bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unified Principal S–N Equation for Friction Stir Welding of 5083 and 6061 Aluminum Alloys
Authors: Li Xiangwei , Fang Ji , Guan Xiaoli 
Published: January 2021

AbstractWith the popularization of friction stir welding (FSW), 5083-H321 and 6061-T6 aluminum alloy materials are widely used during the FSW process. In this study, the fatigue life of friction stir welding with two materials, i.e., 5083-H321 and 6061-T6 aluminum alloy, are studied. Fatigue tests were carried out on the base metal of these two materials as well as on the butt joints and overlapping FSW samples. The principle of the equivalent structural stress method is used to analyze the FSW test data of these two materials. The fatigue resistances of these two materials were compared and a unified principal S–N curve equation was fitted. Two key parameters of the unified principal S–N curve obtained by fitting, Cd is 4222.5, and h is 0.2693. A new method for an FSW fatigue life assessment was developed in this study and can be used to calculate the fatigue life of different welding forms with a single S–N curve. Two main fatigue tests of bending and tension were used to verify the unified principal S–N curve equation. The results show that the fatigue life calculated by the unified mean 50% master S–N curve parameters are the closest to the fatigue test results. The reliability, practicability, and generality of the master S–N curve fitting parameters were verified using the test data. The unified principal S–N curve acquired in this study can not only be used in aluminum alloy materials but can also be applied to other materials.
Renocolic fistula following a partial nephrectomy: a case study
Authors: Dergamoun Hamza , Zaoui Youssef , Amielh David , Volpe Pascal , El Kharroubi Amine 
Published: January 2021

AbstractBackgroundUro-digestive fistulae are uncommon. They frequently manifest themselves with mild symptoms but can, in some cases, be life-threatening leading to septic shock and death. The diagnosis is facilitated by radiological explorations and their management remains mainly surgical.Case presentationWe report the case of a diabetic 62-year-old patient who developed a renocolic fistula revealed by a digestive symptomatology, following a partial nephrectomy that was surgically treated with positive overall outcome.ConclusionThe development of a fistula between the colon and the kidney is very rare. Although the outcome was positive at the price of total nephrectomy and partial colectomy, the diagnosis and management of the fistula were challenging. Urologists should keep in mind the possibility of a fistula developing in the aftermath of a partial nephrectomy.
An Anatolian study on the current knowledge and attitudes of urology operating room staff on ionizing radiation
Authors: Girgin Reha 
Published: January 2021

Abstract
Background
To evaluate current approaches to ionizing radiation by personnel working in urology operating room at all levels of health service in Anatolia, Turkey.

Methods
A questionnaire was e-mailed to urology operating room personnel including MDs at different academic levels, between August and September 2020 in Anatolia, Turkey. The questionnaire included demographic questions and questions about ionizing radiation, exposure and protection.

Results
Of the 173 (11.9%) respondents, 44.5% were doctors, 24.9% were nurses, 20.8% were radiology technicians, and 9.8% were other operating room personnel. While most participants (73.4%) had some knowledge of radiation, only 42.2% stated they had received radiation-specific training. The two most commonly used personal protective equipments (PPEs) among respondents (79.8%) were lead aprons and thyroid protectors. Interestingly, both types of PPE were preferred among those who had not received radiation safety training. Conversely, besides lead aprons and thyroid protectors; gonadal protection, goggles and gloves were the preferred PPEs among respondents who had received radiation training (p < 0.001). Radiology technicians exhibited the highest compliance rate for dosimeter usage (100%), followed by faculty members (37.5%), urology specialists (36.7%) nurses (27.9%), operating room staff (17.6%) and assistants (15%). While differences in compliance were statistically significant (p < 0.001), no significant relationship was found between radiation protection measures and years of experience, daily fluoroscopy exposure or education level.

Conclusions
Despite advances in medical science, our findings suggest that many hospital personnel are still insensitive to the dangers of fluoroscopy, which is of great importance in urology operating rooms.
Mining influential genes based on deep learning
Authors: Kong Lingpeng , Chen Yuanyuan , Xu Fengjiao , Xu Mingmin , Li Zutan , Fang Jingya , Zhang Liangyun , Pian Cong 
Published: January 2021

AbstractBackgroundCurrently, large-scale gene expression profiling has been successfully applied to the discovery of functional connections among diseases, genetic perturbation, and drug action. To address the cost of an ever-expanding gene expression profile, a new, low-cost, high-throughput reduced representation expression profiling method called L1000 was proposed, with which one million profiles were produced. Although a set of ~ 1000 carefully chosen landmark genes that can capture ~ 80% of information from the whole genome has been identified for use in L1000, the robustness of using these landmark genes to infer target genes is not satisfactory. Therefore, more efficient computational methods are still needed to deep mine the influential genes in the genome.ResultsHere, we propose a computational framework based on deep learning to mine a subset of genes that can cover more genomic information. Specifically, an AutoEncoder framework is first constructed to learn the non-linear relationship between genes, and then DeepLIFT is applied to calculate gene importance scores. Using this data-driven approach, we have re-obtained a landmark gene set. The result shows that our landmark genes can predict target genes more accurately and robustly than that of L1000 based on two metrics [mean absolute error (MAE) and Pearson correlation coefficient (PCC)]. This reveals that the landmark genes detected by our method contain more genomic information.ConclusionsWe believe that our proposed framework is very suitable for the analysis of biological big data to reveal the mysteries of life. Furthermore, the landmark genes inferred from this study can be used for the explosive amplification of gene expression profiles to facilitate research into functional connections.
Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics
Authors: Shen Pan , Xu Aishi , Hou Yushan , Wang Huqiang , Gao Chao , He Fuchu , Yang Dong 
Published: January 2021

Abstract
Background
One striking feature of the large KRAB domain-containing zinc finger protein (KZFP) family is its rapid evolution, leading to hundreds of member genes with various origination time in a certain mammalian genome. However, a comprehensive genome-wide and across-taxa analysis of the structural and expressional features of KZFPs with different origination time is lacking. This type of analysis will provide valuable clues about the functional characteristics of this special family.

Results
In this study, we found several conserved paradoxical phenomena about this issue. 1) Ordinary young domains/proteins tend to be disordered, but most of KRAB domains are completely structured in 64 representative species across the superclass of Sarcopterygii and most of KZFPs are also highly structured, indicating their rigid and unique structural and functional characteristics; as exceptions, old-zinc-finger-containing KZFPs have relatively disordered KRAB domains and linker regions, contributing to diverse interacting partners and functions. 2) In general, young or highly structured proteins tend to be spatiotemporal specific and have low abundance. However, by integrated analysis of 29 RNA-seq datasets, including 725 samples across early embryonic development, embryonic stem cell differentiation, embryonic and adult organs, tissues in 7 mammals, we found that KZFPs tend to express ubiquitously with medium abundance regardless of evolutionary age and structural disorder degree, indicating the wide functional requirements of KZFPs in various states. 3) Clustering and correlation analysis reveal that there are differential expression patterns across different spatiotemporal states, suggesting the specific-high-expression KZFPs may play important roles in the corresponding states. In particular, part of young-zinc-finger-containing KZFPs are highly expressed in early embryonic development and ESCs differentiation into endoderm or mesoderm. Co-expression analysis revealed that young-zinc-finger-containing KZFPs are significantly enriched in five co-expression modules. Among them, one module, including 13 young-zinc-finger-containing KZFPs, showed an ‘early-high and late-low’ expression pattern. Further functional analysis revealed that they may function in early embryonic development and ESC differentiation via participating in cell cycle related processes.

Conclusions
This study shows the conserved and special structural, expressional features of KZFPs, providing new clues about their functional characteristics and potential causes of their rapid evolution.
Activation of metabolic and stress responses during subtoxic expression of the type I toxin hok in Erwinia amylovora
Authors: Peng Jingyu , Triplett Lindsay R. , Sundin George W. 
Published: January 2021

Abstract
Background
Toxin-antitoxin (TA) systems, abundant in prokaryotes, are composed of a toxin gene and its cognate antitoxin. Several toxins are implied to affect the physiological state and stress tolerance of bacteria in a population. We previously identified a chromosomally encoded hok-sok type I TA system in Erwinia amylovora, the causative agent of fire blight disease on pome fruit trees. A high-level induction of the hok gene was lethal to E. amylovora cells through unknown mechanisms. The molecular targets or regulatory roles of Hok were unknown.

Results
Here, we examined the physiological and transcriptomic changes of Erwinia amylovora cells expressing hok at subtoxic levels that were confirmed to confer no cell death, and at toxic levels that resulted in killing of cells. In both conditions, hok caused membrane rupture and collapse of the proton motive force in a subpopulation of E. amylovora cells. We demonstrated that induction of hok resulted in upregulation of ATP biosynthesis genes, and caused leakage of ATP from cells only at toxic levels. We showed that overexpression of the phage shock protein gene pspA largely reversed the cell death phenotype caused by high levels of hok induction. We also showed that induction of hok at a subtoxic level rendered a greater proportion of stationary phase E. amylovora cells tolerant to the antibiotic streptomycin.

Conclusions
We characterized the molecular mechanism of toxicity by high-level of hok induction and demonstrated that low-level expression of hok primes the stress responses of E. amylovora against further membrane and antibiotic stressors.
Association of mitochondrial DNA haplogroups J and K with low response in exercise training among Finnish military conscripts
Authors: Kiiskilä Jukka , Jokelainen Jari , Kytövuori Laura , Mikkola Ilona , Härkönen Pirjo , Keinänen-Kiukaanniemi Sirkka , Majamaa Kari 
Published: January 2021

AbstractBackgroundWe have previously suggested that some of the mutations defining mitochondrial DNA (mtDNA) haplogroups J and K produce an uncoupling effect on oxidative phosphorylation and thus are detrimental for elite endurance performance. Here, the association between haplogroups J and K and physical performance was determined in a population-based cohort of 1036 Finnish military conscripts.ResultsFollowing a standard-dose training period, excellence in endurance performance was less frequent among subjects with haplogroups J or K than among subjects with non-JK haplogroups (p = 0.041), and this finding was more apparent among the best-performing subjects (p < 0.001).ConclusionsThese results suggest that mtDNA haplogroups are one of the genetic determinants explaining individual variability in the adaptive response to endurance training, and mtDNA haplogroups J and K are markers of low-responders in exercise training.
A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution
Authors: Li Douyue , Pan Saichao , Zhang Hongxi , Fu Yongzhuo , Peng Zhuli , Zhang Liang , Peng Shan , Xu Fei , Huang Hanrou , Shi Ruixue , Zheng Heping , Peng Yousong , Tan Zhongyang 
Published: January 2021

Abstract
Background
Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps were established, which could clearly display SSR landscape in every bin of 1 k base pairs (Kbp) along the sequenced part of human reference Y-DNA (NC_000024.10), by our developed differential method for improving the existing method to reveal SSR distributional characteristics in large genomic sequences.

Results
The maps show that SSRs accumulate significantly with forming density peaks in at least 2040 bins of 1 Kbp, which involve different coding, noncoding and intergenic regions of the Y-DNA, and 10 especially high density peaks were reported to associate with biological significances, suggesting that the other hundreds of especially high density peaks might also be biologically significant and worth further analyzing. In contrast, the maps also show that SSRs are extremely sparse in at least 207 bins of 1 Kbp, including many noncoding and intergenic regions of the Y-DNA, which is inconsistent with the widely accepted view that SSRs are mostly rich in these regions, and these sparse distributions are possibly due to powerfully regional selection. Additionally, many regions harbor SSR clusters with same or similar motif in the Y-DNA.

Conclusions
These 540 maps may provide the important information of clearly position-related SSR distributional features along the human reference Y-DNA for better understanding the genome structures of the Y-DNA. This study may contribute to further exploring the biological significance and distribution law of the huge numbers of SSRs in human Y-DNA.
Comparison and interpretation of characteristics of Rhizosphere microbiomes of three blueberry varieties
Authors: Zhang Yan , Wang Wei , Shen Zhangjun , Wang Jingjing , Chen Yajun , Wang Dong , Liu Gang , Han Maozhen 
Published: January 2021

Abstract
Background
Studies on the rhizosphere microbiome of various plants proved that rhizosphere microbiota carries out various vital functions and can regulate the growth and improve the yield of plants. However, the rhizosphere microbiome of commercial blueberry was only reported by a few studies and remains elusive. Comparison and interpretation of the characteristics of the rhizosphere microbiome of blueberry are critical important to maintain its health.

Results
In this study, a total of 20 rhizosphere soil samples, including 15 rhizosphere soil samples from three different blueberry varieties and five bulk soil samples, were sequenced with a high-throughput sequencing strategy. Based on these sequencing datasets, we profiled the taxonomical, functional, and phenotypic compositions of rhizosphere microbial communities for three different blueberry varieties and compared our results with a previous study focused on the rhizosphere microbiome of blueberry varieties. Our results demonstrated significant differences in alpha diversity and beta diversity of rhizosphere microbial communities of different blueberry varieties and bulk soil. The distribution patterns of taxonomical, functional, and phenotypic compositions of rhizosphere microbiome differ across the blueberry varieties. The rhizosphere microbial communities of three different blueberry varieties could be distinctly separated, and 28 discriminative biomarkers were selected to distinguish these three blueberry varieties. Core rhizosphere microbiota for blueberry was identified, and it contained 201 OTUs, which were mainly affiliated with Proteobacteria, Actinobacteria, and Acidobacteria. Moreover, the interactions between OTUs of blueberry rhizosphere microbial communities were explored by a co-occurrence network of OTUs from an ecological perspective.

Conclusions
This pilot study explored the characteristics of blueberry’s rhizosphere microbial community, such as the beneficial microorganisms and core microbiome, and provided an integrative perspective on blueberry’s rhizosphere microbiome, which beneficial to blueberry health and production.
Off-pump coronary artery bypass concomitant with retrieval of broken guide wire stuck in the brachial artery: a case report
Authors: Xue Yuan , Dai Lu , Jiang Wenjian , Zhang Hongjia 
Published: January 2021

Abstract
Background
The broken guide wire could get stuck anywhere during coronary artery angiography, but the broken guide wire in the brachial artery is extremely rare.

Case presentation
In this report, we describe our experience with a case of off-pump coronary artery bypass (OPCABG) concomitant with the retrieval of a broken guide wire stuck in the brachial artery: a 56-year-old male patient was referred to our hospital because of tri-vessel disease and a broken guide wire stuck in the right brachial artery. He received OPCABG concomitant with the retrieval of the broken guide wire stuck in the brachial artery under general anesthesia. The patient was discharged uneventfully, and 12 months follow-up showed an excellent surgical outcome.

Conclusion
Open surgery is an effective means for treating patients with a guide wire stuck in the brachial artery during percutaneous coronary intervention.
Macrophage migration inhibitory factor is an early marker of severe acute pancreatitis based on the revised Atlanta classification
Authors: Shen Dingcheng , Tang Caixi , Zhu Shuai , Huang Gengwen 
Published: January 2021

Abstract
Background
Various serum markers for early identification of severe acute pancreatitis (SAP) have been studied. Serum macrophage migration inhibitory factor (MIF) was reported to be correlated with severity of acute pancreatitis (AP) based on the 1992 Atlanta classification. However, MIF has never been proven to be predictive of disease severity based on the revised Atlanta classification (RAC). The potential predictive value of MIF needs to be further validated.

Methods
Consecutive patients with AP within 48 h after symptom onset and 10 healthy control volunteers were enrolled prospectively. Serum MIF levels were measured by enzyme-linked immunosorbent assay (ELISA). The predictive value of MIF, clinical scores and other serum markers were determined.

Results
Among 143 patients with AP, there were 52 (36.4%), 65 (45.5%) and 26 (18.1%) with mild, moderate and severe disease based on the RAC respectively. Compared with healthy volunteers, serum levels of MIF were significantly higher in AP patients, especially those with SAP (P < 0.001). Multivariate regression analysis indicated that increased serum MIF (cut-off 2.30 ng/ml, OR = 3.16, P = 0.008), IL-6 (cut-off 46.8 pg/ml, OR = 1.21, P = 0.043), APACHE II score (cut-off 7.5, OR = 2.57, P = 0.011) and BISAP score (cut-off 1.5, OR = 1.01, P = 0.038) were independent risk factors for predicting SAP (P < 0.05). By using the area under the receiver operating characteristic (ROC) curve (AUC), MIF (AUC 0.950) demonstrated more excellent discriminative power for predicting SAP than APACHE II (AUC 0.899), BISAP (AUC 0.886), and IL-6 (AUC 0.826).

Conclusions
Serum MIF is a valuable early marker for predicting the severity of AP based on the RAC.
Effects of hearing impairment and hearing aid use on the incidence of cognitive impairment among community-dwelling older adults: evidence from the Taiwan Longitudinal Study on Aging (TLSA)
Authors: Tai Chi-Jung , Tseng Tzyy-Guey , Hsiao Yu-Han , Kuo Tsu-Ann , Huang Ching-Ya , Yang Yi-Hsin , Lee Meng-Chih 
Published: January 2021

Abstract
Background
Previous studies have reported associations between hearing impairment (HI) and cognitive impairment, but the evidence is not conclusive while considering concurrent geriatric syndromes. Especially, evidence from previous studies rarely came from Asian studies. This study aimed to evaluate the independent effects of HI and hearing aid use on the incidence of cognitive impairment while considering most geriatric confounders.

Methods
This population-based, propensity-score matched cohort study used cohort from Waves IV–VII (1999–2011) survey of the Taiwan Longitudinal Study on Aging (TLSA). Cognitive impairment was identified based on Short Portable Mental Status Questionnaire (SPMSQ) scores. The hazard ratio (HR) was calculated using the Cox proportional hazard regression adjusting for age, sex, comorbidities, socioeconomic status, Center for Epidemiologic Studies Depression (CES-D) scores, the instrumental activities of daily living scale, mobility condition and quality of life. In addition, social support and participation were also considered as confounders in the analysis. To assess the robustness of our findings, we conducted a sensitivity analysis designed to access unmeasured confounding factors by calculating E-values.

Results
After 1:1 propensity-score matching, we included 709 participants in both the HI and non-HI groups with a mean age of 73.4 years and 39.4% of participants were female. The mean follow-up was 8.9 ± 3.9 years. The HI group had a higher incidence of cognitive impairment than the non-HI group (74.5% vs. 69.1%, respectively), with an adjusted HR of 1.16 (95% confidence interval [CI], 1.03–1.32) based on a 12-year follow up. The E-value was 1.45 for the estimate, which provided evidence for this study’s robustness. Although, a subgroup analysis showed that hearing aid use was associated with lower incidences of cognitive impairment (66.3% vs. 75.6%) when compared to non-users in the HI group, the adjusted HR of 0.82 (95% CI, 0.61–1.09) revealed no significant differences.

Conclusions
HI was an independent risk factor of incident cognitive impairment on top of concurrent geriatric syndromes. Early HI detection may thus be effective for preventing cognitive decline. Further studies are needed to evaluate the effect of hearing aid use on the prevention of cognitive decline.