placebo: 0.721 ± 0.102 to 0.706 ± 0.097 g/cm2), total hip (creatine: 0.879 ± 0.118 to 0.872 ± 0.114; placebo: 0.881 ± 0.111 to 0.873 ± 0.109 g/cm2), or lumbar spine (creatine: 0.932 ± 0.133 to 0.925 ± 0.131; placebo: 0.923 ± 0.145 to 0.915 ± 0.143 g/cm2). Creatine significantly maintained section modulus (1.35 ± 0.29 to 1.34 ± 0.26 vs. placebo 1.34 ± 0.25 to 1.28 ± 0.23 cm3, p = 0.0011), predictive of bone bending strength, and buckling ratio (10.8 ± 2.6 to 11.1 ± 2.2 vs. placebo 11.0 ± 2.6 to 11.6 ± 2.7; p = 0.011), predictive of reduced cortical bending under compressive loads, at the narrow part of the femoral neck. Creatine reduced walking time over 80 meters (48.6 ± 5.6 to 47.1 ± 5.4 vs. placebo 48.3 ± 4.5 to 48.2 ± 4.9 s; p = 0.0008), but had no effect on muscular strength (i.e., 1RM) during the bench press (32.1 ± 12.7 to 42.6 ± 14.1 vs. placebo 30.6 ± 10.9 to 41.4 ± 14 kg) and hack squat (57.6 ± 21.6 to 84.4 ± 28.1 vs. placebo 56.6 ± 24.0 to 82.7 ± 25.0 kg). In sub-analysis of valid completers, creatine increased lean tissue mass compared to placebo (40.8 ± 5.7 to 43.1 ± 5.9 vs. placebo 40.4 ± 5.3 to 42.0 ± 5.2 kg; p = 0.046).

Conclusions
Two years of creatine supplementation and exercise in postmenopausal women had no effect on bone mineral density, yet improved some bone geometric properties at the proximal femur.