bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of fiber-reinforced polylactic acid filaments using untreated/silane-treated trichosanthes cucumerina fibers for additive manufacturing
Authors: Raghunathan Vijay , Ayyappan Vinod , Rangappa Sanjay Mavinkere , Siengchin Suchart
Published: January 2024

Multi-material additive manufacturing is gaining importance due to the enhancement of properties by utilizing different materials in a single additive process, especially in 3D printing. The prime motive is the need for eco-friendly materials, with the waste-to-wealth concept being the current global trend. Trichosanthes Cucumerina stem fiber, which is obtained from the discarded stem of Trichosanthes Cucumerina plant, is used in this work; the treatment of the Trichosanthes Cucumerina fibers was done using silane. Six filaments were developed with varying untreated/silane-treated Trichosanthes Cucumerina contents (3, 6, and 9%) compared with pure PLA filaments for 3D printing. Developed filaments were assessed for ultimate tensile strength, diameter variation, differential scanning calorimetry, water absorption, morphological and surface roughness. The test results elucidated that the 6% silane-treated Trichosanthes Cucumerina fiber-reinforced/PLA filament had the highest tensile strength of 63.5 MPa with better fiber distribution. The 3% silane-treated Trichosanthes Cucumerina fiber-reinforced/PLA filament had the least diameter deviation of 0.0015 mm. Based on the test data, the 6% silane-treated Trichosanthes Cucumerina fiber-reinforced/PLA filament can be utilized to prepare biodegradable components.
Miscellaneous Care: Bridging the In-between of Translational Medicine
Authors: Hernández Isabel Briz
Published: January 2024

Based on fieldwork in China on oncology clinical trials for immunotherapy which involve foreign patients as trial subjects, in this paper, I illustrate how the source material needed for the trial (the patient’s T cells) is a scarce biological substance that needs to be generated and crafted though the efforts of patients, doctors, nurses, or lab technicians, as well as other staff: chauffeurs, translators, and foreign patient coordinators. Among the varied tasks done by these support staff, I focus on the intersubjective practices they perform to respond to the needs at the bench and the bedside, what I call “miscellaneous care.” I argue that although invisible and neglected, these practices are constitutive of the techno-scientific assemblage of translational medicine. Miscellaneous care suggests that the capitalization of life itself does not only refer to the capitalization of biological substances and biological processes, it in fact includes capitalization of intersubjective processes, such as responding to the presence of others.
Understanding Altruism of Nonprofit Workers: The Roles of Motivation Types
Authors: Ugur Zeynep B. , Heermans Gabriela Francisca
Published: January 2024

This paper studies the impact of motivation types on altruism levels among the nonprofit organization (NPO) workforces in Turkey. To measure altruism, we used a probabilistic dictator game with real stakes. In a sample of 228 NPO workers, 73% opted to donate an average of 50 out of approximately 100 USD instead of retaining the entire 100 USD for themselves in the case they might win. Our results show that the NPO workforce’s altruism levels vary greatly depending on their motivation type. Religiously motivated NPO workers show the highest levels of altruism, whereas career-oriented NPO workers show the lowest levels of altruism. Moreover, paid NPO workers show significantly lower levels of altruism compared to unpaid workers. In addition, motivation types partially explain the differences in altruism between unpaid and paid workers.
Multiscale convolutional conditional domain adversarial network with channel attention for unsupervised bearing fault diagnosis
Authors: Wang Haomiao , Li Yibin , Jiang Mingshun , Zhang Faye
Published: January 2024

Unsupervised cross-domain fault diagnosis is an effective technical way to realize the engineering application of bearing fault diagnosis methods. However, there are still two problems that need to be resolved. First, the importance of fault features at different scales is generally not consistent. There is redundant information in the fault features. Second, most methods mainly study how to lessen the marginal distribution difference in source and target domains while ignoring their class information. When the data distribution contains complex multimodal structure, this may lead to failure to capture the multimodal structure. To address the above problems, a multiscale channel attention conditional domain adversarial network is proposed. First, a new channel attention module is designed to assign different weights to different channels, which can highlight valuable features and stamp out superfluous features. Then, conditional domain adversarial is used to fully capture the multimodal structure through cross-covariance dependencies between features and classes. Our method’s capability is validated by diagnose results on public data sets and self-built data sets.
Multimodal imaging of congenital peri-papillary arterial loops presenting with vitreous hemorrage in a young male: A case report
Authors: Lassandro Nicola Vito , Maceroni Martina
Published: January 2024

Introduction

Congenital arterial peripapillary loops are rare entities and very few cases are described in literature.

Case description

A 25-year-old Asian man presented a diffuse vitreous hemorrhage in his Left Eye (LE). OCT-A revealed the presence of bilateral vascular loops at the optic nerve head. Fluorescein angiography (FA) confirmed the vascular abnormality in both eyes, with arterial filling in early phases and no dye leakage. At twenty days of follow up, the vitreous hemorrhage in the LE completely reabsorbed and BCVA improved from 20/63 to 20/20.

Conclusion

Congenital peripapillary loops should be considered in the differential diagnosis of vitreous hemorrhage, especially in young patients with no history of ocular/head trauma. Multimodal imaging is highly recommended to properly manage the patients, avoiding unnecessary therapeutic choices.
Palliative Care for Newborns in India: Patterns of Care in a Neonatal Palliative Care Program at a Tertiary Government Children’s Hospital
Authors: Ishak Tayoob Mohammad , Rayala Spandana , Doherty Megan , Singh Hima Bindu , Alimelu Madireddy , Lingaldinna Swapna , Palat Gayatri
Published: January 2024

Neonatal palliative care is a specialized area within children’s palliative care, which focusses on the needs of infants with life-limiting or life-threatening conditions. Nearly one quarter of global neonatal deaths occur in India, where neonatal palliative care evidence is limited. This study describes the development and implementation of a neonatal palliative care program within a neonatal intensive care unit (NICU) at a government hospital, describing the implementing an 8-month pilot palliative care program for neonates, including the patterns of care, and barriers and enablers of success. The hospital-based palliative care team included trained pediatric palliative care physicians, a nurse, and a counselor. There was a steady increase in monthly referrals. There were 110 referrals in total, including 89 (81%) deaths and 18 (16%) babies were alive at the time of final follow-up, 10 months after the pilot program was completed. The program addressed physical symptoms, including providing morphine, as well as psychosocial and spiritual concerns of families. A model of hospital-based palliative care for neonates can be implemented within NICUs in tertiary government hospitals in India. Neonatal palliative care programs should include partnerships with charitable organizations to support implementation costs and provide palliative care training, mentorship, and capacity-building support.
Evidence-based telehealth interventions for posttraumatic stress disorder, depression, and anxiety: A systematic review and meta-analysis
Authors: Kelber Marija S , Smolenski Derek J , Boyd Courtney , Shank Lisa M , Bellanti Dawn M , Milligan Tiffany , Edwards-Stewart Amanda , Libretto Salvatore , Parisi Kelly , Morgan Maria A , Evatt Daniel P
Published: January 2024

Introduction

The goal of this systematic review was to examine the efficacy of behavioral health care treatments for posttraumatic stress disorder (PTSD), depression, and anxiety delivered via telehealth.

Methods

We searched a combination of keywords related to telehealth, relevant mental health disorders, and evidence-based psychotherapies in three databases (PubMed, PsycInfo, and Embase) from database inception to April 2022. We included randomized controlled trials published in English wherein at least one arm received an evidence-based psychotherapy via telehealth. To be included, studies also had to enroll an adult population with symptoms or diagnosis of PTSD, depressive disorder, or anxiety disorder.

Results

Moderate quality of evidence was consistent with only small differences, if any, in efficacy between video teleconferencing (VTC) and in-person delivery for patients with PTSD ( d = 0.06, 95% CI −0.17, 0.28). However, for those with depression, in-person delivery was associated with better outcomes compared to VTC ( d = 0.28, 95% CI 0.03, 0.54; low quality of evidence). We also found that evidence-based treatments delivered over telephone were more efficacious for depression compared to treatment as usual ( d = -0.47, 95% CI −0.66, −0.28; very low quality of evidence). Very low quality of evidence supported the use of telehealth versus waitlist for anxiety ( d = -0.48, 95% CI −0.89, −0.09).

Conclusions

A synthesis across 29 studies indicates that the efficacy of telehealth for delivery of evidence-based behavioral health interventions varies by target diagnosis and telehealth modality. More research is needed on the efficacy of telehealth treatments for depression and anxiety.
Absence of July effect on trauma outcomes at the start of the academic medical calendar
Authors: Zima Laura , Harvin John A , Deng Hansen , Okonkwo David , Sieg Emily , Alhourani Ahmad , Jagid Jonathan R , Krueger Evan , Taghavi Sharven , Nordham Kristen , Torres Glenda , Lang Stefan , Vetkas Artur , Kitagawa Ryan S , Lozano Andres , Conner Christopher R
Published: January 2024

Purpose

The “July effect” refers to the phenomenon of a higher complication incidence and lower survival rate for patients treated at academic institutions during the beginning of the academic medical calendar. To date, no multi-center study has examined the presence of a “July effect” in a large cohort of trauma patients. We sought to determine if there is a by-month effect on survival and length of stay (LOS) for trauma patients in large academic centers.

Methods

We performed a multicenter, retrospective cohort study between 2010 and 2020 from five high-volume academic trauma centers in the United States. We included all adult motor vehicle collision (MVC) traumas evaluated at all centers in the study population (age >16 years, mechanism of injury classified as “motor vehicle collision”). Data included date and time of injury, injury severity score (ISS), LOS, and mortality. Each injury was classified as minor (ISS 1–8), moderate (9–15), severe (16–24), and very severe (>25). The mortality and LOS for each range over the entire epoch was calculated by month for each ISS classification.

Results

We analyzed 39,668 MVC traumas (mean age 41.83, range 39.9–43.3 among sites, 58.9% male and range 56.1–60.4%, 67.4% white range 42.3–84.7%). Survival for the “very severe” traumas ranged from 86.7–90.3%. Across the five sites, there was no significant change in survival (either increased or decreased mortality) or LOS for MVC patients in July or August for any injury classification level. Both age and ISS had a significant effect on survival (OR 0.02 for ISS >25, 0.22 for patients >65 years-old, both p < 0.05).

Conclusions

In five high-volume centers, there was no significant effect of the July transition on survival or LOS of MVC trauma patients.
Comprehensive Sexual Health Educational Learning Modules for College Students
Authors: Asson Alexa , Roberts Joni K.
Published: January 2024

Sexual health education in the United States continues to be a controversial topic of discussion with no federal regulations. Due to this, the sex education students receive before college varies greatly. Our team discovered that no mandatory, comprehensive sexual health education is required for students once they enter the California State University system. At Cal Poly specifically, it was found that students were engaging in risky sexual behaviors. For example, the 2021 American College Health Association—National College Health Assessment III Fall 2021 Data Report revealed that less than half (42.1%) of students reported regularly using condoms during vaginal sex, and a mere 5.1% of students reported barrier method use during oral sex. To fill in the noticed gaps in our students’ sexual health education, our team developed a set of 10 comprehensive sexual health educational learning modules. The modules cover topics ranging from condom use and STIs to pleasure, porn literacy, and having difficult conversations with a partner. This anonymous online resource provides students with easy-to-read written material and engaging graphics. Future research will focus on user engagement and the effect of the resource on sexual health best practices across our campus.
Expanding Human Response to Automation Failures to Sociotechnical Systems
Authors: Cooke Nancy J.
Published: January 2024

Skraaning and Jamieson raise some interesting issues related to the response of humans to automation failures and offer a taxonomy of failure types that broadens its definition. In this commentary a further attempt to broaden the scope of automation failures is made that places failures within a sociotechnical system of multiple humans and multiple machine components including automation. A suggestion of how one might understand the system’s response to automation failures is offered and the inclusion of autonomy is raised as another complication.
Self-compassion as a factor in the deradicalisation of extremist offenders
Authors: Syafiq Muhammad , Alfithon Achmad Mauluddin , Cherney Adrian , Louis Winnifred R.
Published: January 2024

The present study investigates the role of self-compassion in generating change amongst violent extremists through a study of terrorist prisoners in Indonesia. The aim is to provide insights into the under-explored role of self-transformation and agency in the deradicalisation process by applying Neff’s concept of self-compassion, which comprises psychological processes of self-kindness, perceptions of common humanity, and mindfulness. The study draws on qualitative data derived from interviews with three terrorist inmates incarcerated in Porong Prison, Indonesia. All three participants were at the time of the interview participating in a deradicalisation program implemented in the prison. Interview data indicate that the components of self-compassion play a role in self-change reported by terrorist inmates. This included the expression of remorse, seeking God's forgiveness, the acceptance of consequences and human frailty, and the ability to not linger or fixate on negative thoughts and past decisions and actions. The results of this study indicate that self-compassion is a potentially important element in the deradicalisation process, and that the development of self-compassion is an additional method by which interventions can assist the process of desistance from violent extremism.
An Ambitious Artificial Intelligence Policy in a Decentralised Governance System: Evidence From Indonesia
Authors: Wadipalapa Rendy Pahrun , Katharina Riris , Nainggolan Poltak Partogi , Aminah Sitti , Apriani Tini , Ma’rifah Diana , Anisah Azmi Listya
Published: January 2024

This study investigates Indonesia’s ambitious artificial intelligence (AI) policy within the context of its decentralised governance structure. Through in-depth case studies in Jakarta, Central Java, and East Java, we analyse emerging AI-based policy responses and their challenges in a rapidly evolving technological landscape. Drawing from elite interviews conducted with central and local government officials and documentary research, this study offers rare insights into the local perspective on the struggle to accommodate the central government's ambitious plan with limited resources. This article finds that the divergence in the views and visions of AI between central and local governments has complicated the formulation and implementation of AI-based policies. Central authorities wield a dominant role, evident through regulatory mandates and a centralised decision-making approach that can potentially constrain local autonomy. This power asymmetry, coupled with the lack of specific AI-focused regulations, challenges local governments’ capacity to independently design and manage AI initiatives aligned with their unique contexts. Interestingly, instead of showing their resistance towards the ambitious national plan, local leaders have embraced AI policies, positioning them as innovative tools to enhance popularity in the lead-up to the 2024 general election.
ChatGPT is a promising tool to increase readability of orthopedic research consents
Authors: Gill Bissem , Bonamer John , Kuechly Henry , Gupta Rajul , Emmert Scottie , Kurkowski Sarah , Hasselfeld Kim , Grawe Brian
Published: January 2024

Background/Purpose: Informed consent is a fundamental ethical requirement in medical research, ensuring that participants have a comprehensive understanding of the risks and benefits associated with their participation. Clinical researchers must ensure effective and efficient communication of the implications of participation, but the complexity and length of traditional research consent forms can impede comprehension and create barriers to effective communication between researchers and participants. For this reason, the American Medical Association recommends a 6th grade reading level for all patient-facing medical information. Can the large language model, ChatGPT-3.5, improve readability while simultaneously preserving information necessary for adequate informed consent?. Methods: Nineteen IRB approved Orthopedic surgery research consent forms were entered into ChatGPT with instructions to make the form “readable at a 6th-grade level.” Post ChatGPT consent forms were assessed using commonly used readability metrics. Additionally, a single Orthopedic surgeon who has practiced independently for 15 years assessed the forms for accuracy and retention of imperative informed consent elements. Results: The median differences between pre-ChatGPT and post-ChatGPT were statistically significant for every readability metric (all p < 0.001) and all favored the post-ChatGPT consent as being more readable. Two language metrics, Automated Readability Index and Raygor Grade Level, indicated the post-ChatGPT consent forms could meet the AMA's recommended 6th-grade reading level. Twelve of 19 post-ChatGPT consents had at least one error. Conclusion: ChatGPT can significantly improve the readability of Orthopedic clinical research consent forms, but these edited consents are not without mistakes and cannot reach the AMA's recommended 6th grade reading level. Therefore, ChatGPT should be used as a tool to supplement the writing and editing process of human researchers.
The relationship between body height and plantar pressure distribution in adult handball players: A cross-sectional study
Authors: Abdel-aziem Amr Almaz , Ameer Mariam A
Published: January 2024

Background/purpose

The relationship between a handball player's upper body posture, body weight distribution in relation to body height is poorly understood. So, this study explored the relationship between body height and sagittal spinal curvatures and plantar pressure distribution in handball players.

Method

According to handball player's body height, 63 male handball players were divided into two groups; group A (age, 23.54 ± 1.32 years) consisted of 30 handball players with body height above average, and group B (age, 23.40 ± 1.73 years) consisted of 33 handball players with body height below average. The thoracic and lumbar curvatures and trunk height were measured with the Formetric III 4D spine, and the DIERS Pedoscan device was used to assess the plantar pressure distribution for both groups.

Results

The thoracic kyphosis of group A was significantly higher than that of group B ( p = 0.001), without a significant difference in lumbar lordosis ( p = 0.086). Group A showed a significant increase in the forefeet pressure and a significant decrease in the rearfeet pressure compared to group B ( p = 0.001). There was a high positive correlation between the body height and trunk length, and body height and kyphosis angle ( r = 0.932, r = 0.665, respectively). There was a high positive correlation between the body height and forefoot plantar pressure ( r = 0.665, p < 0.01).

Conclusion

The taller handball players have an increased thoracic kyphosis angle and forefeet pressure compared to shorter handball players.
Millions Saved in Head and Neck Free Flap Reconstruction at a High-Volume Center: A Cost Analysis
Authors: Fraser Hill W.K. , Redwood Jennifer , Thoma Achilles , Hatchell Alexandra , Matthews Jennifer , David McKenzie C. , Hart Robert , Chandarana Shamir P. , Wayne Matthews T. , Dort Joseph C. , Schrag Christiaan
Published: January 2024

Background: Within a resource-limited healthcare system, an emphasis on financial accountability is imperative. Over the past decade at our institution, there have been many operational changes employed to improve patient care during oncologic head and neck resections with free flap (HNFF) reconstruction. The objective of this study is to assess whether these changes are associated with cost savings. Methods: A retrospective cohort study that included consecutive patients treated from January 2007 to February 2020 was performed. The perspective of the third payer party was used and direct costs were considered. The peri-operative period was defined as the day of surgery and subsequent admission. Total peri-operative cost was defined as staffing, material, reconstructive surgeon, anesthetist, and admission costs. Costs are represented in Canadian Dollars ($CAD) adjusted for inflation. Results: There were 590 consecutive cases. Average age was 61 with a male proportion of 69% (n = 409). Tumor type, need for tracheostomy, neck dissection, anatomic region resected, 30-day re-operation, and re-admission did not change significantly over the study period ( P > 0.05). The mean total operative time per case decreased by 4.1 h over the study period. The median length of stay per patient decreased by 4.5 days. The total peri-operative cost per patient during the study period decreased by $19,928. Net cost savings to the third-party payer over the study period was $8,142,962. Conclusion: A culture of improvement-focused teamwork allowed for several advances over the study period. These were associated with improved patient care, operative efficiency, and significant cost savings of HNFF reconstruction.
Nurses’ Documentation Practice and Associated Factors in Eight Public Hospitals, Amhara Region, Ethiopia: A Cross-Sectional Study
Authors: Molla Fitalew , Temesgen Worku Animaw , Kerie Sitotaw , Endeshaw Destaw
Published: January 2024

Background

Nursing care documentation, which is the record of nursing care that is planned for and delivered to individual patients, can enhance patient outcomes while advancing the nursing profession. However, its practice and associated factors among Ethiopian nurses are not well investigated.

Objective

To assess the level of nursing care documentation practice and associated factors among nurses working at public hospitals in Ethiopia.

Methods

An institutional-based cross-sectional study was conducted from May 1 to 30, 2022. A total of 378 nurses and corresponding charts were randomly selected with a multistage sampling technique. Self-administered structured questionnaires and structured checklists were used to collect data about independent variables and nurses’ documentation practice, respectively. Epi Data 4.6 was used for data entry and SPSS version 25 for analysis. Descriptive statistics and binary logistic regression analysis have been employed. The STROBE checklist was used to report the study.

Results

In this study, 372 nurses participated, and 30.4% (95% confidence interval [CI]: 26%–35%) of them had good nursing care documentation practice. Adequate knowledge about nursing care documentation(adjusted odds ratio [AOR] = 4.16, 95% CI: [2.36–7.33]), favorable attitude toward nursing care documentation (AOR = 3.43, 95% CI: [1.85–6.36]), adequacy of documenting sheets (AOR = 2.02, 95% CI: [1.14–3.59]), adequacy of time (AOR = 3.85, 95% CI: [2.11–7.05]), nurse-to-patient ratio (AOR = 2.78, 95% CI: [1.13–6.84]), and caring patients who had no stress, anxiety, pain, and distress (AOR = 3.56, 95% CI: [1.69–7.52]) were significantly associated with proper nursing care documentation practices.

Conclusion

Nursing documentation practice was poor in this study compared to the health sector transformation in quality standards due to the identified factors. Improving nurses’ knowledge and attitude toward nursing care documentation and increasing access to documentation materials can contribute to improving documentation practice.
The Impact of Temporal Reflexivity on Time Performance in NPD Projects: A Mixed-Methods Study
Authors: Zheng Yujuan , Sarker Saonee , Huang Wei (Wayne) , Ma Xufei
Published: January 2024

Timely new product development (NPD) has always been a top priority in NPD projects. Despite realizing its importance, the empirical examination of specific factors that may improve NPD time performance has remained limited. This study investigated how temporal reflexivity influences NPD time performance based on the time, interaction, and performance (TIP) theory. Using a mixed-methods design, our research findings showed that temporal reflexivity significantly and positively influenced temporal coordination. Contrary to our hypothesis, the temporal coordination was insignificantly related to the NPD time performance. Furthermore, temporal leadership significantly and positively moderated the relationship between temporal reflexivity and temporal coordination.
Pro-inflammatory cytokines stimulate CFTR-dependent anion secretion in pancreatic ductal epithelium
Authors: Angyal Dora , Groeneweg Tessa A. , Leung Anny , Desain Max , Dulla Kalyan , de Jonge Hugo R. , Bijvelds Marcel J. C.
Published: January 2024

Background

Loss of CFTR-dependent anion and fluid secretion in the ducts of the exocrine pancreas is thought to contribute to the development of pancreatitis, but little is known about the impact of inflammation on ductal CFTR function. Here we used adult stem cell-derived cell cultures (organoids) obtained from porcine pancreas to evaluate the effects of pro-inflammatory cytokines on CFTR function.

Methods

Organoids were cultured from porcine pancreas and used to prepare ductal epithelial monolayers. Monolayers were characterized by immunocytochemistry. Epithelial bicarbonate and chloride secretion, and the effect of IL-1β, IL-6, IFN-γ, and TNF-α on CFTR function was assessed by electrophysiology.

Results

Immunolocalization of ductal markers, including CFTR, keratin 7, and zonula occludens 1, demonstrated that organoid-derived cells formed a highly polarized epithelium. Stimulation by secretin or VIP triggered CFTR-dependent anion secretion across epithelial monolayers, whereas purinergic receptor stimulation by UTP, elicited CFTR-independent anion secretion. Most of the anion secretory response was attributable to bicarbonate transport. The combination of IL-1β, IL-6, IFN-γ, and TNF-α markedly enhanced CFTR expression and anion secretion across ductal epithelial monolayers, whereas these cytokines had little effect when tested separately. Although TNF-α triggered apoptotic signaling, epithelial barrier function was not significantly affected by cytokine exposure.

Conclusions

Pro-inflammatory cytokines enhance CFTR-dependent anion secretion across pancreatic ductal epithelium. We propose that up-regulation of CFTR in the early stages of the inflammatory response, may serve to promote the removal of pathogenic stimuli from the ductal tree, and limit tissue injury.
Tpgen: a language model for stable protein design with a specific topology structure
Authors: Min Xiaoping , Yang Chongzhou , Xie Jun , Huang Yang , Liu Nan , Jin Xiaocheng , Wang Tianshu , Kong Zhibo , Lu Xiaoli , Ge Shengxiang , Zhang Jun , Xia Ningshao
Published: January 2024

Background

Natural proteins occupy a small portion of the protein sequence space, whereas artificial proteins can explore a wider range of possibilities within the sequence space. However, specific requirements may not be met when generating sequences blindly. Research indicates that small proteins have notable advantages, including high stability, accurate resolution prediction, and facile specificity modification.

Results

This study involves the construction of a neural network model named TopoProGenerator(TPGen) using a transformer decoder. The model is trained with sequences consisting of a maximum of 65 amino acids. The training process of TopoProGenerator incorporates reinforcement learning and adversarial learning, for fine-tuning. Additionally, it encompasses a stability predictive model trained with a dataset comprising over 200,000 sequences. The results demonstrate that TopoProGenerator is capable of designing stable small protein sequences with specified topology structures.

Conclusion

TPGen has the ability to generate protein sequences that fold into the specified topology, and the pretraining and fine-tuning methods proposed in this study can serve as a framework for designing various types of proteins.
SSF-DDI: a deep learning method utilizing drug sequence and substructure features for drug–drug interaction prediction
Authors: Zhu Jing , Che Chao , Jiang Hao , Xu Jian , Yin Jiajun , Zhong Zhaoqian
Published: January 2024

Background

Drug–drug interactions (DDI) are prevalent in combination therapy, necessitating the importance of identifying and predicting potential DDI. While various artificial intelligence methods can predict and identify potential DDI, they often overlook the sequence information of drug molecules and fail to comprehensively consider the contribution of molecular substructures to DDI.

Results

In this paper, we proposed a novel model for DDI prediction based on sequence and substructure features (SSF-DDI) to address these issues. Our model integrates drug sequence features and structural features from the drug molecule graph, providing enhanced information for DDI prediction and enabling a more comprehensive and accurate representation of drug molecules.

Conclusion

The results of experiments and case studies have demonstrated that SSF-DDI significantly outperforms state-of-the-art DDI prediction models across multiple real datasets and settings. SSF-DDI performs better in predicting DDI involving unknown drugs, resulting in a 5.67% improvement in accuracy compared to state-of-the-art methods.
Genome-wide association study identifies genetic variants underlying footrot in Portuguese Merino sheep
Authors: Gaspar Daniel , Ginja Catarina , Carolino Nuno , Leão Célia , Monteiro Helena , Tábuas Lino , Branco Sandra , Padre Ludovina , Caetano Pedro , Romão Ricardo , Matos Claudino , Ramos António Marcos , Bettencourt Elisa , Usié Ana
Published: January 2024

Background

Ovine footrot caused by Dichelobacter nodosus (D. nodosus) is a contagious disease with serious economic and welfare impacts in sheep production systems worldwide. A better understanding of the host genetic architecture regarding footrot resistance/susceptibility is crucial to develop disease control strategies that efficiently reduce infection and its severity. A genome-wide association study was performed using a customized SNP array (47,779 SNPs in total) to identify genetic variants associated to footrot resistance/susceptibility in two Portuguese native breeds, i.e. Merino Branco and Merino Preto, and a population of crossbred animals. A cohort of 1375 sheep sampled across 17 flocks, located in the Alentejo region (southern Portugal), was included in the analyses.

Results

Phenotypes were scored from 0 (healthy) to 5 (severe footrot) based on visual inspection of feet lesions, following the Modified Egerton System. Using a linear mixed model approach, three SNPs located on chromosome 24 reached genome-wide significance after a Bonferroni correction (p < 0.05). Additionally, six genome-wide suggestive SNPs were identified each on chromosomes 2, 4, 7, 8, 9 and 15. The annotation and KEGG pathway analyses showed that these SNPs are located within regions of candidate genes such as the nonsense mediated mRNA decay associated PI3K related kinase (SMG1) (chromosome 24) and the RALY RNA binding protein like (RALYL) (chromosome 9), both involved in immunity, and the heparan sulfate proteoglycan 2 (HSPG2) (chromosome 2) and the Thrombospodin 1 (THBS1) (chromosome 7) implicated in tissue repair and wound healing processes.

Conclusion

This is the first attempt to identify molecular markers associated with footrot in Portuguese Merino sheep. These findings provide relevant information on a likely genetic association underlying footrot resistance/susceptibility and the potential candidate genes affecting this trait. Genetic selection strategies assisted on the information obtained from this study could enhance Merino sheep-breeding programs, in combination with farm management strategies, for a more effective and sustainable long-term solution for footrot control.
Genome-wide identification, characterization, and expression analysis of MIPS family genes in legume species
Authors: Jacob Feba , Hamid Rasmieh , Ghorbanzadeh Zahra , Valsalan Ravisankar , Ajinath Lavale Shivaji , Mathew Deepu
Published: January 2024

Background

Evolutionarily conserved in plants, the enzyme D-myo-inositol-3-phosphate synthase (MIPS; EC 5.5.1.4) regulates the initial, rate-limiting reaction in the phytic acid biosynthetic pathway. They are reported to be transcriptional regulators involved in various physiological functions in the plants, growth, and biotic/abiotic stress responses. Even though the genomes of most legumes are fully sequenced and available, an all-inclusive study of the MIPS family members in legumes is still ongoing.

Results

We found 24 MIPS genes in ten legumes: Arachis hypogea, Cicer arietinum, Cajanus cajan, Glycine max, Lablab purpureus, Medicago truncatula, Pisum sativum, Phaseolus vulgaris, Trifolium pratense and Vigna unguiculata. The total number of MIPS genes found in each species ranged from two to three. The MIPS genes were classified into five clades based on their evolutionary relationships with Arabidopsis genes. The structural patterns of intron/exon and the protein motifs that were conserved in each gene were highly group-specific. In legumes, MIPS genes were inconsistently distributed across their genomes. A comparison of genomes and gene sequences showed that this family was subjected to purifying selection and the gene expansion in MIPS family in legumes was mainly caused by segmental duplication. Through quantitative PCR, expression patterns of MIPS in response to various abiotic stresses, in the vegetative tissues of various legumes were studied. Expression pattern shows that MIPS genes control the development and differentiation of various organs, and have significant responses to salinity and drought stress.

Conclusion

The MIPS genes in the genomes of legumes have been identified, characterized and their expression was analysed. The findings pave way for understanding their molecular functions and evolution, and lead to identify the putative MIPS genes associated with different cell and tissue development.
Comparative transcriptomic analysis of the different developmental stages of ovary in the cuttlefish Sepia pharaonis
Authors: Jiang Maowang , Han Qingxi , Xu Liting , Peng Ruibing , Zhang Tao , Jiang Xiamin
Published: January 2024

The cuttlefish, Sepia pharaonis, is characterized by rapid growth and strong disease resistance, making it an important commercially farmed cephalopod species in the southeastern coastal regions of China. However, in the reproductive process of S. pharaonis, there are challenges such as a low output of eggs, poor quality, and low survival rates of newly hatched juveniles. Therefore, there is an urgent need to study the molecular mechanisms underlying ovarian development in this species. In this study, we conducted the first transcriptomic analysis of the ovary at four developmental stages: the undeveloped stage, developing stage, nearly-ripe stage, and ripe stage, and compared the transcriptomics among these four stages using Illumina sequencing technology. The total numbers of clean reads of the four stages ranged from 40,890,772 to 52,055,714 reads. A total of 136,829 DEGs were obtained, GC base ratios of raw data were between 38.44 and 44.59%, and the number of uniquely mapped reads spanned from 88.08 to 95.90%. The Pearson correlation coefficient demonstrated a strong correlation among different samples within the same group, PCA and Anosim analysis also revealed that the grouping of these four stages was feasible, and each stage could be distinguished from the others. GO enrichment analysis demonstrated that ovarian follicle growth, sex differentiation, and transforming growth factor beta receptor, played a foreshadowing role at the early ovarian development stage, and the terms of small molecule metabolic process, peptide metabolic process, and catalytic activity were prominent at the mature stage. Meanwhile, KEGG analysis showed that the early ovarian development of S. pharaonis was mainly associated with the cell cycle, DNA replication, and carbon metabolism, while the mid-late ovarian development was involved with the signal transduction, endocrine system, and reproduction pathway. RT-qPCR further confirmed the consistent expression patterns of genes such as 17β-HSD, GH, VGS, NFR, and NYR in the ovaries of S. pharaonis, exhibiting elevated levels of expression during the maturation stage. Conversely, ER and OM exhibited high expression levels during the early stages of ovarian development. These transcriptomic data provide insights into the molecular mechanisms of S. pharaonis ovarian development. The findings of this study will contribute to improving the reproduction and development of cuttlefish and enriching the bioinformatics knowledge of cephalopods.
Multi-tissue metabolic and transcriptomic responses to a short-term heat stress in swine
Authors: Huau Guilhem , Liaubet Laurence , Gourdine Jean-Luc , Riquet Juliette , Renaudeau David
Published: January 2024

Background

Heat stress (HS) is an increasing threat for pig production with a wide range of impacts. When submitted to high temperatures, pigs will use a variety of strategies to alleviate the effect of HS. While systemic adaptations are well known, tissue-specific changes remain poorly understood. In this study, thirty-two pigs were submitted to a 5-day HS at 32 °C.

Results

Transcriptomic and metabolomic analyses were performed on several tissues. The results revealed differentially expressed genes and metabolites in different tissues. Specifically, 481, 1774, 71, 1572, 17, 164, and 169 genes were differentially expressed in muscle, adipose tissue, liver, blood, thyroid, pituitary, and adrenal glands, respectively. Regulatory glands (pituitary, thyroid, and adrenal) had a lower number of regulated genes, perhaps indicating an earlier sensitivity to HS. In addition, 7, 8, 2, and 8 metabolites were differentially produced in muscle, liver, plasma, and urine, respectively. The study also focused on the oxidative stress pathway in muscle and liver by performing a correlation analysis between genes and metabolites.

Conclusions

This study has identified various adaptation mechanisms in swine that enable them to cope with heat stress (HS). These mechanisms include a global decrease in energetic metabolism, as well as changes in metabolic precursors that are linked with protein and lipid catabolism and anabolism. Notably, the adaptation mechanisms differ significantly between regulatory (pituitary, thyroid and adrenal glands) and effector tissues (muscle, adipose tissue, liver and blood). Our findings provide new insights into the comprehension of HS adaptation mechanisms in swine.
Integrative genomic analyses reveal putative cell type-specific targets of the Drosophila ets transcription factor Pointed
Authors: Bollepogu Raja Komal Kumar , Yeung Kelvin , Shim Yoon-Kyung , Mardon Graeme
Published: January 2024

The Ets domain transcription factors direct diverse biological processes throughout all metazoans and are implicated in development as well as in tumor initiation, progression and metastasis. The Drosophila Ets transcription factor Pointed (Pnt) is the downstream effector of the Epidermal growth factor receptor (Egfr) pathway and is required for cell cycle progression, specification, and differentiation of most cell types in the larval eye disc. Despite its critical role in development, very few targets of Pnt have been reported previously. Here, we employed an integrated approach by combining genome-wide single cell and bulk data to identify putative cell type-specific Pnt targets. First, we used chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) to determine the genome-wide occupancy of Pnt in late larval eye discs. We identified enriched regions that mapped to an average of 6,941 genes, the vast majority of which are novel putative Pnt targets. Next, we integrated ChIP-seq data with two other larval eye single cell genomics datasets (scRNA-seq and snATAC-seq) to reveal 157 putative cell type-specific Pnt targets that may help mediate unique cell type responses upon Egfr-induced differentiation. Finally, our integrated data also predicts cell type-specific functional enhancers that were not reported previously. Together, our study provides a greatly expanded list of putative cell type-specific Pnt targets in the eye and is a resource for future studies that will allow mechanistic insights into complex developmental processes regulated by Egfr signaling.
Genome-wide association study for stayability at different calvings in Nellore beef cattle
Authors: Silva Diogo Osmar , Fernandes Júnior Gerardo Alves , Fonseca Larissa Fernanda Simielli , Mota Lúcio Flávio Macedo , Bresolin Tiago , Carvalheiro Roberto , de Albuquerque Lucia Galvão
Published: January 2024

Backgrounding

Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal’s life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female’s productive life.

Results

The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant.

Conclusion

Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.
High frequency of antimicrobial resistance in Salmonella and Escherichia coli causing diarrheal diseases at the Yirimadio community health facility, Mali
Authors: Diarra Bintou , Guindo Ibréhima , Koné Boī , Dembélé Maīmouna , Cissé Ibrahim , Thiam Souleymane , Konaté Kadidia , Tékété Mamadou , Maīga Almoustapha , Maīga Oumou , Timbiné Lassina , Djimde Abdoulaye
Published: January 2024

Background

Diarrhoea is a public health problem, especially in developing countries where it is the second leading cause of child mortality. In Low Income Countries like in Mali, self-medication and inappropriate use of antibiotics due to the scarcity of complementary diagnostic systems can lead to the development of multidrug-resistant bacteria causing diarrhoea. The objective of this work was to determine the microorganisms responsible for diarrhoea in children under 15 years of age and to characterize their sensitivity to a panel of antibiotics used in a peri-urban community in Mali. The study involved outpatient children visiting the Yirimadio Community Health Centre and diagnosed with diarrhoea. Stool samples from those patients were collected and analysed by conventional stools culture and the susceptibility to antibiotics of detected bacteria was determined by the disc diffusion method in an agar medium.

Result

Overall, 554 patients were included. Children under the age of 3 years accounted for 88.8% (492 of 554) of our study population. Two bacterial species were isolated in this study, Escherichia coli 31.8% (176 of 554) and Salmonella 2.9% (16 of 554). In the 176, E. coli strains resistance to amoxicillin and to cotrimoxazole was seen in 93.8% (165 of 176) and 92.6% ( 163 of 176), respectively. The ESBL resistance phenotype accounted for 39,8% (70 of 176) of E. coli. Sixteen (16) strains of Salmonella were found, of which one strain (6.3%) was resistant to amoxicillin and to amoxicillin + clavulanic acid. Another one was resistant to chloramphenicol (6.3%). Two strains of Salmonella were resistant to cotrimoxazole (12.5%) and two others were resistant to cefoxitin (12.5%).

Conclusions

The data suggest that E. coli is frequently involved in diarrhoea in children under 3 years of age in this peri-urban setting of Bamako, Mali, with a high rate of resistance to amoxicillin and cotrimoxazole, the most widely used antibiotics in the management of diarrhoea in this setting.