bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in clinical isolates of Salmonella Typhimurium
Authors: Baker Stephen , Tran Tuan-Anh , Srid Sushmita , Reece Stephen , Lunguya Octavie , Jacobs Jan , Puyvelde Sandra Van , Marks Florian , Dougan Gordon , Thomson Nick , Nguyen Binh , Bao Pham The 
Published: October 2023

Abstract

Antimicrobial resistance (AMR) is a growing public health crisis that requires innovative solutions. Presently we rely on exposing single organisms to an antimicrobial and growth to determine susceptibility; throughput and interpretation hinder our ability to rapidly distinguish between antimicrobial-susceptible and -resistant organisms isolated from clinical samples. Salmonella Typhimurium (S. Typhimurium) is an enteric pathogen responsible for severe gastrointestinal illness in immunocompetent individuals and can also cause invasive disease in immunocompromised people. Despite widespread resistance, ciprofloxacin remains a common treatment, particularly in lower-resource settings, where the drug is given empirically. Here, we exploited high-content imaging to generate deep phenotyping of various S. Typhimurium isolates longitudinally exposed to increasing concentrations of ciprofloxacin. We applied machine learning algorithms to the resulting imaging data and demonstrated that individual isolates display distinct growth and morphological characteristics that clustered by time point and susceptibility to ciprofloxacin, which occurred independently of ciprofloxacin exposure. We used a further set of S. Typhimurium clinical isolates to test the ability of our algorithm to distinguish between ciprofloxacin-susceptible and -resistant isolates. We found that a random forest classifier could accurately predict how the organism would respond to ciprofloxacin without exposure to it or any prior knowledge of ciprofloxacin susceptibility. These results provide the first proof-of-principle for the use of high-content imaging with machine learning algorithms to predict drug susceptibility of clinical bacterial isolates. This technique can be exploited to identify drug-resistant bacteria more rapidly and accurately and may be an important tool in understanding the phenotypic impact of antimicrobials on the bacterial cell in order to identify drugs with new modes of action.
WWOX promotes osteosarcoma development via upregulation of Myc
Authors: Aqeilan Rami , Akkawi Rania , Hidmi Osama , Yahia Ameen Haj , Drier Yotam , Monin Jonathan , Diment Judith , Stein Gary 
Published: October 2023

Abstract
Osteosarcoma (OS) is an aggressive bone tumor that primarily affects children and adolescents. This malignant tumor is highly aggressive, associated with poor clinical outcomes, and metastasizes mainly to the lungs. Due to its rarity and biological heterogeneity, limited studies of its molecular basis exist, thus hindering the development of effective therapies. WW domain-containing oxidoreductase (WWOX) spans one of the most active and common fragile sites that is frequently altered in human OS. The combined deletion of Wwox and Trp53 using Osterix1-Cre transgenic mice has been shown to accelerate OS development. In this study, we generated a traceable OS mouse model, SKO-Trp53 or DKO-Wwox/Trp53, expressing a tdTomato reporter. By tracking tomato expression at different time points, we detected the early presence of tdTomato-positive cells in the bone marrow (BM) mesenchymal stem cells (MSCs) of non-OS bearing mice, young BM (yBM). We found that DKO yBM cells, but not SKO yBM cells, exhibited tumorigenic traits both in vitro and in vivo. Molecular and cellular characterization of these DKO yBM cells revealed their resemblance to OS tumor cells. Interestingly, one of the observed significant transcriptomic changes in DKO yBM was the upregulation of Myc and its target genes, as compared to SKO yBM cells. Intriguingly, Myc-chromatin immunoprecipitation sequencing (ChIP-Seq) revealed increased enrichment on Myc targets, which were upregulated in DKO yBM cells. Restoration of WWOX in DKO-yBM cells reduced Myc protein levels. As a prototype target, we demonstrated upregulation of MCM7, a known Myc target, in DKO yBM relative to SKO yBM. Inhibition of MCM7 expression using Simvastatin resulted in reduced proliferation and tumor cell growth of DKO yBM cells. Our findings revealed BM-MSCs as a platform to study OS and Myc and its targets as WWOX effectors and early molecular events during osteosarcomagenesis.
Clinical effectiveness/child-patient and parent satisfaction of two topical fluoride treatments for caries: a randomised clinical trial
Authors: Maldupa Ilze , Innes Nicola , Viduskalne Ilona , Brinkmane Anda , Senakola Egita , Krumina Karina , Uribe Sergio E. 
Published: October 2023

Abstract
Knowledge gaps exist regarding optimal silver diammine fluoride (SDF) regimens and the efficacy of new products for arresting dental caries in young children. We evaluated the effectiveness of 38%-SDF(SDI-RivaStar), Tiefenfluorid(TF) comparing with Placebo(P), all in conjunction with behavioural modification(BM), in preventing major complications (endodontic/extractions/pain) —a patient-centred outcome— due to early childhood caries over 12 months in children under 71-months. A six-arm, patient/parent-blinded, superiority, placebo-controlled randomised control trial at the university clinic in Riga, Latvia, from 1/9/20-31/8/22 (Protocol registration ISRCTN17005348). The trial tested six protocols, using three compounds (P/SDF/TF) under two regimes: annual and biannual (P1/P2/TF1/TF2/SDF1/SDF2) for major complications. Secondary outcomes included minor complications and parental satisfaction. All groups received BM. 373/427 randomised children (87.3%) completed the study. SDF2 had a significantly lower rate and risk of major (21.5%, OR=0.28, 95%CI[0.11, 0.72], p<0.05) and minor complications (OR=0.16 (95%CI [0.05, 0.50], p=0.002). Overall satisfaction was 96%(p>0.05). SDF biannual application with BM effectively prevented major complications of early childhood caries and was well accepted by children and their parents. Trial registration number: ISRCTN17005348, principal investigator: Ilze Maldupa, registration date: 30/06/2021.
Efficient mesophyll-derived protoplast manipulation system as a versatile tool for characterization of genes responding to multiple stimuli in mulberry
Authors: Zhou Hong , Lei Yali , Hou Zhiwei , Yuan Jianglian , He Ningjia 
Published: October 2023

Abstract
Versatile protoplast manipulation systems have been established in a variety of plant species for gene functional studies, especially on physiological perceptions and responses to hormones, metabolites, environmental stimuli. However, efficient protoplast-based systems are still lacking for the economically important woody plant mulberry, of which functional genomics research is hindered by its long life cycle and recalcitrance to genetic transformation. In this study, we set up sterile cultures for a hybrid mulberry resource and established an efficient protocol for isolating mesophyll-derived protoplast via optimizing the starting materials and maceration conditions. With sufficient viable protoplasts, polyethylene glycol (PEG)-mediated transient gene expression has been carried out and a transformation efficiency of nearly 50% was achieved through optimizing the incubation strategy. The transient gene expression system was validated by subcellular localization assays of the mulberry nuclear marker gene MaHTR6 and chloroplast marker gene MaTRX. Subsequently, the system was used for functional characterization of putative mulberry cytokinin response factors (MaCRFs) in response to phytohormone and environmental stimuli. Combined the established system with RT-qPCR to test the CRFs transcriptional regulation, we found that among the three MaCRFs, conserved with Arabidopsis CRF2, MaCRF1 turned out to function primarily as a response factor to cytokinin and auxin. While MaCRF2 and MaCRF3 respond not only to phytohormones but also to environmental stresses. In summary, we have established an efficient mesophyll-derived protoplast manipulation system in mulberry, thereby facilitating transient function analysis of genes in response to multiple external stimuli.
Influence of unidirectional loading pusher head structure on the deformation law of bionic egg-shaped shell parts in internal high-pressure bulging
Authors: sun zhiying , Shen Mingting , Shi Zhengxian , Cheng Huiming 
Published: October 2023

Abstract

A solid particle medium flexible bulging technology is proposed to solve the problems of low molding precision, poor stability, and uneven deformation that may occur when processing bionic egg-shaped shells by the traditional bulging process. By optimizing the mold parameters, such as the angle and height of the pusher head, the flow characteristics of the granular material are improved, resulting in improved machining accuracy and surface quality when molding egg-shaped plastic shells. In this paper, we utilize a ø0.8-1 mm yttria-stabilized zirconia ceramic bead to serve as a pressure-transfer medium during the granular media forming process. Several different shapes of pusher heads with cone angles of 45°, 60°, 75°, and 90° and heights of 10mm, 25mm, and 40mm were designed and manufactured. The numerical model of simulation was verified by the analysis of strain inhomogeneity coefficient, and the maximum thinning rate at the apex of bulging of the egg-shaped test was measured and calculated. The results show that the maximum thinning rate at the apex of bulging is the largest for the pusher head with 45° cone angle and 25mm height, and the strain distribution is the most uniform and the expansion effect is the best. The study shows that the optimization of the process parameters of the pusher head shape can effectively improve the uniformity of the strain distribution and thickness distribution during the egg-shaped shell forming process, thus improving the machining accuracy of the plastic deformation of the bionic egg-shaped tube test piece.
Pregnancy outcomes of Jehovah’s Witnesses: case series over fifteen years in a tertiary teaching hospital
Authors: Ng Vivian Wai Yan , Seto Mimi Tin Yan , Cheung Ka Wang 
Published: October 2023

Abstract
Background
More than 5000 Jehovah’s Witnesses resided in Hong Kong. Higher morbidity and mortality rates in pregnancy were associated with this specific group of women than the general population. We aim to assess the obstetric and neonatal outcomes of Jehovah’s Witnesses (JW) mothers in a teaching hospital and to evaluate the acceptance rate of blood fractions and blood transfusion alternatives.
Methods
This is a retrospective case-control study. Women who delivered from 1st January 2005 to 31st December 2020 were analysed from the electronic Clinical Data Analysis and Reporting System (CDARS). Patients who identified themselves as JW were reviewed. The immediate next age-matched non-JW patient in the antenatal care booking register was recruited as control.
Results
There were 83 JW women identified within the study period. 35 delivered overseas or in the private sector, leaving 48 women for analysis. 8 (16.7%) accepted blood transfusion; 11 (22.9%) accepted some minor fractions, 29 (60.4 %) refused all blood components. 42 (87.5%) had consultant review and anaesthesiologist consultation before delivery with confirmation of their advanced directives. JW mothers had similar haemoglobin levels to controls at different time points – at booking, third trimester, delivery and the postnatal period (p=0.53-0.857). Pregnant JW were more likely to receive iron supplements in the antenatal period (p=0.006) compared with age-matched control. In terms of obstetrics outcome, there was no difference in mode of delivery compared with control. 30 (62.5%) had normal vaginal deliveries, 4 (8.3 %) had instrumental births and 14 (29.1%) had Caesarean births in JW arm. There was no increase in blood loss at delivery for JW mothers (p=0.19). Neonatal outcome in terms of mean birthweight (3266 grams vs 3041 grams, p=0.188) and 5-min Apgar score (9.8 vs 9.9, p=0.448) were comparable between JW and non-JW group. There were no maternal deaths, no hysterectomy and no admissions to the adult intensive care unit in either arms.
Conclusion
Pregnant JW who received optimised obstetric care had similar outcomes to controls who were non-JW. The risk of morbidity could be mitigated with precautions and JW mothers should not be discriminated on the choice of blood product refusal.
Postponing Spinal Surgery in Patients Recovered from COVID-19 based on Coagulation Test Results, Effective or Ineffective Strategy?
Authors: Mohsenzadeh Mahdi , Zamani Majid , Mokhtari AliMohammad , Talaie Alireza , Sajjadi SeyedHadi , Pouladkhay Fatemeh 
Published: October 2023

Abstract
Background
The COVID-19 pandemic has posed numerous challenges across medical disciplines, including laboratory testing. Alterations in blood parameters caused by the virus have raised concerns regarding the reliability of certain laboratory tests. This study aimed to investigate whether relying on hematology test results to postpone surgeries remains a dependable practice, particularly in the context of spinal interventions.
Methods
A retrospective analysis was conducted on the medical records of 220 patients who had undergone spinal surgery between October 2021 and June 2023 and whose COVID-19 status was documented. Inclusion criteria encompassed individuals without a history of blood disorders, pregnancy, drug or smoking addiction, or recent surgical procedures. Data were extracted using a checklist and analyzed utilizing SPSS software. Descriptive methods and statistical tests, such as independent samples t-test and chi-square test, were employed, with statistical significance set at p < 0.05.
Results
Among the analyzed patients, 56.4% were male and 43.6% were female. Fusion surgery was performed on 82.7% of individuals, while laminectomy surgery was performed on 17.3%. Approximately 65.9% had no underlying conditions, and 67.3% had a history of prior COVID-19 infection. Postoperative thrombotic complications were observed in 2.2%. Comparisons between patients with and without coagulation complications revealed no significant differences in demographic information, history of COVID-19 infection, or coagulation test results. Furthermore, a comparison of D-dimer test outcomes between individuals with normal D-dimer levels (54 people) and those with levels exceeding 500 (55 people) demonstrated no significant distinction (P > 0.05).
Conclusion
Based on the findings, this study concludes that for major and extensive spinal surgeries in patients with a history of COVID-19, evaluating D-dimer test results does not offer significant assistance in decision-making.
The Relationship Between Alarm Fatigue with Clinical Competence in Neonatal Intensive Care Nurses in Kermanshah-Iran, 2022.
Authors: Begjani Jamaloddin , Moheb Nasim Bagheri , Haghani Shima , Takhtgahi Homa Babaei 
Published: October 2023

Abstract
Background: Inadequate qualifications of nurses are one of the predisposing factors for the occurrence of clinical errors in care units, which can lead to doubling the amount of care. On the other hand, false alarms reduce the response time and nurses' trust in alarms, which can cause them to suffer from alarm fatigue in the long run. This study was conducted with the aim of determining the relationship between alarm fatigue andclinical competence in neonatal intensive care nurses in Iran, Kermanshah, 2022.
Methods: In this cross-sectional study, 140 neonatal intensive care nurses were selected by the census method. The data collection tools included a demographic questionnaire, the “Nurse Competence Scale” and an “Alarm fatigue questionnaire”. Data were analysed using descriptive and analytical statistics.
Results: The average alarm fatigue score was 21.61 ± 7.45 and above average. Most of the researched nurses, that means 75% of them, had very good clinical qualifications. The average score of clinical competence in nurses was 174.76± 26.74 and was evaluated at a very good level. The clinical competence of nurses in the subscale of managing situations, with an average of 83.72 ±14.53, is the highest, and in the subscale of ensuring quality, with an average of 75.31± 18.26, the lowest average score has been obtained among other subscales of clinical competence. This study shows the relationship between alarm fatigue and clinical competence in the teaching–coaching subscale among nurses in the neonatal intensive care unit of Kermanshah city, so that with the increase in alarm fatigue in nurses, the clinical competence in the teaching–coaching subscale decreases (p= 0/019).
Conclusion: Clinicalcompetence was scored at a very good level, and alarm fatigue was above average. This study shows the relationship between alarm fatigue and clinical competence in the teaching–coaching subscale among NICU nurses. The findings showed that the clinical competence of nurses obtained the highest average score in the managing situations subscale and the lowest average score in the ensuring quality subscale. It is appropriate to take measures to strengthen the aspect of ensuring quality, which is mostly evidence-based nursing. Additionally, according to the needs of nurses in hospitals, more planning should be done to improve education. It is necessary to adopt solutions according to standard guidelines to reduce alarms and to monitor the physiological monitoring systems in hospitals because not paying attention to these issues leads to the fatigue of the alarms of nurses, which itself has many consequences for nurses and patients.
Effectiveness of a Social Justice Curriculum Intervention on Cultural Competency among Internal Medicine Residents
Authors: Trivedi Bhavi , Mares Adriana , Mukherjee Debabrata , Harindranathan Priya , Hechanova Aimee , Edwards Brian , Dwivedi Alok , Deoker Abhizith 
Published: October 2023

Abstract

Introduction:
There is a nationwide need to include social justice topics in medical education to reduce health disparities of culturally diverse patients. Cultural competence acts as a link between cultural diversity and social justice to foster health equity among patients. We implemented a Social Justice in Medicine curriculum in the Internal Medicine residency program to prepare cultural competencies for social justice among residents. We sought to investigate the impact of curriculum implementation on residents' cultural competency.
Methods
The social justice in medicine included a variety of educational strategies including online curriculum modules, immersive clinical experiences in continuity clinics, community engagement, a lecture series (Social Determinants of Health, social injustices, resident activism etc.), and the use of reflective practices (bias assessments, group discussions). We conducted a pre-post quasi-experimental study to evaluate the effect of implementation of an educational intervention on competency as measured by the Inventory for Assessing the Process of Cultural Competence Among Healthcare Professionals - Revised, a 25-item 4-point Likert scale. This instrument assesses cultural awareness, knowledge, skill, encounters, and desire. The effect size was summarized with mean difference (MD) and 95% confidence interval (CI).
Results
A total of 40 residents participated in the study. Overall 11.7% relative improvement in cultural competency was observed following the intervention (MD = 7.7; 95%CI: 4.72, 10.68, p < 0.001). The intervention improved all the domains of competency including awareness (MD = 0.93; 95%CI: -0.02, 1.87), p = 0.05), knowledge (MD = 2.20; 95%CI: 1.33, 3.07, p < 0.001), skill (MD = 1.90; 95%CI: 1.12, 2.68, p < 0.001), encounters (MD = 1.10; 95%CI: 0.23, 1.97, p = 0.014), and desire (MD = 1.58; 95%CI: 0.80, 2.35, p < 0.001).
Conclusions
The implementation of social justice in medicine curriculum improved the cultural competencies among internal medicine residents in our study. Future longitudinal studies are required to investigate challenges, barriers, and modes of implementation strategies in a larger setting.
Up-to-dateness of patient versions of clinical practice guidelines and potential influencing factors: a mixed-methods analysis
Authors: Hellbrecht Irma , Könsgen Nadja , Pieper Dawid , Prediger Barbara , Breuing Jessica 
Published: October 2023

Abstract
Background:
Clinical practice guidelines (CPGs) provide recommendations and are a fundamental part of clinical practice. Following and based on CPGs, many guideline organisations also produce patient versions of CPGs (PVGs). The main objective of this study was to perform a mixed-methods analysis on the up-to-dateness of German PVGs and potential methodological influence factors.
Methods:
A mixed-methods analysis was conducted. First, a literature search to identify PVGs was performed between October 2022 and January 2023. PVGs fulfilling the following criteria were included: published in German, free accessible, explicit link to corresponding CPG, final version, date of literature search of CPG and publication date of PVG available (no publication date restriction). Second, interviews with experts in the PVG development were conducted and analysed using qualitative content analysis (following Mayring) with MAXQDA software.
Results:
49 PVGs were included and analysed. A median of 36 months elapsed between the literature search of CPGs and the publication of PVGs. Six interviews were conducted and interviewees mostly perceived PVGs as up-to-date. However, they identified exceptions in the up-to-dateness depending on the topic or thematic chapters of PVGs. Interviewees mentioned different influencing factors such as the scientific progress and the editorial process of PVGs.
Conclusion:
Our findings shed light on potential issues with regard to the up-to-dateness of PVGs. In the context of a fast-moving evidence basis, it seems doubtful whether PVGs actually reflect the current state of knowledge, especially in fields with high research activity. However, some factors may not be modifiable because they essentially contribute to the quality assurance of PVGs. Further research is desirable to investigate which measures may be feasible to improve the up-to-dateness of PVGs.
Beta Diversity Assessment of Odonata Communities in Amazonian Streams with Altered Environments
Authors: Silva Samantha Ribeiro , de Lima Edgar Luiz , Gonçalves Myckey Kenzy e Silva , Oliveira-Junior José Max Barbosa , Dias-Silva Karina , Juen Leandro , Brasil Leandro Schlemmer 
Published: October 2023

Abstract
Beta diversity has been widely used in studies to understand the spatial distribution patterns of species and to assess the effects of anthropic impacts on aquatic environments. Dissimilarity indices, such as Sorensen and Jaccard, are widely used to calculate beta diversity, and show differences in their way of evaluating and valuing biodiversity components, which result in different patterns. Despite this variation, the efficiency and performance of beta diversity to measure environmental impacts in communities remains unexplored. In this study, we In this study, we evaluate changes in the composition of Odonata species adult in Amazonian streams using different beta diversity indices. The Odonata were sampling in 98 small streams in two regions of the eastern Amazon. We compared the beta diversity of preserved and altered streams in each region using the Sorensen and Jaccard indices. Our results show that all methods used are effective in detecting changes in Odonata species composition when comparing preserved and altered stream communities. However, the Sorensen index was more able to reflect these changes, possibly due to its lower sensitivity to rare species compared to the Jaccard index. Even with a subtle difference in detection power, we should consider it, especially when environmental changes are less pronounced, using methods with greater accuracy increases the probability of detecting the effects of human actions on natural communities.