bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetics and”democracy”
Authors: Marchetti Federico , Corsello Giovanni 
Published: December 2022

Abstract
Background
The spread of knowledge on the important implications of a diagnosis of genetic disease does not correspond to a sharing of the knowledge and equal rights of children.

Main body
It is estimated that about 5% of newborns may have a rare disease that in some cases, if diagnosed early, could have specific treatments that may be able to modify the natural history of the disease. However, in most countries the diagnosis during the first hours of life is limited to a few diseases, due to the high costs and time required for genetic investigations with classical methods. Recently, experimental projects to subject all newborns to a complete DNA analysis, with Next Generation Sequencing techniques, to detect any genetic pathologies as early as possible, have been reported in some countries. The late diagnosis of some genetic diseases that have treatment plans, such as spinal muscular atrophy, can be a serious damage, for anyone who has seen and accompanied the life of a child with this disease and his/her family, before and after, the recent availability of therapies which, if started very early, can lead to an almost normal life. Rapid sequencing and genetic diagnosis are a crucial part of directing inpatient management and this resource should be accessible not only to academic medical centers but also in community settings.

Conclusions
It is time for a profound reflection that places in Italy, as in other countries, the use of genetic tests in neonatal and pediatric age based on principles of evidence, ethics, and democracy and on clear national guidelines, which also consider organizational aspects.
Breath-by-breath P0.1 measured on quasi-occlusion via Hamilton C6 may result in underestimation of respiratory drive and inspiratory effort
Authors: Takane Ryo , Nakajima Mikio , Miwa Maki , Kaszynski Richard H. , Nakano Tomotsugu , Goto Hideaki , Takeuchi Muneyuki 
Published: December 2022

AbstractWe aimed to identify the threshold for P0.1 in a breath-by-breath manner measured by the Hamilton C6 on quasi-occlusion for high respiratory drive and inspiratory effort. In this prospective observational study, we analyzed the relationships between airway P0.1 on quasi-occlusion and esophageal pressure (esophageal P0.1 and esophageal pressure swing). We also conducted a linear regression analysis and derived the threshold of airway P0.1 on quasi-occlusion for high respiratory drive and inspiratory effort. We found that airway P0.1 measured on quasi-occlusion had a strong positive correlation with esophageal P0.1 measured on quasi-occlusion and esophageal pressure swing, respectively. Additionally, the P0.1 threshold for high respiratory drive and inspiratory effort were calculated at approximately 1.0 cmH2O from the regression equations. Our calculations suggest a lower threshold of airway P0.1 measured by the Hamilton C6 on quasi-occlusion than that which has been previously reported.
Extensive testing of a multi-locus sequence typing scheme for Giardia duodenalis assemblage A confirms its good discriminatory power
Authors: Klotz Christian , Sannella Anna Rosa , Weisz Filip , Chaudhry Umer , Sroka Jacek , Tůmová Pavla , Nohýnková Eva , Ignatius Ralf , Aebischer Toni , Betson Martha , Troell Karin , Cacciò Simone M. 
Published: December 2022

Abstract
Background
The flagellated parasite Giardia duodenalis is a major and global cause of diarrhoeal disease. Eight genetically very distinct groups, known as assemblages A to H, have been recognized in the G. duodenalis species complex, two of which (assemblages A and B) infect humans and other mammalian hosts. Informative typing schemes are essential to understand transmission pathways, characterize outbreaks and trace zoonotic transmission. In this study, we evaluated a published multi-locus sequence typing (MLST) scheme for G. duodenalis assemblage A, which is based on six polymorphic markers.

Methods
We genotyped 60 human-derived and 11 animal-derived G. duodenalis isolates collected in Europe and on other continents based on the published protocol. After retrieving previously published genotyping data and excluding isolates whose sequences showed allelic sequence heterozygosity, we analysed a dataset comprising 146 isolates.

Results
We identified novel variants at five of the six markers and identified 78 distinct MLST types in the overall dataset. Phylogenetic interpretation of typing data confirmed that sub-assemblage AII only comprises human-derived isolates, whereas sub-assemblage AI comprises all animal-derived isolates and a few human-derived isolates, suggesting limited zoonotic transmission. Within sub-assemblage AII, isolates from two outbreaks, which occurred in Sweden and Italy, respectively, had unique and distinct MLST types. Population genetic analysis showed a lack of clustering by geographical origin of the isolates.

Conclusion
The MLST scheme evaluated provides sufficient discriminatory power for epidemiological studies of G. duodenalis assemblage A.

Graphical Abstract
Altered DNA methylation in estrogen-responsive repetitive sequences of spermatozoa of infertile men with shortened anogenital distance
Authors: Stenz Ludwig , Beyens Matthias , Gill Mark E. , Paoloni-Giacobino Ariane , De Geyter Christian 
Published: December 2022

Abstract
Background
It has been suggested that antenatal exposure to environmental endocrine disruptors is responsible for adverse trends in male reproductive health, including male infertility, impaired semen quality, cryptorchidism and testicular cancer, a condition known as testicular dysgenesis syndrome. Anogenital distance (AGD) is an anthropomorphic measure of antenatal exposure to endocrine disruptors, with higher exposure levels leading to shortened AGD. We hypothesized that exposure to endocrine disruptors could lead to changes in DNA methylation during early embryonic development, which could then persist in the sperm of infertile men with shortened AGD.

Results
Using fluorescence activated cell sorting based on staining with either YO-PRO-1 (YOPRO) or chromomycin-3 (CMA3), we isolated four sperm fractions from eleven infertile men with short AGD and ten healthy semen donors. We examined DNA methylation in these sorted spermatozoa using reduced representation bisulfite sequencing. We found that fractions of spermatozoa from infertile men stained with CMA3 or YOPRO were more likely to contain transposable elements harboring an estrogen receptor response element (ERE). Abnormal sperm (as judged by high CMA3 or YOPRO staining) from infertile men shows substantial hypomethylation in estrogenic Alu sequences. Conversely, normal sperm fractions (as judged by low CMA3 or YO-PRO-1 staining) of either healthy donors or infertile patients were more likely to contain hypermethylated Alu sequences with ERE.

Conclusions
Shortened AGD, as related to previous exposure to endocrine disruptors, and male infertility are accompanied by increased presence of hormonal response elements in the differentially methylated regulatory sequences of the genome of sperm fractions characterized by chromatin decondensation and apoptosis.
In Silico functional and phylogenetic analyses of fungal immunomodulatory proteins of some edible mushrooms
Authors: Ramlal Ayyagari , Samanta Aveek 
Published: December 2022

AbstractMushrooms are a well known source of many bioactive and nutritional compounds with immense applicability in both the pharmaceutical and food industries. They are widely used to cure various kinds of ailments in traditional medicines. They have a low amount of fats and cholesterol and possess a high number of proteins. Immunomodulators have the ability which can improve immunity and act as defensive agents against pathogens. One such class of immunomodulators is fungal immunomodulatory proteins (FIPs). FIPs have potential roles in the treatment of cancer, and immunostimulatory effects and show anti-tumor activities. In the current study, 19 FIPs from edible mushrooms have been used for comparison and analysis of the conserved motifs. Phylogenetic analysis was also carried out using the FIPs. The conserved motif analysis revealed that some of the motifs strongly supported their identity as FIPs while some are novel. The fungal immunomodulatory proteins are important and have many properties which can be used for treating ailments and diseases and this preliminary study can be used for the identification and functional characterization of the proposed novel motifs and in unraveling the potential roles of FIPs for developing newer drugs.
A novel promising diagnosis model for colorectal advanced adenoma and carcinoma based on the progressive gut microbiota gene biomarkers
Authors: Xu Junfeng , Zheng Zhijun , Yang Lang , Li Ruoran , Ma Xianzong , Zhang Jie , Yin Fumei , Liu Lin , Xu Qian , Shen Qiujing , Shen Xiuping , Wu Chunyan , Liu Jing , Qin Nan , Sheng Jianqiu , Jin Peng 
Published: December 2022

Abstract
Background
Colorectal cancer (CRC), a commonly diagnosed cancer often develops slowly from benign polyps called adenoma to carcinoma. Altered gut microbiota is implicated in colorectal carcinogenesis. It is warranted to find non-invasive progressive microbiota biomarkers that can reflect the dynamic changes of the disease. This study aimed to identify and evaluate potential progressive fecal microbiota gene markers for diagnosing advanced adenoma (AA) and CRC.

Results
Metagenome-wide association was performed on fecal samples from different cohorts of 871 subjects (247 CRC, 234 AA, and 390 controls). We characterized the gut microbiome, identified microbiota markers, and further constructed a colorectal neoplasms classifier in 99 CRC, 94 AA, and 62 controls, and validated the results in 185 CRC, 140 AA, and 291 controls from 3 independent cohorts. 21 species and 277 gene markers were identified whose abundance was significantly increased or decreased from normal to AA and CRC. The progressive gene markers were distributed in metabolic pathways including amino acid and sulfur metabolism. A diagnosis model consisting of four effect indexes was constructed based on the markers, the sensitivities of the Adenoma Effect Index 1 for AA, Adenoma Effect Index 2 for high-grade dysplasia (HGD) adenoma were 71.3% and 76.5%, the specificities were 90.5% and 90.3%, respectively. CRC Effect Index 1 for all stages of CRC and CRC Effect Index 2 for stage III–IV CRC to predict CRC yielded an area under the curve (AUC) of 0.839 (95% CI 0.804–0.873) and 0.857 (95% CI 0.793–0.921), respectively. Combining with fecal immunochemical test (FIT) significantly improved the sensitivity of CRC Effect Index 1 and CRC Effect Index 2 to 96.7% and 100%.

Conclusions
This study reports the successful diagnosis model establishment and cross-region validation for colorectal advanced adenoma and carcinoma based on the progressive gut microbiota gene markers. The results suggested that the novel diagnosis model can significantly improve the diagnostic performance for advanced adenoma.
Lack of sex-related analysis and reporting in Cochrane Reviews: a cross-sectional study
Authors: Antequera Alba , Cuadrado-Conde M. Ana , Roy-Vallejo Emilia , Montoya-Martínez María , León-García Montserrat , Madrid-Pascual Olaya , Calderón-Larrañaga Sara ,   on behalf of Research for gender equity collaboration
Published: December 2022

Abstract
Background
Sex-specific analysis and reporting may allow a better understanding of intervention effects and can support the decision-making process. Well-conducted systematic reviews (SRs), like those carried out by the Cochrane Collaboration, provide clinical responses transparently and stress gaps of knowledge. This study aimed to describe the extent to which sex is analysed and reported in a cross-section of Cochrane SRs of interventions, and assess the association with the gender of main authorships.

Methods
We searched SRs published during 2018 within the Cochrane Database of Systematic Reviews. An investigator appraised the sex-related analysis and reporting across sections of SRs and collected data on gender and country of affiliation of the review first and last authors, and a second checked for accuracy. We conducted descriptive statistics and bivariate logistic regression to explore the association between the gender of the authors and sex-related analysis and reporting.

Results
Six hundred and ten Cochrane SRs were identified. After removing those that met no eligibility criteria, 516 reviews of interventions were included. Fifty-six reviews included sex-related reporting in the abstract, 90 considered sex in their design, 380 provided sex-disaggregated descriptive data, 142 reported main outcomes or performed subgroup analyses by sex, and 76 discussed the potential impact of sex or the lack of such on the interpretations of findings. Women represented 53.1 and 42.2% of first and last authorships, respectively. Women authors (in first and last position) had a higher possibility to report sex in at least one of the review sections (OR 2.05; CI 95% 1.12–3.75, P=0.020) than having none.

Conclusions
Sex consideration amongst Cochrane SRs was frequently missing. Structured guidance to sex-related analysis and reporting is needed to enhance the external validity of findings. Likewise, including gender diversity within the research workforce and relevant authorship positions may foster equity in the evidence generated.
Does particle radiation have superior radiobiological advantages for prostate cancer cells? A systematic review of in vitro studies
Authors: Du Tian-Qi , Liu Ruifeng , Zhang Qiuning , Luo Hongtao , Chen Yanliang , Tan Mingyu , Wang Qian , Wu Xun , Liu Zhiqiang , Sun Shilong , Yang Kehu , Tian Jinhui , Wang Xiaohu 
Published: December 2022

Abstract
Background
Charged particle beams from protons to carbon ions provide many significant physical benefits in radiation therapy. However, preclinical studies of charged particle therapy for prostate cancer are extremely limited. The aim of this study was to comprehensively investigate the biological effects of charged particles on prostate cancer from the perspective of in vitro studies.

Methods
We conducted a systematic review by searching EMBASE (OVID), Medline (OVID), and Web of Science databases to identify the publications assessing the radiobiological effects of charged particle irradiation on prostate cancer cells. The data of relative biological effectiveness (RBE), surviving fraction (SF), standard enhancement ratio (SER) and oxygen enhancement ratio (OER) were extracted.

Results
We found 12 studies met the eligible criteria. The relative biological effectiveness values of proton and carbon ion irradiation ranged from 0.94 to 1.52, and 1.67 to 3.7, respectively. Surviving fraction of 2 Gy were 0.17 ± 0.12, 0.55 ± 0.20 and 0.53 ± 0.16 in carbon ion, proton, and photon irradiation, respectively. PNKP inhibitor and gold nanoparticles were favorable sensitizing agents, while it was presented poorer performance in GANT61. The oxygen enhancement ratio values of photon and carbon ion irradiation were 2.32 ± 0.04, and 1.77 ± 0.13, respectively. Charged particle irradiation induced more G0-/G1- or G2-/M-phase arrest, more expression of γ-H2AX, more apoptosis, and lower motility and/or migration ability than photon irradiation.

Conclusions
Both carbon ion and proton irradiation have advantages over photon irradiation in radiobiological effects on prostate cancer cell lines. Carbon ion irradiation seems to have further advantages over proton irradiation.

Graphical Abstract
Automated quantitative assessment of pediatric blunt hepatic trauma by deep learning-based CT volumetry
Authors: Huang Shungen , Zhou Zhiyong , Qian Xusheng , Li Dashuang , Guo Wanliang , Dai Yakang 
Published: December 2022

Abstract
Background
To develop an end-to-end deep learning method for automated quantitative assessment of pediatric blunt hepatic trauma based on contrast-enhanced computed tomography (CT).

Methods
This retrospective study included 170 children with blunt hepatic trauma between May 1, 2015, and August 30, 2021, who had undergone contrast-enhanced CT. Both liver parenchyma and liver trauma regions were manually segmented from CT images. Two deep convolutional neural networks (CNNs) were trained on 118 cases between May 1, 2015, and December 31, 2019, for liver segmentation and liver trauma segmentation. Liver volume and trauma volume were automatically calculated based on the segmentation results, and the liver parenchymal disruption index (LPDI) was computed as the ratio of liver trauma volume to liver volume. The segmentation performance was tested on 52 cases between January 1, 2020, and August 30, 2021. Correlation analysis among the LPDI, trauma volume, and the American Association for the Surgery of Trauma (AAST) liver injury grade was performed using the Spearman rank correlation. The performance of severity assessment of pediatric blunt hepatic trauma based on the LPDI and trauma volume was evaluated using receiver operating characteristic (ROC) analysis.

Results
The Dice, precision, and recall of the developed deep learning framework were 94.75, 94.11, and 95.46% in segmenting the liver and 72.91, 72.40, and 76.80% in segmenting the trauma regions. The LPDI and trauma volume were significantly correlated with AAST grade (rho = 0.823 and rho = 0.831, respectively; p < 0.001 for both). The area under the ROC curve (AUC) values for the LPDI and trauma volume to distinguish between high-grade and low-grade pediatric blunt hepatic trauma were 0.942 (95% CI, 0.882–1.000) and 0.952 (95% CI, 0.895–1.000), respectively.

Conclusions
The developed end-to-end deep learning method is able to automatically and accurately segment the liver and trauma regions from contrast-enhanced CT images. The automated LDPI and liver trauma volume can act as objective and quantitative indexes to supplement the current AAST grading of pediatric blunt hepatic trauma.
Increased expression of ECT2 predicts the poor prognosis of breast cancer patients
Authors: Yi Ming , Zhang Di , Song Bin , Zhao Bin , Niu Mengke , Wu Yuze , Dai Zhijun , Wu Kongming 
Published: December 2022

AbstractBreast cancer is the most common malignancy and the second leading cause of cancer-related death in women. Recent studies have indicated that aberrant activation of Rho GTPases relates to the malignant properties of breast cancer cells. As the guanine nucleotide exchange factor of Rho GTPases, the role of ECT2 (epithelial cell transforming 2) in breast cancer is still unclear. Tissue microarrays and multiple public databases were utilized to investigate the relationship between ECT2 level and clinical-pathological features of breast cancer patients. Kaplan Meier-plotter online tool and tissue microarray with survival information were used to investigate the predictive value for breast cancer. Here, we found increased ECT2 level was highly associated with advanced TNM stage, poor differentiation, and loss of hormone receptors of breast cancer. Gene expression profile showed that ECT2 level was closely correlated to cell-proliferation-associated pathways. Integration analysis using public databases and tissue microarray indicated that high ECT2 was an adverse prognostic factor for breast cancer patients. We believe the ECT2 level might be a valuable complement for commercially available predictors such as the 21 genes test. Furthermore, ECT2 would be a novel target for drug development for breast cancer.
Inequality in remote learning quality during COVID-19: student perspectives and mitigating factors
Authors: Kennedy Alec I. , Mejía-Rodríguez Ana María , Strello Andrés 
Published: December 2022

Abstract
Background
Remote learning, or synchronous or asynchronous instruction provided to students outside the classroom, was a common strategy used by schools to ensure learning continuity for their students when many school buildings were forced to shut down due to the COVID-19 pandemic. Differences in technology infrastructures, digital competencies of students and teachers, and home supports for learning likely led to inequalities in the way remote learning reached and was perceived by students. This study seeks to understand how student perspectives on remote learning varied across and within several countries.

Methods
Building off a conceptual framework developed to understand remote learning success and using data from the Responses to Education Disruption Survey (REDS) student questionnaire from seven countries, we construct measures of student perceptions of three essential components of successful remote learning: Access to Suitable Technology, Effective Teachers, and Engaged Students. We then compare values on these scales across and within countries to identify inequalities in remote learning quality during school closures. We also investigate the extent to which schools implemented supports for remote learning across countries.

Results
We find evidence of across country variation in remote learning quality with certain countries having much lower values on our remote learning quality scales compared to other countries in our sample. Furthermore, we identify within-country inequalities in access to and confidence in using technology with low-SES students, girls, and those living in rural areas having lower values on these measures. Furthermore, we find some evidence of within-country inequalities in student engagement across socioeconomic groups. In contrast, we do not find as many inequalities in our measures of effective teachers. In most countries, schools provided several supports to improve remote learning.

Conclusions
While inequalities in remote learning experiences were anticipated and confirmed by our results, we find it promising that, in some countries, inequalities in access to and confidence in using technology as well as student engagement did not extend to inequalities in perceptions of teacher effectiveness and support. Schools’ efforts to support remote learning, regardless of student background, should be seen as a positive and illustrate their resilience in the face of many challenges.
NEPSscaling: plausible value estimation for competence tests administered in the German National Educational Panel Study
Authors: Scharl Anna , Zink Eva 
Published: December 2022

AbstractEducational large-scale assessments (LSAs) often provide plausible values for the administered competence tests to facilitate the estimation of population effects. This requires the specification of a background model that is appropriate for the specific research question. Because the German National Educational Panel Study (NEPS) is an ongoing longitudinal LSA, the range of potential research questions and, thus, the number of potential background variables for the plausible value estimation grow with each new assessment wave. To facilitate the estimation of plausible values for data users of the NEPS, the R package NEPSscaling allows their estimation following the scaling standards in the NEPS without requiring in-depth psychometric expertise in item response theory. The package requires the user to prepare the data for the background model only. Then, the appropriate item response model including the linking approach adopted for the NEPS is selected automatically, while a nested multiple imputation scheme based on the chained equation approach handles missing values in the background data. For novice users, a graphical interface is provided that only requires minimal knowledge of the R language. Thus, NEPSscaling can be used to estimate cross-sectional and longitudinally linked plausible values for all major competence assessments in the NEPS.