bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microplate bioassay to examine the effects of grapevine-isolated stilbenoids on survival of root knot nematodes
Authors: Wallis Christopher M. 
Published: June 2022

Abstract
Objectives
Root knot nematodes can be major pests in vineyards and cause significant yield losses over time. Control involves the use of different resistant grapevine rootstocks, but it remains unclear the mechanisms that such rootstocks possess to limit root knot nematode infections. Defense-associated compounds called stilbenoids, a type of phenolic compound, are present in relatively substantial amounts in grapevine root tissues. Therefore, experiments were performed to assess how different stilbenoid compounds impact nematode survival in microplate assays. Data generated were part of a larger effort to understand potential mechanisms that resistant grapevine rootstocks have to limit root knot infections. Data description: The percentage of surviving root knot nematodes was assessed 1, 3, and 5 days after J2 juveniles were placed into microplate wells amended with 0, 1.25, 2.5, 5, or 10 ppm of piceid, ε-viniferin, a resveratrol trimer putatively identified as miyabenol C, or a putative mixture of resveratrol tetramers putatively identified as vitisin B and hopeaphenol. Both ε-viniferin and the resveratrol tetramers significantly reduced root knot survival at the higher concentrations. These data provide insight about one potential mechanism that grapevine rootstocks might possess to combat nematodes.
Reduced CSF orexin levels in rats and patients with systemic inflammation: a preliminary study
Authors: Ogawa Yasuhiro , Shimojo Nobutake , Ishii Akiko , Tamaoka Akira , Kawano Satoru , Inoue Yoshiaki 
Published: June 2022

Abstract
Objective
Sepsis is a lethal condition characterized by systemic inflammation and multiple organ failure; this condition was initially defined as systemic inflammatory response syndrome (SIRS) due to infection. We previously reported that the hypothalamic neuropeptide orexin improved survival in a murine model of sepsis by mainly acting in the medullary raphe nucleus through orexin type-2 receptors. We hypothesized that orexin treatment enhances recovery from sepsis by reversing the reduction in orexin levels in the cerebrospinal fluid (CSF). We recently reported a case in which CSF orexin levels were reduced in a patient with sepsis. Herein, we attempted to further investigate CSF orexin levels in rats and patients with systemic inflammation. This patient study was a single-center, retrospective observational study.

Results
CSF orexin levels were low in rats with lipopolysaccharide-induced systemic inflammation. We enrolled 14 patients with meningitis/encephalitis. Six patients were diagnosed with SIRS, of whom 5 patients had infections (“sepsis” by the previous definition). CSF orexin levels were low in SIRS patients. The results support the hypothesis that orexin treatment enhances recovery from sepsis by reversing the reduction in CSF orexin levels.
Mitochondrial DNA methylation profiling of the human prefrontal cortex and nucleus accumbens: correlations with aging and drug use
Authors: Huang Chia-Hung , Chang Man-Chen , Lai Yung-Chun , Lin Chun-Yen , Hsu Cho-Hsien , Tseng Bo-Yuan , Hsiao Chuhsing Kate , Lu Tzu-Pin , Yu Sung-Liang , Hsieh Sung-Tsang , Chen Wei J. 
Published: June 2022

Abstract
Background
Despite the brain’s high demand for energy, research on its epigenetics focuses on nuclear methylation, and much of the mitochondrial DNA methylation remains seldom investigated. With a focus on the nucleus accumbens (NAcc) and the prefrontal cortex (PFC), we aimed to identify the mitochondrial methylation signatures for (1) distinguishing the two brain areas, (2) correlating with aging, and (3) reflecting the influence of illicit drugs on the brain.

Result
We collected the brain tissue in the NAcc and the PFC from the deceased individuals without (n = 39) and with (n = 14) drug use and used whole-genome bisulfite sequencing to cover cytosine sites in the mitochondrial genome. We first detected differential methylations between the NAcc and the PFC in the nonusers group (P = 3.89 × 10–9). These function-related methylation differences diminished in the drug use group due to the selective alteration in the NAcc. Then, we found the correlation between the methylation levels and the chronological ages in the nonusers group (R2 = 0.34 in the NAcc and 0.37 in the PFC). The epigenetic clocks in illicit drug users, especially in the ketamine users, were accelerated in both brain regions by comparison with the nonusers. Finally, we summarized the effect of the illicit drugs on the methylation, which could significantly differentiate the drug users from the nonusers (AUC = 0.88 in the NAcc, AUC = 0.94 in the PFC).

Conclusion
The mitochondrial methylations were different between different brain areas, generally accumulated with aging, and sensitive to the effects of illicit drugs. We believed this is the first report to elucidate comprehensively the importance of mitochondrial DNA methylation in human brain.
Safety, efficacy and biomarkers analysis of mesenchymal stromal cells therapy in ARDS: a systematic review and meta-analysis based on phase I and II RCTs
Authors: Wang Jianbao , Luo Fenbin , Suo Ye , Zheng Yuxin , Chen Kaikai , You Deyuan , Liu Yuqi 
Published: June 2022

Abstract
Background
Mesenchymal stromal cells (MSCs) therapy for acute respiratory distress syndrome (ARDS) is an emerging treatment, but most of the current trials of MSCs stay in the animal experimental stage, and the safety and efficacy of MSCs in clinical application are not clear. We aimed to analyze the safety, efficacy and biomarkers of mesenchymal stromal cells in the treatment of ARDS.

Methods
For this systematic review and meta-analysis, we searched PubMed, Embase, Cochrane Central Register of Controlled Trials, Web of science, CNKI, VIP and Wan Fang data, studies published between database inception and Mar 17, 2022. All randomized controlled trials (RCT) of stem cell interventions for ARDS were included, without language or date restrictions. We did separate meta-analyses for mortality, subjects with adverse events (AEs) and subjects with serious adverse events (SAEs). Since the trials data are dichotomous outcomes, the odds ratio (OR) is adopted for meta-analysis. The quality of the evidence was assessed with the Cochrane risk of bias tool.

Findings
In total, 5 trials involving 171 patients with ARDS were included in this meta-analysis. A total of 99 individuals were randomly assigned to receive MSCs treatment, and 72 were randomly assigned to receive placebo treatment. Treatment with MSCs appeared to increase the occurrence of adverse events, but this result was not statistically significant (OR, 1.58; 95%CI, 0.64–3.91; P = 0.32). The occurrence of serious adverse events was lower in the MSCs group than in the placebo group (OR, 0.57; 95%CI, 0.14–2.32; P = 0.43); there seems to be no significant difference between the two groups in terms of 28 days mortality (OR, 0.93; 95%CI, 0.45–1.89); oxygenation index and biomarkers showed a tendency to improve in treatment, but there was a lack of more statistically significant clinical evidence to support them.

Interpretation
Based on the current clinical trials, MSCs intervention has some safety for ARDS patients, but its effectiveness and predictive value of airspace biomarkers need to be determined by more large-scale, standard randomized controlled trials.
Sympathetic-mediated blunting of forearm vasodilation is similar between young men and women
Authors: Gentilin Alessandro , Moghetti Paolo , Cevese Antonio , Schena Federico , Tarperi Cantor 
Published: June 2022

Abstract
Background
The in-vivo regulation of vascular conductance (VC) is a continuous balance between endothelial vasodilation and sympathetic vasoconstriction. Although women may report blunted sympathetic vasoconstriction along with higher endothelial vasodilation than men, it is currently unknown whether the interaction between vasoconstriction and vasodilation leads to different regulation of VC between sexes. This study assessed sex differences in sympathetic-mediated blunting of endothelial vasodilation after a brief period of ischemia and whether any restriction of vasodilation blunts tissue blood flow (BF) and re-oxygenation.

Methods
13 young women and 12 young men underwent two 5-min forearm circulatory occlusions followed by reperfusion, one in basal conditions and the other during cold pressor test-induced sympathetic activation (SYMP). Brachial artery diameter and BF, mean arterial pressure, total peripheral resistance (TPR), and thenar eminence oxygenation were collected. Percent changes normalized to baseline values of forearm VC, brachial artery BF and flow-mediated dilation (FMD), TPR, and hand oxygenation after circulatory reperfusion were calculated.

Results
TPR increased during SYMP in men (p = 0.019) but not in women (p = 0.967). Women showed a greater brachial artery FMD than men (p = 0.004) at rest, but sex differences disappeared after normalization to shear rate and baseline diameter (p > 0.11). The percent increases from baseline of peak and average forearm VC after circulatory reperfusion did not differ between sexes in basal conditions (p > 0.98) or during SYMP (p > 0.97), and were restrained by SYMP similarly in both sexes (p < 0.003) without impairing the hand re-oxygenation (p > 0.08) or average hyperemic response (p > 0.09).

Conclusions
Although women may report blunted sympathetic vasoconstriction than men when assessed separately, the similar sympathetic-mediated restriction of vasodilation suggests a similar dynamic regulation of VC between sexes. SYMP-mediated restrictions of the normal forearm vasodilation do not impair the average hyperemic response and hand re-oxygenation in both sexes.
Clinical significance of pancreatic calcifications: a 15-year single-center observational study
Authors: Wang Wei , Chai Li , Zhu Naiyi , Wang Qingrou , Zhou Yiran , Chai Weimin 
Published: June 2022

Abstract
Objectives
Pancreatic calcifications (PC) are considered specific for chronic pancreatitis (CP), but PC may also be present in non-CP diseases. The aims are to understand the pattern of calcifications in different diseases and to determine they were related to malignant diseases.

Methods
A retrospective study was performed including patients with PC or CP undergoing surgery in the Department of General Surgery of Ruijin Hospital from January 2003 to June 2018.

Results
PC were observed in 168 (4.5%) of the 3755 patients with pancreatic lesions treated during the study period. The majority of patients with PC had three kinds of CP (73.2%) while 26.8% had other five kinds of non-CP diseases. In patients with non-CP diseases, the incidence of PC in malignant intraductal papillary mucinous neoplasm (IPMN) was significantly higher than benign IPMN (8.3% vs. 0.7%, p = 0.004). In patients of CP with pancreatic mass (n = 81), PC (Odds ratio = 28.6, p = 0.000), advanced age (> 55 years) and parenchymal atrophy were independent predictors for malignancy. In patients of CP without pancreatic mass (n = 110), there were 82 cases (74.5%) with PC and 5 cases (4.5%) with pancreatic ductal adenocarcinoma. The regression model of risk factors was not successful.

Conclusions
The disease spectrum with PC was very diverse. PC may be related to malignant IPMN in non-CP diseases and is related to malignancy in the patients of CP with pancreatic mass and indications for resection.
Burden and factors associated with schistosomiasis and soil-transmitted helminth infections among school-age children in Huambo, Uige and Zaire provinces, Angola
Authors: Bartlett Adam W. , Sousa-Figueiredo Jose C. , van Goor Roelofje C. , Monaghan Paul , Lancaster Warren , Mugizi Rukaaka , Mendes Elsa P. , Nery Susana Vaz , Lopes Sergio 
Published: June 2022

AbstractBackgroundSchistosomiasis and soil-transmitted helminths (STHs) contribute high disease burdens amongst the neglected tropical diseases (NTDs) and are public health problems in Angola. This study reports the prevalence, intensity and risk factors for schistosomiasis and STH infection in Huambo, Uige and Zaire provinces, Angola, to inform a school-based preventive chemotherapy program.MethodsA two-stage cluster design was used to select schools and schoolchildren to participate in parasitological and water, sanitation and hygiene (WASH) surveys across Huambo, Uige, and Zaire provinces. Point-of-care circulating cathodic antigen and urinalysis rapid diagnostic tests (RDTs) were used to determine the prevalence ofSchistosoma mansoniandS. haematobium, respectively. Kato-Katz was used to identify and quantify STH species and quantify and compare with RDTs forS. mansoni. Urine filtration was used to quantify and compare with RDTs forS. haematobium. Descriptive statistics were used for prevalence and infection intensity of schistosomiasis and STH infection. Performance of RDTs was assessed through specificity and Cohen’s Kappa agreement with microscopy. A multivariate regression analysis was used to determine demographic and WASH factors associated with schistosomiasis and STH infection.ResultsA total 575 schools and 17,093 schoolchildren participated in the schistosomiasis survey, of which 121 schools and 3649 schoolchildren participated in the STH survey. Overall prevalence ofS. mansoniwas 21.2% (municipality range 0.9–74.8%) andS. haematobium13.6% (range 0–31.2%), with an overall prevalence of schistosomiasis of 31.4% (range 5.9–77.3%). Overall prevalence ofAscaris lumbricoideswas 25.1% (range 0–89.7%), hookworm 5.2% (range 0–42.6%), andTrichuris trichiura3.6% (range 0–24.2%), with an overall prevalence of STH infection of 29.5% (range 0.8–89.7%). Ecological zone and ethnicity were factors associated with schistosomiasis and STH infection, with older age and female sex additional risk factors forS. haematobium.ConclusionsMost municipalities met World Health Organization defined prevalence thresholds for a schistosomiasis preventive chemotherapy program. A STH preventive chemotherapy program is indicated for nearly all municipalities in Uige and select municipalities in Huambo and Zaire. The association between ecological zone and ethnicity with schistosomiasis and STH infection necessitates further evaluation of home and school environmental, sociodemographic and behavioural factors to inform targeted control strategies to complement preventive chemotherapy programs.
The crustal stress field of Germany: a refined prediction
Authors: Ahlers Steffen , Röckel Luisa , Hergert Tobias , Reiter Karsten , Heidbach Oliver , Henk Andreas , Müller Birgit , Morawietz Sophia , Scheck-Wenderoth Magdalena , Anikiev Denis 
Published: June 2022

AbstractInformation about the absolute stress state in the upper crust plays a crucial role in the planning and execution of, e.g., directional drilling, stimulation and exploitation of geothermal and hydrocarbon reservoirs. Since many of these applications are related to sediments, we present a refined geomechanical–numerical model for Germany with focus on sedimentary basins, able to predict the complete 3D stress tensor. The lateral resolution of the model is 2.5 km, the vertical resolution about 250 m. Our model contains 22 units with focus on the sedimentary layers parameterized with individual rock properties. The model results show an overall good fit with magnitude data of the minimum (Shmin) and maximum horizontal stress (SHmax) that are used for the model calibration. The mean of the absolute stress differences between these calibration data and the model results is 4.6 MPa for Shmin and 6.4 MPa for SHmax. In addition, our predicted stress field shows good agreement to several supplementary in-situ data from the North German Basin, the Upper Rhine Graben and the Molasse Basin.
Machine learning model for malaria risk prediction based on mutation location of large-scale genetic variation data
Authors: Tai Kah Yee , Dhaliwal Jasbir 
Published: June 2022

AbstractIn recent malaria research, the complexity of the disease has been explored using machine learning models via blood smear images, environmental, and even RNA-Seq data. However, a machine learning model based on genetic variation data is still required to fully explore individual malaria risk. Furthermore, many Genome-Wide Associations Studies (GWAS) have associated specific genetic markers, i.e., single nucleotide polymorphisms (SNPs), with malaria. Thus, the present study improves the current state-of-the-art genetic risk score by incorporating SNPs mutation location on large-scale genetic variation data obtained from GWAS. Nevertheless, it becomes computationally expensive for hyperparameter optimization on large-scale datasets. Therefore, this study proposes a machine learning model that incorporates mutation location as well as a Genetic Algorithm (GA) to optimize hyperparameters. Besides that, a deep learning model is also proposed to predict individual malaria risk as an alternative approach. The analysis is performed on the Malaria Genomic Epidemiology Network (MalariaGEN) dataset comprising 20,817 individuals from 11 populations. The findings of this study demonstrated that the proposed GA could overcome the curse of dimensionality and improve resource efficiency compared to commonly used methods. In addition, incorporating the mutation location significantly improved the machine learning models in predicting the individual malaria risk; a Mean Absolute Error (MAE) score of 8.00E−06. Moreover, the deep learning model obtained almost similar MAE scores to the machine learning models, indicating an alternative approach. Thus, this study provides relevant knowledge of genetic and technical deliberations that can improve the state-of-the-art methods for predicting individual malaria risk.
specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data
Authors: Darcy John L. , Amend Anthony S. , Swift Sean O. I. , Sommers Pacifica S. , Lozupone Catherine A. 
Published: June 2022

AbstractBackgroundUnderstanding the factors that influence microbes’ environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, “specificity” is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao’s (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3 ) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.ResultsWe present our R packagespecificityfor performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.Conclusionsspecificityis well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers usingspecificity’s companion package,specificity.shiny.
Amino acid availability enhanced through glucose coadministration of amino acid supplementation during hemodiafiltration: two case reports
Authors: Fujiwara Masako , Ando Itiro , Shishido You , Imai Yutaka , Terawaki Hiroyuki 
Published: June 2022

Abstract
Background
Intravenous administration of amino acid (AA) formulation (IVAA) as intradialytic parenteral nutrition is widely used for malnourished patients with end-stage kidney disease (ESKD) treated with hemodialysis (HD) or hemodiafiltration (HDF). Although various therapy recipes such as AA compositions or simultaneous administration of glucose and/or lipids have been attempted, the specific effects of each recipe on AA behaviors and metabolic consequences have not been well investigated. To clarify the effect of simultaneous glucose administration with IVAA, we investigated the behavior of AAs, insulin as a metabolic hormone, and energy-related metabolites during an HDF session in two patients.

Case presentation
We aimed to determine the effect of IVAA with or without simultaneous glucose administration. The plasma levels of AAs, branched-chain AAs (leucine, isoleucine, and valine), major nonessential AAs (alanine and glutamine with glutamate), insulin, glucose, and ketone bodies were measured before HDF and at the second hour (prior to the meal in the HDF session). Lost AAs in the spent dialysate were also measured for the first two hours during the HDF session.

Conclusion
In the absence of glucose administration, plasma AA levels and the loss of AAs in the dialysate increased owing to IVAA, with the increase in plasma levels in ketone bodies occurring because of scarce secretion of plasma insulin. In the presence of glucose administration, plasma levels and the loss of AA decreased even when the same amount of AAs was injected, possibly because of the profound secretion of insulin with a decrease in ketone bodies. The present findings suggest that the metabolic effects of simultaneous glucose administration on IVAAs enhanced AA uptake into the body during HDF sessions, which might increase the effectiveness of IVAAs.