bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parametric Subharmonic Instability of Diurnal Internal Tides in the Abyssal South China Sea
Authors: Hu Qianwen , Huang Xiaodong , Xu Qinbo , Zhou Chun , Guan Shoude , Xu Xing , Zhao Wei , Yang Qingxuan , Tian Jiwei 
Published: October 2022

Abstract
Internal waves close to the seafloor of abyssal oceans are the key energy suppliers driving near-bottom mixing and the upwelling branches of meridional overturning circulation, but their spatiotemporal variability and intrinsic mechanisms remain largely unclear. In this study, measurements from 10 long-term moorings were used to investigate the internal wave activities in the abyssal South China Sea, which is an important upwelling zone. Strong near-inertial internal waves (NIWs) with current velocity pulses exceeding 5 cm s−1 were observed to dominate the near-bottom internal wave field at approximately 14°N. These abyssal NIWs were phase-coupled with diurnal internal tides (D1), and both displayed common seasonal variations that were larger in winter and summer, providing evidence of diurnal parametric subharmonic instability (PSI) near its critical latitudes (CLs). Emitted from the bottom, near-inertial kinetic energy rapidly decreased by one order of magnitude from depths of ∼120 to ∼620 m above the bottom. Near rough topographies, the abyssal PSI was shifted poleward to approximately 14.8°N by negative relative vorticities of passing anticyclonic eddies or topographic Rossby waves. Compared with flat topography, PSI near rough topography was significantly promoted by topographic-localized strong D1 with high-mode structures, creating abyssal NIW bursts. Bottom-reaching shipboard conductivity–temperature–depth profiles revealed that the bottom mixed layers became much thicker when approaching CLs, suggesting that abyssal PSI potentially accelerates the ventilation and upwelling of bottom water. The observational results presented here illustrate notable spatiotemporal variations in abyssal NIWs regulated by PSI and call for consideration of PSI to better understand near-bottom mixing and upwelling.
Substance P Inhibitor Promotes Tendon Healing in a Collagenase-Induced Rat Model of Tendinopathy
Authors: Ko Kyung Rae , Han Soo-Hong , Choi Sujin , An Hyun-Ju , Kwak Eun-Bee , Jeong Yunhui , Baek Minjung , Lee Jusung , Choi Junwon , Kim Il-Su , Lee Soonchul 
Published: October 2022

Background:The substance P–neurokinin 1 receptor pathway has been proposed as a therapeutic target for tendinopathy. However, there is a lack of evidence regarding its practical applications.Purpose:To investigate the therapeutic effects of substance P inhibitor (SPI) on inflamed tenocytes in vitro and in a collagenase-induced rat model of tendinopathy in vivo.Study Design:Controlled laboratory study.Methods:We analyzed the mRNA levels of inflammatory (cyclooxygenase [COX]-2 and interleukin [IL]-6) and tenogenic (Mohawk and scleraxis [SCX]) markers using reverse transcription quantitative polymerase chain reaction to demonstrate the effects of SPI on lipopolysaccharide-treated (inflamed) tenocytes. A collagenase-induced rat model of tendinopathy was created by injecting 20 µL of collagenase into the Achilles tendon. A behavior test using an incapacitance apparatus was performed to detect changes in postural equilibrium. The tendon specimens were obtained, and their gross findings were examined. The tensile strength was measured, and histopathological evaluation was performed (hematoxylin and eosin, alcian blue, and immunohistochemical staining).Results:The mRNA levels of COX-2, IL-6, Mohawk, and SCX differed significantly between inflamed tenocytes and those treated with SPI. SPI improved the weight burden in a rat model of tendinopathy in a behavioral test. The specimens of the SPI group showed a normal tendon-like appearance. In the biomechanical test, the tensile strength of the SPI group was significantly greater than that of the tendinopathy group. In the histopathological evaluation, the degree of collagen matrix breakdown was mild in the SPI group. In alcian blue staining, only small focal depositions of proteoglycans and glycosaminoglycans were observed in the SPI group. The SPI group showed decreased expression of IL-6 and neurokinin 1 receptor.Conclusion:This study suggests that SPI has therapeutic effects on tendon healing and restoration in a collagenase-induced rat model of tendinopathy.Clinical Relevance:SPI is a promising agent for tendinopathy in humans.
Ultrasound-guided versus conventional peribulbar anaesthesia in cataract surgery: A randomised controlled study
Authors: Naguib Nader N , Mohasseb Tariq M , Ezzat Azza M , Hussien Gomaa Z , Khattab Rehab S , Aboul Fetouh Eman S , Dobal Nasser M 
Published: October 2022

Background: Blind ophthalmic anaesthetic techniques may have serious complications. Aim: To assess the safety of ultrasound as a guide in ophthalmic blocks. Methods: Fifty adult patients undergoing cataract surgery under peribulbar block anaesthesia were randomly assigned to ultrasound-guided and conventional block groups. In the ultrasound-guided block group, a large amount of the standard ultrasound gel was applied to the closed eyelids. The globes were scanned in both sagittal and transverse planes. The patients were asked to look straight ahead with closed eyes without clenching the eyelids. The depth and gain were adjusted before performing the block. The primary outcome was the rate of complications. Secondary outcomes included the volume of injected anaesthetics and surgeon and patients’ satisfaction. Results: The local anaesthetic volume used was not significantly different between the two groups (7.08 ± 1.66 and 6.72 ± 1.97ml). The block onset, time and quality were comparable in both groups. No complications were reported, and there were no significant differences regarding surgeons’ or patients’ satisfaction with either procedure. Conclusion: The ultrasound-guided local ophthalmic block is as safe as the conventional method. Although its use was not superior to the conventional procedure, direct visualisation with ultrasound may be important to avoid vulnerable structures such as staphylomas.
Stabilizing effect of an elbow orthosis with an adjustable hinge axis after lateral collateral ligament injury: A biomechanical study
Authors: Badre Armin , Axford David T , Kotzer Sara , Johnson James A , King Graham JW 
Published: October 2022

Background Current commercial elbow braces have a straight hinge that does not account for the native carrying angle of the elbow. The objective of this study was to determine the effectiveness of a custom-designed hinged elbow orthosis (HEO) with variable valgus angulations in stabilizing a lateral collateral ligament (LCL) deficient elbow. Methods Eight cadaveric upper extremities were mounted in an elbow motion simulator in the abducted varus gravity-loaded position. The specimens were examined before and after simulated LCL injury and then with the addition of the custom-designed HEO with 0°, 10°, and 20° of valgus angulation. Kinematic data were recorded using an electromagnetic tracking system. Results The LCL injured state with or without the brace resulted in significant increases in varus angulation of the elbow compared to the intact state in both pronation and supination ( P < 0.05). There were no significant differences in varus-valgus angulation or ulnohumeral rotation between any of the brace angles and the LCL injured state with the forearm pronated and supinated. Discussion The custom-designed HEO did not provide any additional stability to the LCL injured elbow. The varus arm position should be avoided during the rehabilitation of an LCL injured elbow even when an HEO is used.
Genomic characterization of Bacillus cereus sensu stricto 3A ES isolated from eye shadow cosmetic products
Authors: Yossa Nadine , Bell Rebecca , Tallent Sandra , Brown Eric , Binet Rachel , Hammack Thomas 
Published: October 2022

Abstract
Background
The Bacillus cereus group, also known as B. cereus sensu lato (s.l.) contains ubiquitous spore-forming bacteria found in the environment including strains from the B. cereus sensu stricto (s.s.) species. They occur naturally in a wide range of raw materials and in consumer products. Characterizing isolates that have survived in consumer products allows us to better understand the mechanisms that permit spores to persist and potentially cause illness. Here we characterize the draft genome sequence of B. cereus s. s. 3A-ES, originally isolated from eye shadow and since investigated in several cosmetic studies and compared it to other top ten published complete genome sequences of B. cereus s.l. members.

Results
The draft genome sequence of B. cereus s.s. 3A ES consisted of an average of 90 contigs comprising approximately 5,335,727 bp and a GC content of 34,988%, and with 5509 predicted coding sequences. Based on the annotation statistics and comparison to other genomes within the same species archived in the Pathosystems Resource Integration Center (PATRIC), this genome “was of good quality. Annotation of B. cereus s.s. 3A ES revealed a variety of subsystem features, virulence factors and antibiotic resistant genes. The phylogenetic analysis of ten B. cereus group members showed B. cereus s.s. 3A-ES to be a closely related homolog of B. cereus s.s. ATCC 14,579, an established reference strain that is not adapted for cosmetic microbiological studies. Survival of 3A-ES in eye shadow could be linked to predicted stress-response genes and strengthened by additional stress-response genes such as VanB-type, VanRB, CAT15/16, BcrA, BcrB, Lsa(B), and recA that are lacking in B. cereus s.s. ATCC 14,579.

Conclusion
Our genomic analysis of B. cereus s.s. 3A-ES revealed genes, which may allow this bacterium to withstand the action of preservatives and inhibitors in cosmetics, as well as virulence factors that could contribute to its pathogenicity. Having a well-characterized strain obtained from eye-shadow may be useful for establishing a reference strain for cosmetics testing.
Lipopolysaccharide downregulates the expression of ZO-1 protein through the Akt pathway
Authors: Zou Peicen , Yang Fan , Ding Yijun , Zhang Di , Liu Ying , Zhang Jinjing , Wu Dan , Wang Yajuan 
Published: October 2022

Abstract
Background
Neonatal bacterial meningitis is a common neonatal disease with high morbidity, and can cause serious sequelae when left untreated. Escherichia coli is the common pathogen, and its endotoxin, lipopolysaccharide (LPS) can damage the endothelial cells, increasing the permeability of the blood-brain barrier (BBB), leading to intracranial inflammation. However, the specific mechanism of bacterial meningitis induced by LPS damaging BBB remains unclear. In this study, the mouse brain microvascular endothelial (bEND.3) cells were used as a research object to investigate whether LPS damage BBB through the PI3K/Akt pathway.

Methods
The bEND.3 cells were stimulated with different concentrations of LPS for 12 h, and the expression of tight junction proteins (ZO-1, claudin-5, occludin) was detected using western blotting. The cells were challenged with the same concentration of LPS (1ug/ml) across different timepoints (0, 2 h, 4 h, 6 h, 12 h, 24 h). Expression of TJ proteins and signal pathway molecules (PI3K, p-PI3K, Akt, p-Akt) were detected. The distribution of ZO-1 in bEND.3 cells were detected by immunofluorescence staining.

Results
A negative correlation is observed between ZO-1 and LPS concentration. Moreover, a reduced expression of ZO-1 was most significant under 1 ug/ml of LPS, and the difference was statistically significant (P < 0.05). Additionally, there is a negative correlation between ZO-1 and LPS stimulation time. Meanwhile, the expression of claudin-5 and occludin did not change significantly with the stimulation of LPS concentration and time. The immunofluorescence assay showed that the amount of ZO-1 on the surface of bEND.3 cells stimulated with LPS was significantly lower than that of the control group. After LPS stimulation, p-Akt protein increased at 2 h and peaked at 4 h. The titer of p-PI3K did not change significantly with time.

Conclusion
LPS can downregulate the expression of ZO-1; however, its effect on claudin-5 and occludin is minimal. Akt signal pathway may be involved in the regulation of ZO-1 expression induced by LPS in bEND.3 cells.
A prospective study on the application of HINTS in distinguishing the localization of acute vestibular syndrome
Authors: Qiu Tao , Dai Xiaoyan , Xu Xiaoya , Zhang Guiqin , Huang Linming , Gong Qingping 
Published: October 2022

Abstract
Background
Acute vestibular syndrome (AVS) is a common clinical syndrome in neurology clinics and emergency department. Canonical standard for AVS diagnosis requires the presence of persistent vertigo for more than 24 h. HINTS (head impulse-nystagmus-test of skew) is an emerging scheme in the diagnosis of AVS. In this prospective study, we evaluated the specificity and sensitivity of HINTS in distinguishing between central and peripheral AVS.

Methods
A cohort of 239 cases with complete clinical record was recruited in the study. All patients completed emergency brain CT examination to exclude hemorrhagic stroke. HINTS examination was conducted to distinguish between central AVS and peripheral AVS, and all patients completed head MRI, BAEP and vestibular function examinations within one week. Patients diagnosed as central AVS were subject to angiography (CTA/MRA/DSA), and patients with peripheral AVS were considered for a 3-month follow-up to correct the initial diagnosis.

Results
Patients with central AVS were associated with an elder age, higher incidences of hypertension, atrial fibrillation, family history of stroke and previous history of stroke. Posterior circulation cerebral infarction, vestibular migraine and cerebellitis were the dominant diseases associated with central AVS. The sensitivities of HIT, GE, and TS in the diagnosis of central AVS were 73.5%, 61.2%, and 26.5%, and the specificities were 97.9%, 92.6%, and 93.2% respectively.

Conclusions
The sensitivity of HINTS for central AVS diagnosis is 89.8% and the specificity is 84.2%. HINTS is an easy-to-operate, low-cost, high-sensitivity and specific examination technique, which is practical in neurology outpatient clinics and emergency departments.
EVI1 expression in early-stage breast cancer patients treated with neoadjuvant chemotherapy
Authors: Leichsenring Jonas , Vladimirova Valentina , Solbach Christine , Karn Thomas , Ataseven Beyhan , Sinn Bruno Valentin , Barinoff Jana , Müller Volkmar , Blohmer Jens-Uwe , Schem Christian , Engels Knut , Marmé Frederik , Fisseler-Eckhoff Annette , Fasching Peter A. , Stickeler Elmar , van Mackelenbergh Marion , Denkert Carsten , Stenzinger Albrecht , Loibl Sibylle , Gröschel Stefan 
Published: October 2022

Abstract
Background
Overexpression of the EVI1 (ecotropic viral integration site 1) oncogene has recently been implicated as a prognostic factor in breast cancer (BC), particularly in triple-negative BC (TNBC). In this study we aimed to investigate frequency and clinical relevance of EVI1 expression in newly diagnosed BC treated with neoadjuvant chemotherapy.

Methods
EVI1 expression was determined by immunohistochemistry using H-score as a cumulative measurement of protein expression in pretherapeutic biopsies of BC patients treated with anthracycline/taxane based neoadjuvant chemotherapy within the GeparTrio trial. EVI1 was analyzed as a continuous variable and dichotomized into low or high based on median expression. Endpoints were pathological complete response (pCR), disease-free survival (DFS) and overall survival (OS).

Results
Of the 993 tumors analyzed, 882 had available subtype information: 50.8% were HR + /HER2-, 15% HR + /HER2 + , 9.8% HR-/HER2 + , and 24.5% TNBC. Median EVI1 H-score was 112.16 (range 0.5–291.4). High EVI1 expression was significantly associated with smaller tumor size (p = 0.002) but not with BC subtype. Elevated EVI1 levels were not significantly associated with therapy response and survival in the entire cohort or within BC subtypes. However, TNBC patients with high EVI1 showed a trend towards increased pCR rates compared to low group (37.7% vs 27.5%, p = 0.114; odds ratio 1.60 (95%CI 0.90–2.85, p = 0.110) and numerically better DFS (HR = 0.77 [95%CI 0.48–1.23], log-rank p = 0.271) and OS (HR = 0.76 [95% 0.44–1.31], log-rank p = 0.314) without reaching statistical significance.

Conclusion
EVI1 was not associated with response to neoadjuvant therapy or patient survival in the overall cohort. Further analyses are needed to verify our findings especially in the pathological work-up of early-stage HER2-negative BC patients.

Trial registration
NCT00544765.
Prognosis of lasso-like penalized Cox models with tumor profiling improves prediction over clinical data alone and benefits from bi-dimensional pre-screening
Authors: Jardillier Rémy , Koca Dzenis , Chatelain Florent , Guyon Laurent 
Published: October 2022

Abstract
Background
Prediction of patient survival from tumor molecular ‘-omics’ data is a key step toward personalized medicine. Cox models performed on RNA profiling datasets are popular for clinical outcome predictions. But these models are applied in the context of “high dimension”, as the number p of covariates (gene expressions) greatly exceeds the number n of patients and e of events. Thus, pre-screening together with penalization methods are widely used for dimensional reduction.

Methods
In the present paper, (i) we benchmark the performance of the lasso penalization and three variants (i.e., ridge, elastic net, adaptive elastic net) on 16 cancers from TCGA after pre-screening, (ii) we propose a bi-dimensional pre-screening procedure based on both gene variability and p-values from single variable Cox models to predict survival, and (iii) we compare our results with iterative sure independence screening (ISIS).

Results
First, we show that integration of mRNA-seq data with clinical data improves predictions over clinical data alone. Second, our bi-dimensional pre-screening procedure can only improve, in moderation, the C-index and/or the integrated Brier score, while excluding irrelevant genes for prediction. We demonstrate that the different penalization methods reached comparable prediction performances, with slight differences among datasets. Finally, we provide advice in the case of multi-omics data integration.

Conclusions
Tumor profiles convey more prognostic information than clinical variables such as stage for many cancer subtypes. Lasso and Ridge penalizations perform similarly than Elastic Net penalizations for Cox models in high-dimension. Pre-screening of the top 200 genes in term of single variable Cox model p-values is a practical way to reduce dimension, which may be particularly useful when integrating multi-omics.
Association of levels of metabolites with the safe margin of rectal cancer surgery: a metabolomics study
Authors: Zhang Shaopeng , Pan Guoqiang , Liu Zhifeng , Kong Yuan , Wang Daguang 
Published: October 2022

AbstractBackgroundRectal cancer is one of the most lethal of gastrointestinal malignancies. Metabonomics has gradually developed as a convenient, inexpensive and non-destructive technique for the study of cancers.MethodsA total of 150 tissue samples from 25 rectal cancer patients were analyzed by liquid chromatography–mass spectrometry (LC–MS), and 6 tissue samples were collected from each patient (group 1: tumor; group 2: 0.5 cm from tumor; group 3:1 cm from tumor; group 4:2 cm from tumor; group 5:3 cm from tumor and group 6:5 cm from tumor). The differential metabolites of tumor tissues and 5 cm from the tumor (normal tissues) were first selected. The differential metabolites between tumor tissues and normal tissues were regrouped by hierarchical clustering analysis, and further selected by discriminant analysis according to the regrouping of clustering results. The potential safe margin of clinical T(cT)1,cT2 stage rectal cancer and cT3,cT4 stage rectal cancer at the metabolomic level was further identified by observing the changes in the level of differential metabolites within the samples from group 1 to group 6.ResultsWe found 22 specific metabolites to distinguish tumor tissue and normal tissue. The most significant changes in metabolite levels were observed at 0.5 cm (cT1, cT2) and 2.0 cm (cT3, cT4) from the tumor, while the changes in the tissues afterwards showed a stable trend.ConclusionsThere are differential metabolites between tumor tissues and normal tissues in rectal cancer. Based on our limited sample size, the safe distal incision margin for rectal cancer surgery in metabolites may be 0.5 cm in patients with cT1 and cT2 stage rectal cancer and 2.0 cm in patients with cT3 and cT4 stage rectal cancer.
Association between obese phenotypes and risk of carotid artery plaque among chinese male railway drivers
Authors: Pan Jia , Wang Zihang , Dong Chaohui , Yang Bo , Tang Lei , Jia Peng , Yang Shujuan , Zeng Honglian 
Published: October 2022

Abstract
Background
China has the world’s highest rail transportation network density, and the prevalence of obesity among railway workers in China is more than twice that of adults in the world. Carotid artery plaque (CAP) is a simple and noninvasive predictor of early atherosclerosis, while the association between different obese phenotypes and CAP risk among Chinese male railway drivers is unclear.

Methods
This cross-sectional study was performed among 8,645 Chinese male railway drivers. Obese phenotypes were assessed based on the obesity status (the body mass index ≥ 28 kg/m2 as obesity vs. < 28 kg/m2 as non-obesity) and metabolic status (metabolically healthy vs. metabolically unhealthy). Metabolically unhealthy was defined as the presence of at least one dysfunction, including elevated blood pressure, elevated fasting blood glucose, elevated triglyceride, and reduced high-density-lipoprotein cholesterol. Four obese phenotypes were defined based on the body mass index and metabolic status, i.e., metabolically healthy non-obesity (MHNO), metabolically healthy obesity (MHO), metabolically unhealthy obesity (MUO), and metabolically unhealthy non-obesity (MUNO). Multivariable logistic regression was employed to estimate the association between different obese phenotypes and the risk of CAP. Subgroup analysis was performed to examine the variation of the association by age, circadian rhythm disorders, and history of smoking and drinking.

Results
The prevalence of CAP among male railway drivers in MHO, MUO, MUNO, and MHNO was 8.75%, 18.67%, 17.82%, and 5.36%, respectively. Compared to those with MHNO, an increased risk for CAP was observed among those with MHO (OR = 2.18, 95% CI: 0.82, 5.10), MUO (OR = 1.78, 95% CI:1.44, 2.21), and MUNO (OR = 2.20, 95% CI: 1.67, 2.89). The subgroup analysis showed that both of the metabolically unhealthy groups (MUNO and MUO) aged < 45 years were prone to a higher risk of CAP (for the MUNO group, OR = 4.27, 95% CI:2.71, 7.10; for the MUO group, OR = 4.00, 95%CI: 2.26, 7.17).

Conclusion
The obese phenotypes are associated with CAP risk in male railway drivers, especially those with metabolically unhealthy conditions aged < 45 years.