bluuebunny/crossref_metadata_2025_split huggingface dataset:
sRNAdeep: a novel tool for bacterial sRNA prediction based on DistilBERT encoding mode and deep learning algorithms
Authors: Qian Weiye , Sun Jiawei , Liu Tianyi , Yang Zhiyuan , Tsui Stephen Kwok-Wing 
Published: October 2024

Abstract
Background
Bacterial small regulatory RNA (sRNA) plays a crucial role in cell metabolism and could be used as a new potential drug target in the treatment of pathogen-induced disease. However, experimental methods for identifying sRNAs still require a large investment of human and material resources.

Methods
In this study, we propose a novel sRNA prediction model called sRNAdeep based on the DistilBERT feature extraction and TextCNN methods. The sRNA and non-sRNA sequences of bacteria were considered as sentences and then fed into a composite model consisting of deep learning models to evaluate classification performance.

Results
By filtering sRNAs from BSRD database, we obtained a validation dataset comprised of 2438 positive and 4730 negative samples. The benchmark experiments showed that sRNAdeep displayed better performance in the various indexes compared to previous sRNA prediction tools. By applying our tool to Mycobacterium tuberculosis (MTB) genome, we have identified 21 sRNAs within the intergenic and intron regions. A set of 272 targeted genes regulated by these sRNAs were also captured in MTB. The coding proteins of two genes (lysX and icd1) are implicated in drug response, with significant active sites related to drug resistance mechanisms of MTB.

Conclusion
In conclusion, our newly developed sRNAdeep can help researchers identify bacterial sRNAs more precisely and can be freely available from https://github.com/pyajagod/sRNAdeep.git.
Patient iPSC-derived neural progenitor cells display aberrant cell cycle control, p53, and DNA damage response protein expression in schizophrenia
Authors: Stahl Aaron , Heider Johanna , Wüst Richard , Fallgatter Andreas J. , Schenke-Layland Katja , Volkmer Hansjürgen , Templin Markus F. 
Published: October 2024

Abstract
Background
Schizophrenia (SCZ) is a severe psychiatric disorder associated with alterations in early brain development. Details of underlying pathomechanisms remain unclear, despite genome and transcriptome studies providing evidence for aberrant cellular phenotypes and pathway deregulation in developing neuronal cells. However, mechanistic insight at the protein level is limited.

Methods
Here, we investigate SCZ-specific protein expression signatures of neuronal progenitor cells (NPC) derived from patient iPSC in comparison to healthy controls using high-throughput Western Blotting (DigiWest) in a targeted proteomics approach.

Results
SCZ neural progenitors displayed altered expression and phosphorylation patterns related to Wnt and MAPK signaling, protein synthesis, cell cycle regulation and DNA damage response. Consistent with impaired cell cycle control, SCZ NPCs also showed accumulation in the G2/M cell phase and reduced differentiation capacity. Furthermore, we correlated these findings with elevated p53 expression and phosphorylation levels in SCZ patient-derived cells, indicating a potential implication of p53 in hampering cell cycle progression and efficient neurodevelopment in SCZ.

Conclusions
Through targeted proteomics we demonstrate that SCZ NPC display coherent mechanistic alterations in regulation of DNA damage response, cell cycle control and p53 expression. These findings highlight the suitability of iPSC-based approaches for modeling psychiatric disorders and contribute to a better understanding of the disease mechanisms underlying SCZ, particularly during early development.
Medical students and house officers’ perception, attitude and potential barriers towards artificial intelligence in Egypt, cross sectional survey
Authors: Allam Rasha Mahmoud , Abdelfatah Dalia , Khalil Marwa Ibrahim Mahfouz , Elsaieed Mohamed Mahmoud , El Desouky Eman D. 
Published: October 2024

Abstract
Background
Artificial intelligence (AI) is one of the sectors of medical research that is expanding the fastest right now in healthcare. AI has rapidly advanced in the field of medicine, helping to treat a variety of illnesses and reducing the number of diagnostic and follow-up errors.

Objective
This study aims to assess the perception and attitude towards artificial intelligence (AI) among medical students & house officers in Egypt.

Methods
An online cross-sectional study was done using a questionnaire on the Google Form website. The survey collected demographic data and explored participants’ perception, attitude & potential barriers towards AI.

Results
There are 1,346 responses from Egyptian medical students (25.8%) & house officers (74.2%). Most participants have inadequate perception (76.4%) about the importance and usage of AI in the medical field, while the majority (87.4%) have a negative attitude. Multivariate analysis revealed that age is the only independent predictor of AI perception (AOR = 1.07, 95% CI 1.01–1.13). However, perception level and gender are both independent predictors of attitude towards AI (AOR = 1.93, 95% CI 1.37–2.74 & AOR = 1.80, 95% CI 1.30–2.49, respectively).

Conclusion
The study found that medical students and house officers in Egypt have an overall negative attitude towards the integration of AI technologies in healthcare. Despite the potential benefits of AI-driven digital medicine, most respondents expressed concerns about the practical application of these technologies in the clinical setting. The current study highlights the need to address the concerns of medical students and house officers towards AI integration in Egypt. A multi-pronged approach, including education, targeted training, and addressing specific concerns, is necessary to facilitate the wider adoption of AI-enabled healthcare.
Co-designing postpartum contraceptive services with and for immigrant women in Sweden: lessons learned from the IMPROVE-it project
Authors: Herzig van Wees Sibylle , Kilander Helena , Salah Khadija , Saidarab Sahra , Wängborg Anna , Larsson Elin C. 
Published: October 2024

Abstract
Background and aim
Immigrant women in many high-income countries including Sweden, report unmet need of sexual and reproductive health and rights, and face worse pregnancy outcomes and higher risk of unintended pregnancies. Postpartum contraceptive services are often inadequate to meet their needs. Co-design has shown to reduce health inequities, yet little is known about using this method for postpartum contraceptive service development and even less in collaborating with immigrant populations. The aim of this paper is to describe the co-design process and the strategies that were developed to help develop tailored and acceptable postpartum contraceptive services for immigrant women in Sweden.

Methods
The paper describes a co-design process that took place during 2022–2023, including the cyclical digital consultations with Arabic and Somali speaking immigrant women, midwives and researchers, as well as the outputs from the process. The theoretical framework for the co-design process was the ‘Double Diamond’ Design Process Model. Data analysis included qualitative content analysis.

Results
The co-design process led to the joint development of intervention materials and strategies to improve postpartum contraceptive services. Specifically, the process revealed ideas on how to improve contraceptive counseling within three pre-identified areas of change: improve physical access to contraceptive services; improved communication strategies using visual aids and information charts; and empowerment strategies that focus on reflective practice without assumptions about what a group of women might expect. We found that participants contributed actively to the process with ideas and suggestions, and that the co-design process facilitated positive reflections on ongoing counseling practices.

Conclusion
The co-design process resulted in the successful and participative development of innovative tools and activities to improve contraceptive counseling services. This approach is original because it involves both immigrant women, often left behind, and midwives delivering the services. Whilst this interplay allowed for careful refinement of services and tools by using an iterative process, it also facilitated reflective midwifery practice.
Establishment of the auxin inducible degron system for Babesia duncani: a conditional knockdown tool to study precise protein regulation in Babesia spp.
Authors: Chen Bo , Zhang Qi , Wang Sen , Guan Xing-ai , Luo Wan-xin , Li Dong-fang , He Yue , Huang Shu-jing , Zhou Ya-ting , Zhao Jun-long , He Lan 
Published: October 2024

Abstract
Background
Babesia duncani is a pathogen within the phylum Apicomplexa that causes human babesiosis. It poses a significant threat to public health, as it can be transmitted not only through tick bites but also via blood transfusion. Consequently, an understanding of the gene functions of this pathogen is necessary for the development of drugs and vaccines. However, the absence of conditional gene knockdown tools has hindered the research on this pathogen. The auxin-inducible degron (AID) system is a rapid, reversible conditional knockdown system widely used in gene function studies. Thus, there is an urgent need to establish the AID system in B. duncani to study essential gene functions.

Methods
The endogenous genes of the Skp1-Cullin-F-box (SCF) complex in B. duncani were identified and confirmed through multiple sequence alignment and conserved domain analysis. The expression of the F-box protein TIR1 from Oryza sativa (OsTIR1) was achieved by constructing a transgenic parasite strain using a homologous recombination strategy. Polymerase chain reaction (PCR), western blot, and indirect immunofluorescence assay (IFA) were used to confirm the correct monoclonal parasite strain. The degradation of enhanced green fluorescent protein (eGFP) tagged with an AID degron was detected through western blot and live-cell fluorescence microscopy after treatment of indole-3-acetic acid (IAA).

Results
In this study, Skp1, Cul1, and Rbx1 of the SCF complex in B. duncani were identified through sequence alignment and domain analysis. A pure BdTIR1 strain with expression of the OsTIR1 gene was constructed through homologous recombination and confirmed. This strain showed no significant differences from the wild type (WT) in terms of growth rate and proportions of different parasite forms. The eGFP tagged with an AID degron was successfully induced for degradation using 500 μM IAA. Grayscale analysis of western blot indicated a 61.3% reduction in eGFP expression levels, while fluorescence intensity analysis showed a 77.5% decrease in fluorescence intensity. Increasing the IAA concentration to 2 mM accelerated eGFP degradation and enhanced the extent of degradation.

Conclusions
This study demonstrated the functionality of the AID system in regulating protein levels by inducing rapid degradation of eGFP using IAA, providing an important research tool for studying essential gene functions related to invasion, egress, and virulence of B. duncani. Moreover, it also offers a construction strategy for apicomplexan parasites that have not developed an AID system.

Graphical Abstract
Point-of-care test of blood Plasmodium RNA within a Pasteur pipette using a novel isothermal amplification without nucleic acid purification
Authors: Xie Lyu , Xu Jiyu , Fan Lihua , Sun Xiaodong , Zheng Zhi 
Published: October 2024

Abstract
Background
Resource-limited regions face a greater burden of infectious diseases due to limited access to molecular tests, complicating timely diagnosis and management. Current molecular point-of-care tests (POCTs) either come with high costs or lack adequate sensitivity and specificity. To facilitate better prevention and control of infectious diseases in underserved areas, we seek to address the need for molecular POCTs that better align with the World Health Organization (WHO)’s ASSURED criteria—Affordable, Sensitive, Specific, User-friendly, Rapid and robust, Equipment-free, and Deliverable to end users.

Methods
A novel molecular POCT, Pasteur Pipette-assisted isothermal probe amplification (pp-IPA), was developed for malaria detection. Without any microfluidics, this method captures Plasmodium 18S rRNA in a modified Pasteur pipette using tailed genus-specific probes. After washing, the bound tailed probes are ligated to form a template for subsequent novel isothermal probe amplification using a pair of generic primers, bypassing nucleic acid extraction and reverse transcription. The method was assessed using cultured Plasmodium and compared with real-time quantitative reverse transcription PCR (RT-qPCR) or reverse transcription loop-mediated isothermal amplification (RT-LAMP) in clinical blood samples.

Results
The entire assay is completed in 60–80 min with minimal hands-on time, using only a Pasteur pipette and a water bath. The pp-IPA’s analytical sensitivity is 1.28 × 10–4 parasites/μl, with 100% specificity against various blood-borne pathogens causing malaria-like symptoms. Additionally, pp-IPA needs only liquid-transfer skill for operation and the cost is around USD 0.25 per test, making it at least 300 times lower than mainstream POCT platforms.

Conclusions
Designed to improve the accessibility of molecular detection in resource-limited settings, pp-IPA’s simplicity, affordability, high sensitivity/specificity, and minimal equipment requirements make it a promising point-of-care pathogen identification tool in resource-constrained regions.

Graphical Abstract
Application of a recently developed method of oriented drill coring to accumulative tephra layers: identification of the Matuyama–Brunhes geomagnetic reversal in Akan caldera-forming eruption deposits
Authors: Hasegawa Takeshi , Kusu Chie , Okada Makoto , Hiratsuka Aoi , Nishiki Kuniaki , Sato Yuki , Koshigai Masaru , Matsuzaki Takuya , Yamamoto Yuhji 
Published: October 2024

AbstractWe adapted a recently developed technique of oriented drill coring (100 m in depth) for paleomagnetic measurements, including additional techniques such as half-cutting of the drill cores and accurate cube sampling using an apparatus that precisely guides the cube into the half-cut drill core surface. Our techniques were successfully applied to sequential tephra layers (including loess) at Akan Quaternary caldera volcano in eastern Hokkaido, Japan. Directions of remanent magnetization for a total of 129 specimens were measured by Spinner magnetometer with thermal and alternating field demagnetizations. We detected clear Matuyama–Brunhes geomagnetic reversal between the depths of 20.59 m and 21.30 m, where inclinations change from 65.1 to –44.3°. With these techniques, we can in future obtain useful geologic information (e.g., radiometric ages and absolute paleo-intensities) from volcanic rocks around the Matuyama–Brunhes boundary in Akan volcano. This will clarify more detailed processes of the geomagnetic polarity transition. Our study demonstrates the utility of oriented drill cores from successive tephra and loess layers for high resolution investigate of continuous paleo-geomagnetic records. The new techniques can be adopted to other geological fields on Earth, like in studies of marine sediments, providing continuous paleomagnetic direction data from drill core.
Graphical Abstract
Evaluation of cosmetic efficacy of lychee seed fermentation liquid
Authors: Yan Yaqian , Fu Hao , Tang Yuling , Huang Tiantian , Zou Xun , Su Ning , Wang Dongdong , Wang Changtao , Li Meng 
Published: October 2024

Abstract
Background
Lychee seeds were fermented by three kinds of bacteria (Lactobacillus plantarum, Saccharomyces cerevillus and ganoderma lucidum mycelium), and two effective strains were selected by two indexes of activity content and antioxidant, so as to further verify whether lychee seeds have waste multiplication effect and can protect cells damaged by oxidation from anti-inflammatory, anti-aging and safety.

Results
The contents of polyphenols, flavonoids and proteins in the solution fermented by Ganoderma lucidum mycelium did not increase, thus affecting the antioxidant capacity of the solution was far less than that of the water extract. The active content of the other two fermentation solutions was higher than that of the water extract, and the ability of scavenging free radicals of the two solutions increased with the increase of the volume fraction. At the cellular level, the two fermentation solutions showed repair effects on UVA-induced damaged cells. The contents of type I collagen (COL-1), total antioxidant capacity and ELN were increased, the contents of reactive oxygen species and MDA were decreased, and the expressions of inflammatory factors IL-6, TNF-a, iNOS and COX-2 were decreased in HaCaT cells. From the gene level, the mRNA contents of IL-6, TNF-a, Caspase-3, Caspase-9, Bax and Bcl were significantly decreased. The test of chick embryo chorioallantoic membrane (HTET CAM) showed that there was no bleeding and litchi seed fermentation liquid was not irritating.

Conclusions
Therefore, two kinds of litchi seed fermentation can be used as natural plant raw materials for cosmetics, and have strong antioxidant, anti-inflammatory and anti-aging functions on skin, and also have good human safety.

Graphical Abstract
The progesterone prime protocol: an affordable option for ICSI in Egypt
Authors: Elnahas Tamer , Mohamed Reham , Abdel-Rasheed Mazen , Salem Sondos , Nasr Mohamed , Elnahas Ahmed , Hassan Eman , Salama Ehab 
Published: October 2024

Abstract
Background
The two main input indicators needed to assess the success of assisted reproductive technology (ART) strategies are cost-effectiveness and clinical outcome. Therefore, we focused in our study on the direct cost associated with the Progesterone Prime Ovulation Induction Protocol (P-P-OP protocol) compared to other protocols, and the clinical outcomes of this strategy were measured in their effect on implantation and pregnancy rates.

Methods
A pilot single-armed study was conducted on 47 infertile women coming for an ICSI cycle. Progesterone priming was started with 10 mg dydrogesterone along with HMG 150–300 IU from the second day of the menstrual cycle and was maintained until the day of ovulation trigger. The primary outcome was the cost per cycle, while the secondary outcome was the clinical pregnancy rate. The cost per cycle, including the cryopreservation cost, was calculated for economic evaluation.

Results
Per each cycle, the number of retrieved oocytes was 14.87 ± 8.09, the number of mature oocytes was 9.81 ± 4.67, the number of total embryos was 8.74 ± 4.28 (grade A = 67.40%, grade B = 11.92%, grade C = 20.68%), and the number of transferred embryos was 2.43 ± 0.68. The clinical pregnancy rate in our study was 42.5%. Economically, the cost of the P-P-OP protocol for each patient was only 56 USD.

Conclusion
The P-P-OP protocol is a simplified approach suitable for freeze-only strategies, offering the benefits of positive results, fewer injections, lower costs, and increased patient convenience.
Electrical cardiometry significance in postoperative cardiac ICU; a single center study
Authors: Samir Mohamed , Mostafa Fatma Alzahraa , Sobhy Rodina , El-Sisi Amal , Tantawy Amira El , Sakr Hesham Mohammed , Afifi Ahmed 
Published: October 2024

Abstract
Background
Hemodynamic monitoring is a cornerstone of critical care; in fact, the techniques available for this purpose are either unreliable or operator-dependent or intermittent (echocardiography) and invasive (thermodilution). Objectives: To evaluate the effectiveness of electrical cardiometry (EC) in assessing hemodynamics in pediatric postoperative cardiac intensive care unit (ICU) and the agreement between EC and trans-thoracic echocardiography (TTE) as bedside tools for hemodynamic monitoring and early diagnosis of cardiovascular compromise. We included 70 pediatric patients from the postoperative cardiac ICU. All participants underwent history-taking and clinical examination. emphasising vital signs, manifestations or signs of hemodynamic instability, calculation of RACH score and vasoactive inotropic score. EC was applied for all patients, and TTE.

Results
The study included 40 males and 30 females with a mean age of 2.6 ± 3.49 years, ranging between 2 weeks and 13 years, with a male to female ratio of 1.3:1. The median of EC parameters were comparable to TTE parameters stroke volume (SV) (9 vs. 8 p = 0.2), stroke index (SI) (23.5 vs. 22 p = 0.2), cardiac output (CO) (1.25 vs. 1.1 p = 0.3), and cardiac index (CI) (3.2 vs. 3.15 p = 0.2). Hemodynamic parameters correlated significantly between EC and echocardiography, with significantly observed agreement between them. Four equations were postulated successfully based on a linear regression model to predict echocardiographic hemodynamic parameters in comparable groups of children, i.e., SV, SI, CO, and CI.

Conclusion
EC is an excellent alternative to echocardiography in hemodynamic assessment of cardiac patients in the postoperative ICU.
Low back pain myths: a narrative review
Authors: Kripa Sai , Kadiresan Mathivadhani 
Published: October 2024

AbstractPeople all around the world suffer from low back pain (LBP), which frequently results in disability and a lower quality of life. Myths and misconceptions around LBP are still prevalent in both the general public and hospital settings, despite its ubiquitous prevalence. Through dispelling these myths and advocating for evidence-based knowledge, medical professionals can enhance patient education, lessen stigma, and anxiety related to life with post-traumatic stress disorder and enable more successful management techniques. Furthermore, dispelling myths regarding low back pain in the broader public can enable people to actively participate in their own care and support improved outcomes for those who have this crippling illness. The purpose of this evaluation of the literature is to identify and dispel prevalent misconceptions about LBP by examining the available data.
Wound healing after surgical therapy for multiple myeloma: a case–control study
Authors: Shi Xiangjun , Zhou Yanyou , Du Boran , Yao Xingchen , Du Xinru 
Published: October 2024

Objective: The aim of this study was to observe the surgical wound healing process in patients with multiple myeloma who had undergone surgery. Method: We collected clinical data on patients with multiple myeloma and observed wound healing following surgical therapy. Additionally, we compared the expression of angiogenesis markers in patients with and without multiple myeloma (undergoing surgical excision of other tumour tissues). In patients who had multiple myeloma bone disease, we examined several clinical features: haemoglobin levels; albumin levels; blood glucose levels; and surgery programme. We then compared expression levels of the angiogenesis markers CD31, CD34 and vascular endothelial growth factor (VEGF) in samples scraped from the skin margin of the surgical incision in 12 patients without multiple myeloma (control) and nine patients with multiple myeloma. Results: All 61 patients with multiple myeloma observed showed no disunion, no delayed union and no infection in their wound healing. CD31 and VEGF expression was higher in the nine patients with multiple myeloma compared with the 12 control patients without. We observed no difference in CD34 expression between control and experimental groups. Conclusion: The results of this study suggest that patients with multiple myeloma who have undergone surgery recover well and produce higher quantities of new vessels compared with patients without multiple myeloma. This occurs through increased expression of CD31 and VEGF, angiogenic factors which promote wound healing. We did not observe higher expression of these factors contributing to increased incisional implantation metastasis.