bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toxoplasmosis in immunocompetent Saudi women: Correlation with vitamin D
Authors: Rasheed Zafar , Shariq Ali , AlQefari Ghaida B , Alwahbi Ghayda S , Aljuaythin Amal I , Alsuhaibani Fidaa S , Alotaibi Daliyah F , Aljohani Shahad S , Alghasham Ruqiah , Alsaeed Thamir , Alharbi Nada A , Rugaie Osamah Al , Abdulmonem Waleed Al , Sharaf Osama F 
Published: September 2021

Objective: Toxoplasma gondii ( T. gondii) is a life-threatening parasite particularly infecting the immunocompromised women. Deficiency of vitamin D is well reported in several infectious disorders. This study was undertaken to investigate a correlation of vitamin D deficiency with the onset of T. gondii infection in immunocompetent women from the central of Saudi Arabia. Methods: Blood samples were collected from 304 Saudi women from the Qassim region of Saudi Arabia. Specific immunoassays were used to determine the levels of T. gondii immunoglobulin G and vitamin D. The SPSS and the Prism Graph Pad statistical software were used for the data analysis. Results: Out of 304 women, 18.8% were found to be positive for toxoplasmosis. Interestingly, the serum levels of vitamin D in toxoplasma positive cases were found to be significantly low as compared with the levels of vitamin D in toxoplasma negative cases. Moreover, sociodemographic risk factors such as age, residence location, and consumption of fruits/vegetables were also found to be associated with vitamin D deficiency and with the seroprevalence of toxoplasmosis. Conclusion: This study investigated a direct correlation of vitamin D deficiency with the severity of the toxoplasmosis in Saudi women. Therefore, it is predicted that vitamin D supplementation may provide protection against toxoplasma infection.
Ramucirumab plus paclitaxel as second-line treatment in patients with advanced gastric or gastroesophageal junction adenocarcinoma: a nationwide real-world outcomes in Korea study (KCSG-ST19-16)
Authors: Han Hye Sook , Kim Bum Jun , Jee Hee-Jung , Ryu Min-Hee , Park Se Hoon , Rha Sun Young , Kim Jong Gwang , Bae Woo Kyun , Lee Keun-Wook , Oh Do-Youn , Kim In-Ho , Sym Sun Jin , Oh So Yeon , Kim Hyeong Su , Byun Ji-Hye , Kim Dong Sook , Suh Young Ju , An Hyonggin , Zang Dae Young 
Published: September 2021

Background: Ramucirumab as monotherapy or in combination with paclitaxel is a second-line treatment option recommended for patients with locally advanced unresectable or metastatic gastric or gastroesophageal junction (GEJ) adenocarcinoma. However, real-world data from large study cohorts focused on ramucirumab plus paclitaxel in gastric cancer are limited. Methods: The study population comprised all patients with gastric or GEJ cancer who received ramucirumab plus paclitaxel in South Korea between 1 May 2018 and 31 December 2018. We included patients with advanced gastric or GEJ adenocarcinoma and disease progression after first-line platinum and fluoropyrimidine-containing combination chemotherapy. Results: In total, 1063 patients were included in the present study. The objective response rate and disease control rate were 15.1% and 57.7%, respectively. The median progression-free survival was 4.03 months (95% confidence interval, 3.80–4.27) and the median overall survival was 10.03 months (95% confidence interval, 9.33–10.73). Grade 3 or higher treatment-related adverse events with incidence of ⩾5% were neutropenia (35.1%) and anemia (10.5%). Based on multivariable analysis, overall survival was negatively associated with Eastern Cooperative Oncology Group performance status ⩾2, weight loss ⩾10% in the previous 3 months, GEJ of primary tumor, poor or unknown histologic grade, number of metastatic sites ⩾3, presence of peritoneal metastasis, no prior gastrectomy, and time to second-line since first-line treatment <6 months. Conclusion: Our large-scale, nationwide, real-world data analysis of an unselected real-world population adds evidence for the efficacy and safety of second-line ramucirumab plus paclitaxel in patients with locally advanced unresectable or metastatic gastric or GEJ adenocarcinoma.
Ultrasound-guided erector spinae interfascial plane block for spinal surgery in three cats
Authors: Alza Salvatierra Diego N , Herrera Linares Manuel E , Motta Luca , Martinez Miguel 
Published: September 2021

Case series summary The erector spinae plane (ESP) block consists of an interfascial injection of local anaesthetic between the erector spinae muscle group and the transverse processes of the thoracic vertebrae. This block targets the dorsal rami of the thoracic spinal nerves to desensitise the cutaneous area near the dorsal midline, the paraspinal muscles, the dorsal vertebral laminae and the facet joints. The purpose of this case series is to describe the perioperative analgesic effect and complications of ultrasound-guided ESP block with bupivacaine in three cats undergoing spinal surgery. Only one cardiovascular response was recorded in this case series. Just one cat received intraoperative rescue analgesia. Cats 1 and 2 recorded just one high pain score in the first 24 h postoperatively, and cat 3 recorded three high pain scores. The total amount of methadone given in the 24 h postoperatively was 0.6 mg/kg in cat 1, 0.9 mg/kg in cat 2 and 0.8 mg/kg in cat 3. All three cats suffered mild and transient intraoperative complications, which were easily addressed. There were no postoperative complications. Relevance and novel information This case series documents a novel locoregional anaesthesia technique as an alternative to traditional systemic analgesia. The technique is part of a multimodal analgesia approach for spinal surgery in cats. Perioperative analgesic effect and complications presented in this case series are evaluated and discussed.
Neural-Fuzzy-Based Adaptive Sliding Mode Automatic Steering Control of Vision-based Unmanned Electric Vehicles
Authors: Guo Jinghua , Li Keqiang , Fan Jingjing , Luo Yugong , Wang Jingyao 
Published: September 2021

AbstractThis paper presents a novel neural-fuzzy-based adaptive sliding mode automatic steering control strategy to improve the driving performance of vision-based unmanned electric vehicles with time-varying and uncertain parameters. Primarily, the kinematic and dynamic models which accurately express the steering behaviors of vehicles are constructed, and in which the relationship between the look-ahead time and vehicle velocity is revealed. Then, in order to overcome the external disturbances, parametric uncertainties and time-varying features of vehicles, a neural-fuzzy-based adaptive sliding mode automatic steering controller is proposed to supervise the lateral dynamic behavior of unmanned electric vehicles, which includes an equivalent control law and an adaptive variable structure control law. In this novel automatic steering control system of vehicles, a neural network system is utilized for approximating the switching control gain of variable structure control law, and a fuzzy inference system is presented to adjust the thickness of boundary layer in real-time. The stability of closed-loop neural-fuzzy-based adaptive sliding mode automatic steering control system is proven using the Lyapunov theory. Finally, the results illustrate that the presented control scheme has the excellent properties in term of error convergence and robustness.
Efficacy and safety of erenumab in Japanese migraine patients with prior preventive treatment failure or concomitant preventive treatment: subgroup analyses of a phase 3, randomized trial
Authors: Hirata Koichi , Sakai Fumihiko , Takeshima Takao , Imai Noboru , Matsumori Yasuhiko , Yoshida Ryuji , Numachi Yotaro , Peng Cheng , Mikol Daniel D. , Cheng Sunfa 
Published: September 2021

Abstract
Background
These subgroup analyses of a Phase 3, randomized, double-blind, placebo-controlled study evaluated the efficacy and safety of erenumab 70 mg in Japanese migraine patients with/without prior preventive treatment failure(s) (“failed-yes” and “failed-no” subgroups) and with/without concomitant preventive treatment (“concomitant preventive-yes” and “concomitant preventive-no” subgroups).

Methods
Overall, 261 patients were randomized; 130 and 131 patients to erenumab 70 mg and placebo, respectively. Subgroup analyses evaluated the change from baseline to Months 4–6 in mean monthly migraine days (MMD) (primary endpoint), achievement of a ≥50% reduction in mean MMD, and change from baseline in mean monthly acute migraine-specific medication (MSM) treatment days. Treatment-emergent adverse events were also evaluated.

Results
Of the 261 patients randomized, 117 (44.8%) and 92 (35.3%) patients were in the failed-yes and concomitant preventive-yes subgroups, respectively. Erenumab 70 mg demonstrated consistent efficacy across all subgroups, with greater reductions from baseline in mean MMD versus placebo at Months 4–6 (treatment difference versus placebo [95% CI], failed-yes: − 1.9 [− 3.3, − 0.4]; failed-no: − 1.4 [− 2.6, − 0.3]; concomitant preventive-yes: − 1.7 [− 3.3, 0.0]; concomitant preventive-no: − 1.6 [− 2.6, − 0.5]). Similar results were seen for achievement of ≥50% reduction in mean MMD and change from baseline in mean monthly acute MSM treatment days. The safety profile of erenumab 70 mg was similar across subgroups, and similar to placebo in each subgroup.

Conclusion
Erenumab was associated with clinically relevant improvements in all efficacy endpoints and was well tolerated across all subgroups of Japanese migraine patients with/without prior preventive treatment failure(s) and with/without concomitant preventive treatment.

Trial registration
Clinicaltrials.gov. NCT03812224. Registered January 23, 2019.
Return to physical activity and change in body mass index after hypoallergenic medial mobile-bearing unicompartmental knee arthroplasty
Authors: D’Ambrosi Riccardo , Nuara Alessandro , Mariani Ilaria , Corona Katia , Mogos Stefan , Catellani Francesco , Hantes Michael , Ursino Nicola 
Published: September 2021

Abstract
Background
The primary purpose of the present prospective study was to consecutively analyse the outcomes of the return to sports activity of patients with positive patch tests undergoing a medial mobile-bearing titanium niobium nitride (TiNbN) unicompartmental knee arthroplasty (UKA). The secondary purpose was to ascertain if a higher grade of physical activity leads to a reduction in the body mass index (BMI) of the patients.

Material and methods
Forty-one patients with positive skin patch tests were included in this prospective study. The clinical evaluation consisted of the University of California, Los Angeles (UCLA) activity scale and the High-Activity Arthroplasty Score (HAAS). Each patient was evaluated the day before surgery (T0), after 12.37 ± 0.70 months (T1), and on the day of the final follow-up, after 67.03 ± 18.2 months (T2). Furthermore, the BMI of each patient was analysed before surgery and during the final follow-up.

Results
The UCLA and HAAS mean preoperative values ranged from 3.68 ± 1.1.7 and 6.15 ± 0.76 to 6.1 ± 0.76 and 10.34 ± 1.3, respectively, at T1 (p < 0.0001) and to the final values of 6.34 ± 0.62 and 11.0 ± 8.9, respectively, at T2 (UCLA: T2 versus T1: p = 0.132; T2 versus T0: p < 0.0001; HAAS: T2 versus T1: p = 0.0027; T2 versus T0: p < 0.001). BMI ranged from a preoperative value of 27.97 ± 3.63 to a final value of 26.84 ± 3.11 (p < 0.0001). The only differences within the subgroups concerned patients with BMI ≥ 28, showing a superior HAAS at each follow-up (p < 0.05). A positive correlation was found between BMI and HAAS at T0 and T2 (p < 0.05).

Conclusions
This is the first study to evaluate the rate of the return to sports activities and change in BMI following hypoallergenic UKA. The majority of patients reduced their weight following UKA and improved their physical activity, showing outcomes that were comparable to the standard cobalt–chrome (CoCr) prostheses, regardless of gender, age, BMI and implant size.

Level of evidence
IV – Prospective Cohort Study.
Trial registration researchregistry5978—Research Registry www.researchregistry.com
Limited value of serum neutrophil-to-lymphocyte ratio in the diagnosis of chronic periprosthetic joint infection
Authors: Ye Yongyu , Chen Weishen , Gu Minghui , Liu Qiaoli , Xian Guoyan , Pan Baiqi , Zheng Linli , Chen Xiaoling , Zhang Ziji , Sheng Puyi 
Published: September 2021

Abstract
Background
Diagnosing chronic periprosthetic joint infection (PJI) is challenging. No single biomarker can accurately recognize PJI preoperatively in a timely manner. Therefore, the aim of the present study was to investigate the usefulness of the serum neutrophil-to-lymphocyte ratio (NLR) in aiding the diagnosis of chronic PJI.

Materials and methods
We retrospectively evaluated the medical records of 158 patients who had undergone revision arthroplasty (104 with aseptic mechanic failure and 54 with chronic PJI) from July 2011 to July 2020. Univariate analysis followed by multivariate logistic regression was applied to compare NLR, C-reactive protein (CRP), and erythrocyte sedimentation ratio (ESR) between the two groups. The receiver operating characteristic (ROC) curve was used to assess the diagnostic performance of NLR alone and in combination with CRP and ESR.

Results
NLR, CRP, and ESR were significantly higher in patients with chronic PJI than in the aseptic revision group (p < 0.05). ROC curve analysis revealed that NLR had a sensitivity of 57.41% and a specificity of 77.88% with an optimal threshold of 2.56. The optimal threshold for CRP and ESR was 7.00 mg/L (sensitivity 62.50% and specificity 83.12%) and 43 mm/h (sensitivity 59.38% and specificity 80.52%), respectively. The combined diagnostic value of NLR with CRP and ESR was shown to have no additional diagnostic value in predicting chronic PJI.

Conclusion
Compared with traditional inflammatory biomarkers (ESR and CRP), the value of serum NLR alone or combined with CRP and ESR for diagnosing chronic PJI is limited.

Level of evidence
Level 3.
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction
Authors: Solana Jimena , Garrote-Sánchez Emilio , Gil Rosario 
Published: September 2021

Abstract
Background
The study of gene essentiality is fundamental to understand the basic principles of life, as well as for applications in many fields. In recent decades, dozens of sets of essential genes have been determined using different experimental and bioinformatics approaches, and this information has been useful for genome reduction of model organisms. Multiple in silico strategies have been developed to predict gene essentiality, but no optimal algorithm or set of gene features has been found yet, especially for non-model organisms with incomplete functional annotation.

Results
We have developed DELEAT v0.1 (DELetion design by Essentiality Analysis Tool), an easy-to-use bioinformatic tool which integrates an in silico gene essentiality classifier in a pipeline allowing automatic design of large-scale deletions in any bacterial genome. The essentiality classifier consists of a novel logistic regression model based on only six gene features which are not dependent on experimental data or functional annotation. As a proof of concept, we have applied this pipeline to the determination of dispensable regions in the genome of Bartonella quintana str. Toulouse. In this already reduced genome, 35 possible deletions have been delimited, spanning 29% of the genome.

Conclusions
Built on in silico gene essentiality predictions, we have developed an analysis pipeline which assists researchers throughout multiple stages of bacterial genome reduction projects, and created a novel classifier which is simple, fast, and universally applicable to any bacterial organism with a GenBank annotation file.
Fast and exact quantification of motif occurrences in biological sequences
Authors: Prosperi Mattia , Marini Simone , Boucher Christina 
Published: September 2021

Abstract
Background
Identification of motifs and quantification of their occurrences are important for the study of genetic diseases, gene evolution, transcription sites, and other biological mechanisms. Exact formulae for estimating count distributions of motifs under Markovian assumptions have high computational complexity and are impractical to be used on large motif sets. Approximated formulae, e.g. based on compound Poisson, are faster, but reliable p value calculation remains challenging. Here, we introduce ‘motif_prob’, a fast implementation of an exact formula for motif count distribution through progressive approximation with arbitrary precision. Our implementation speeds up the exact calculation, usually impractical, making it feasible and posit to substitute currently employed heuristics.

Results
We implement motif_prob in both Perl and C+ + languages, using an efficient error-bound iterative process for the exact formula, providing comparison with state-of-the-art tools (e.g. MoSDi) in terms of precision, run time benchmarks, along with a real-world use case on bacterial motif characterization. Our software is able to process a million of motifs (13–31 bases) over genome lengths of 5 million bases within the minute on a regular laptop, and the run times for both the Perl and C+ + code are several orders of magnitude smaller (50–1000× faster) than MoSDi, even when using their fast compound Poisson approximation (60–120× faster). In the real-world use cases, we first show the consistency of motif_prob with MoSDi, and then how the p-value quantification is crucial for enrichment quantification when bacteria have different GC content, using motifs found in antimicrobial resistance genes. The software and the code sources are available under the MIT license at https://github.com/DataIntellSystLab/motif_prob.

Conclusions
The motif_prob software is a multi-platform and efficient open source solution for calculating exact frequency distributions of motifs. It can be integrated with motif discovery/characterization tools for quantifying enrichment and deviation from expected frequency ranges with exact p values, without loss in data processing efficiency.
A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers
Authors: Hong Zhou , Liao Xuezhu , Ye Yuanjun , Zhang Ningnan , Yang Zengjiang , Zhu Weidong , Gao Wei , Sharbrough Joel , Tembrock Luke R. , Xu Daping , Wu Zhiqiang 
Published: September 2021

Abstract
Background
Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers.

Results
We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as a single circular structure of 435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386 bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome.

Conclusion
For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.
Altered expression of microRNAs in the rat diaphragm in a model of ventilator-induced diaphragm dysfunction after controlled mechanical ventilation
Authors: Wang Pengcheng , Zhou Xianlong , Li Gang , Ma Haoli , Liu Ruining , Zhao Yan 
Published: September 2021

AbstractBackgroundVentilator-induced diaphragm dysfunction (VIDD) is a common complication of life support by mechanical ventilation observed in critical patients in clinical practice and may predispose patients to severe complications such as ventilator-associated pneumonia or ventilator discontinuation failure. To date, the alterations in microRNA (miRNA) expression in the rat diaphragm in a VIDD model have not been elucidated. This study was designed to identify these alterations in expression.ResultsAdult male Wistar rats received conventional controlled mechanical ventilation (CMV) or breathed spontaneously for 12 h. Then, their diaphragm tissues were collected for RNA extraction. The miRNA expression alterations in diaphragm tissue were investigated by high-throughput microRNA-sequencing (miRNA-seq). For targeted mRNA functional analysis, gene ontology (GO) analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were subsequently conducted. qRT-PCR validation and luciferase reporter assays were performed. We successfully constructed a model of ventilator-induced diaphragm dysfunction and identified 38 significantly differentially expressed (DE) miRNAs, among which 22 miRNAs were upregulated and 16 were downregulated. GO analyses identified functional genes, and KEGG pathway analyses revealed the signaling pathways that were most highly correlated, which were the MAPK pathway, FoxO pathway and Autophagy–animal. Luciferase reporter assays showed that STAT3 was a direct target of both miR-92a-1-5p and miR-874-3p and that Trim63 was a direct target of miR-3571.ConclusionsThe current research supplied novel perspectives on miRNAs in the diaphragm, which may not only be implicated in diaphragm dysfunction pathogenesis but could also be considered as therapeutic targets in diaphragm dysfunction.