bluuebunny/crossref_metadata_2025_split huggingface dataset:
Online supervised versus workplace corrective exercises for upper crossed syndrome: a protocol for a randomized controlled trial
Authors: Yaghoubitajani Zohreh , Gheitasi Mehdi , Bayattork Mohammad , Andersen Lars Louis 
Published: December 2021

Abstract
Background and objective
Musculoskeletal disorders (MSDs) including upper crossed syndrome (UCS) are considered as the leading cause of work-related issues worldwide among office workers. Therefore, the present study aims to evaluate the effect of workplace-based versus online-supervised home-based corrective exercises among office workers with UCS.

Methods and design
To this end, 45 subjects within the age range of 30–45 years are randomly assigned to three groups in the present parallel-group, randomized control trial using a pretest-posttest design. These groups include the subjects who receive online-supervised exercise and workplace exercise containing three sessions of intervention for 8 weeks and the control group receives no intervention while performing routine activities. The primary outcome variables are neck-shoulder pain (NSP) and consequent sick leave due to NSP, followed by alignment, workability, and the surface electromyography of upper, middle, and lower trapezius (UT, MT, and LT), sternocleidomastoid (SCM), and serratus anterior (SA) as the secondary variables.

Discussion
The present study seeks to assess the effect of workplace versus online-supervised corrective exercise interventions among 45 office workers suffering from UCS. It is expected to improve and reduce the related symptoms including postural malalignment and imbalance muscles after 8 weeks of corrective exercises. If effective, the findings may lead to adherence and work performance among the office workers, and individuals subjected to UCS can use the benefits of an online-supervised intervention. In addition, the findings may be useful in different workplaces as the evidence for employers to benefit from the reduction in the related costs and side effects of work-related neck/shoulder disorders including work disability, productivity loss, time expense, social insurance, work absenteeism, and treatment costs. Finally, clinicians and corrective exercise therapists can consider it as a clinical based-evidence intervention for their further actions.

Trial registration
Iranian Registry of Clinical Trials IRCT20200729048249N1. Registered on 5 October 2020 (https://en.irct.ir/user/trial/49992/view)
Feasibility of remote neurocognitive assessment: pandemic adaptations for a clinical trial, the Cognition and Obstructive Sleep Apnea in Parkinson’s Disease, Effect of Positive Airway Pressure Therapy (COPE-PAP) study
Authors: Lajoie Annie C. , Crane Joelle , Robinson Ann R. , Lafontaine Anne-Louise , Benedetti Andrea , Kimoff R. John , Kaminska Marta 
Published: December 2021

Abstract
Background
The COVID-19 pandemic poses challenges for timely outcome assessment in randomized clinical trials (RCT). Our aim was to describe our remote neurocognitive testing (NCT) protocol administered by telephone in patients with Parkinson’s disease (PD) and obstructive sleep apnea (OSA).

Methods
We studied PD patients with OSA and Montreal Cognitive Assessment (MoCA) score ≤ 27 participating in a RCT assessing OSA treatment impact on cognition. Trial outcomes included change in MoCA and specific cognitive domains from baseline to 3 and 6 months. With COVID19 pandemic-related restrictions, 3-month visits were converted from in-person to telephone administration with materials mailed to participants for compatible tests and retrieved by courier the same day. In exploratory analyses, we compared baseline vs. 3-month results in the control arm, which were not expected to change significantly (test-re-test), using a paired t-test and assessed agreement with the intraclass correlation coefficient (ICC).

Results
Seven participants were approached and agreed to remote NCT at 3-month follow-up. Compared to the in-person NCT control arm group, they were younger (60.6 versus 70.6 years) and had a shorter disease course (3.9 versus 9.2 years). Remote NCT data were complete. The mean test-retest difference in MoCA was similar for in-person and remote NCT control-arm groups (between group difference − 0.69; 95%CI − 3.67, 2.29). Agreement was good for MOCA and varied for specific neurocognitive tests.

Conclusion
Telephone administration of the MoCA and a modified neurocognitive battery is feasible in patients with PD and OSA. Further validation will require a larger sample size.
One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics
Authors: Vishnu Udayakumar S. , Estève Pierre-Olivier , Chin Hang Gyeong , Pradhan Sriharsa 
Published: December 2021

Abstract
Background
Accessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development. Chromatin accessibility along with integrated multiomics approaches have been used for determining molecular subtypes of cancer in patient samples.

Results
One-pot Universal NicE-seq (One-pot UniNicE-seq) is an improved accessible chromatin profiling method that negate DNA purification and incorporate sonication free enzymatic fragmentation before library preparation and is suited to a variety of mammalian cells. One-pot UniNicE-seq is versatile, capable of profiling 4% formaldehyde fixed chromatin in as low as 25 fixed cells. Accessible chromatin profile is more efficient on formaldehyde-fixed cells using one-pot UniNicE-seq compared to Tn5 transposon mediated methods, demonstrating its versatility.

Conclusion
One-pot UniNicE-seq allows the entire process of accessible chromatin labeling and enrichment in one pot at 4% formaldehyde cross-linking conditions. It doesn’t require enzyme titration, compared to other technologies, since accessible chromatin is labelled with 5mC incorporation and deter degradation by nicking enzyme, thus opening the possibility for automation.
A method for monitoring the coupling evolution of microservice-based architectures
Authors: Apolinário Daniel R.F. , de França Breno B.N. 
Published: December 2021

AbstractThe microservice architecture is claimed to satisfy ongoing software development demands, such as resilience, flexibility, and velocity. However, developing applications based on microservices also brings some drawbacks, such as the increased software operational complexity. Recent studies have also pointed out the lack of methods to prevent problems related to the maintainability of these solutions. Disregarding established design principles during the software evolution may lead to the so-called architectural erosion, which can end up in a condition of unfeasible maintenance. As microservices can be considered a new architecture style, there are few initiatives to monitoring the evolution of software microservice-based architectures. In this paper, we introduce the SYMBIOTE method for monitoring the coupling evolution of microservice-based systems. More specifically, this method collects coupling metrics during runtime (staging or production environments) and monitors them throughout software evolution. The longitudinal analysis of the collected measures allows detecting an upward trend in coupling metrics that could represent signs of architectural degradation. To develop the proposed method, we performed an experimental analysis of the coupling metrics behavior using artificially generated data. The results of these experiment revealed the metrics behavior in different scenarios, providing insights to develop the analysis method for the identification of architectural degradation. We evaluated the SYMBIOTE method in a real-case open source project called Spinnaker. The results obtained in this evaluation show the relationship between architectural changes and upward trends in coupling metrics for most of the analyzed release intervals. Therefore, the first version of SYMBIOTE has shown potential to detect signs of architectural degradation during the evolution of microservice-based architectures.
The value of MRI compared to conventional radiography in analysing morphologic changes in the spine in axial spondyloarthritis
Authors: Adelsmayr Gabriel , Haidmayer Andreas , Spreizer Christopher , Janisch Michael , Quehenberger Franz , Klocker Eva , Graninger Winfried , Fuchsjäger Michael , Hermann Josef 
Published: December 2021

Abstract
Background
Imaging of morphologic changes in the vertebral spine in axial spondyloarthritis (SpA) is routinely performed with conventional radiography limited by superposition in the thoracic segments and radiation exposure. The objective was to assess the reliability of MRI compared to conventional radiography in depicting morphologic vertebral lesions in patients with axial SpA. Forty patients diagnosed with axial SpA were included in this cross-sectional study. Patients underwent MRI of the whole spine with T1-weighted and TIRM sequences in the sagittal plane and conventional radiography of the cervical and lumbar spine in lateral projections. Morphologic changes (syndesmophytes and erosions) in the anterior vertebral endplates on MRI and conventional radiography were independently evaluated by two radiologists. Inter-modality and interobserver agreement were calculated using Cohen’s Kappa.

Results
Inter-modality agreement was low for cervical and lumbar syndesmophytes and erosions (κ ≤ 0.2 ± 0.07–0.1). Interobserver agreement on conventional radiography was highest for cervical and lumbar anterior syndesmophytes/bridging (κ = 0.92 ± 0.02–0.03). Syndesmophytes in thoracic anterior vertebral units were the most frequent MRI finding with a high interobserver agreement (κ = 0.83 ± 0.05).

Conclusions
In imaging morphologic changes in the spine in patients with axial SpA, MRI was shown to be not an equivalent substitute but a complementary imaging modality to conventional radiography. Conventional radiography seems superior to depict morphologic cervical and lumbar vertebral changes compared to MRI, whereas MRI may visualise morphologic lesions in the thoracic spine.
CMR Characteristics, gene variants and long-term outcome in patients with left ventricular non-compaction cardiomyopathy
Authors: Zhou Di , Li Shijie , Sirajuddin Arlene , Wu Weichun , Huang Jinghan , Sun Xiaoxin , Zhao Shihua , Pu Jielin , Lu Minjie 
Published: December 2021

AbstractBackgroundAs the paucity of data focusing on evaluating cardiac structure and function in patients with or without gene mutation, this study was sought to investigate the correlation between genotype and cardiac magnetic resonance (CMR) phenotype in patients with left ventricular non-compaction cardiomyopathy (LVNC) and to explore prognostic relevance in this cohort if possible.MethodsPatients with LVNC who underwent CMR and targeted gene sequencing between 2006 and 2016 were retrospectively evaluated. Demographic data, clinical presentation, genetic analysis, CMR data and follow-up data of all participants were collected.ResultsCompared to negative genotype (G−) group, patients with positive genotype (G+) had larger left atrial volume (LAV), and carriers of multiple variants had lower left ventricular (LV) ejection fraction and cardiac index, increased LV fibrosis, larger LA volume, reduced LV global circumferential strain, LA reservoir strain and booster pump strain (allp < 0.05). LA volume was able to discriminate patients with G + (allp < 0.05), as well as those with multiple genetic mutation (allp < 0.01). During a median follow-up of 5.1 years, Kaplan–Meier survival analysis revealed worse primary endpoint-free survival among carriers of multiple variants compared to G− group.ConclusionsCMR feature tracking is a remarkable tool to evaluate implication, genetics cascade screen and predict outcome in LVNC population. LA volume is a sensitive and robust indicator for genetic mutational condition, of which facilities to guide clinical management and intensity of follow-up for patients and their relatives.
Intensity of arterial structure acquired by Silent MRA estimates cerebral blood flow
Authors: Hwang Zhen-An , Li Chia-Wei , Lin Chien-Yuan Eddy , Chen Jyh-Horng , Chen Chia-Yuen , Chan Wing P. 
Published: December 2021

Abstract
Background
Cerebral blood flow (CBF) and the morphology of the cerebral arteries are important for characterizing cerebrovascular disease. Silent magnetic resonance angiography (Silent MRA) is a MRA technique focusing on arterial structural delineation. This study was conducted to investigate the correlation between Silent MRA and CBF quantification, which has not yet been reported.

Methods
Both the Silent MRA and time-of-flight magnetic resonance angiography scans were applied in seventeen healthy participants to acquire the arterial structure and to find arterial intensities. Phase-contrast MRA (PC-MRA) was then used to perform the quantitative CBF measurement of 13 cerebral arteries. Due to different dataset baseline signal level of Silent MRA, the signal intensities of the selected 13 cerebral arteries were normalized to the selected ROIs of bilateral internal carotid arteries. The normalized signal intensities were used to determine the relationship between Silent MRA and CBF.

Results
The image intensity distribution of arterial regions generated by Silent MRA showed similar laminar shape as the phase distribution by PC-MRA (correlation coefficient > 0.62). Moreover, in both the results of individual and group-leveled analysis, the intensity value of arterial regions by Silent MRA showed positively correlation with the CBF by PC-MRA. The coefficient of determination (R2) of individual trends ranged from 0.242 to 0.956, and the R2 of group-leveled result was 0.550.

Conclusions
This study demonstrates that Silent MRA provides valuable CBF information despite arterial structure, rendering it a potential tool for screening for cerebrovascular disease.
Bone marrow derived-mesenchymal stem cell improves diabetes-associated fatty liver via mitochondria transformation in mice
Authors: Bi Youkun , Guo Xuejun , Zhang Mengqi , Zhu Keqi , Shi Chentao , Fan Baoqi , Wu Yanyun , Yang Zhiguang , Ji Guangju 
Published: December 2021

Abstract
Background
Non-alcoholic fatty liver disease (NAFLD) has become a global epidemic disease. Its incidence is associated with type 2 diabetes mellitus (T2DM). Presently, there is no approved pharmacological agents specially developed for NAFLD. One promising disease-modifying strategy is the transplantation of stem cells to promote metabolic regulation and repair of injury.

Method
In this study, a T2DM model was established through 28-week high-fat diet (HFD) feeding resulting in T2DM-associated NAFLD, followed by the injection of bone marrow mesenchymal stem cells (BMSCs). The morphology, function, and transfer of hepatocyte mitochondria were evaluated in both vivo and in vitro.

Results
BMSC implantation resulted in the considerable recovery of increasing weight, HFD-induced steatosis, liver function, and disordered glucose and lipid metabolism. The treatment with BMSC transplantation was accompanied by reduced fat accumulation. Moreover, mitochondrial transfer was observed in both vivo and vitro studies. And the mitochondria-recipient steatotic cells exhibited significantly enhanced OXPHOS activity, ATP production, and mitochondrial membrane potential, and reduced reactive oxygen species levels, which were not achieved by the blocking of mitochondrial transfer.

Conclusion
Mitochondrial transfer from BMSCs is a feasible process to combat NAFLD via rescuing dysfunction mitochondria, and has a promising therapeutic effect on metabolism-related diseases.
ChemTables: a dataset for semantic classification on tables in chemical patents
Authors: Zhai Zenan , Druckenbrodt Christian , Thorne Camilo , Akhondi Saber A. , Nguyen Dat Quoc , Cohn Trevor , Verspoor Karin 
Published: December 2021

AbstractChemical patents are a commonly used channel for disclosing novel compounds and reactions, and hence represent important resources for chemical and pharmaceutical research. Key chemical data in patents is often presented in tables. Both the number and the size of tables can be very large in patent documents. In addition, various types of information can be presented in tables in patents, including spectroscopic and physical data, or pharmacological use and effects of chemicals. Since images of Markush structures and merged cells are commonly used in these tables, their structure also shows substantial variation. This heterogeneity in content and structure of tables in chemical patents makes relevant information difficult to find. We therefore propose a new text mining task of automatically categorising tables in chemical patents based on their contents. Categorisation of tables based on the nature of their content can help to identify tables containing key information, improving the accessibility of information in patents that is highly relevant for new inventions. For developing and evaluating methods for the table classification task, we developed a new dataset, calledChemTables, which consists of 788 chemical patent tables with labels of their content type. We introduce this data set in detail. We further establish strong baselines for the table classification task in chemical patents by applying state-of-the-art neural network models developed for natural language processing, including TabNet, ResNet and Table-BERT onChemTables. The best performing model, Table-BERT, achieves a performance of 88.66 micro-averaged$$F_1$$F1score on the table classification task. TheChemTablesdataset is publicly available athttps://doi.org/10.17632/g7tjh7tbrj.3, subject to the CC BY NC 3.0 license. Code/models evaluated in this work are in a Github repositoryhttps://github.com/zenanz/ChemTables.
Processing binding data using an open-source workflow
Authors: Samuel Errol L. G. , Holmes Secondra L. , Young Damian W. 
Published: December 2021

AbstractThe thermal shift assay (TSA)—also known as differential scanning fluorimetry (DSF), thermofluor, and Tm shift—is one of the most popular biophysical screening techniques used in fragment-based ligand discovery (FBLD) to detect protein–ligand interactions. By comparing the thermal stability of a target protein in the presence and absence of a ligand, potential binders can be identified. The technique is easy to set up, has low protein consumption, and can be run on most real-time polymerase chain reaction (PCR) instruments. While data analysis is straightforward in principle, it becomes cumbersome and time-consuming when the screens involve multiple 96- or 384-well plates. There are several approaches that aim to streamline this process, but most involve proprietary software, programming knowledge, or are designed for specific instrument output files. We therefore developed an analysis workflow implemented in the Konstanz Information Miner (KNIME), a free and open-source data analytics platform, which greatly streamlined our data processing timeline for 384-well plates. The implementation is code-free and freely available to the community for improvement and customization to accommodate a wide range of instrument input files and workflows.
Graphical Abstract
Low-cost production and application of lipopeptide for bioremediation and plant growth by Bacillus subtilis SNW3
Authors: Umar Aiman , Zafar Aneeqa , Wali Hasina , Siddique Meh Para , Qazi Muneer Ahmed , Naeem Afshan Hina , Malik Zulfiqar Ali , Ahmed Safia 
Published: December 2021

AbstractAt present time, every nation is absolutely concern about increasing agricultural production and bioremediation of petroleum-contaminated soil. Hence, with this intention in the current study potent natural surfactants characterized as lipopeptides were evaluated for low-cost production by Bacillus subtilis SNW3, previously isolated from the Fimkessar oil field, Chakwal Pakistan. The significant results were obtained by using substrates in combination (white beans powder (6% w/v) + waste frying oil (1.5% w/v) and (0.1% w/v) urea) with lipopeptides yield of about 1.17 g/L contributing 99% reduction in cost required for medium preparation. To the best of our knowledge, no single report is presently describing lipopeptide production by Bacillus subtilis using white beans powder as a culture medium. Additionally, produced lipopeptides display great physicochemical properties of surface tension reduction value (SFT = 28.8 mN/m), significant oil displacement activity (ODA = 4.9 cm), excessive emulsification ability (E24 = 69.8%), and attains critical micelle concentration (CMC) value at 0.58 mg/mL. Furthermore, biosurfactants produced exhibit excellent stability over an extensive range of pH (1–11), salinity (1–8%), temperature (20–121°C), and even after autoclaving. Subsequently, produced lipopeptides are proved suitable for bioremediation of crude oil (86%) and as potent plant growth-promoting agent that significantly (P < 0.05) increase seed germination and plant growth promotion of chili pepper, lettuce, tomato, and pea maximum at a concentration of (0.7 g/100 mL), showed as a potential agent for agriculture and bioremediation processes by lowering economic and environmental stress.
Graphical Abstract
Single-cell RNA-sequencing reveals distinct immune cell subsets and signaling pathways in IgA nephropathy
Authors: Zeng Honghui , Wang Le , Li Jiajia , Luo Siweier , Han Qianqian , Su Fang , Wei Jing , Wei Xiaona , Wu Jianping , Li Bin , Huang Jingang , Tang Patrick , Cao Chunwei , Zhou Yiming , Yang Qiongqiong 
Published: December 2021

AbstractBackgroundIgA nephropathy (IgAN) is the most common primary glomerulonephritis globally. Increasing evidence suggests the importance of host immunity in the development of IgAN, but its dynamics during the early stage of IgAN are still largely unclear.ResultsHere we successfully resolved the early transcriptomic changes in immune cells of IgAN by conducting single-cell RNA-sequencing (scRNA-seq) with peripheral blood mononuclear cells. The differentially expressed genes (DEGs) between control and IgAN were predominantly enriched in NK cell-mediated cytotoxicity and cell killing pathways. Interestingly, we discovered that the number and cytotoxicity of NK cells are significantly reduced in IgAN patients, where both the number and marker genes of NK cells were negatively associated with the clinical parameters, including the levels of urine protein creatinine ratio (UPCR), serum galactose-deficient IgA1 and IgA. A distinctive B cell subset, which had suppressed NFκB signaling was predominantly in IgAN and positively associated with disease progression. Moreover, the DEGs of B cells were enriched in different viral infection pathways. Classical monocytes also significantly changed in IgAN and a monocyte subset expressing interferon-induced genes was positively associated with the clinical severity of IgAN. Finally, we identified vast dynamics in intercellular communications in IgAN.ConclusionsWe dissected the immune landscape of IgAN at the single-cell resolution, which provides new insights in developing novel biomarkers and immunotherapy against glomerulonephritis.