bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gdaphen, R pipeline to identify the most important qualitative and quantitative predictor variables from phenotypic data
Authors: Muñiz Moreno Maria del Mar , Gavériaux-Ruff Claire , Herault Yann 
Published: January 2023

AbstractBackgroundIn individuals or animals suffering from genetic or acquired diseases, it is important to identify which clinical or phenotypic variables can be used to discriminate between disease and non-disease states, the response to treatments or sexual dimorphism. However, the data often suffers from low number of samples, high number of variables or unbalanced experimental designs. Moreover, several parameters can be recorded in the same test. Thus, correlations should be assessed, and a more complex statistical framework is necessary for the analysis. Packages already exist that provide analysis tools, but they are not found together, rendering the decision method and implementation difficult for non-statisticians.ResultWe present Gdaphen, a fast joint-pipeline allowing the identification of most important qualitative and quantitative predictor variables to discriminate between genotypes, treatments, or sex. Gdaphen takes as input behavioral/clinical data and uses a Multiple Factor Analysis (MFA) to deal with groups of variables recorded from the same individuals or anonymize genotype-based recordings. Gdaphen uses as optimized input the non-correlated variables with 30% correlation or higher on the MFA-Principal Component Analysis (PCA), increasing the discriminative power and the classifier’s predictive model efficiency. Gdaphen can determine the strongest variables that predict gene dosage effects thanks to the General Linear Model (GLM)-based classifiers or determine the most discriminative not linear distributed variables thanks to Random Forest (RF) implementation. Moreover, Gdaphen provides the efficacy of each classifier and several visualization options to fully understand and support the results as easily readable plots ready to be included in publications. We demonstrate Gdaphen capabilities on several datasets and provide easily followable vignettes.ConclusionsGdaphen makes the analysis of phenotypic data much easier for medical or preclinical behavioral researchers, providing an integrated framework to perform: (1) pre-processing steps as data imputation or anonymization; (2) a full statistical assessment to identify which variables are the most important discriminators; and (3) state of the art visualizations ready for publication to support the conclusions of the analyses. Gdaphen is open-source and freely available athttps://github.com/munizmom/gdaphen, together with vignettes, documentation for the functions and examples to guide you in each own implementation.
Ion-pumping microbial rhodopsin protein classification by machine learning approach
Authors: Selvaraj Muthu Krishnan , Thakur Anamika , Kumar Manoj , Pinnaka Anil Kumar , Suri Chander Raman , Siddhardha Busi , Elumalai Senthil Prasad 
Published: January 2023

Abstract
Background
Rhodopsin is a seven-transmembrane protein covalently linked with retinal chromophore that absorbs photons for energy conversion and intracellular signaling in eukaryotes, bacteria, and archaea. Haloarchaeal rhodopsins are Type-I microbial rhodopsin that elicits various light-driven functions like proton pumping, chloride pumping and Phototaxis behaviour. The industrial application of Ion-pumping Haloarchaeal rhodopsins is limited by the lack of full-length rhodopsin sequence-based classifications, which play an important role in Ion-pumping activity. The well-studied Haloarchaeal rhodopsin is a proton-pumping bacteriorhodopsin that shows promising applications in optogenetics, biosensitized solar cells, security ink, data storage, artificial retinal implant and biohydrogen generation. As a result, a low-cost computational approach is required to identify Ion-pumping Haloarchaeal rhodopsin sequences and its subtype.

Results
This study uses a support vector machine (SVM) technique to identify these ion-pumping Haloarchaeal rhodopsin proteins. The haloarchaeal ion pumping rhodopsins viz., bacteriorhodopsin, halorhodopsin, xanthorhodopsin, sensoryrhodopsin and marine prokaryotic Ion-pumping rhodopsins like actinorhodopsin, proteorhodopsin have been utilized to develop the methods that accurately identified the ion pumping haloarchaeal and other type I microbial rhodopsins. We achieved overall maximum accuracy of 97.78%, 97.84% and 97.60%, respectively, for amino acid composition, dipeptide composition and hybrid approach on tenfold cross validation using SVM. Predictive models for each class of rhodopsin performed equally well on an independent data set. In addition to this, similar results were achieved using another machine learning technique namely random forest. Simultaneously predictive models performed equally well during five-fold cross validation. Apart from this study, we also tested the own, blank, BLAST dataset and annotated whole-genome rhodopsin sequences of PWS haloarchaeal isolates in the developed methods. The developed web server (https://bioinfo.imtech.res.in/servers/rhodopred) can identify the Ion Pumping Haloarchaeal rhodopsin proteins and their subtypes. We expect this web tool would be useful for rhodopsin researchers.

Conclusion
The overall performance of the developed method results show that it accurately identifies the Ionpumping Haloarchaeal rhodopsin and their subtypes using known and unknown microbial rhodopsin sequences. We expect that this study would be useful for optogenetics, molecular biologists and rhodopsin researchers.
TeCD: The eccDNA Collection Database for extrachromosomal circular DNA
Authors: Guo Jing , Zhang Ze , Li Qingcui , Chang Xiao , Liu Xiaoping 
Published: January 2023

Abstract
Background
Extrachromosomal circular DNA (eccDNA) is a kind of DNA that widely exists in eukaryotic cells. Studies in recent years have shown that eccDNA is often enriched during tumors and aging, and participates in the development of cell physiological activities in a special way, so people have paid more and more attention to the eccDNA, and it has also become a critical new topic in modern biological research.

Description
We built a database to collect eccDNA, including animals, plants and fungi, and provide researchers with an eccDNA retrieval platform. The collected eccDNAs were processed in a uniform format and classified according to the species to which it belongs and the chromosome of the source. Each eccDNA record contained sequence length, start and end sites on the corresponding chromosome, order of the bases, genomic elements such as genes and transposons, and other information in the respective sequencing experiment. All the data were stored into the TeCD (The eccDNA Collection Database) and the BLAST (Basic Local Alignment Search Tool) sequence alignment function was also added into the database for analyzing the potential eccDNA sequences.

Conclusion
We built TeCD, a platform for users to search and obtain eccDNA data, and analyzed the possible potential functions of eccDNA. These findings may provide a basis and direction for researchers to further explore the biological significance of eccDNA in the future.
Direct leaf-peeling method for areca protoplasts: a simple and efficient system for protoplast isolation and transformation in areca palm (Areca catechu)
Authors: Wang Yaodi , Wang Linxi , Liu Hongjun , Gou Bei , Hu Weiyao , Qin Li , Shen Wentao , Wang Aiming , Cui Hongguang , Dai Zhaoji 
Published: January 2023

Abstract
Background
Areca palm (Areca catechu) is a woody perennial plant of both economical and medicinal importance grown in tropical and subtropical climates. Yet, the molecular biology study of areca palm is extremely impeded by its unavailability of a transformation method. An efficient protoplast isolation and transformation system could be highly desirable to overcome this barrier.

Results
Here, we described a simple and efficient method for protoplast isolation and transformation from the perennial plant areca palm. A high yield of protoplasts (2.5 × 107 protoplasts per gram of fresh leaf tissues) was obtained from the fresh light green leaflet from the newly-emerged leaf digested overnight in the enzyme solution [2% (w/v) cellulase R10, 0.5% (w/v) macerozyme R10, 0.7 M mannitol, 10 mM CaCl2, 20 mM KCl, 20 mM MES and 0.1% (w/v) BSA, pH 5.7] by the direct leaf-peeling method. The isolated areca protoplasts maintain viability of 86.6% and have been successfully transformed with a green fluorescent protein (GFP)-tagged plasmid (pGreen0029-GFP, 6.0 kb) via the polyethylene glycol (PEG)-mediated transformation. Moreover, the mannitol concentration (optimal: 0.7 M) was determined as a key factor affecting areca protoplast isolation. We also demonstrated that the optimal density of areca protoplast for efficient transformation was at 1.0–1.5 × 106 cells/ml. With the optimization of transformation parameters, we have achieved a relatively high transformation efficiency of nearly 50%.

Conclusion
We have established the first efficient protocol for the high-yield isolation and transformation of areca palm protoplasts. This method shall be applied in various biological studies of areca palm, such as gene function analysis, genome editing, protein trafficking and localization and protein–protein interaction. In addition, the protoplast system offers a great genetic transformation approach for the woody perennial plant-areca palm. Moreover, the established platform may be applied in protoplast isolation and transformation for other important species in the palm family, including oil palm and coconut.
Effect of Leventhal’s self-regulatory intervention on the hypertensive patients’ illness perception and lifestyle: a randomized controlled trial
Authors: Saranjam Fatemeh , Afrasiabifar Ardashir , Alamdari Alikaram , Hosseini Nazafarin 
Published: January 2023

Abstract
Background
The perception of illness may lead to improving the hypertensive patients’ lifestyle, but no study was found in this regard. Therefore, this study was conducted to determine the effect of intervention based on Leventhal’s self-regulatory model on the illness perception and lifestyle of patients with hypertension.

Methods
In the present randomized controlled trial study, ninety eligible patients with primary hypertension were randomly assigned to one of the two groups of intervention and control. Patients in the intervention group received five sessions of Leventhal’s self-regulatory intervention, each of 60 min and weekly. However the control group received routine care. The outcomes were illness perception and lifestyle of the patients with hypertension. The Revised Illness Perception Questionnaire and the Lifestyle Questionnaire were administered to assess illness perception and lifestyle before the treatment to establish a baseline and subsequently 12 weeks after the intervention. The collected data were analyzed using statistical IMB SPSS software, version 21. Qualitative data were analyzed using Chi-Square test or Fisher’s Exact test, and the Independent Sample t- test and Paired Sample t- test were used for analyzing quantitative data.

Results
Leventhal’s self-regulatory intervention improved subscales of illness perception (p < 0.05) except for emotional representations and consequences. The global mean scores of the hypertensive patients ̓ lifestyle in the intervention group significantly increased from 102.8 ± 2.3 at the baseline to 112.1 ± 3 post-intervention.

Conclusions
Interventions based on Leventhal’s self-regulatory model could improve the illness perception and lifestyle of patients with hypertension.
Trial registration The present randomized controlled trial study was registered on the Iranian Registry of Clinical Trials Website (IRCT); ID: IRCT20141222020401N6 on 8/5/2019.
Two cases of Ramsay-Hunt syndrome following varicella zoster viral meningitis in young immunocompetent men: case reports
Authors: Hwang Yun Su , Kim Young Seo , Shin Byoung-Soo , Kang Hyun Goo 
Published: January 2023

Abstract
Background
Ramsay-Hunt syndrome (RHS) due to varicella zoster virus (VZV) infection is commonly reported in individuals aged at least 50 years or immunocompromised individuals. VZV infection may invade the central nervous system (CNS) and cause meningitis or encephalitis, which are more likely to occur in patients with chronic diseases such as diabetes and chronic renal failure. However, cases with VZV-induced concurrent RHS and CNS infections are rare.

Case presentation
Two young male patients, aged 32 and 43 years, with no underlying disease developed VZV meningitis, followed by RHS involving cranial nerves VII and VIII. Both patients presented with symptoms of peripheral facial palsy, and dizziness accompanied by tinnitus and hearing loss, which appeared several days after the onset of fever and headache. These symptoms were documented as facial neuropathy and sensorineural hearing loss in the electrophysiologic studies. Lymphocyte-dominant pleocytosis and VZV positivity were confirmed from cerebrospinal fluid examination and polymerase chain reaction, respectively. The patients were treated with intravenous acyclovir and oral steroids simultaneously. Following the treatment completion, both patients were relieved of their headaches and fever; however, facial palsy, dizziness, and tinnitus persisted. They were followed up at the outpatient clinic.

Conclusion
These cases confirmed that RHS and CNS infections can co-exist even in young adults with normal immune function and more importantly, that CNS infection can precede RHS. Since early detection and treatment of RHS improve the prognosis, it is critical to closely monitor patients with VZV meningitis or encephalitis considering the possible superimposition of RHS.
Safety and efficacy of trifluridine/tipiracil in previously treated metastatic colorectal cancer: final results from the phase IIIb single-arm PRECONNECT study by duration of therapy
Authors: Taieb Julien , Price Timothy , Vidot Loïck , Chevallier Bénédicte , Wyrwicz Lucjan , Bachet Jean-Baptiste 
Published: January 2023

Abstract
Background
PRECONNECT was an international, phase IIIb trial evaluating the safety and efficacy of trifluridine/tipiracil (FTD/TPI) for metastatic colorectal cancer (mCRC).

Methods
Patients with mCRC received FTD/TPI 35 mg/m2 twice-daily on days 1–5 and 8–12 of each 28-day cycle for third- or later-line treatment. Primary endpoint: safety and time to deterioration of Eastern Cooperative Oncology Group performance status [ECOG PS] to ≥2). Secondary endpoints included progression-free survival (PFS). Potential prognostic factors for PFS were explored.

Results
Of 914 patients, 69% completed 0–3, 24% completed 4–7, and 7% completed ≥8 cycles of FTD/TPI. Drug-related grade ≥ 3 adverse events included neutropenia (38.1%), anaemia (7.2%) and asthenia (3.4%). Median [95% CI] time to ECOG PS deterioration was 8.7 [8.1-not calculable] months and increased with duration of treatment (DoT). Median PFS was 2.8 [2.7–3.0] months and increased with duration of treatment DoT. Prognostic factors associated with longer PFS included time since diagnosis of first metastasis, number of metastatic sites, baseline ECOG PS, presence/absence of liver metastasis or previous regorafenib treatment, and laboratory variables.

Conclusions
No new safety concerns for FTD/TPI were identified and PFS increased with DoT. These data provide confidence for the use of FTD/TPI, including the use of multiple cycles, in routine practice.

Trial registration
EudraCT Number: 2016-002311-18; registered 19/09/2016.
https://clinicaltrials.gov/ct2/show/NCT03306394; registered 11/10/2017.
Perceived stress in adolescence and labour market participation in young adulthood - a prospective cohort study
Authors: Winding Trine Nøhr , Nielsen Mette Lykke , Grytnes Regine 
Published: January 2023

Abstract
Background
Adolescence is a key-developmental stage for physical, neurological, psychological, and social changes. In this developmental stage, a large number of people struggle with mental health problems like stress, anxiety, or depression. Psychological vulnerability in adolescence has previously been found to be negatively related to future low labour market participation. However, studies are lacking that investigate the impact of stress during adolescence on labour market participation in early adulthood using register data. The aim of this prospective study was therefore to examine the association between perceived stress during adolescence and labour market participation in young men and women in early adulthood.

Methods
A Danish cohort of 3038 participants born in 1989 was followed with use of questionnaires from age 15 to age 28. The exposure, self-reported perceived stress, was collected by questionnaires at ages 15, 18, and 21. The outcome, labour market participation, was based on register information on social benefits, such as unemployment benefits, sickness benefits, and disability benefits, collected on a weekly basis during a 4-year period. Information about the socioeconomic confounders was also gleaned from registers.

Results
The study found consistent associations between perceived stress from age 15 to age 21 and low labour market participation from age 25 to age 29 in both women and men after adjusting for mental health and socioeconomic confounders. The strongest associations between perceived stress and low labour market participation were seen among men who reported stress several times during adolescence.

Conclusions
The results indicate that although, women in general, reported being more stressed than men during adolescence and had lower labour market participation in early adulthood, there was a small group of men who had experienced stress during adolescence who were at particularly high risk of being marginalised in the labour market.
Application of plasma donor-derived cell free DNA for lung allograft rejection diagnosis in lung transplant recipients
Authors: Ju Chunrong , Xu Xin , Zhang Jianheng , Chen Ao , Lian Qiaoyan , Liu Feng , Liu Haitao , Cai Yuhang , Zou Yanjun , Yang Yalan , Zhou Yang , He Jianxing 
Published: January 2023

Abstract
Background
Donor-derived cell-free DNA (dd-cfDNA) has been applied to monitor acute rejection (AR) in kidney and heart transplantation. This study was aimed to investigate the application of dd-cfDNA levels in the diagnosis of AR and chronic lung allograft dysfunction (CLAD) among the lung transplantation recipients (LTRs).

Methods
One hundred and seventy LTRs were enrolled at the First Affiliated Hospital of Guangzhou Medical University between 1 June 2015 and 30 March 2021. Patients were divided into 4 groups: stable group, AR group, infection group and CLAD group. The level of dd-cfDNA was analyzed using target region sequencing and the performance characteristics of dd-cfDNA for diagnosis of AR and CLAD were determined, respectively.

Results
Kruskal–Wallis test showed that there were some significant differences in the level of dd-cfDNA (%) among the 4 groups, with p < 0.001. Among them, the level of dd-cfDNA (%) was highest (median 2.17, IQR [1.40–3.82]) in AR group, and higher in CLAD group (median 1.07, IQR [0.98–1.31]), but lower in infection group (median 0.71, IQR [0.57–1.07]) and lowest in stable group (median 0.71, IQR [0.61–0.84]). AUC-ROC curve analysis showed that the threshold of dd-cfDNA for AR was 1.17%, with sensitivity being 89.19% and specificity being 86.47%, and the optimal threshold of 0.89% was determined of CLAD, with sensitivity being 95.00% and specificity of 76.99%.

Conclusions
Plasma dd-cfDNA could be a useful tool for the assessment of lung allograft rejection, including AR and CLAD, and holds promise as a noninvasive biomarker for “allograft injury” in both acute and chronic rejection following lung transplantation.
Gunshot injury to the colon by expanding bullets in combat patients wounded in hybrid period of the Russian-Ukrainian war during 2014–2020
Authors: Gumeniuk Kostiantyn , Lurin Igor A. , Tsema Ievgen , Malynovska Lesia , Gorobeiko Maksym , Dinets Andrii 
Published: January 2023

Abstract
Background
A gunshot wound to the colon is a frequent injury in armed conflicts. An example of a high-energy modern weapon is hollow-point bullets, which is associated with increased tissue damage and lethal outcome. The aim of this study was to evaluate gunshot injuries to the colon in combat patients and to assess the difference in clinical features of patients with colon injuries by hollow-point versus shape-stable bullets.

Patients and methods
Analyses of clinical data were performed on 374 male soldiers from the Armed Forces of Ukraine with gunshot abdominal wounds with injury to the colon in East Ukraine between 2014 and 2020. Out of 374 injured, 112 (29.9%) patients were diagnosed with penetrating gunshot bullet wounds: 69/112 (61.6%) were injured by shape-stable bullets, and the hollow-point bullets injured 43/112 (38.4%) patients.

Results
More severe hemorrhagic shock stages were in patients injured by hollow-point bullets: shock stages III-IV was in 25 (58.1%) patients injured by the hollow-point bullets vs. 17 (24.6%) patients injured by shape-stable bullets (p = 0.0004). Left colon parts were more frequently injured as compared to the right colon side or transverse colon: 21 (48.8%) patients were injured by the hollow-point bullets (p < 0.0001), and 41 (59.4%) patients were injured by the shape-stable bullets (p = 0.032). A significant difference was identified for the frequent injury to the middle colon within the entire cohort (p = 0.023). Patients injured by the hollow-point bullets demonstrated a higher frequency of 3–5 areas of colon gunshot defects, which was detected in 18 (41.8%) patients injured by hollow-point bullets and none with shape-stable bullets injury (p = 0.0001). Colon Injury Scale (CIS) IV was detected in 7 (16.3%) patients injured by the hollow-point bullets as compared to 2 (2.9%) patients injured by shape-stable bullets (p = 0.011). Colostomy was performed in 14 (69%) patients injured by shape-stable bullets and in 12 (27.9%) patients injured by hollow-point bullets (p > 0.05). 15 (35%) patients died after injury by the hollow-point bullet, whereas 9 (13%) patients after damage by the shape-stable bullets (p = 0.0089).

Conclusions
All patients should be suspected to have an injury by bullet with expanding properties in case of penetrating abdominal injury (absent of outlet wound) and careful revision of the abdomen must be performed to identify possible multiorgan injury as well as multiple gunshot defects of the intestine.