bluuebunny/crossref_metadata_2025_split huggingface dataset:
Update on known and emergent viruses affecting human male genital tract and fertility
Authors: Dabizzi Sara , Maggi Mario , Torcia Maria Gabriella 
Published: March 2024

AbstractMany viruses infect the male genital tract with harmful consequences at individual and population levels. In fact, viral infections may induce damage to different organs of the male genital tract (MGT), therefore compromising male fertility. The oxidative stress, induced during viral-mediated local and systemic inflammation, is responsible for testicular damage, compromising germinal and endocrine cell functions. A reduction in sperm count, motility, number of normal sperm and an increase in DNA fragmentation are all common findings in the course of viral infections that, however, generally regress after infection clearance. In some cases, however, viral shedding persists for a long time leading to unexpected sexual transmission, even after the disappearance of the viral load from the blood.The recent outbreak of Zika and Ebola Virus evidenced how the MGT could represent a reservoir of dangerous emergent viruses and how new modalities of surveillance of survivors are strongly needed to limit viral transmission among the general population.Here we reviewed the evidence concerning the presence of relevant viruses, including emergent and re-emergent, on the male genital tract, their route of entry, their adverse effects on male fertility and the pattern of viral shedding in the semen.We also described laboratory strategies to reduce the risk of horizontal or vertical cross-infection in serodiscordant couples undergoing assisted reproductive technologies.
StackDPP: a stacking ensemble based DNA-binding protein prediction model
Authors: Ahmed Sheikh Hasib , Bose Dibyendu Brinto , Khandoker Rafi , Rahman M Saifur 
Published: March 2024

Abstract
Background
DNA-binding proteins (DNA-BPs) are the proteins that bind and interact with DNA. DNA-BPs regulate and affect numerous biological processes, such as, transcription and DNA replication, repair, and organization of the chromosomal DNA. Very few proteins, however, are DNA-binding in nature. Therefore, it is necessary to develop an efficient predictor for identifying DNA-BPs.

Result
In this work, we have proposed new benchmark datasets for the DNA-binding protein prediction problem. We discovered several quality concerns with the widely used benchmark datasets, PDB1075 (for training) and PDB186 (for independent testing), which necessitated the preparation of new benchmark datasets. Our proposed datasets UNIPROT1424 and UNIPROT356 can be used for model training and independent testing respectively. We have retrained selected state-of-the-art DNA-BP predictors in the new dataset and reported their performance results. We also trained a novel predictor using the new benchmark dataset. We extracted features from various feature categories, then used a Random Forest classifier and Recursive Feature Elimination with Cross-validation (RFECV) to select the optimal set of 452 features. We then proposed a stacking ensemble architecture as our final prediction model. Named Stacking Ensemble Model for DNA-binding Protein Prediction, or StackDPP in short, our model achieved 0.92, 0.92 and 0.93 accuracy in 10-fold cross-validation, jackknife and independent testing respectively.

Conclusion
StackDPP has performed very well in cross-validation testing and has outperformed all the state-of-the-art prediction models in independent testing. Its performance scores in cross-validation testing generalized very well in the independent test set. The source code of the model is publicly available at https://github.com/HasibAhmed1624/StackDPP. Therefore, we expect this generalized model can be adopted by researchers and practitioners to identify novel DNA-binding proteins.
The application of lasers in vital pulp therapy: clinical and radiographic outcomes
Authors: Afkhami Farzaneh , Rostami Golriz , Xu Chun , Peters Ove A. 
Published: March 2024

AbstractThe main purpose of vital pulp therapy (VPT) is to preserve the integrity and function of the pulp. A wide variety of materials and techniques have been proposed to improve treatment outcomes, and among them, the utilization of lasers has gained significant attention. The application of lasers in different stages of VPT has witnessed remarkable growth in recent years, surpassing previous approaches.This study aimed to review the applications of lasers in different steps of VPT and evaluate associated clinical and radiographic outcomes. An electronic search using Scopus, MEDLINE, Web of Science and Google Scholar databases from 2000 to 2023 was carried out by two independent researchers. The focus was on human studies that examined the clinical and/or radiographic effects of different laser types in VPT. A total of 4243 studies were included in this narrative review article. Based on the compiled data, it can be concluded that although current literature suggests laser may be proposed as an adjunct modality for some procedural steps in VPT, more research with standardized methodologies and criteria is needed to obtain more reliable and conclusive results.
Analysis of drug-induced interstitial lung disease caused by herbal medicine using the Japanese Adverse Drug Event Report database
Authors: Oura Keita , Tanaka Mizuki , Matsumoto Kiyoka , Satake Riko , Inoue Misaki , Yoshida Yu , Wakabayashi Wataru , Hasegawa Shiori , Iwata Mari , Suzuki Takaaki , Maezawa Mika , Nakao Satoshi , Liao Jun , Iguchi Kazuhiro , Nakamura Mitsuhiro 
Published: March 2024

Abstract
Background
Drug-induced interstitial lung disease (DIILD) is a severe adverse event leading to morbidity and mortality. This study evaluated the adverse event indicators of DIILD and time-to-onset profiles following the daily intake of herbal drugs (Scutellariae radix [“ogon” in Japanese], Bupleuri radix [“saiko” in Japanese], and Pinelliae tuber [“hange” in Japanese]) using the Japanese Adverse Drug Event Report database. DIILD was defined in accordance with the Medical Dictionary for Regulatory Activities.

Methods
The Japanese Adverse Drug Event Report database contained 830,079 reports published between April 2004 and April 2023. The association between herbal medicines and DILLD was evaluated using the pharmacovigilance index as the reporting odds ratio (ROR), logistic regression models, propensity score-matching techniques, and Weibull shape parameters.

Results
The adjusted RORs using multivariate logistic regression models for Scutellariae radix (daily intake), Pinelliae tuber (daily intake), sex (male), age (≥ 60 years), Scutellariae radix (daily intake)*age (≥ 60 years), and Scutellariae radix (daily intake)* Pinelliae tuber (daily intake) were 1.47 (1.36 − 1.59), 1.05 (1.01 − 1.10), 1.45 (1.34 − 1.57), 1.92 (1.74 − 2.11), 3.35 (3.12 − 3.60), and 1.49 (1.46 − 1.53), respectively. DIILD onset profiles were evaluated using the Weibull shape parameter. A logistic plot of daily intake and onset of DIILD was drawn. ROR signals were detected in 32 of 54 herbal medicines, including Scutellariae radix, Bupleuri radix, and Pinelliae tuber. The median duration (days) (interquartile range) to DIILD onset was 36.0 (27.0–63.0) for Saikokaryukotsuboreito, 35.0 (21.0–55.0) for Saireito, and 31.0 (13.5–67.5) for Shosaikoto. The Weibull shape parameter beta (95% confidence interval) values for Saikokaryukotsuboreito, Saireito, and Shosaikoto were 1.36 (1.08–1.67), 1.36 (1.20–1.52), and 1.31 (0.98–1.68), respectively.

Conclusions
DIILD demonstrated a dose-dependent to crude drugs. Clinicians should strive for the early detection of DIILD and avoid the inadvertent administration of herbal medicines.
Aligning organisational priorities and implementation science for cancer research
Authors: Best Stephanie , Thursky Karin , Buzza Mark , Klaic Marlena , Peters Sanne , Guccione Lisa , Trainer Alison , Francis Jillian 
Published: March 2024

Abstract
Background
The challenge of implementing evidence into routine clinical practice is well recognised and implementation science offers theories, models and frameworks to promote investigation into delivery of evidence-based care. Embedding implementation researchers into health systems is a novel approach to ensuring research is situated in day-to-day practice dilemmas. To optimise the value of embedded implementation researchers and resources, the aim of this study was to investigate stakeholders’ views on opportunities for implementation science research in a cancer setting that holds potential to impact on care. The research objectives were to: 1) Establish stakeholder and theory informed organisation-level implementation science priorities and 2) Identify and prioritise a test case pilot implementation research project.

Methods
We undertook a qualitative study using semi-structured interviews. Participants held either a formal leadership role, were research active or a consumer advocate and affiliated with either a specialist cancer hospital or a cancer alliance of ten hospitals. Interview data were summarised and shared with participants prior to undertaking both thematic analysis, to identify priority areas for implementation research, and content analysis, to identify potential pilot implementation research projects. The selected pilot Implementation research project was prioritised using a synthesis of an organisational and implementation prioritisation framework – the organisational priority setting framework and APEASE framework.

Results
Thirty-one people participated between August 2022 and February 2023. Four themes were identified: 1) Integration of services to address organisational priorities e.g., tackling fragmented services; 2) Application of digital health interventions e.g., identifying the potential benefits of digital health interventions; 3) Identification of potential for implementation research, including deimplementation i.e., discontinuing ineffective or low value care and; 4) Focusing on direct patient engagement e.g., wider consumer awareness of the challenges in delivering cancer care. Six potential pilot implementation research projects were identified and the EMBED project, to support clinicians to refer appropriate patients with cancer for genetic testing, was selected using the synthesised prioritisation framework.

Conclusions
Using a theory informed and structured approach the alignment between strategic organisational priorities and implementation research priorities can be identified. As a result, the implementation research focus can be placed on activities with the highest potential impact.
Effects of changes in residential fast-food outlet exposure on Body Mass Index change: longitudinal evidence from 92,211 Lifelines participants
Authors: van Erpecum Carel-Peter L. , van Zon Sander K.R. , Bültmann Ute , Smidt Nynke 
Published: March 2024

Abstract
Background
Evidence on the association between fast-food outlet exposure and Body Mass Index (BMI) remains inconsistent and is primarily based on cross-sectional studies. We investigated the associations between changes in fast-food outlet exposure and BMI changes, and to what extent these associations are moderated by age and fast-food outlet exposure at baseline.

Methods
We used 4-year longitudinal data of the Lifelines adult cohort (N = 92,211). Participant residential addresses at baseline and follow-up were linked to a register containing fast-food outlet locations using geocoding. Change in fast-food outlet exposure was defined as the number of fast-food outlets within 1 km of the residential address at follow-up minus the number of fast-food outlets within 1 km of the residential address at baseline. BMI was calculated based on objectively measured weight and height. Fixed effects analyses were performed adjusting for changes in covariates and potential confounders. Exposure-moderator interactions were tested and stratified analyses were performed if p < 0.10.

Results
Participants who had an increase in the number of fast-food outlets within 1 km had a greater BMI increase (B(95% CI): 0.003 (0.001,0.006)). Decreases in fast-food outlet exposure were not associated with BMI change (B(95% CI): 0.001 (-0.001,0.004)). No clear moderation pattern by age or fast-food outlet exposure at baseline was found.

Conclusions
Increases in residential fast-food outlet exposure are associated with BMI gain, whereas decreases in fast-food outlet exposure are not associated with BMI loss. Effect sizes of increases in fast-food outlet exposure on BMI change were small at individual level. However, a longer follow-up period may have been needed to fully capture the impact of increases in fast-food outlet exposure on BMI change. Furthermore, these effect sizes could still be important at population level considering the rapid rise of fast-food outlets across society. Future studies should investigate the mechanisms and changes in consumer behaviours underlying associations between changes in fast-food outlet exposure and BMI change.
Harmony in nature: understanding the cultural and ecological aspects of plant use in Ladakh
Authors: Angmo Kunzes , Adhikari Bhupendra S. , Bussmann Rainer W. , Rawat Gopal S. 
Published: March 2024

Abstract
Background
Traditional knowledge (TK) in Ladakh encapsulates a repository of experimental wisdom cultivated over millennia. Despite this cultural wealth, dwindling interest among the younger generations in the region’s age-old practices underscores the urgency to document TK. The current study investigates the diverse usage of plants in Surru, Wakha and Lower Indus valleys of Western Ladakh exploring the influence of socioeconomic and ecological factors.

Methods
A stratified random sample approach was adopted to select 540 respondents for gathering information of useful plants through interviews and questionnaires. Participant observation, questionnaires, open-ended and semi-structured interviews were conducted for data collection. Free listing was done to create an extensive list of plants and their uses. Ethnobotanical metrics such as relative frequency of citation (RFC), relative importance index (RI), cultural value (CV) index and cultural importance (CI) index were computed to assess species applicability. Additionally, one-way analysis of variance (ANOVA) was utilized to discern significant differences in knowledge levels based on valleys, gender, education and religion using TK as a response variable.

Results
Altogether, we recorded 246 plant species under various ethnobotanical uses from Western Ladakh. These include medicinal (126), fodder (124), wild ornamentals (86), food (81), fuel wood (54), dye (20), religious (31) and others (34). Novel plant reports include Berberis brandisiana Ahrendt and Dactylorhiza kafiriana Renz. The dominant plant family is Asteraceae with 35 species. Suru valley exhibits the highest number of cited plants followed by Wakha-chu and Lower Indus valleys (192, 168 and 152 species, respectively).

Conclusion
Disparities in plant use understanding are evident among different groups, prompting further investigation through intercultural comparisons. Plants such as Arnebia euchroma, Juniperus semiglobosa, and Artemisia species emerge with cultural importance. Gender, valley affiliation, religious background and the remoteness of a village all influence local plant knowledge. These variations are linked to socioeconomic disparities among communities.
Channel-wise attention enhanced and structural similarity constrained cycleGAN for effective synthetic CT generation from head and neck MRI images
Authors: Gong Changfei , Huang Yuling , Luo Mingming , Cao Shunxiang , Gong Xiaochang , Ding Shenggou , Yuan Xingxing , Zheng Wenheng , Zhang Yun 
Published: March 2024

Abstract
Background
Magnetic resonance imaging (MRI) plays an increasingly important role in radiotherapy, enhancing the accuracy of target and organs at risk delineation, but the absence of electron density information limits its further clinical application. Therefore, the aim of this study is to develop and evaluate a novel unsupervised network (cycleSimulationGAN) for unpaired MR-to-CT synthesis.

Methods
The proposed cycleSimulationGAN in this work integrates contour consistency loss function and channel-wise attention mechanism to synthesize high-quality CT-like images. Specially, the proposed cycleSimulationGAN constrains the structural similarity between the synthetic and input images for better structural retention characteristics. Additionally, we propose to equip a novel channel-wise attention mechanism based on the traditional generator of GAN to enhance the feature representation capability of deep network and extract more effective features. The mean absolute error (MAE) of Hounsfield Units (HU), peak signal-to-noise ratio (PSNR), root-mean-square error (RMSE) and structural similarity index (SSIM) were calculated between synthetic CT (sCT) and ground truth (GT) CT images to quantify the overall sCT performance.

Results
One hundred and sixty nasopharyngeal carcinoma (NPC) patients who underwent volumetric-modulated arc radiotherapy (VMAT) were enrolled in this study. The generated sCT of our method were more consistent with the GT compared with other methods in terms of visual inspection. The average MAE, RMSE, PSNR, and SSIM calculated over twenty patients were 61.88 ± 1.42, 116.85 ± 3.42, 36.23 ± 0.52 and 0.985 ± 0.002 for the proposed method. The four image quality assessment metrics were significantly improved by our approach compared to conventional cycleGAN, the proposed cycleSimulationGAN produces significantly better synthetic results except for SSIM in bone.

Conclusions
We developed a novel cycleSimulationGAN model that can effectively create sCT images, making them comparable to GT images, which could potentially benefit the MRI-based treatment planning.
Engaging Fathers for Effective Child Nutrition and Development in Tanzania (EFFECTS): study protocol for a five-arm, cluster-randomized trial
Authors:   EFFECTS Study Investigators, Lyaatu Isaac , Mosha Dominic , Sando Mary Mwanyika , Jeong Joshua , Yousafzai Aisha , PrayGod George , Evarist Roman , Galvin Lauren , Kieffer Mary Pat , Kumalija Elfrida , Simpson Jennifer , Ambikapathi Ramya , Boncyk Morgan , Matangi Evidence , Gunaratna Nilupa S. 
Published: March 2024

Abstract
Background
Globally, 144 million children under 5 years are undernourished and 250 million do not meet their developmental potential. Multi-input interventions, such as bundled nutrition and parenting interventions, are designed to mitigate risks for multiple child outcomes. There is limited evidence that bundled interventions have additive benefits to nutrition, growth, or development outcomes. These outcomes share common risks; therefore, designing interventions to tackle these risks using a common theory of change may optimize effectiveness. Emerging evidence suggests explicit engagement of fathers may benefit child outcomes, but few trials have tested this or included data collected from fathers.

Methods
Engaging Fathers for Effective Child Nutrition and Development in Tanzania (EFFECTS) is a community-based cluster-randomized controlled trial that will be implemented in the rural Mara Region, Tanzania. The trial aims (1) to test a bundled nutrition and parenting program delivered to mothers’ groups, with or without fathers’ groups, over 12 months on child and caregiving outcomes compared to a nutrition program alone, and (2) to test nutrition or bundled nutrition and parenting programs delivered to mothers’ and fathers’ groups over 12 months on child and caregiving outcomes compared to programs delivered to mothers alone. The trial comprises five arms: (1) mothers’ groups receiving a nutrition program, (2) mothers’ groups receiving a bundled nutrition and parenting program, (3) mothers’ and fathers’ groups receiving a nutrition program, (4) mothers’ and fathers’ groups receiving a bundled nutrition and parenting program, and (5) control receiving standard of care health services. The primary outcomes are child dietary diversity and early child development (mental and motor development). Parents with a child under 18 months will be enrolled in peer groups and receive twice monthly intervention by trained community health workers. Data will be collected from mothers, fathers, and children at baseline (pre-intervention), midline, and endline (post-intervention).

Discussion
EFFECTS will generate evidence on the effects of bundled nutrition and parenting interventions on child nutrition, growth, and development outcomes; determine the benefits of engaging fathers on child, caregiving, and caregiver outcomes; and investigate common and unique pathways between treatments and child outcomes.

Trial registration
ClinicalTrials.gov NCT03759821. Registered on November 30, 2018
New thiazole, thiophene and 2-pyridone compounds incorporating dimethylaniline moiety: synthesis, cytotoxicity, ADME and molecular docking studies
Authors: Metwally Heba M. , Younis Norhan M. , Abdel-Latif Ehab , El-Rayyes Ali 
Published: March 2024

AbstractVarious sets of thiazole, thiophene, and 2-pyridone ring structures containing a dimethylaniline component were synthesized. Substituted thiazoles 2–3 and thiophenes 5–7 were produced by reacting thiocarbamoyl compound 4 with α-halogenated reagents in different basic conditions. Also, a series of 2-pyridone derivatives 9a–f substituted with dimethylaniline was synthesized through Michael addition of malononitrile to α,β-unsaturated nitrile derivatives 8a–f. The synthesized products were structurally proven by spectroscopic methods such as IR, 1H NMR, 13C NMR, and MS data. Furthermore, the anti-cancer efficacy of the compounds was assessed using the MTT assay on two cell lines: hepatocellular carcinoma (HepG-2) and breast cancer (MDA-MB-231). The results showed the highest growth inhibition for derivatives 2, 6, 7, and 9c, which were further examined for their IC50 values. The IC50 for compound 2 showed equipotent activity (IC50 = 1.2 µM) against the HepG-2 cell line compared to Doxorubicin (IC50 = 1.1 µM). Compounds 2, 6, 7 and 9c showed very good ADME assessments for further drug administration. Moreover, the PASS theoretical prediction for the compounds showed high antimitotic and antineoplastic activities for compounds 2, 6, 7, and 9c, as well as potent inhibition activity for the insulysin enzyme (IDE). Molecular docking stimulations were performed on CDK1/CyclinB1/CKS2 (PDB ID: 4y72) and BPTI (PDB ID: 2ra3). When docked into (PDB ID: 4y72), all of the tested compounds showed considerable inhibition, and the 2-pyridone derivative 9d had the maximum binding affinity (− 8.1223 kcal/mol). While thiophene derivative 6 offered the maximum binding affinity (− 7.5094 kcal/mol) when docked into (PDB ID: 2ra3).
Graphical Abstract