bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing learning outcomes of two collaborative activities on random genetic drift in an upper-division genetics course
Authors: True John R. , Abreu Evan 
Published: February 2024

Abstract
Background
Random genetic drift is a difficult concept for biology undergraduates to understand. Active learning activities in a collaborative setting have the potential to improve student learning outcomes compared to traditional lectures alone and have been shown to help foster success for underrepresented students. However, few activities in this content area have been evaluated for effectiveness in improving student outcomes using peer-reviewed instruments backed by evidence of their validity and reliability. Our aim in this study was to use the Genetic Drift Instrument (GeDI) to evaluate and compare student learning gains in an upper division genetics course in which two different genetic drift activities, a faculty-developed collaborative exercise and a commercially published lab tutorial, were administered in an active-learning classroom with students working in small groups.

Methods
The GeDI was administered in both pre- and post-testing in two semesters (n = 95 and 98 students), with the semesters differing in which activity was assigned. Instrument dimensionality, person and item fit, and reliability were evaluated using Rasch analysis. Hierarchical Linear Models (HLMs) with two-way interactions were fitted to assess whether being in a certain Intervention Type, Race/ethnicity, Gender, or First Generation Status affected learning gains. HLMs with three-way interactions were used to assess whether the activities benefited students of all backgrounds equivalently.

Results
We found that the GeDI demonstrated unidimensionality, with high item reliability and relatively low person reliability, consistent with previous studies. Both the faculty-developed activity and the commercially available lab tutorial were associated with significant learning gains on genetic drift concepts. Students in the SimBio group had higher learning gains but the difference in effect size was small. No significant differences in learning gains were found between students from different demographic groups, and both activities appeared to benefit students of different backgrounds equivalently.

Conclusions
The GeDI instrument could be improved by adding items that more consistently differentiate students of different ability levels, especially at high ability levels. The greater impact on learning gains in the SimBio group while statistically significant does not translate into actual meaningful differences in student understanding. While students of different background variables in the sample have equivalent learning gains and are benefitted equivalently by the different interventions, our interventions did not ameliorate inequities in genetic drift understanding as measured by the GeDI that were uncovered in pre-testing.
Predicting the duration of motorway incidents using machine learning
Authors: Corbally Robert , Yang Linhao , Malekjafarian Abdollah 
Published: February 2024

AbstractMotorway incidents are frequent & varied in nature. Incident management on motorways is critical for both driver safety & road network operation. The expected duration of an incident is a key parameter in the decision-making process for control room operators, however, the actual duration for which an incident will impact the network is never known with true certainty. This paper presents a study which compares the ability of different machine learning algorithms to estimate the duration of motorway incidents on Ireland’s M50 motorway, using an extensive historical incident database. Results show that the support vector machine has the best performance in most cases, but a different method may need to be used to improve accuracy in some situations. Results highlight the main challenges in accurately forecasting incident durations in real time & recommendations are made for improving prediction accuracy through systematic recording of various additional incident details.
What happens to Bifidobacterium adolescentis and Bifidobacterium longum ssp. longum in an experimental environment with eukaryotic cells?
Authors: Jakubczyk Dominika , Leszczyńska Katarzyna , Pacyga-Prus Katarzyna , Kozakiewicz Dominika , Kazana-Płuszka Wioletta , Gełej Dominika , Migdał Paweł , Kruszakin Roksana , Zabłocka Agnieszka , Górska Sabina 
Published: February 2024

Abstract
Background
The impact of probiotic strains on host health is widely known. The available studies on the interaction between bacteria and the host are focused on the changes induced by bacteria in the host mainly. The studies determining the changes that occurred in the bacteria cells are in the minority. Within this paper, we determined what happens to the selected Bifidobacterium adolescentis and Bifidobacterium longum ssp. longum in an experimental environment with the intestinal epithelial layer. For this purpose, we tested the bacteria cells' viability, redox activity, membrane potential and enzymatic activity in different environments, including CaCo-2/HT-29 co-culture, cell culture medium, presence of inflammatory inductor (TNF-α) and oxygen.

Results
We indicated that the external milieu impacts the viability and vitality of bacteria. Bifidobacterium adolescentis decrease the size of the live population in the cell culture medium with and without TNF-α (p < 0.001 and p < 0.01 respectively). In contrast, Bifidobacterium longum ssp. longum significantly increased survivability in contact with the eukaryotic cells and cell culture medium (p < 0.001). Bifidobacterium adolescentis showed significant changes in membrane potential, which was decreased in the presence of eukaryotic cells (p < 0.01), eukaryotic cells in an inflammatory state (p < 0.01), cell culture medium (p < 0.01) and cell culture medium with TNF-α (p < 0.05). In contrast, Bifidobacterium longum ssp. longum did not modulate membrane potential. Instead, bacteria significantly decreased the redox activity in response to milieus such as eukaryotic cells presence, inflamed eukaryotic cells as well as the culture medium (p < 0.001). The redox activity was significantly different in the cells culture medium vs the presence of eukaryotic cells (p < 0.001). The ability to β-galactosidase production was different for selected strains: Bifidobacterium longum ssp. longum indicated 91.5% of positive cells, whereas Bifidobacterium adolescentis 4.34% only. Both strains significantly reduced the enzyme production in contact with the eukaryotic milieu but not in the cell culture media.

Conclusion
The environmental-induced changes may shape the probiotic properties of bacterial strains. It seems that the knowledge of the sensitivity of bacteria to the external environment may help to select the most promising probiotic strains, reduce research costs, and contribute to greater reproducibility of the obtained probiotic effects.
A comprehensive study on non-cancer-related mortality risk factors in elderly gastric cancer patients post-curative surgery
Authors: Ushimaru Yuki , Nagano Shinnosuke , Nishikawa Kazuhiro , Kawabata Ryohei , Takeoka Tomohira , Kitagawa Akihiro , Ohara Nobuyoshi , Tomihara Hideo , Maeda Sakae , Imazato Mitsunobu , Noura Shingo , Miyamoto Atsushi 
Published: February 2024

Abstract
Background
The increasing incidence of gastric cancer in the elderly underscores the need for an in-depth understanding of the challenges and risks associated with surgical interventions in this demographic. This study aims to investigate the risk factors and prognostic indicators for non-cancer-related mortality following curative surgery in elderly gastric cancer patients.

Methods
This retrospective analysis examined 684 patients with pathological Stage I—III gastric cancer who underwent curative resection between January 2012 and December 2021. The study focused on patients aged 70 years and above, evaluating various clinical and pathological variables. Univariate analysis was utilized to identify potential risk factors with to non-cancer-related mortality and to access prognostic outcomes.

Results
Out of the initial 684 patients, 244 elderly patients were included in the analysis, with 33 succumbing to non-cancer-related causes. Univariate analysis identified advanced age (≥ 80 years), low body mass index (BMI) (< 18.5), high Charlson Comorbidity Index (CCI), and the presence of overall surgical complications as significant potential risk factors for non-cancer related mortality. These factors also correlated with poorer overall survival and prognosis. The most common cause of non-cancer-related deaths were respiratory issues and heart failure.

Conclusion
In elderly gastric cancer patients, managing advanced age, low BMI, high CCI, and minimizing postoperative complications are essential for reducing non-cancer-related mortality following curative surgery.
Clinical and genomic evaluations of a persistent fatal SARS-CoV-2 infection in a goods syndrome patient: a case report
Authors: Tabarsi Payam , Maleki Ali , Abtahian Zahra , khabbaz Alieh , Fereydouni Zahra , Rezaie Jahangir , Tavakoli Mahsa , Sanati Parastoo Yektay , Salehi-Vaziri Mostafa 
Published: February 2024

AbstractThe coronavirus disease of 2019 (COVID-19) resulted from an infection by severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) which is the main cause of acute respiratory distress syndrome (ARDS) in global population from 2019 on. It may contribute to higher rate of death among the patients with immunodeficiency based on recent reports. In addition, Good syndrome (GS) as a result of thymoma removal might cause in some long-lasting microbial infections. We described clinical aspects and viral mutations on a case of GS suffering from COVID-19. A 46-year-old man with fever, common respiratory disease symptoms and positive COVID-19 polymerase chain reaction (PCR) test, with the history of thymoma removal surgery was admitted to Masih Daneshvari Hospital, Tehran, Iran. Lung radiographs and oxygen saturation measurement disclosed considerable implication resulted in application of several anti-microbial medication. The delta variant (B.1.617.2 (21 J Clade)) was the strain isolated from the patient by sequencing methods done by the COVID-19 National Reference Laboratory (CNRL), Pasteur Institute of Iran, while the dominant strain circulated mostly among population was Omicron (B.1.1.529) at the time of sampling. Unfortunately, the patient had passed away a month later by sudden respiratory failure progressed in refractory septic shock. Despite the fact that opportunistic infections may lead the GS patients to a major health problematic condition, unusual persistent of infections such as non-dominant variant of SARS-Cov-2 could be observed through the disease timeline. Therefore, a fully screening of thymoma plus intra-host evolution monitoring of SARS-CoV-2 is highly recommended in immunocompromised patients.
Establishing the Kidney dIsease in the National guarD (KIND) registry: an opportunity for epidemiological and clinical research in Saudi Arabia
Authors: Tawhari Mohammed , Alhamadh Moustafa , Alhabeeb Abdulrahman , Ureeg Abdulaziz , Alghnam Suliman , Alhejaili Fayez , Alnasser Lubna A. , Sayyari Abdullah 
Published: February 2024

Abstract
Background
In Saudi Arabia (SA), there has been an alarming increase in the prevalence of chronic kidney diseases (CKD) over the last three decades. Despite being one of the largest countries in the Middle East, renal conditions remain understudied, and there is limited data on their epidemiology and outcomes in SA.

Objectives
To document the experience of establishing a local renal registry assessing the epidemiology of CKD and identifying potential areas for improving the quality and delivery of care for CKD patients.

Methods
This is a multi-center retrospective registry. Potential participants were identified through the ICD-10 codes from five hospitals serving the National Guard affiliates in SA. Patients aged ≥ 18 years treated in any National Guard hospital since 2010 for glomerulonephritis, CKD, or received hemodialysis, peritoneal dialysis, or renal transplant were enrolled. Once enrolled in the registry, patients were followed to the last visit date. RedCap was used to create and host the online registry platform.

Results
A total of 2,912 patients were included, and more than half were younger than 60 years old. Two-thirds of the patients were overweight (25%) or obese (37%). Glomerulonephritis was diagnosed in 10% of the patients, and dialysis-dependent and kidney transplant patients accounted for 31.4% and 24.4%, respectively. Hypertension and diabetes mellitus were detected among 52% and 43% of the participants, respectively. Hemodialysis was the most prevalent dialysis method, with patients spending 3.6 ± 0.4 h per session to receive this treatment. One in every five participants had a kidney biopsy taken (21%). Several barriers and facilitators of the success of this registry were identified.

Conclusions
The KIND registry provides much-needed information about CKD in Saudi Arabia and serves as a model for future projects investigating the natural history and progression of the spectrum of renal diseases. Logistic and financial challenges to the sustainability of registries are identified and discussed.
Differential expression of Semaphorin-7A /CD163-positive macrophages in large artery and cardiogenic stroke
Authors: Jiang Yi , Sun Zhichao , Ge Zhonglin , Tao Zhonghai , Liu Mengqian , Zhong Wen , Dong Nan , Xu Lei , Wang Hui , Xu Yiwen , Shen Xiaozhu 
Published: February 2024

Abstract
Background
Identification of the causes of stroke of undetermined etiology, specifically cardioembolism (CE) and non-CE causes, can inform treatment planning and prognosis prediction. The objective of this study was to analyze the disparities in thrombus composition, particularly Semaphorin-7A (Sema7A) and CD163, between patients diagnosed with large-artery atherosclerosis (LAA) and those with CE, and to investigate their potential association with prognosis.

Methods
Thrombi were collected from patients who underwent mechanical thrombectomy at two hospitals. The patients were categorized into two groups: LAA and CE. We compared the levels of Sema7A and CD163 between these groups and analyzed their relationships with stroke severity, hemorrhagic transformation and prognosis.

Results
The study involved a total of 67 patients. Sema7A expression was found to be significantly higher in the CE group compared to LAA (p < 0.001). Conversely, no statistically significant differences were observed for CD163 between the groups. The presence of Sema7A/CD163 did not show any associations with stroke severity or hemorrhagic transformation (all p > 0.05). However, both Sema7A (OR, 2.017; 95% CI, 1.301–3.518; p = 0.005) and CD163 (OR, 2.283; 95% CI, 1.252–5.724; p = 0.03) were associated with the poor prognosis for stroke, after adjusting for stroke severity.

Conclusion
This study highlights that CE thrombi exhibited higher levels of Sema7A expression compared to LAA thrombi. Moreover, we found a positive correlation between Sema7A/CD163 levels and the poor prognosis of patients with acute ischemic stroke.
Predictive factors of perinatal depression among women with gestational diabetes mellitus in the UAE: a cross-sectional clinical study
Authors: Alzarooni Khadija I. , Abusnana Salah , Zakaria Hala , Hussein Amal , Mussa Bashair M. , Mohammed Ghada 
Published: February 2024

Abstract
Background
Gestational Diabetes Mellitus (GDM) is responsible for the development of 30–50% of type 2 diabetes mellitus that predisposes later to adverse consequences among affected mothers and their offspring. Several studies have suggested that GDM increases the risk of developing perinatal depression (PND); however, factors that are involved in this association are yet to be determined. This study aims to identify factors that interrelate GDM and PND among pregnant and postnatal women in the United Arab Emirates (UAE).

Methods
A total of 186 women between 18 and 45 years old attending the obstetrics clinic during their 3rd trimester or up to 6 months postnatal were recruited between October 2021 and April 2022. Women who were known to have pre-existing diabetes mellitus (type 1 or type 2), kidney disease, liver disease, and those receiving hormonal therapy were excluded. Participants completed a structured questionnaire including sociodemographic data and the Edinburgh Postnatal Depression Scale (EPDS). Based on their EPDS scores, study participants were categorized into three groups: no depression (> 9), possible depression (9–11), and high possibility/strong positive depression (≥ 12). SPSS 26 was used for data analysis.

Results
Among the 186 participants, 81% (n = 151) were Emirati, 41% (n = 76) had no GDM, and 58% (n = 110) had GDM. Of the study participants, 34.4% had a high possibility of strong positive depression, 40.9% had possible depression, and only 6.5% had no depression. The association between GDM and PND was clinically and statistically insignificant, with a calculated odds ratio (OR) of 1.574 (p value = 0.204) and a 95% confidence interval (0.781—3.172). However, age, personal history of depression, and BMI were found to be strong predictors of depression among pregnant/postpartum women in the UAE.

Conclusions
The study findings propose that age, personal history of depression, and obesity are strong predictors of depression during pregnancy. The strong correlation between obesity (which is a known strong predictor of GDM) and PND suggests that further studies with longitudinal designs and longer observational periods might better reveal the relationship between GDM and PND.

Trial registration
Retrospectively registered study by Research Ethics Committees of the University Hospital Sharjah and the University of Sharjah (Ref. No.: UHS-HERC- 025–17122019) December 17, 2019.
Transcriptomics analysis revealed that TAZ regulates the proliferation of KIRC cells through mitophagy
Authors: He Zhen , Shi Jianxi , Zhu Bing , Tian Zhentao , Zhang Zhihong 
Published: February 2024

AbstractTranscriptional Co-Activator with PDZ-Binding Motif (TAZ, also known as WWTR1) is a downstream effector of the Hippo pathway, involved in the regulation of organ regeneration and cell differentiation in processes such as development and regeneration. TAZ has been shown to play a tumor-promoting role in various cancers. Currently, many studies focus on the role of TAZ in the process of mitophagy. However, the molecular mechanism and biological function of TAZ in renal clear cell carcinoma (KIRC) are still unclear. Therefore, we systematically analyzed the mRNA expression profile and clinical data of KIRC in The Cancer Genome Atlas (TCGA) dataset. We found that TAZ expression was significantly upregulated in KIRC compared with normal kidney tissue and was closely associated with poor prognosis of patients. Combined with the joint analysis of 36 mitophagy genes, it was found that TAZ was significantly negatively correlated with the positive regulators of mitophagy. Finally, our results confirmed that high expression of TAZ in KIRC inhibits mitophagy and promotes KIRC cell proliferation. In conclusion, our findings reveal the important role of TAZ in KIRC and have the potential to be a new target for KIRC therapy.
Ocular parameters associated with visual performance of enhanced monofocal intraocular lens
Authors: Kim Da Ran , Yoon Young Chae , Whang Woong-Joo , Hwang Ho Sik , Na Kyung-Sun 
Published: February 2024

Abstract
Background
An enhanced monofocal intraocular lenses (IOLs) (Tecnis Eyhance ICB00 and Tecnis Eyhance Toric DIU) has been developed to enhance intermediate vision while avoiding the disadvantages of multifocal IOLs. Although many studies have demonstrated the improvement of intermediate visual acuity with enhanced monofocal IOLs, it is not known specifically for which patients these IOLs should be recommended or avoided. In this study, we aim to find out which ocular parameters affect vision performance and photic phenomenon of ICB00 or DIU at different distances.

Methods
Patients who underwent cataract surgery with ICB00 or DIU, performed by a single surgeon, were included. Before surgery, the patients’ age, gender, axial length, anterior chamber depth, spherical aberration Z (4,0), vertical coma, horizontal coma, angle kappa (κ), angle alpha (α), and other ocular parameters were investigated. One month after surgery, uncorrected near visual acuity (UNVA at 40 cm), uncorrected intermediate visual acuity (UIVA at 66 cm), uncorrected distance logMAR visual acuity (UDVA), IOL decentration, and quality of vision (QoV) questionnaires were conducted.

Results
A total of 43 patients (58 eyes) were included. The results of the univariate linear regression analyses showed a negative correlation between spherical aberration and logMAR UNVA and UIVA (p = 0.003, β=-0.51 and p = 0.018, β=-0.23, respectively) and a positive correlation between angle α and logMAR UIVA (p = 0.036, β = 0.19). Deeper anterior chamber depth (ACD) was associated with poorer total QoV (p = 0.018, β = 14.43), particularly in glare, halo, blur, and fluctuation perception. A higher degree of IOL decentration tended to decrease UNVA and UIVA (Pearson correlation coefficient, r = 0.336 and r = 0.221, respectively); however, no significant effect was observed on UDVA (Pearson correlation coefficient, r = 0.042).

Conclusions
In enhanced monofocal IOLs, a higher level of spherical aberration is associated with better performance in UNVA and UIVA, whereas a larger angle α has a negative impact. A deeper ACD negatively affects the QoV.
The association between sex and neonatal respiratory distress syndrome
Authors: Fang Keren , Yue Shaojie , Wang Shuo , Wang Mingjie , Yu Xiaohe , Ding Ying , Lv Mei , Liu Yang , Cao Chuanding , Liao Zhengchang 
Published: February 2024

Abstract
Background
To investigate the association between sex and neonatal respiratory distress syndrome (NRDS).

Methods
Neonates born at our hospital and transferred to the neonatal department within 1 h were retrospectively analyzed. Depending on whether they developed NRDS during their hospital stay, the neonates was divided into NRDS and non-NRDS groups. There were 142 neonates in the NRDS group (95 males and 47 females) and 310 neonates in the non-NRDS group (180 males and 140 females). The neonates’ data on gestational age (GA), sex, birth weight, white blood cell count (WBC), platelet count (PLT), C-reactive protein (CRP), total immunoglobulin M (total IgM), gestational diabetes mellitus(GDM), antenatal steroids use, meconium-stained amniotic fluid, and preterm premature rupture of membranes(PPROM) were gathered.

Results
452 neonates (265 males and 187 females) were involved for the purpose of collecting basic characteristic. Multivariate analysis, males had a 1.87 times higher risk of NRDS than females (P < 0.05) after controlling for the confounding effects of GA, birth weight, WBC, PLT, CRP, total IgM, GDM, antenatal steroids use, meconium-stained amniotic fluid, and PPROM.

Conclusions
Sex was associated with NRDS; males had a considerably higher risk of NRDS than females.