bluuebunny/crossref_metadata_2025_split huggingface dataset:
Massive expansion of P-selectin genes in two Venerida species, Sinonovacula constricta and Mercenaria mercenaria: evidence from comparative genomics of Bivalvia
Authors: Xu Yuanfeng , Dong Xumeng , Ma Shuonan , Luo Cheng , Xu Jilin 
Published: September 2022

Abstract
Background
P-selectin is a molecule participating in the inflammatory response through mediating cellular adhesion and essential for wound repair. However, studies regarding P-selectin in Bivalvia are rare. This study identified 90 P-selectin genes among nine bivalve genomes and classified them into 4 subfamilies according to phylogenetic analysis.

Results
Notable P-selectin gene expansion was observed in two Venerida species, Sinonovacula constricta and Mercenaria mercenaria. The synteny analysis revealed that P-selectin gene expansion was mostly caused by tandem duplication. In addition, the expression profiles of P-selectin genes in S. constricta showed that many P-selectins were specifically highly expressed in the gills, and the P-selectin expression patterns changed dramatically under low salt stress and ammonia nitrogen stress.

Conclusions
The massive expansion of P-selectins may facilitate the tolerance to environmental stresses. This study sheds light on the characterizations and expression profiles of P-selectin genes in Bivalvia and provides an integrated framework for further investigation of the role of P-selectins in the environmental tolerance of bivalves.
A robust and transformation-free joint model with matching and regularization for metagenomic trajectory and disease onset
Authors: Li Qian , Vehik Kendra , Li Cai , Triplett Eric , Roesch Luiz , Hu Yi-Juan , Krischer Jeffrey 
Published: September 2022

Abstract
Background
To identify operational taxonomy units (OTUs) signaling disease onset in an observational study, a powerful strategy was selecting participants by matched sets and profiling temporal metagenomes, followed by trajectory analysis. Existing trajectory analyses modeled individual OTU or microbial community without adjusting for the within-community correlation and matched-set-specific latent factors.

Results
We proposed a joint model with matching and regularization (JMR) to detect OTU-specific trajectory predictive of host disease status. The between- and within-matched-sets heterogeneity in OTU relative abundance and disease risk were modeled by nested random effects. The inherent negative correlation in microbiota composition was adjusted by incorporating and regularizing the top-correlated taxa as longitudinal covariate, pre-selected by Bray-Curtis distance and elastic net regression. We designed a simulation pipeline to generate true biomarkers for disease onset and the pseudo biomarkers caused by compositionality. We demonstrated that JMR effectively controlled the false discovery and pseudo biomarkers in a simulation study generating temporal high-dimensional metagenomic counts with random intercept or slope. Application of the competing methods in the simulated data and the TEDDY cohort showed that JMR outperformed the other methods and identified important taxa in infants’ fecal samples with dynamics preceding host disease status.

Conclusion
Our method JMR is a robust framework that models taxon-specific trajectory and host disease status for matched participants without transformation of relative abundance, improving the power of detecting disease-associated microbial features in certain scenarios. JMR is available in R package mtradeR at https://github.com/qianli10000/mtradeR.
Interleukin-22 protects from endotoxemia by inducing suppressive F4/80+Ly6GhiLy6Chi cells population
Authors: Yu Chang , Ling Qihua , Jiao Junzhe , Liu Juhong , Huang Zhihua , Wang Fang , Sun Xuehua , Kong Xiaoni 
Published: September 2022

Abstract
Background
Excessive inflammatory response is the primary cause of early death in patients with endotoxemia. Interleukin 22 (IL-22) has been shown to play critical roles in the modulation of infectious diseases, but its function in regulating immune responses during endotoxemia remains unclear.

Methods
Lipopolysaccharide (LPS) was used to induce endotoxemia mouse model with or without a recombinant fusion protein containing human IL-22 (F-652). IL-6, TNF-α, IL-1β, and MCP-1 were measured by ELISA assays. The type of macrophage was assessed by flow cytometry. Real-time PCR was used to detect the expression of S100A9.

Results
We found that F-652 injection significantly improved the survival rates and reduced pro-inflammatory cytokines (IL-6, TNF-a, IL-1β, MCP-1) in LPS-induced endotoxemia mice. However, the mice injected with F-652 had a higher number of infiltrated immune cells after LPS treatment, suggesting an impaired immune response. Flow cytometry analysis showed a higher number of F4/80+Ly6GhiLy6Chi cells that highly expressed M2-like macrophage markers (Ym1, Arg, CCL17) in the peritoneal cavity of the F-652-treated endotoxemia mice. Further investigation found that these suppressive M2 macrophages might be induced by F-652 since the F-652 treatment could increase S100A9 in vitro.

Conclusions
Our study suggests that IL-22 has a protective role against endotoxemia by inducing the development of immunosuppressive cells through S100A9.
Comparisons of electrophysiological characteristics, pacing parameters and mid- to long-term effects in right ventricular septal pacing, right ventricular apical pacing and left bundle branch area pacing
Authors: Li Wenhua , Ding Yu , Gong Chao , Zhou Genqing , Lu Xiaofeng , Wei Yong , Peng Shi , Cai Lidong , Yuan Tianyou , Li Fangfang , Liu Shaowen , Chen Songwen 
Published: September 2022

Abstract
Background
As a near-physiological pacing innovation, left bundle branch area pacing (LBBAP) has drawn much attention recently. This study was aimed to investigate the electrophysiological characteristics, unipolar/bipolar pacing parameters and mid- to long-term effects and safety of three different pacing methods and identify possible predictors of adverse left ventricular remodeling.

Methods
Ninety-two patients were divided into the LBBAP group, right ventricular septal pacing (RVSP) group and right ventricular apical pacing (RVAP) group. Baseline information, electrophysiological, pacing and echocardiographic parameters were collected.

Results
The three pacing methods were performed with a similar high success rate. The paced QRSd was significantly different among the LBBAP, RVSP and RVAP groups (105.93 ± 15.85 ms vs. 143.63 ± 14.71 ms vs. 155.39 ± 14.17 ms, p < 0.01). The stimulus to left ventricular activation time (Sti-LVAT) was the shortest in the LBBAP group, followed by the RVSP and RVAP groups (72.80 ± 12.07 ms vs. 86.29 ± 8.71 ms vs. 94.14 ± 10.14 ms, p < 0.001). LBBAP had a significantly lower tip impedance during the procedure and 3-month follow up as compared to RVSP and RVAP (p < 0.001). Higher bipolar captured thresholds were observed in LBBAP during the procedure (p < 0.001). Compared to the baseline values, there was a greater reduction in left ventricular end-diastolic dimension (LVEDD) in the LBBAP group (p = 0.046) and a significant enlargement in LVEDD in the RVAP group (p = 0.008). Multiple regression analysis revealed that the Sti-LVAT was a significant predictor of LVEDD at 12 months post-procedure. At the 24-h post-procedure, significant elevations were observed in the cTnI levels in LBBAP (p < 0.001) and RVSP (p < 0.05). More transient RBB injury was observed in LBBAP. But no significant difference was found in cardiac composite endpoints among three groups (p > 0.05).

Conclusions
LBBAP demonstrated a stable captured threshold, a low tip impedance and a high R-wave amplitude during the 12-month follow-up. Left ventricular remodeling was improved at 12 months post-procedure through LBBAP. The Sti-LVAT was a significant predictor of left ventricular remodeling. LBBAP demonstrated its feasibility, effectiveness, safety and some beneficial electrophysiological characteristics during this mid- to long-term follow-up, which should be confirmed by further studies.
Improving the accuracy of self-reported height and weight in surveys: an experimental study
Authors: Van Dyke Nina , Drinkwater Eric J. , Rachele Jerome N. 
Published: September 2022

Abstract
Background
Many studies rely on self-reported height and weight. While a substantial body of literature exists on misreporting of height and weight, little exists on improving accuracy. The aim of this study was to determine, using an experimental design and a comparative approach, whether the accuracy of self-reported height and weight data can be increased by improving how these questions are asked in surveys, drawing on the relevant evidence from the psychology and survey research literatures.

Methods
Two surveys from two separate studies were used to test our hypotheses (Science Survey, n = 1,200; Eating Behaviours Survey, n = 200). Participants were randomly assigned to one of six conditions, four of which were designed to improve the accuracy of the self-reported height and weight data (“preamble”), and two of which served as the control conditions ( “no preamble”). Four hypotheses were tested: (H1) survey participants read a preamble prior to being asked their height and weight will report lower heights and higher weights than those not read a preamble; (H2) the impact of question-wording (i.e., preamble vs. no preamble) on self-reported weight will be greater for participants with higher BMIs; (H3) the impact of question-wording on height will be greater for older participants; (H4) either version of the weight question – standard or “weight-specific”—may result in participants reporting more accurate self-reported weight. One-way MANOVA was conducted to test Hypothesis 1; two-way analysis of variance were conducted to test Hypothesis 2; moderation analysis was used to test Hypothesis 3; independent samples t-test was conducted to test Hypothesis 4.

Results
None of the hypotheses was supported.

Conclusions
This paper provides an important starting point from which to inform further work exploring how question wording can improve self-reported measurement of height and weight. Future research should explore how question preambles may or may not operationalise hypothesised underlying mechanisms, the sensitivity or intrusiveness of height and weight questions, individual beliefs about one’s height and weight, and survey context.
A logical analysis of null hypothesis significance testing using popular terminology
Authors: McNulty Richard 
Published: September 2022

Abstract
Background
Null Hypothesis Significance Testing (NHST) has been well criticised over the years yet remains a pillar of statistical inference. Although NHST is well described in terms of statistical models, most textbooks for non-statisticians present the null and alternative hypotheses (H0 and HA, respectively) in terms of differences between groups such as (μ1 = μ2) and (μ1 ≠ μ2) and HA is often stated to be the research hypothesis. Here we use propositional calculus to analyse the internal logic of NHST when couched in this popular terminology. The testable H0 is determined by analysing the scope and limits of the P-value and the test statistic’s probability distribution curve.

Results
We propose a minimum axiom set NHST in which it is taken as axiomatic that H0 is rejected if P-value< α. Using the common scenario of the comparison of the means of two sample groups as an example, the testable H0 is {(μ1 = μ2) and [($$\overline{x}$$

x
¯

1 ≠ $$\overline{x}$$

x
¯

2) due to chance alone]}. The H0 and HA pair should be exhaustive to avoid false dichotomies. This entails that HA is ¬{(μ1 = μ2) and [($$\overline{x}$$

x
¯

1 ≠ $$\overline{x}$$

x
¯

2) due to chance alone]}, rather than the research hypothesis (HT). To see the relationship between HA and HT, HA can be rewritten as the disjunction HA: ({(μ1 = μ2) ∧ [($$\overline{x}$$

x
¯

1 ≠ $$\overline{x}$$

x
¯

2) not due to chance alone]} ∨ {(μ1 ≠ μ2) ∧ [$$(\overline{x}$$

(

x
¯

1 ≠ $$\overline{x}$$

x
¯

2) not due to (μ1 ≠ μ2) alone]} ∨ {(μ1 ≠ μ2) ∧ [($$\overline{\boldsymbol{x}}$$

x

¯

1≠$$\overline{\boldsymbol{x}}$$

x

¯

2) due to (μ1 ≠ μ2) alone]}). This reveals that HT (the last disjunct in bold) is just one possibility within HA. It is only by adding premises to NHST that HT or other conclusions can be reached.

Conclusions
Using this popular terminology for NHST, analysis shows that the definitions of H0 and HA differ from those found in textbooks. In this framework, achieving a statistically significant result only justifies the broad conclusion that the results are not due to chance alone, not that the research hypothesis is true. More transparency is needed concerning the premises added to NHST to rig particular conclusions such as HT. There are also ramifications for the interpretation of Type I and II errors, as well as power, which do not specifically refer to HT as claimed by texts.
Does potential antibody-dependent enhancement occur during SARS-CoV-2 infection after natural infection or vaccination? A meta-analysis
Authors: Gan Lin , Chen Yan , Tan Jinlin , Wang Xuezhi , Zhang Dingmei 
Published: September 2022

AbstractCoronavirus disease 2019 (COVID-19) continues to constitute an international public health emergency. Vaccination is a prospective approach to control this pandemic. However, apprehension about the safety of vaccines is a major obstacle to vaccination. Amongst health professionals, one evident concern is the risk of antibody-dependent enhancement (ADE), which may increase the severity of COVID-19. To explore whether ADE occurs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and increase confidence in the safety of vaccination, we conducted a meta-analysis to investigate the relationship between post-immune infection and disease severity from a population perspective. Databases, including PubMed, EMBASE, Chinese National Knowledge Infrastructure, SinoMed, Scopus, Science Direct, and Cochrane Library, were searched for articles on SARS-CoV-2 reinfection published until 25 October 2021. The papers were reviewed for methodological quality, and a random effects model was used to analyse the results. Heterogeneity was assessed using the I2 statistic. Publication bias was evaluated using a funnel plot and Egger’s test. Eleven studies were included in the final meta-analysis. The pooled results indicated that initial infection and vaccination were protective factors against severe COVID-19 during post-immune infection (OR = 0.55, 95%CI = 0.31–0.98). A subgroup (post-immune infection after natural infection or vaccination) analysis showed similar results. Primary SARS-CoV-2 infection and vaccination provide adequate protection against severe clinical symptoms after post-immune infection. This finding demonstrates that SARS-CoV-2 may not trigger ADE at the population level.
The effect of two types of diet on apoptosis indexes, lipid profile and histopathological outcome in acute kidney injury during exercise
Authors: Sabet Nazanin , Soltani Zahra , Khaksari Mohammad , Iranpour Maryam , Afshar Reza Malekpour , Mehdiabadi Fatemeh Mousavi , Raji-Amirhasani Alireza 
Published: September 2022

Abstract
Background
Exercise and some pre-AKI diets have been shown to improve injury, apoptosis, and lipid profile. In this study, the effect of two different diets along with exercise training on acute kidney injury (AKI) was investigated.

Materials and methods
Laboratory rats were randomly divided into four groups of control, standard diet + exercise, exercise + calorie restriction (CR) and exercise + time restriction (TR). Each group was divided into two subgroups of AKI and no AKI. The animals received endurance training and diet regimens before AKI. Fasting blood glucose, serum creatinine, Bcl-2-associated X protein (Bax), B-cell lymphoma 2 (Bcl2) and histopathological outcome of renal tissue as well as serum lipid profile of animals were assessed 24 h after AKI.

Results
The percentage of changes in renal Bcl2 and Bax after AKI in the group with previous exercise was lower than the group without previous exercise (p < 0.01). After induction of AKI, serum lipid profile changed in non-exercised rats (p < 0.001). Also, after injury, fasting blood glucose levels increased in non-exercised rats (p < 0.05). After injury, the start of both CR and TR diets during exercise caused less change in Bcl2 and Bax of non-exercised rats compared to exercised rats (p < 0.001). CR diet along with exercise improved lipid profile, and also CR diet along exercise decreased fasting blood glucose levels (p < 0.001). Also, both the CR and TR diets during exercise caused fewer changes in histopathological outcome after AKI.

Conclusion
Exercise alone decreased changes in apoptotic and histopathological indexes, fasting blood glucose, as well as lipid profile of rats after AKI. Reduction of apoptosis and improvement of histopathological outcome after AKI appeared more when CR and TR diets were commenced during exercise. The reduction of lipid profile changes was more pronounced in the group that received CR diet during exercise.
The systemic immune response due to cholesterol crystal embolization syndrome: a case report
Authors: Sakamoto Tetsu , Yamakawa Takafumi , Hirano Keita , Kobayashi Arisa , Kasai Mio , Koizumi Kiyoshi , Yokoo Takashi , Komatsumoto Satoru , Murohisa Toshimitsu , Shimizu Taro 
Published: September 2022

Abstract
Background
Cholesterol crystal embolization syndrome (CES) occurs when an atherosclerotic plaque causes small-vessel embolization, resulting in multi-organ damage. Although CES is pathologically characterized by an infiltration of eosinophils, the implication of the systemic inflammatory response represented by hypereosinophilia is unclear in clinical practice. Herein we present the case of a patient diagnosed with CES who developed multiple allergic organ injuries, including daptomycin-related dermatitis and later vancomycin-induced acute tubulointerstitial nephritis, which was successfully treated by the withdrawal of each medicine with or without corticosteroid therapy, one by one.

Case presentation
A 76-year-old Japanese man diagnosed with thoracic aneurysm rupture underwent total arch replacement through the open stent graft technique. Postoperatively, he developed methicillin-resistant Staphylococcus epidermidis bacteremia, which was treated with daptomycin. Subsequently, he presented with palpable purpura on both dorsal feet, erythema around his body, and hypereosinophilia. Daptomycin was replaced with vancomycin due to suspicion of drug-induced erythema. The erythema gradually faded. On nine days after vancomycin therapy, the systemic erythema rapidly reappeared followed by acute renal failure. The renal function decline prompted hemodialysis. A skin biopsy revealed cholesterol embolization, whereas a kidney biopsy revealed acute tubulointerstitial nephritis. After vancomycin discontinuation and initiation of systemic corticosteroid treatment, his kidney function was restored to the baseline level.

Conclusions
The present case highlights cholesterol embolization can cause allergic complications in addition to direct organ damage.
Clinical significance and oncogenic function of NR1H4 in clear cell renal cell carcinoma
Authors: Huang Shiyu , Hou Yanguang , Hu Min , Hu Juncheng , Liu Xiuheng 
Published: September 2022

Abstract
Background
Nuclear receptor subfamily 1 group H member 4 (NR1H4) have been reported in various cancer types, however, little is known about the clinical values and biological function in clear cell Renal cell carcinoma (ccRCC).

Methods
The expression pattens of NR1H4 in ccRCC were investigated in clinical specimens, cell lines and publicly‑available databases. Cell Counting Kit-8 (CCK-8), colony formation, 5-ethynyl-2' -deoxyuridine (EdU), transwell and cell wound healing assays were performed to assess the biological functions of NR1H4 in 786-O ccRCC cells. Gene set enrichment analysis (GSEA), Flow Cytometry, quantitative real‐time PCR (qRT-PCR), western blot and immunofluorescence were performed to explore the molecular mechanism of NR1H4 in ccRCC. We explored the early diagnostic value, prognostic value, genetic mutation and DNA methylation of NR1H4 by a comprehensive bioinformatics analysis based on the data published in the following databases: The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Kaplan‐Meier Plotter, Gene Expression Profiling Interactive Analysis (GEPIA), UNIVERSITY OF CALIFORNIA SANTA CRUZ Xena (UCSC Xena), cBio Cancer Genomics Portal, MethSurv, SurvivalMeth and The University of ALabama at Birmingham CANcer data analysis Portal (UALCAN). Its correlation with tumor-infiltrating immune cells in ccRCC was analyzed by Tumor Immune Estimation Resource 2.0 (TIMER2.0) and Tumor Immune System Interactions Database (TISIDB).

Results
In this study, NR1H4 was found to be highly expressed in ccRCC tissues and ccRCC cell lines. Knockdown of NR1H4 significantly suppressed cancer cell proliferation, migration and invasion. Mechanistically, tumor‐associated signaling pathways were enriched in the NR1H4 overexpression group and si-NR1H4 could induce the downregulation of Cyclin E2 (CCNE2). By bioinformatics analysis, NR1H4 was identified as highly expressed in stage I ccRCC with a high diagnostic accuracy (area under the receiver operating characteristic curve > 0.8). Genetic alteration and DNA methylation of NR1H4 were significantly associated with prognosis in ccRCC patients. Moreover, NR1H4 expression associated with immune cell infiltration levels in ccRCC, which provides a new idea for immunotherapy.

Conclusions
Our study indicated that NR1H4 might be a potential tumor biomarker and therapeutic target for ccRCC which could promote cancer cell proliferation, migration and invasion via regulating CCNE2.
Clinical characteristics of glaucoma patients with various risk factors
Authors: Omodaka Kazuko , Kikawa Tsutomu , Kabakura Sayaka , Himori Noriko , Tsuda Satoru , Ninomiya Takahiro , Takahashi Naoki , Pak Kyongsun , Takeda Noriyasu , Akiba Masahiro , Nakazawa Toru 
Published: September 2022

Abstract
Background
Glaucoma is multifactorial, but the interrelationship between risk factors and structural changes remains unclear. Here, we adjusted for confounding factors in glaucoma patients with differing risk factors, and compared differences in structure and susceptible areas in the optic disc and macula.

Methods
In 458 eyes with glaucoma, we determined confounding factors for intraocular pressure (IOP), central corneal thickness (CCT), axial length (AL), LSFG-measured ocular blood flow (OBF), which was assessed with laser speckle flowgraphy-measured mean blur rate in the tissue area (MT) of the optic nerve head, biological antioxidant potential (BAP), and systemic abnormalities in diastolic blood pressure (dBP). To compensate for measurement bias, we also analyzed corrected IOP (cIOP; corrected for CCT) and corrected MT (cMT; corrected for age, weighted retinal ganglion cell count, and AL). Then, we determined the distribution of these parameters in low-, middle-, and high-value subgroups and compared them with the Kruskal–Wallis test. Pairwise comparisons used the Steel–Dwass test.

Results
The high-cIOP subgroup had significantly worse mean deviation (MD), temporal, superior, and inferior loss of circumpapillary retinal nerve fiber layer thickness (cpRNFLT), and large cupping. The low-CCT subgroup had temporal cpRNFLT loss; the high-CCT subgroup had low cup volume. The high-AL subgroup had macular ganglion cell complex thickness (GCCT) loss; the low-AL subgroup had temporal cpRNFLT loss. The high-systemic-dBP subgroup had worse MD, total, superior, and inferior cpRNFLT loss and macular GCCT loss. The low-BAP subgroup had more male patients, higher dBP, and cpRNFLT loss in the 10 o’clock area. The high-OBF subgroup had higher total, superior and temporal cpRNFLT and macular GCCT.

Conclusions
Structural changes and local susceptibility to glaucomatous damage show unique variations in patients with different risk factors, which might suggest that specific risk factors induce specific types of pathogenesis and corresponding glaucoma phenotypes. Our study may open new avenues for the development of precision medicine for glaucoma.