bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inpatient glycemic control and outcome of COVID-19 patients: A retrospective cohort
Authors: Lesniak Christopher , Ong Raquel , Akula Monika S , Douedi Steven , Akoluk Arda , Soomro Rabail , Copca-Alvarez Albino , Purewal Tiffany , Patel Ishan , Upadhyaya Vandan , Cheng Jennifer , Jain Ashali , Asif Arif , Chalasani Krishna , Hossain Mohammad A 
Published: August 2021

Objectives: Although there have been associations between diabetes and mortality in COVID-19 patients, it is unclear whether this is driven by the disease itself or whether it can be attributed to an inability to exhibit effective glucose control. Methods: We conducted a retrospective cohort study of 292 patients admitted to a tertiary referral center to assess the association of mortality and glycemic control among COVID-19-positive patients. We used a logistic regression model to determine whether average fasting glycemic levels were associated with in-hospital mortality. Results: Among the diabetic and non-diabetic patients, there were no differences between mortality or length of stay. Mean glucose levels in the first 10 days of admission were higher on average among those who died (150–185 mg/dL) compared with those who survived (125–165 mg/dL). When controlling for multiple variables, there was a significant association between mean fasting glucose and mortality (odds ratio = 1.014, p < 0.001). The associations between glucose and mortality remained when controlled for comorbidities and glucocorticoid use. Conclusion: The results of this retrospective study show an association between mortality and inpatient glucose levels, suggesting that there may be some benefit to tighter glucose control in patients diagnosed with COVID-19.
Unstable Bony Chance Fracture Successfully Treated With Teriparatide in Patient With Ankylosed Spine: A Case Report and Review of the Literature
Authors: Park Hyung-Youl , Ha Kee-Yong , Kim Ki-Won , Rhyu Kee-Won , Kim Young-Hoon , Lee Jun-Seok , Kim Sang-Il , Park Soo-Bin 
Published: August 2021

Background: Ankylosed spines with ankylosing spondylitis or diffuse idiopathic skeletal hyperostosis (DISH) are prone to fractures due to osteoporosis and fracture instability from long lever arm. In such cases, surgical management is the main treatment option. Case presentation: We report a first case of successful treatment of unstable bony Chance fracture at thoracolumbar junction in DISH patient using teriparatide and review previous literature on ankylosed spine fractures treated with teriparatide. An 82-year-old male patient presented with back pain after falling from a 3 m height 3 months ago. Imaging studies showed L1 unstable flexion-distraction injury (bony Chance fracture) and intravertebral vacuum cleft in ankylosed spine due to DISH. Conservative treatment, teriparatide and orthosis, was determined as the most appropriate approach because the patient declined surgery and presented with tolerable mechanical back pain without any neurologic deficits. Solid bony union was successfully achieved without any complications after 1-year treatment. Conclusion: Although surgical management is strongly recommended for unstable fracture in ankylosed spine, non-surgical treatment including teriparatide and orthosis might be safer and effective options in bony Chance fracture without neurologic deficits and intractable mechanical pain.
Comparison of Endoscopic Discectomy Versus Non-Endoscopic Discectomy for Symptomatic Lumbar Disc Herniation: A Systematic Review and Meta-Analysis
Authors: Li Wei-Shang , Yan Qi , Cong Lin 
Published: August 2021

Study Design: Systematic review. Objective: The authors aimed to systematically compare the effectiveness and safety of endoscopic discectomy (ED) with non-endoscopic discectomy (NED) for treatment of symptomatic lumbar disc herniation (LDH). Methods: A systematic search was performed on PubMed, EMBASE, the Cochrane Library and China National Knowledge Infrastructure for randomized controlled trial from inception until August 13, 2020. Trials which investigated multiple operative approaches on lumbar disc herniation were identified without language restrictions. Results: In total, 25 trials involving 2258 patients with symptomatic LDH were included. Twenty trials performed the comparison between ED and NED. Five trials performed the comparison between percutaneous endoscopic transforaminal discectomy (PETD) and percutaneous endoscopic interlaminar discectomy (PEID). The operative time of micro-endoscopic discectomy (MED) was longer than open discectomy (OD). The length of hospital stay of percutaneous endoscopic lumbar discectomy (PELD) was shorter than fenestration discectomy (FD). Significant differences in intraoperative blood loss volumes were found between PELD with FD and MED with OD. The complication rate of PELD was lower than FD (PELD: 4.3%; FD: 14.6%) and the complication rate of full-endoscopic discectomy (FE) was lower than microscopic discectomy (MD) (FE: 13.4%; MD: 32.1%). Conclusions: PELD and FE have the advantage of limiting intraoperative damages. ED and NED can be both considered sufficient to achieve good clinical outcomes. PETD and PEID are able to achieve similar results but the learning curve of PETD was steeper. More independent high-quality RCTs with sufficiently large sample sizes performing cost-effectiveness analyzes are needed.
AO Spine Adult Spinal Deformity Patient Profile: A Paradigm Shift in Comprehensive Patient Evaluation in Order to Optimize Treatment and Improve Patient Care
Authors: Naresh-Babu J , Kwan Kenny Yat Hong , Wu Yabin , Yilgor Caglar , Alanay Ahmet , Cheung Kenneth M. C. , Polly David W. , Park Jong-Beom , Ito Manabu , Lenke Lawrence G. , van Hooff Miranda L. , Kleuver Marinus de ,   AO Spine Knowledge Forum Deformity
Published: August 2021

Study Design: Modified Delphi study. Objective: Adult spinal deformity (ASD) is an increasingly recognized condition, comprising a spectrum of pathologies considerably impacting patients’ health and functional status. Patients present with a combination of pain, disability, comorbidities and radiological deformity. The study aims to propose a systematic approach of gathering information on the factors that drive decision-making by developing a patient profile. Methods: The present study comprises of 3 parts. Part 1: Development of prototype of patient profile: The data from the Core Outcome Study on SCOlisis (COSSCO) by Scoliosis Research Society (SRS) was categorized into a conceptual framework. Part 2: Modified Delphi study: Items reaching >70% agreement were included in a 4 round iterative process with 51 panellists across the globe. Part 3: Pilot testing—feasibility: Content validity and usability were evaluated quantitatively. Results: The profile consisted of 4 domains. 1. General health with demographics and comorbidities, 2.Spine-specific health with spine related health and neurological status, 3. Imaging with radiographic and MRI parameters and 4. Deformity type. Each domain consisted of 1 or 2 components with various factors and their measuring instruments. Profile was found to have an excellent content validity (I-CVIr 0.78-1.00; Ave-CVI 0.92) appropriateness, relevance and usefulness. Conclusions: The present study, is first to provide a universally applicable multimodal ASD patient profile to methodically describe patients. Physicians are encouraged to assess ASD patients holistically using this profile and not just based on radiographic findings.
Rapid sequence intubation: a survey of current practice in the South African pre-hospital setting
Authors: Botha Johanna Catharina , Lourens Andrit , Stassen Willem 
Published: August 2021

Abstract
Background
Rapid sequence intubation (RSI) is an advanced airway skill commonly performed in the pre-hospital setting globally. In South Africa, pre-hospital RSI was first approved for non-physician providers by the Health Professions Council of South Africa in 2009 and introduced as part of the scope of practice of degree qualified Emergency Care Practitioners (ECPs) only. The research study aimed to investigate and describe, based on the components of the minimum standards of pre-hospital RSI in South Africa, specific areas of interest related to current pre-hospital RSI practice.

Methods
An online descriptive cross-sectional survey was conducted amongst operational ECPs in the pre-hospital setting of South Africa, using convenience and snowball sampling strategies.

Results
A total of 87 participants agreed to partake. Eleven (12.6%) incomplete survey responses were excluded while 76 (87.4%) were included in the data analysis. The survey response rate could not be calculated. Most participants were operational in Gauteng (n = 27, 35.5%) and the Western Cape (n = 25, 32.9%). Overall participants reported that their education and training were perceived as being of good quality. The majority of participants (n = 69, 90.8%) did not participate in an internship programme before commencing duties as an independent practitioner. Most RSI and post-intubation equipment were reported to be available; however, our results found that introducer stylets and/or bougies and end-tidal carbon dioxide devices are not available to some participants. Only 50 (65.8%) participants reported the existence of a clinical governance system within their organisation. Furthermore, our results indicate a lack of clinical feedback, deficiency of an RSI database, infrequent clinical review meetings and a shortage of formal consultation frameworks.

Conclusion
The practice of safe and effective pre-hospital RSI, performed by non-physician providers or ECPs, relies on comprehensive implementation and adherence to all the components of the minimum standards. Although there is largely an apparent alignment with the minimum standards, recurrent revision of practice needs to occur to ensure alignment with recommendations. Additionally, some areas may benefit from further research to improve current practice.
Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data
Authors: ElAbd Hesham , Degenhardt Frauke , Koudelka Tomas , Kamps Ann-Kristin , Tholey Andreas , Bacher Petra , Lenz Tobias L. , Franke Andre , Wendorff Mareike 
Published: August 2021

AbstractBackgroundThe human leukocyte antigen (HLA) proteins play a fundamental role in the adaptive immune system as they present peptides to T cells. Mass-spectrometry-based immunopeptidomics is a promising and powerful tool for characterizing the immunopeptidomic landscape of HLA proteins, that is the peptides presented on HLA proteins. Despite the growing interest in the technology, and the recent rise of immunopeptidomics-specific identification pipelines, there is still a gap in data-analysis and software tools that are specialized in analyzing and visualizing immunopeptidomics data.ResultsWe present the IPTK library which is an open-source Python-based library for analyzing, visualizing, comparing, and integrating different omics layers with the identified peptides for an in-depth characterization of the immunopeptidome. Using different datasets, we illustrate the ability of the library to enrich the result of the identified peptidomes. Also, we demonstrate the utility of the library in developing other software and tools by developing an easy-to-use dashboard that can be used for the interactive analysis of the results.ConclusionIPTK provides a modular and extendable framework for analyzing and integrating immunopeptidomes with different omics layers. The library is deployed intoPyPIathttps://pypi.org/project/IPTKL/and intoBiocondaathttps://anaconda.org/bioconda/iptkl, while the source code of the library and the dashboard, along with the online tutorials are available athttps://github.com/ikmb/iptoolkit.
CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes
Authors: Polit Lélia , Kerdivel Gwenneg , Gregoricchio Sebastian , Esposito Michela , Guillouf Christel , Boeva Valentina 
Published: August 2021

Abstract
Background
Multiple studies rely on ChIP-seq experiments to assess the effect of gene modulation and drug treatments on protein binding and chromatin structure. However, most methods commonly used for the normalization of ChIP-seq binding intensity signals across conditions, e.g., the normalization to the same number of reads, either assume a constant signal-to-noise ratio across conditions or base the estimates of correction factors on genomic regions with intrinsically different signals between conditions. Inaccurate normalization of ChIP-seq signal may, in turn, lead to erroneous biological conclusions.

Results
We developed a new R package, CHIPIN, that allows normalizing ChIP-seq signals across different conditions/samples when spike-in information is not available, but gene expression data are at hand. Our normalization technique is based on the assumption that, on average, no differences in ChIP-seq signals should be observed in the regulatory regions of genes whose expression levels are constant across samples/conditions. In addition to normalizing ChIP-seq signals, CHIPIN provides as output a number of graphs and calculates statistics allowing the user to assess the efficiency of the normalization and qualify the specificity of the antibody used. In addition to ChIP-seq, CHIPIN can be used without restriction on open chromatin ATAC-seq or DNase hypersensitivity data. We validated the CHIPIN method on several ChIP-seq data sets and documented its superior performance in comparison to several commonly used normalization techniques.

Conclusions
The CHIPIN method provides a new way for ChIP-seq signal normalization across conditions when spike-in experiments are not available. The method is implemented in a user-friendly R package available on GitHub: https://github.com/BoevaLab/CHIPIN
Dysregulated long noncoding RNAs in the brainstem of the DBA/1 mouse model of SUDEP
Authors: Chen Deng , Zhu Lina , Lin Xin , Zhou Dong , Liu Ling 
Published: August 2021

Abstract
Background
Long noncoding RNAs (lncRNAs) play an important role in many neurological diseases. This study aimed to investigate differentially expressed lncRNAs and messenger RNAs (mRNAs) in the susceptibility gaining process of primed DBA/1 mice, a sudden unexpected death in epilepsy (SUDEP) model, to illustrate the potential role of lncRNAs in SUDEP.

Methods
The Arraystar mouse lncRNA Microarray V3.0 (Arraystar, Rockville, MD) was applied to identify the aberrantly expressed lncRNAs and mRNAs between primed DBA/1 mice and normal controls. The differences were verified by qRT-PCR. We conducted gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and coexpression analyses to explore the possible function of the dysregulated RNAs.

Results
A total of 502 lncRNAs (126 upregulated and 376 downregulated lncRNAs) and 263 mRNAs (141 upregulated and 122 downregulated mRNAs) were dysregulated with P < 0.05 and a fold change over 1.5, among which Adora3 and Gstt4 were possibly related to SUDEP. GO analysis revealed that chaperone cofactor-dependent protein refolding and misfolded protein binding were among the top ten downregulated terms, which pointed to Hspa1a, Hspa2a and their related lncRNAs. KEGG analysis identified 28 upregulated and 10 downregulated pathways. Coexpression analysis showed fifteen dysregulated long intergenic noncoding RNAs (lincRNAs) and three aberrantly expressed antisense lncRNAs, of which AK012034 and NR_040757 are potentially related to SUDEP by regulating LMNB2 and ITPR1, respectively.

Conclusions
LncRNAs and their coexpression mRNAs are dysregulated in the priming process of DBA/1 in the brainstem. Some of these mRNAs and lncRNAs may be related to SUDEP, including Adora3, Lmnb2, Hspa1a, Hspa1b, Itrp1, Gstt4 and their related lncRNAs. Further study on the mechanism of lncRNAs in SUDEP is needed.
Carboxymethyl-γ-cyclodextrin, a novel selective relaxant binding agent for the reversal of neuromuscular block induced by aminosteroid neuromuscular blockers: an ex vivo laboratory study
Authors: Fábián Ákos I. , Tassonyi Edömér , Csernoch Vera , Fedor Marianna , Sohajda Tamás , Szente Lajos , Fülesdi Béla 
Published: August 2021

Abstract
Background
Residual neuromuscular block at the end of surgery may compromise the patient’s safety. The risk of airway complications can be minimized through monitoring of neuromuscular function and reversal of neuromuscular block if needed. Effective reversal can be achieved with selective relaxant binding agents, however, sugammadex is the only clinically approved drug in this group.
We investigated the concentration–response properties of a novel selective relaxant binding agent, carboxymethyl-γ-cyclodextrin for the reversal of neuromuscular block. We evaluated the hypothesis that it is equally potent for reversing neuromuscular block as sugammadex.

Methods
Phrenic nerve – hemidiaphragm tissue preparations were isolated from male Wistar rats and suspended in a tissue holder allowing electrical stimulation of the nerve and monitoring of muscle contraction force. Concentration–response relationships were constructed for the neuromuscular blocking agents rocuronium, pipecuronium, and vecuronium. The half-effective concentrations of sugammadex and carboxymethyl-γ-cyclodextrin for reversal of neuromuscular block were determined.

Results
The half effective concentrations (95% confidence interval, CI) were 7.50 (6.93–8.12) μM for rocuronium, 1.38 (1.33–1.42) μM for pipecuronium, and 3.69 (3.59–3.80) μM for vecuronium. The half effective concentrations (95% CI) of carboxymethyl-γ-cyclodextrin and sugammadex were 35.89 (32.67–39.41) μM and 3.67 (3.43–3.92) μM, respectively, for the reversal of rocuronium-induced block; 10.14 (9.61–10.70) μM and 0.67 (0.62–0.74) μM, respectively, for the reversal of pipecuronium-induced block; and 376.1 (341.9–413.8) μM and 1.45 (1.35–1.56) μM, respectively, for the reversal of vecuronium-induced block.

Conclusions
Carboxymethyl-γ-cyclodextrin is an effective, but less potent agent for reversal of neuromuscular block than sugammadex.
Increased ratio of sST2/LVMI predicted cardiovascular mortality and heart failure rehospitalization in heart failure with reduced ejection fraction patients: a prospective cohort study
Authors: Li Fuhai , Xu Mengying , Fu Mingqiang , Cui Xiaotong , Lian Zhexun , Xin Hui , Zhou Jingmin , Ge Junbo 
Published: August 2021

Abstract
Background
Inflammation is one of the principal triggering mechanisms for left ventricular fibrosis and remodeling in heart failure, leading to adverse clinical outcomes. Soluble suppression of tumorigenicity 2 (sST2), a member of the interleukin-1 receptor family, is assumed to play a significant role in the fibrotic response to inflammation. Left ventricular mass index (LVMI) is a parameter of the prefibrotic inflammatory phase of heart failure preceding remodeling. The present study aimed to investigate the prognostic value of the sST2/LVMI ratio in heart failure with reduced ejection fraction.

Methods
This was a prospective cohort study. A total of 45 consecutive patients with heart failure with reduced ejection fraction, treated between September 2015 and December 2016, were enrolled. The sST2/LVMI ratio was measured at baseline. The primary endpoint was a composite of cardiovascular mortality and readmission for heart failure. The prognostic impact of the sST2/LVMI ratio was evaluated using a multivariable Cox proportional hazards regression model.

Results
Forty-five patients were enrolled in this study. Their average age was 48 ± 14 years, and approximately 20% of them were men. Patients were followed for 9 months, during which the primary outcome occurred in 15 patients. Kaplan–Meier analysis showed that patients with a high sST2/LVMI ratio (≥ 0.39) had shorter event-free survival than those with intermediate (between 0.39 and 0.24) and low ratios (< 0.24) (log-rank, P = 0.022). The fully adjusted multivariable Cox regression analysis showed that the sST2/LVMI ratio was positively associated with the composite outcome in patients with heart failure with reduced ejection fraction after adjusting for confounders (hazard ratio 1.64, 95% confidence interval 1.06 to 2.54). By subgroup analysis, a stronger association was found with age between 40 and 55 years, systolic blood pressure < 115 or ≥ 129 mmHg, diastolic blood pressure < 74 mmHg, hematocrit < 44.5%, and interventricular septum thickness ≥ 8.5 mm.

Conclusion
In patients with heart failure with reduced ejection fraction, the relationship between the sST2/LVMI ratio and the composite outcome was linear. A higher baseline ratio of sST2/LVMI was associated with an increased risk of cardiovascular mortality and heart failure rehospitalization in the short-term follow-up.
Mucormycosis-induced upper gastrointestinal ulcer perforation in immunocompetent patients: a report of two cases
Authors: Huang Hongyun , Xie Lang , Zheng Zheng , Yu Hanhui , Tu Lingjing , Cui Chunhui , Yu Jinlong 
Published: August 2021

Abstract
Background
Gastrointestinal mucormycosis (GIM) is a rare, opportunistic fungal infection with poor prognosis. Clinically, it is difficult to diagnose GIM owing to its nonspecific clinical symptoms and poor suspicion. The estimated incidence of GIM is inaccurate, and most cases are diagnosed accidentally during surgery or upon postmortem examination. GIM usually occurs in patients with immune deficiencies or diabetes. Here, we report two cases of immunocompetent young patients with GIM who had good prognosis after treatment. Compared to other case reports on GIM, our cases had unusual infection sites and no obvious predisposing factors, which make it important to highlight these cases.

Case presentation
The first case was that of a 16-year-old immunocompetent boy who was admitted with gastrointestinal bleeding and perforation due to a gastric ulcer. Strategies used to arrest bleeding during emergency gastroscopy were unsuccessful. An adhesive mass was then discovered through laparoscopy. The patient underwent type II gastric resection. Pathological examination of the mass revealed bacterial infection and GIM. The second case was of a 33-year-old immunocompetent woman with a recent history of a lower leg sprain. The patient subsequently became critically ill and required ventilatory support. After hemodynamic stabilization and extubation, she presented with hematemesis due to exfoliation and necrosis of the stomach wall. The patient underwent total gastrectomy plus jejunostomy. The pathology results revealed severe bacterial infection and fungal infection that was confirmed as GIM. The patient fully recovered after receiving anti-infective and antifungal treatments.

Conclusions
Neither patient was immunosuppressed, and both patients presented with gastrointestinal bleeding. GIM was confirmed via pathological examination. GIM is not limited to immunocompromised patients, and its diagnosis mainly relies on pathological examination. Early diagnosis, timely surgical treatment, and early administration of systemic drug treatment are fundamental to improving its prognosis.