bluuebunny/crossref_metadata_2025_split huggingface dataset:
scMEB: a fast and clustering-independent method for detecting differentially expressed genes in single-cell RNA-seq data
Authors: Zhu Jiadi , Yang Youlong 
Published: May 2023

Abstract
Background
Cell clustering is a prerequisite for identifying differentially expressed genes (DEGs) in single-cell RNA sequencing (scRNA-seq) data. Obtaining a perfect clustering result is of central importance for subsequent analyses, but not easy. Additionally, the increase in cell throughput due to the advancement of scRNA-seq protocols exacerbates many computational issues, especially regarding method runtime. To address these difficulties, a new, accurate, and fast method for detecting DEGs in scRNA-seq data is needed.

Results
Here, we propose single-cell minimum enclosing ball (scMEB), a novel and fast method for detecting single-cell DEGs without prior cell clustering results. The proposed method utilizes a small part of known non-DEGs (stably expressed genes) to build a minimum enclosing ball and defines the DEGs based on the distance of a mapped gene to the center of the hypersphere in a feature space.

Conclusions
We compared scMEB to two different approaches that could be used to identify DEGs without cell clustering. The investigation of 11 real datasets revealed that scMEB outperformed rival methods in terms of cell clustering, predicting genes with biological functions, and identifying marker genes. Moreover, scMEB was much faster than the other methods, making it particularly effective for finding DEGs in high-throughput scRNA-seq data. We have developed a package scMEB for the proposed method, which could be available at https://github.com/FocusPaka/scMEB.
Detection of blaNDM−1,mcr-1 and MexB in multidrug resistant Pseudomonas aeruginosa isolated from clinical specimens in a tertiary care hospital of Nepal
Authors: Sharma Samikshya , Devkota Madhu Dixit , Pokhrel Bharat Mani , Banjara Megha Raj 
Published: May 2023

Abstract
Introduction
Pseudomonas aeruginosa is an opportunistic pathogen, which causes healthcare-associated infections in immunosuppressed patients. They exhibit resistance to multiple classes of antibiotics via various mechanisms such as the over-expression of efflux pumps, decreased production of the outer membrane protein (D2 porin), over-expression of the chromosomally encoded AmpC cephalosporinase, modification of drugs, and mutation(s) at the target site of the drug. The bacteria also develop antibiotic resistance through the acquisition of resistance genes carried on mobile genetic elements. Limited data on phenotypic as well as genotypic characterization of MDR P. aeruginosa in Nepal infers the needs for this study. This study was carried out to determine the prevalence rate of metallo-β-lactamase (MBL-producer) as well as colistin resistant multidrug resistant (MDR) P. aeruginosa in Nepal and also to detect MBL, colistin resistance, and efflux pump encoding genes i.e. blaNDM−1, mcr-1 and MexB respectively in MDR P. aeruginosa isolated from clinical samples.

Methods/methodology
A total of 36 clinical isolates of P. aeruginosa were collected. All bacterial isolates were phenotypically screened for antibiotic susceptibility using Kirby Bauer Disc Diffusion method. All the multidrug resistant P. aeruginosa were phenotypically screened for MBL producer by Imipenem-EDTA combined disc diffusion test (CDDT). Similarly, MIC value for colistin was also determined by broth microdilution method. Genes encoding carbapenemase (blaNDM−1), colistin resistant (mcr-1) and efflux pump activity (MexB) were assayed by PCR.

Results
Among 36 P. aeruginosa, 50% were found to be MDR among which 66.7% were found to be MBL producer and 11.2% were found to be colistin resistant. Among MDR P. aeruginosa, 16.7%, 11.2% and 94.4% were found to be harbouring blaNDM−1, mcr-1 and MexB genes respectively.

Conclusion
In our study, carbapenemase production (encoded by blaNDM−1), colistin resistant enzyme production (encoded by mcr-1), and expression of efflux pump (encoded by MexB) are found to be one of the major causes of antibiotic resistance in P. aeruginosa. Therefore, periodic phenotypic as well as genotypic study in Nepal on P. aeruginosa would provide the scenario of resistance pattern or mechanisms in P. aeruginosa. Furthermore, new policies or rules can be implemented in order to control the P. aeruginosa infections.
Preoptimisation in patients with acute obstructive colon cancer (PREOCC) – a prospective registration study protocol
Authors: Boeding Jeske R. E. , Gobardhan Paul D. , Rijken Arjen M. , Seerden Tom C. J. , Verhoef Cornelis , Schreinemakers Jennifer M. J. 
Published: May 2023

Abstract
Background
Postoperative mortality and morbidity rates are high in patients with obstructing colon cancer (OCC). Different treatment options have been evaluated over the years, mainly for left sided OCC. Optimising the preoperative health condition in elective colorectal cancer (CRC) treatment shows promising results. The aim of this study is to determine whether preoptimisation is feasible in patients with OCC, with a special interest/focus on right-sided OCC, and if, ultimately, optimisation reduces mortality and morbidity (stoma rates, major and minor complications) rates in OCC.

Methods
This is a prospective registration study including all patients presenting with OCC in our hospital. Patients with OCC, treated with curative intent, will be screened for eligibility to receive preoptimisation before surgery. The preoptimisation protocol includes; decompression of the small bowel with a NG-tube for right sided obstruction and SEMS or decompressing ileostomy or colostomy, proximal to the site of obstruction, for left sided colonic obstructions. For the additional work-up, additional nutrition by means of parenteral feeding (for patients who are dependent on a NG tube) or oral/enteral nutrition (in case the obstruction is relieved) is provided. Physiotherapy with attention to both cardio and muscle training prior surgical resection is provided. The primary endpoint is complication-free survival (CFS) at the 90 day period after hospitalisation. Secondary outcomes include pre- and postoperative complications, patient- and tumour characteristics, surgical procedures, total in hospital stay, creation of decompressing and/or permanent ileo- or colostomy and long-term (oncological) outcomes.

Discussion
Preoptimisation is expected to improve the preoperative health condition of patients and thereby reduce postoperative complications.

Trial registration
Trial Registry: NL8266 date of registration: 06-jan-2020.

Study status
Open for inclusion.
Oxidative balance score and dietary phytochemical index can reduce the risk of colorectal cancer in Iranian population
Authors: Bentyaghoob Shahrooz , Dehghani Fereshteh , Alimohammadi Arezoo , Shateri Zainab , Kahrizsangi Masoud Amini , Nejad Elham Tavassoli , Nouri Mehran , Rashidkhani Bahram 
Published: May 2023

Abstract
Background
No previous study has assessed the association between oxidative balance score (OBS) and dietary phytochemical index (DPI) with colorectal cancer (CRC) simultaneously. Therefore, this study investigated the association between OBS and DPI with the odds of CRC among the Iranian population.

Methods
This hospital-based age and sex-matched case–control study was conducted between September 2008 and January 2010 (142 controls and 71 cases were entered for analysis). New diagnosed CRC cases were selected from the Cancer Institute, Imam Khomeini Hospital of Tehran. Dietary intakes were determined by a semi-quantitative food frequency questionnaire (FFQ). Then, dietary indices were calculated by food items and nutrient intake. Logistic regression was utilized for assessing the tertiles of OBS and DPI.

Results
In multivariate analysis, OBS was associated with a 77% reduction in CRC odds in the last tertile than the first tertile (odds ratio (OR) = 0.23, confidence interval (CI): 0.07–0.72, Ptrend = 0.017). Also, we found a 64% reduction in CRC odds in the last tertile of DPI compared to the first tertile (OR = 0.36, CI: 0.15–0.86, Ptrend = 0.015).

Conclusions
A diet rich in phytochemicals and anti-oxidants, including fruits and vegetables (citrus fruits, colored berries, and dark-green leafy vegetables) and whole grains, may reduce the CRC odds.
Long term changes in thrombocytopenia and leucopenia after HCV eradication with direct-acting antivirals
Authors: Tajiri Kazuto , Okada Kazuhiko , Ito Hiroyuki , Kawai Kengo , Kashii Yoshiro , Tokimitsu Yoshiharu , Muraishi Nozomu , Murayama Aiko , Hayashi Yuka , Minemura Masami , Takahara Terumi , Shimizu Yukihiro , Yasuda Ichiro 
Published: May 2023

Abstract
Background
Thrombocytopenia due to hypersplenism is a major complication of hepatitis C virus (HCV)-associated cirrhosis. HCV eradication improves these complications in some patients, but the long-term effects of HCV eradication on these complications remain unclear, especially in patients treated with direct acting antivirals (DAAs). The aim was to evaluate long term changes in thrombocytopenia and leucopenia after HCV eradication with DAAs.

Methods
The present multicenter study retrospectively evaluated changes over 5 years in thrombocytopenia and leukocytopenia, as well as changes in liver fibrosis markers and spleen size, in 115 patients with HCV-cirrhosis treated with DAAs.

Results
Thrombocytopenia and leukocytopenia were improved 4 weeks after DAA administration, with thrombocytopenia show further gradual improvement over the next year. Fib-4 index was markedly reduced 1 year after DAA, followed by subsequent gradual reduction over the next 4 years. Spleen size showed gradual annual reductions, with patients experiencing spleen size reduction characterized at baseline by bilirubinemia.

Conclusions
Rapid DAA-associated HCV eradication might lead to rapid disappearance of liver inflammation and bone marrow suppression due to HCV infection. HCV eradication may gradually improve portal hypertension, reducing spleen size.
Brain‐oscillation-synchronized stimulation to enhance motor recovery in early subacute stroke: a randomized controlled double‐blind three‐ arm parallel‐group exploratory trial comparing personalized, non‐ personalized and sham repetitive transcranial magnetic stimulation (Acronym: BOSS-STROKE)
Authors: Lieb Anne , Zrenner Brigitte , Zrenner Christoph , Kozák Gábor , Martus Peter , Grefkes Christian , Ziemann Ulf 
Published: May 2023

Abstract
Background
Stroke is a major cause of death and the most frequent cause of permanent disability in western countries. Repetitive transcranial brain stimulation (rTMS) has been used to enhance neuronal plasticity after stroke, yet with only moderate effect sizes. Here we will apply a highly innovative technology that synchronizes rTMS to specific brain states identified by real-time analysis of electroencephalography.

Methods
One hundred forty-four patients with early subacute ischemic motor stroke will be included in a multicenter 3-arm parallel, randomized, double-blind, standard rTMS and sham rTMS-controlled exploratory trial in Germany. In the experimental condition, rTMS will be synchronized to the trough of the sensorimotor µ-oscillation, a high-excitability state, over ipsilesional motor cortex. In the standard rTMS control condition the identical protocol will be applied, but non-synchronized to the ongoing µ-oscillation. In the sham condition, the same µ-oscillation-synchronized protocol as in experimental condition will be applied, but with ineffective rTMS, using the sham side of an active/placebo TMS coil. The treatment will be performed over five consecutive work days (1,200 pulses per day, 6,000 pulses total). The primary endpoint will be motor performance after the last treatment session as measured by the Fugl-Meyer Assessment Upper Extremity.

Discussion
This study investigates, for the first time, the therapeutic efficacy of personalized, brain-state-dependent rTMS. We hypothesize that synchronization of rTMS with a high-excitability state will lead to significantly stronger improvement of paretic upper extremity motor function than standard or sham rTMS. Positive results may catalyze a paradigm-shift towards personalized brain-state-dependent stimulation therapies.

Trial registration
This study was registered at ClinicalTrials.gov (NCT05600374) on 10–21-2022.
The relationship between personality traits and individual factors with perinatal depressive symptoms: a cross-sectional study
Authors: Serra Riccardo , Giacchetti Nicoletta , Bersani Francesco Saverio , Cappannini Gaia , Martucci Melania , Panfili Matteo , Sogos Carla , Aceti Franca 
Published: May 2023

Abstract
Background
Pregnancy is a crucial transition moment exposing women to potential mental health problems, especially depressive disturbances. Sociodemographic, pregnancy-related, and psychological factors have been related to depressive symptoms in the perinatal period. This study aims at (1) exploring personality and individual factors related with perinatal depressive symptoms, and (2) testing the mediating role of personality in the relation between characteristics of the woman’s family of origin and depressive symptoms.

Methods
Women in the perinatal period admitted to the gynecology unit for motherhood-related routine assessments (n = 241) were included in the study. A survey on individual sociodemographic, clinical, and pregnancy-related factors was administered, also including the Edinburgh Postnatal Depression Scale (EPDS) and the BIG-5 personality test.

Results
Couple conflict and neuroticism were independent and directly correlated with EPDS total score (respectively: B = 2.337; p = .017; B = 0.303; p < .001). Neuroticism was a significant mediator of the relation between the presence of a psychiatric disorder diagnosis in participant’s parents and the EPDS total score (indirect b = 0.969; BCCI95%=0.366—1.607).

Conclusions
Couple relation and neuroticism traits are individual factors related to depressive symptoms in the perinatal period. The family of origin also plays an indirect role on perinatal depressive symptoms. Screening of these factors could lead to early recognition and more tailored treatments, ultimately leading to better outcome for the entire family.
CT radiomics features of meso-esophageal fat in predicting overall survival of patients with locally advanced esophageal squamous cell carcinoma treated by definitive chemoradiotherapy
Authors: Yan Shuo , Li Fei-Ping , Jian Lian , Zhu Hai-Tao , Zhao Bo , Li Xiao-Ting , Shi Yan-Jie , Sun Ying-Shi 
Published: May 2023

Abstract
Objective
To investigate the value of CT radiomics features of meso-esophageal fat in the overall survival (OS) prediction of patients with locally advanced esophageal squamous cell carcinoma (ESCC).

Methods
A total of 166 patients with locally advanced ESCC in two medical centers were retrospectively analyzed. The volume of interest (VOI) of meso-esophageal fat and tumor were manually delineated on enhanced chest CT using ITK-SNAP. Radiomics features were extracted from the VOIs by Pyradiomics and then selected using the t-test, the Cox regression analysis, and the least absolute shrinkage and selection operator. The radiomics scores of meso-esophageal fat and tumors for OS were constructed by a linear combination of the selected radiomic features. The performance of both models was evaluated and compared by the C-index. Time-dependent receiver operating characteristic (ROC) analysis was employed to analyze the prognostic value of the meso-esophageal fat-based model. A combined model for risk evaluation was constructed based on multivariate analysis.

Results
The CT radiomic model of meso-esophageal fat showed valuable performance for survival analysis, with C-indexes of 0.688, 0.708, and 0.660 in the training, internal, and external validation cohorts, respectively. The 1-year, 2-year, and 3-year ROC curves showed AUCs of 0.640–0.793 in the cohorts. The model performed equivalently compared to the tumor-based radiomic model and performed better compared to the CT features-based model. Multivariate analysis showed that meso-rad-score was the only factor associated with OS.

Conclusions
A baseline CT radiomic model based on the meso-esophagus provide valuable prognostic information for ESCC patients treated with dCRT.
Dual-stage cognitive assessment: a two-stage screening for cognitive impairment in primary care
Authors: Cui Liang , Zhang Zhen , Huang Lin , Li Qinjie , Guo Yi-Han , Guo Qi-Hao 
Published: May 2023

Abstract
Background
Aging population has led to an increased proportion of older adults and cognitively impaired. We designed a brief and flexible two-stage cognitive screening scale, the Dual-Stage Cognitive Assessment (DuCA), for cognitive screening in primary care settings.

Method
In total, 1,772 community-dwelling participants were recruited, including those with normal cognition (NC, n = 1,008), mild cognitive impairment (MCI, n = 633), and Alzheimer’s disease (AD, n = 131), and administered a neuropsychological test battery and the DuCA. To improve performance, the DuCA combines visual and auditory memory tests for an enhanced memory function test.

Results
The correlation coefficient between DuCA-part 1 and DuCA-total was 0.84 (P < 0.001). The correlation coefficients of DuCA-part 1 with Addenbrooke’s Cognitive Examination III (ACE-III) and Montreal Cognitive Assessment Basic (MoCA-B) were 0.66 (P < 0.001) and 0.85 (P < 0.001), respectively. The correlation coefficients of DuCA-total with ACE-III and MoCA-B were 0.78 (P < 0.001) and 0.83 (P < 0.001), respectively. DuCA-Part 1 showed a similar discrimination ability for MCI from NC (area under curve [AUC] = 0.87, 95%CI 0.848–0.883) as ACE III (AUC = 0.86, 95%CI 0.838–0.874) and MoCA-B (AUC = 0.85, 95%CI 0.830–0.868). DuCA-total had a higher AUC (0.93, 95%CI: 0.917–0.942). At different education levels, the AUC was 0.83–0.84 for DuCA-part 1, and 0.89–0.94 for DuCA-total. DuCA-part 1 and DuCA-total’s ability to discriminate AD from MCI was 0.84 and 0.93, respectively.

Conclusion
DuCA-Part 1 would aid rapid screening and supplemented with the second part for a complete assessment. DuCA is suited for large-scale cognitive screening in primary care, saving time and eliminating the need for extensively training assessors.
Combined pituitary hormone deficiency harboring CHD7 gene missense mutation without CHARGE syndrome: a case report
Authors: Obata Yoshinari , Takayama Kana , Nishikubo Hideyuki , Tobimatsu Aoki , Matsuda Izumi , Uehara Yuhei , Maruo Yumiko , Sho Hiroyuki , Kosugi Motohiro , Yasuda Tetsuyuki 
Published: May 2023

Abstract
Background
Heterozygous loss-of-function mutations in the chromodomain helicase DNA-binding protein 7 (CHD7) gene cause CHARGE syndrome characterized by various congenital anomalies. A majority of patients with CHARGE syndrome present with congenital hypogonadotropic hypogonadism (HH), and combined pituitary hormone deficiency (CPHD) can also be present. Whereas CHD7 mutations have been identified in some patients with isolated HH without a diagnosis of CHARGE syndrome, it remains unclear whether CHD7 mutations can be identified in patients with CPHD who do not fulfill the criteria for CHARGE syndrome.

Case presentation
A 33-year-old woman was admitted to our hospital. She had primary amenorrhea and was at Tanner stage 2 for both pubic hair and breast development. She was diagnosed with CPHD (HH, growth hormone deficiency, and central hypothyroidism), and a heterozygous rare missense mutation (c.6745G > A, p.Asp2249Asn) in the CHD7 gene was identified. Our conservation analysis and numerous in silico analyses suggested that this mutation had pathogenic potential. She had mild intellectual disability, a minor feature of CHARGE syndrome, but did not fulfill the criteria for CHARGE syndrome.

Conclusions
We report a rare case of CPHD harboring CHD7 mutation without CHARGE syndrome. This case provides valuable insights into phenotypes caused by CHD7 mutations. CHD7 mutations can have a continuous phenotypic spectrum depending on the severity of hypopituitarism and CHARGE features. Therefore, we would like to propose a novel concept of CHD7-associated syndrome.
Favorable cervical cancer mortality-to-incidence ratios of countries with good human development index rankings and high health expenditures
Authors: Shen Tzu-Tsen , Long Cheng-Yu , Wu Ming-Ping 
Published: May 2023

Abstract
Background
Cervical cancer is highly preventable. The mortality-to-incidence ratio (MIR) is a marker that reflects the available screening interventions and clinical outcomes of cancer treatments. The association between the MIR for cervical cancer and cancer screening disparities among countries is an interesting issue but rarely investigated. The present study sought to understand the association between the cervical cancer MIR and the Human Development Index (HDI).

Methods
Cancer incidence and mortality rates were obtained from the GLOBOCAN database. The MIR was defined as the ratio of the crude mortality rate to the incidence rate. We used linear regression to analyze the correlation of MIRs with the HDI and current health expenditure (CHE) in 61 countries selected based on data quality.

Results
The results showed lower incidence and mortality rates and MIRs in more developed regions. In terms of regional categories, Africa had the highest incidence and mortality rates and MIRs. The incidence and mortality rates and MIRs were lowest in North America. Furthermore, favorable MIRs were correlated with a good HDI and high CHE as a percentage of gross domestic product (CHE/GDP) (both p < 0.0001).

Conclusions
The MIR variation for cervical cancer is associated with the ranking of the health system and health expenditure, which further supports the role of cancer screening and treatment disparities in clinical outcomes. The promotion of cancer screening programs can reduce the cervical cancer global incidence and mortality rates and MIRs.