bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow
Authors: Eschrich Steven A. , Yu Xiaoqing , Teer Jamie K. 
Published: April 2023

Abstract
Background
Massively parallel sequencing includes many liquid handling steps which introduce the possibility of sample swaps, mixing, and duplication. The unique profile of inherited variants in human genomes allows for comparison of sample identity using sequence data. A comparison of all samples vs. each other (all vs. all) provides both identification of mismatched samples and the possibility of resolving swapped samples. However, all vs. all comparison complexity grows as the square of the number of samples, so efficiency becomes essential.

Results
We have developed a tool for fast all vs. all genotype comparison using low level bitwise operations built into the Perl programming language. Importantly, we have also developed a complete workflow allowing users to start with either raw FASTQ sequence files, aligned BAM files, or genotype VCF files and automatically generate comparison metrics and summary plots. The tool is freely available at https://github.com/teerjk/TimeAttackGenComp/.

Conclusions
A fast and easy to use method for genotype comparison as described here is an important tool to ensure high quality and robust results in sequencing studies.
Genomic and functional characterization of carbapenem-resistant Klebsiella pneumoniae from hospital wastewater
Authors: Xie Zhiqiang , Huang Jiangqing , zhang Shengcen , Xu BinBin , Zhang Qianwen , Li Bin 
Published: April 2023

AbstractBackgroundThe emergence of carbapenem-resistantKlebsiella pneumoniae(CRKP) attracted extensive attention. Information on CRKP from hospital wastewater (HWW) is limited. The aims of this study were to investigate the genomic characteristics and to evaluate the survivability characteristics of 11 CRKP from HWW in a Chinese teaching hospital in Fujian province.ResultsA total of 11 CRKP from HWW were recovered in this study. All CRKP from HWW were resistant to most antibiotics. Comparative genetic analysis demonstrated that all CRKP isolates were clustered into the three distinct phylogenetic clades and clade 2 and clade 3 were mixtures of samples collected from both HWW and clinical settings. Varieties of resistance genes, virulence genes and plasmid replicon types were detected in CRKP from HWW. In vitro transfer ofblaKPC-2was successful for 3blaKPC-2-positive CRKP from HWW with high conjugation frequency. Our study demonstrated that the genetic environments ofblaKPC−2shared core structure with ISKpn27-blaKPC−2-ISKpn6. Group analysis showed that CRKP from HWW had a lower survivability in serum compared to clinical CRKP (p < 005); and CRKP from HWW had no significant difference in survivability in HWW compared to clinical CRKP (p > 005).ConclusionsWe analyzed the genomic and survivability characteristics of CRKP from HWW in a Chinese teaching hospital. These genomes represent a significant addition of genomic data from the genus and could serve as a valuable resource for future genomic studies about CRKP from HWW.
The Preventiometer - reliability of a cardiovascular multi-device measurement platform and its measurement agreement with a cohort study
Authors: Junge Martin , Krüger Markus , Wahner-Roedler Dietlind L. , Bauer Brent A. , Dörr Marcus , Bahls Martin , Chenot Jean-François , Biffar Reiner , Schmidt Carsten O. 
Published: April 2023

Abstract
Background
Multimedia multi-device measurement platforms may make the assessment of prevention-related medical variables with a focus on cardiovascular outcomes more attractive and time-efficient. The aim of the studies was to evaluate the reliability (Study 1) and the measurement agreement with a cohort study (Study 2) of selected measures of such a device, the Preventiometer.

Methods
In Study 1 (N = 75), we conducted repeated measurements in two Preventiometers for four examinations (blood pressure measurement, pulse oximetry, body fat measurement, and spirometry) to analyze their agreement and derive (retest-)reliability estimates. In Study 2 (N = 150), we compared somatometry, blood pressure, pulse oximetry, body fat, and spirometry measurements in the Preventiometer with corresponding measurements used in the population-based Study of Health in Pomerania (SHIP) to evaluate measurement agreement.

Results
Intraclass correlations coefficients (ICCs) ranged from .84 to .99 for all examinations in Study 1. Whereas bias was not an issue for most examinations in Study 2, limits of agreement for most examinations were very large compared to results of similar method comparison studies.

Conclusion
We observed a high retest-reliability of the assessed clinical examinations in the Preventiometer. Some disagreements between Preventiometer and SHIP examinations can be attributed to procedural differences in the examinations. Methodological and technical improvements are recommended before using the Preventiometer in population-based research.
Comparison of correctly and incorrectly classified patients for in-hospital mortality prediction in the intensive care unit
Authors: Stenwig Eline , Salvi Giampiero , Salvo Rossi Pierluigi , Skjærvold Nils Kristian 
Published: April 2023

Abstract
Background
The use of machine learning is becoming increasingly popular in many disciplines, but there is still an implementation gap of machine learning models in clinical settings. Lack of trust in models is one of the issues that need to be addressed in an effort to close this gap. No models are perfect, and it is crucial to know in which use cases we can trust a model and for which cases it is less reliable.

Methods
Four different algorithms are trained on the eICU Collaborative Research Database using similar features as the APACHE IV severity-of-disease scoring system to predict hospital mortality in the ICU. The training and testing procedure is repeated 100 times on the same dataset to investigate whether predictions for single patients change with small changes in the models. Features are then analysed separately to investigate potential differences between patients consistently classified correctly and incorrectly.

Results
A total of 34 056 patients (58.4%) are classified as true negative, 6 527 patients (11.3%) as false positive, 3 984 patients (6.8%) as true positive, and 546 patients (0.9%) as false negatives. The remaining 13 108 patients (22.5%) are inconsistently classified across models and rounds. Histograms and distributions of feature values are compared visually to investigate differences between groups.

Conclusions
It is impossible to distinguish the groups using single features alone. Considering a combination of features, the difference between the groups is clearer. Incorrectly classified patients have features more similar to patients with the same prediction rather than the same outcome.
Ischemia prediction score (IsPS) in patients with strangulated small bowel obstruction: a retrospective cohort study
Authors: Murao Shuhei , Fujino Shiki , Danno Katsuki , Takeda Takashi , Yamamoto Kei , Higashiguchi Masaya , Noguchi Kozo , Hirao Takafumi , Oka Yoshio 
Published: April 2023

Abstract
Backgrounds
Intestinal ischemia of strangulated small bowel obstruction (SSBO) requires prompt identification and early intervention. This study aimed to evaluate the risk factors and develop a prediction model of intestinal ischemia requiring bowel resection in SSBO.

Methods
This was a single-center, retrospective cohort study of consecutive patients underwent emergency surgery for SSBO from April 2007 to December 2021. Univariate analysis was performed to identify the risk factors for bowel resection in these patients. Two clinical scores (with contrasted computed tomography [CT] and without contrasted CT) were developed to predict intestinal ischemia. The scores were validated in an independent cohort.

Results
A total of 127 patients were included, 100 in the development cohort (DC) and 27 in the validation cohort (VC). Univariate analysis showed that high white blood cell count (WBC), low base excess (BE), ascites and reduced bowel enhancement were significantly associated with bowel resection. The ischemia prediction score (IsPS) comprised 1 point each for WBC ≥ 10,000/L, BE ≤ -1.0 mmol/L, ascites, and 2 points for reduced bowel enhancement. The simple IsPS (s-IsPS, without contrasted CT) of 2 or more had a sensitivity of 69.4%, specificity of 65.4%. The modified IsPS (m-IsPS, with contrasted CT) of 3 or more had a sensitivity of 86.7%, specificity of 76.0%. AUC of s-IsPS was 0.716 in DC and 0.812 in VC, and AUC of m-IsPS was 0.838 and 0.814.

Conclusion
IsPS predicted possibility of ischemic intestinal resection with high accuracy and can help in the early identification of intestinal ischemia in SSBO.
Rapidly progressive IgA nephropathy with membranoproliferative glomerulonephritis-like lesions in an elderly man following the third dose of an mRNA COVID-19 vaccine: a case report
Authors: Morimoto Nobuhisa , Mori Takayasu , Shioji Shingo , Taguchi Towako , Watanabe Hatsumi , Sakai Keigo , Mori Katsuo , Yamamura Ayumi , Hanioka Asami , Akagi Yuichiro , Fujiki Tamami , Mandai Shintaro , Mori Yutaro , Ando Fumiaki , Susa Koichiro , Iimori Soichiro , Naito Shotaro , Sohara Eisei , Ohashi Kenichi , Uchida Shinichi 
Published: April 2023

Abstract
Background
As messenger RNA (mRNA)-based vaccines for coronavirus disease 2019 (COVID-19) have been administered to millions of individuals worldwide, cases of de novo and relapsing glomerulonephritis after mRNA COVID-19 vaccination are increasing in the literature. While most previous publications reported glomerulonephritis after the first or second dose of an mRNA vaccine, few reports of glomerulonephritis occurring after the third dose of an mRNA vaccine currently exist.

Case presentation
We report a case of rapidly progressive glomerulonephritis in a patient following the third dose of an mRNA COVID-19 vaccine. A 77-year-old Japanese man with a history of hypertension and atrial fibrillation was referred to our hospital for evaluation of anorexia, pruritus, and lower extremity edema. One year before referral, he received two mRNA vaccines (BNT162b2) for COVID-19. Three months before the visit, he received a third mRNA vaccine (mRNA-1273) for COVID-19. On admission, the patient presented severe renal failure with a serum creatinine level of 16.29 mg/dL, which had increased from 1.67 mg/dL one month earlier, prompting us to initiate hemodialysis. Urinalysis showed nephrotic-range proteinuria and hematuria. Renal biopsy revealed mild mesangial proliferation and expansion, a lobular appearance, and double contours of the glomerular basement membrane. Renal tubules had severe atrophy. Immunofluorescence microscopy showed strong mesangial staining for IgA, IgM, and C3c. Electron microscopy exhibited mesangial and subendothelial electron-dense deposits, leading to a diagnosis of IgA nephropathy with membranoproliferative glomerulonephritis-like changes. The kidney function remained unchanged after steroid therapy.

Conclusions
Although the link between renal lesions and mRNA vaccines remains unclear, a robust immune response induced by mRNA vaccines may play a role in the pathogenesis of glomerulonephritis. Further studies of the immunological effects of mRNA vaccines on the kidney are warranted.
Longitudinal prospective cohort study to assess peripheral motor function with extensive electrophysiological techniques in patients with Spinal Muscular Atrophy (SMA): the SMA Motor Map protocol
Authors: Ros Leandra A. A. , Goedee H. Stephan , Franssen Hessel , Asselman Fay-Lynn , Bartels Bart , Cuppen Inge , van Eijk Ruben P. A. , Sleutjes Boudewijn T. H. M. , van der Pol W. Ludo , Wadman Renske I. 
Published: April 2023

Abstract
Background
Hereditary spinal muscular atrophy (SMA) is a motor neuron disorder with a wide range in severity in children and adults. Two therapies that alter splicing of the Survival Motor Neuron 2 (SMN2) gene, i.e. nusinersen and risdiplam, improve motor function in SMA, but treatment effects vary. Experimental studies indicate that motor unit dysfunction encompasses multiple features, including abnormal function of the motor neuron, axon, neuromuscular junction and muscle fibres. The relative contributions of dysfunction of different parts of the motor unit to the clinical phenotype are unknown. Predictive biomarkers for clinical efficacy are currently lacking. The goals of this project are to study the association of electrophysiological abnormalities of the peripheral motor system in relation to 1) SMA clinical phenotypes and 2) treatment response in patients treated with SMN2-splicing modifiers (nusinersen or risdiplam).

Methods
We designed an investigator-initiated, monocentre, longitudinal cohort study using electrophysiological techniques (‘the SMA Motor Map’) in Dutch children (≥ 12 years) and adults with SMA types 1–4. The protocol includes the compound muscle action potential scan, nerve excitability testing and repetitive nerve stimulation test, executed unilaterally at the median nerve. Part one cross-sectionally assesses the association of electrophysiological abnormalities in relation to SMA clinical phenotypes in treatment-naïve patients. Part two investigates the predictive value of electrophysiological changes at two-months treatment for a positive clinical motor response after one-year treatment with SMN2-splicing modifiers. We will include 100 patients in each part of the study.

Discussion
This study will provide important information on the pathophysiology of the peripheral motor system of treatment-naïve patients with SMA through electrophysiological techniques. More importantly, the longitudinal analysis in patients on SMN2-splicing modifying therapies (i.e. nusinersen and risdiplam) intents to develop non-invasive electrophysiological biomarkers for treatment response in order to improve (individualized) treatment decisions.

Trial registration
NL72562.041.20 (registered at https://www.toetsingonline.nl. 26–03-2020).
Virtual Reality Experience during Labour (VIREL); a qualitative study
Authors: Musters A. , Vandevenne A. S. , Franx A. , Wassen M. M. L. H. 
Published: April 2023

Abstract
Background
There is increasing evidence that virtual reality (VR) is effective in the reduction of labour pain. The implementation of alternative methods like VR to reduce labour pain can contribute to reduce patient request for pharmacological pain management methods and associated side effects. The aim of this study is to examine women’s experiences, preferences and satisfaction in regard to the use of VR during labour.

Methods
A qualitative interview study was conducted in a non-university teaching hospital in The Netherlands. Two VR applications, respectively a guided meditation and an interactive game were tested in eligible women with a singleton pregnancy, scheduled for induction of labour. For the primary outcome, patients’ VR experience and application preference (meditation vs. game) were examined using a post-intervention questionnaire and a semi-structured interview. Three categories (with sub-categories) were used to guide interviews: “The VR experience”, “Pain reduction”, and “Usability of the VR application”. Labour pain before and directly after VR was evaluated using the NRS score.

Results
Twenty-four women, of whom 14 were nulliparous and ten multiparous, were included and 12 of these women participated in semi-structured interviews. Using within-subject paired t-test comparisons, compared to pain pre-VR, patients reported a highly significant 26% decrease in mean NRS scores during VR meditation (pain pre-VR = 6.71 + − 1.65 vs. pain after VR = 4.96 + − 2.01) [p < 0.001]. Compared to pain before VR game, patients also reported a highly significant 19% decrease in mean NRS scores during VR game (pain before VR game = 6.89 + − 1.88 vs. pain after VR game = 5.61 + − 2.23) [p = 0.001].

Conclusion
All women were highly satisfied with VR use during labour. Patients reported a highly significant reduction in pain during the interactive VR game and during meditation, patients preferred guided meditation. These results can contribute to the development of a potential promising new non-pharmacological tool to reduce labour pain.

Trial registration
ClinicalTrials.gov Identifier: NCT04858984, date of registration: 26/04/2021 (retrospectively registered).
The role of serum metrics in anti- VEGF treatment for macular edema induced by retinal vein occlusion
Authors: Wang Yun-Chang , Zhou Chuan-Qi , Li Rong-Rong , Cai Yi , Wang Meng-Meng , Yuan Li-Fei , He Yi-Qing 
Published: April 2023

Abstract
Aim
To evaluate association between pretreatment serum metrics and best corrected visual acuity ( BCVA) of patients with macular edema secondary to retinal vein occlusion and its subtypes after intravitreal ranibizumab or conbercept implant.

Methods
This prospective research included 201 patients(201 eyes) who were diagnosed with macular edema secondary to retinal vein occlusion at Heibei Eye Hospital between January 2020 and January 2021, who all received intravitreal anti- vascular endothelial growth factor treatment. Serum metrics were measured before the first treatment, and correlations between BCVA and each of four parameters— platelets, neutrophil- to- lymphocyte ratio(NLR), platelet- to- lymphocyte ratio(PLR) and monocyte- to- lymphocyte ratio(MLR)— were analyzed to identify predictors of effective intravitreal injection treatment outcomes.

Results
The mean platelets was significantly different in the effective and ineffective group for RVO-ME (273.02 ± 41.49 × 109/L,214.54 ± 44.08 × 109/L P < 0.01),BRVO-ME (269.43 ± 49.52 × 109/L,214.72 ± 40.42 × 109/L P < 0.01), and CRVO-ME (262.32 ± 32.41 × 109/L,209.27 ± 42 0.91 × 109/L P < 0.01). The cutoff value of the platelets was 266.500, the area under the curve was 0.857,and the sensitivity and specificity were 59.8% and 93.6%, respectively. The mean PLR was significantly different in the effective and ineffective group for RVO-ME (154.66 ± 49.60, 122.77± 44.63 P < 0.01),BRVO-ME (152.24 ± 54.99, 124.72 ± 41.46 P = 0.003), and CRVO-ME (152.06±44.23, 118.67 ± 41.80 P = 0.001). The cutoff value of the platelets was 126.734, the area under the curve was 0.699, and the sensitivity and specificity were 70.7% and 63.3%, respectively. There were no statistical differencies between the effective and ineffective group(RVO- ME and its subtypes) in NLR and MLR.

Conclusion
Higher pretreatment platelets and PLR were associated with BCVA in patients with RVO- ME and its subtypes who were treated with anti- VEGF drugs. The platelets and PLR may be used as predictive and prognostic tools for effective intravitreal injection treatment outcomes.
Multi-drug resistant Klebsiella-induced corneal ulcer following pterygium surgery: a case report
Authors: Calisir Kenan , Mohamed Hassan Muhumed , Yussuf Aisha Abdirahman 
Published: April 2023

Abstract
Background
Management of pterygium is dependent on the grading of pterygium and its clinical presentation (inflamed or quiescent), and surgical excision is the final choice of treatment for the pterygium extending beyond the limbus. Infectious keratitis is one of the most commonly reported complications in recent years. To the best of our knowledge, Klebsiella keratitis after pterygium surgery has not been described in the current literature. Here, we report a patient with corneal ulcer formation following pterygium surgical excision.

Case presentation
A 62-year-old woman presented with complaints of pain, blurred vision, photophobia and redness in her left eye for a month. She had a history of pterygium surgical excision two months ago. Slit-lamp examination showed conjunctival congestion, a central whitish corneal ulcer with a central epithelial defect, and hypopyon. Corneal scraped sample revealed multidrug resistant (MDR) Klebsiella pneumonia and the strain was found to be sensitive to cefoxitin and ciprofloxacin. Intracameral cefuroxime (1 mg/0.1 mL) injection, fortified cefuroxime ophthalmic suspension (50 mg/mL) and moxifloxacin ophthalmic suspension (0.5%) were successfully administered to control the infection. Since residual central stromal opacification remained persistent, final visual acuity did not improve beyond finger counting at two meters.

Conclusions
Klebsiella keratitis is a rare and sight-threatening complication following pterygium excision. This report emphasizes the importance of close follow-up examination following pterygium surgeries.
Dose–response relationship between active smoking and lung cancer mortality/prevalence in the Chinese population: a meta-analysis
Authors: Ai Feiling , Zhao Jian , Yang Wenyi , Wan Xia 
Published: April 2023

Abstract
Background
The dose‒response relationship-based relative risk (RR) of smoking exposure could better predict the risk of lung cancer than the dichotomous RR. To date, there is a lack of large-scale representative studies illustrating the dose‒response relationship between smoking exposure and lung cancer deaths, and no study has systematically pooled the current evidence in the Chinese population.

Objectives
To elucidate the dose‒response relationship of smoking and the risk of lung cancer mortality in the Chinese population.

Methods
Data were derived from studies on dose‒response relationships of smoking exposure and the risk of lung cancer among Chinese adults published before June 30th, 2021. Based on smoking exposure indicators and RR of lung cancer mortality, a series of dose‒response relationship models were developed. For smokers, 10 models were built to fit the dose‒response relationships between pack-years and RR of lung cancer deaths. For quitters, quit-years and corresponding RRs were used, and the pooled dichotomous RR value was used as the starting point to avoid overestimation. Finally, the results were compared with the estimates from 2019 Global Burden of Disease (GBD) study.

Results
A total of 12 studies were included. Among 10 dose‒response relationship models of pack-years with the RR of lung cancer mortality, the integrated-exposure–response (IER) model achieved the best fit. In all models, less than 60 pack-years presented RRs below 10. For former smokers, the RR decreased to 1 when quit-years reached up to 7 years. Both smokers and quitters had much lower RRs than that of the global level estimated by GBD.

Conclusion
The risk of lung cancer mortality rose with pack-years and decreased with quit-years among Chinese adults, and both values were far below global level. The results suggested that the dose–response RR of lung cancer deaths associated with smoking in China should be estimated separately.