Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibiogram profiles and efficacy of antibiotic regimens of bacterial isolates from chronic osteomyelitis of the appendicular skeleton: A developing-world perspective.

BACKGROUND Empirical antibiotic strategies in the treatment of chronic osteomyelitis should ideally be based on local microbiological antibiograms. OBJECTIVES To review the antibiogram profiles of bacterial isolates of patients undergoing surgical treatment for chronic osteomyelitis and identify the most appropriate empirical antibiotic strategy. METHODS A retrospective review of clinical records and microbial culture reports was performed for all patients who underwent treatment for chronic osteomyelitis at two orthopaedic units in Western Cape Province, South Africa, between March 2016 and December 2019. Reported antibiotic susceptibility data were used to predict the potential efficacy of different empirical antibiotic regimens, according to underlying aetiology (fracture related, contiguous, haematogenous). RESULTS Two hundred patients with chronic osteomyelitis of the appendicular skeleton underwent surgical management. Antibiogram profiles for 218 organisms, isolated from 169 patients, were evaluated. Staphylococcus aureus (41%) and Enterobacterales (30%) were the most common organisms isolated. The combinations of meropenem plus vancomycin, and piperacillin-tazobactam plus amikacin plus vancomycin, as empirical postoperative antibiotics would both effectively treat 78% of chronic osteomyelitis cases overall. The most effective practical oral combinations were co-amoxiclav plus ciprofloxacin (61%) and co-trimoxazole plus ciprofloxacin (61%). CONCLUSIONS This study reports antibiogram profiles in the developing-world setting that could potentially guide empirical antibiotic choices in the management of chronic osteomyelitis.
Daily Training efficiency during computerized cognitive rehabilitation training (CCRT): an analysis from a randomized trial in Ugandan children with and without severe malaria

ABSTRACT Children in Uganda are at risk for significant cognitive sequelae from severe malaria. Computerized cognitive rehabilitation training (CCRT) represents a potential method to improve working memory, behavior, and executive functioning, cognitive domains most at risk following severe malaria. The primary aim of this study was to complete a secondary analysis of data from a concluded CCRT randomized control trial in order to compare the training efficiency of a commonly used CCRT program under conditions of titrated (adaptive) or non-titrated (non-adaptive) training and with children with increasing malaria severity to determine how various factors may affect potential CCRT improvement. A total of 201 school-aged children (66.2% boys) who were either healthy (n = 102) or previously diagnosed with severe or cerebral malaria (n = 99) were randomized into two active treatment arms (titrated and non-titrated learning). Each child received 24 one-hour sessions of training over 8 weeks using Captain’s Log® CCRT by BrainTrain, which includes a comprehensive set of CCRT tasks. Children generally benefited from CCRT over the 24 training sessions, but titrated CCRT showed a clear advantage over non-titrated. Severity of illness or factors such as BMI, did not moderate CCRT performance indicators. These findings support our hypothesis that titrated CCRT would result in steeper improvement in learning, but do not support our hypothesis that history of recent significant illness would affect learning proficiency. Findings were evident across all CCRT performance scores, even given that children were from generally rural, low-resource settings and were generally unfamiliar with computers. ABBREVIATIONS: Computerized Cognitive Rehabilitation Training (CCRT); Mental Processing Index (MPI); Home Observation for the Measurement of the Environment (HOME); Socioeconomic Status (SES); least square means (LSM)
Assessing the Job Satisfaction of Registered Nurses Using Sentiment Analysis and Clustering Analysis

Job satisfaction is a critical component of the professional work environment and is often ascertained through surveys that include structured or open-ended questions. Using data from 24,543 respondents to California Board of Registered Nursing biennial surveys, this study examines the job satisfaction of registered nurses (RNs) by applying clustering analysis to structured job satisfaction items and sentiment analysis to free-text comments. The clustering analysis identified three job satisfaction groups (low, medium, and high satisfaction). Sentiment analysis scores were significantly associated with the job satisfaction groups in both bivariate and multivariate analyses. Differences between the job satisfaction clusters were mostly driven by satisfaction with workload, adequacy of the clerical support services, adequacy of the number of RN staff, and skills of RN colleagues. In addition, there was dispersion in satisfaction related to involvement in management and policy decisions, recognition for a job well done, and opportunities for professional development.
New insight into the role of a combination of zinc oxide and turmeric rhizome liquid extract in osteogenic marker expression

Aim: This research was aimed to determine the potential for treating osteogenesis with a combination of zinc oxide and turmeric (ZOT) rhizome liquid extract. Setting and Design: In vivo, post test-control group design. Material and Methods: The mandibular incisors of Wistar rats were extracted and left untreated or received an application of zinc oxideeugenol (ZOE) 10% or ZOT rhizome liquid extract at various concentrations (10%, 20%, and 40%). The mandible was then subjected to immunohistochemical analysis to detect RUNX2 and alkaline phosphatase (ALP) activity. Statistical Analysis Used: One-way ANOVA and Tukey HSD using SPSS software. Results: All groups demonstrated increasing RUNX2 and ALP activity. ZOT 40% showed the highest activity in all groups on day 3 and day 7, although there were no significant differences with ZOE 10%. Conclusion: A combination of ZOT rhizome liquid extract can induce the osteogenic process in postextraction sockets. The results highlight the need for further investigation of the potential osteogenesis of curcumin in humans.
Cancer cells are highly susceptible to accumulation of templated insertions linked to MMBIR

Abstract Microhomology-mediated break-induced replication (MMBIR) is a DNA repair pathway initiated by polymerase template switching at microhomology, which can produce templated insertions that initiate chromosomal rearrangements leading to neurological and metabolic diseases, and promote complex genomic rearrangements (CGRs) found in cancer. Yet, how often templated insertions accumulate from processes like MMBIR in genomes is poorly understood due to difficulty in directly identifying these events by whole genome sequencing (WGS). Here, by using our newly developed MMBSearch software, we directly detect such templated insertions (MMB-TIs) in human genomes and report substantial differences in frequency and complexity of MMB-TI events between normal and cancer cells. Through analysis of 71 cancer genomes from The Cancer Genome Atlas (TCGA), we observed that MMB-TIs readily accumulate de novo across several cancer types, with particularly high accumulation in some breast and lung cancers. By contrast, MMB-TIs appear only as germline variants in normal human fibroblast cells, and do not accumulate as de novo somatic mutations. Finally, we performed WGS on a lung adenocarcinoma patient case and confirmed MMB-TI-initiated chromosome fusions that disrupted potential tumor suppressors and induced chromothripsis-like CGRs. Based on our findings we propose that MMB-TIs represent a trigger for widespread genomic instability and tumor evolution.
Endometrial preparation does not affect the risk of hypertensive disorders of pregnancy in low-risk women undergoing frozen embryo transfer

Abstract Objective Frozen embryo transfer (FET) is associated with a higher risk of hypertensive disorders in pregnancy. The objective of the present study is to evaluate the effect of different protocols of endometrial preparation on the risk of these disorders. Methods We conducted a retrospective cohort study on 594 singleton pregnancies achieved by embryo transfer of single frozen-thawed blastocysts. Women with preexisting risk factors for hypertensive disorders were excluded. Women were divided into two groups according to the endometrial preparation protocol: either natural cycle (n = 495) or programming cycle with hormonal replacement therapy (n = 97). The primary outcome was the frequency of hypertensive disorders in pregnancy: specifically, gestational hypertension and preeclampsia. Results No differences emerged between women following the natural cycle and those following the programming cycle in the frequency of gestational hypertension (5 vs. 4%) and preeclampsia (1.1 vs. 1.2%). No impact emerged also after multivariate analyses. Conclusions Women receiving hormonal replacement therapy have the same risk of gestational hypertension and preeclampsia as women following natural cycles when considering low-risk singleton pregnancies.
Controlled ovarian stimulation outcomes of fertility preservation procedures in newly diagnosed breast cancer patients: a retrospective study from a single-tertiary-IVF centre

Abstract The aim of this study was to evaluate the effectiveness of controlled ovarian stimulation (COS) using the letrozole-supplemented stimulation protocol in breast cancer (BC) patients prior to their cancer treatment. Sixty-one BC patients (Stages 0–3) who were referred to a university IVF unit for fertility preservation (FP) and underwent embryo and/or oocyte cryopreservation between 2008 − 2020 were included in this retrospective study. Time intervals between breast surgery and initial fertility consultation (IFC)/completion of FP procedures were evaluated. COS outcomes were assessed and compared between the early follicular phase (EFP) and the random-start (RS) protocols. The patients’ mean age was 33.3 ± 4.9 years. The mean time interval between breast surgery and IFC was 20.6 ± 11 (day, mean ± SD) and from IFC to completion of FP procedure was 14.7 ± 5.3. Overall, 9.1 ± 5.9 mature oocytes were obtained, with a peak serum oestradiol level of 388 ± 358 pg/mL. The number of oocytes obtained (11.5 ± 9.3 vs. 10.9 ± 6.9, p = .9) and maturation rates (84.3 ± 17.5% vs. 89.2 ± 11.7, p = .5) were not statistically different between the EPF and RS protocols. The study results support that oocyte or embryo freezing can be performed effectively in a limited time period with letrozole-supplemented COS protocols before the initiation of oncological treatments in breast cancer patients. Impact statement What is already known on this subject? Currently, embryo and oocyte freezing are considered the most established fertility preservation (FP) methods for newly diagnosed cancer patients. What do the results of this study add? This study reports the COS outcomes of newly diagnosed breast cancer patients for FP over a period of twelve years from a single IVF unit. The results support that a considerable number of oocytes can be harvested with letrozole-supplemented COS protocol, which appears to be an effective protocol for BC patients. What are the implications of these findings for clinical practice and/or further research? There is a need for additional studies evaluating long-term follow-up of patients with their pregnancy outcomes.
DeepFusionDTA: Drug-Target Binding Affinity Prediction With Information Fusion and Hybrid Deep-Learning Ensemble Model

Identification of drug-target interaction (DTI) is the most important issue in the broad field of drug discovery. Using purely biological experiments to verify drug-target binding profiles takes lots of time and effort, so computational technologies for this task obviously have great benefits in reducing the drug search space. Most of computational methods to predict DTI are proposed to solve a binary classification problem, which ignore the influence of binding strength. Therefore, drug-target binding affinity prediction is still a challenging issue. Currently, lots of studies only extract sequence information that lacks feature-rich representation, but we consider more spatial features in order to merge various data in drug and target spaces. In this study, we propose a two-stage deep neural network ensemble model for detecting drug-target binding affinity, called DeepFusionDTA, via various information analysis modules. First stage is to utilize sequence and structure information to generate fusion feature map of candidate protein and drug pair through various analysis modules based deep learning. Second stage is to apply bagging-based ensemble learning strategy for regression prediction, and we obtain outstanding results by combining the advantages of various algorithms in efficient feature abstraction and regression calculation. Importantly, we evaluate our novel method, DeepFusionDTA, which delivers 1.5 percent CI increase on KIBA dataset and 1.0 percent increase on Davis dataset, by comparing with existing prediction tools, DeepDTA. Furthermore, the ideas we have offered can be applied to in-silico screening of the interaction space, to provide novel DTIs which can be experimentally pursued. The codes and data are available from https://github.com/guofei-tju/DeepFusionDTA.
Porcine Reproductive and Respiratory Syndrome Virus Infection Upregulates Negative Immune Regulators and T-Cell Exhaustion Markers

Porcine reproductive and respiratory syndrome virus (PRRSV) is widespread in many swine-producing countries, causing substantial economic losses to the swine industry. Porcine alveolar macrophage (PAM) is considered the primary target for PRRSV replication in pigs. ABSTRACT Porcine alveolar macrophage (PAM) is one of the primary cellular targets for porcine reproductive and respiratory syndrome virus (PRRSV), but less than 2% of PAMs are infected with the virus during the acute stage of infection. To comparatively analyze the host transcriptional response between PRRSV-infected PAMs and bystander PAMs that remained uninfected but were exposed to the inflammatory milieu of an infected lung, pigs were infected with a PRRSV strain expressing green fluorescent protein (PRRSV-GFP), and GFP+ (PRRSV infected) and GFP− (bystander) cells were sorted for RNA sequencing (RNA-seq). Approximately 4.2% of RNA reads from GFP+ and 0.06% reads from GFP− PAMs mapped to the PRRSV genome, indicating that PRRSV-infected PAMs were effectively separated from bystander PAMs. Further analysis revealed that inflammatory cytokines, interferon-stimulated genes, and antiviral genes were highly upregulated in GFP+ compared to GFP− PAMs. Importantly, negative immune regulators, including NF-κB inhibitors (NFKBIA, NFKBID, NFKBIZ, and TNFAIP3) and T-cell exhaustion markers (programmed death ligand-1 [PD-L1], PD-L2, interleukin-10 [IL-10], IDO1, and transforming growth factor β2 [TGFB2]) were highly upregulated in GFP+ cells compared to GFP− cells. By using an in situ hybridization assay, RNA transcripts of tumor necrosis factor (TNF) and NF-κB inhibitors were detected in PRRSV-infected PAMs cultured ex vivo and lung sections of PRRSV-infected pigs during the acute stage of infection. Collectively, the results suggest that PRRSV infection upregulates expression of negative immune regulators and T-cell exhaustion markers in PAMs to modulate the host immune response. Our findings provide further insight into PRRSV immunopathogenesis. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) is widespread in many swine-producing countries, causing substantial economic losses to the swine industry. Porcine alveolar macrophage (PAM) is considered the primary target for PRRSV replication in pigs. However, less than 2% of PAMs from acutely infected pigs are infected with the virus. In the present study, we utilized a PRRSV strain expressing green fluorescent protein to infect pigs and sorted infected and bystander PAMs from the pigs during the acute stage of infection for transcriptome analysis. PRRSV-infected PAMs showed a distinctive gene expression profile and contained many uniquely activated pathways compared to bystander PAMs. Interestingly, upregulated expression of NF-κB signaling inhibitors and T-cell exhaustion molecules were observed in PRRSV-infected PAMs. Our findings provide additional knowledge on the mechanisms that PRRSV employs to modulate the host immune system.
A retrospective, observational study of medicolegal cases against obstetricians and gynaecologists in South Africa's private sector.

BACKGROUND The viability of obstetric practice in the private sector has been threatened as a result of steep increases in professional indemnity fees over the past 10 years. Despite this, empirical research investigating key aetiological factors to target risk management interventions has been lacking. OBJECTIVES To explore private practice medicolegal data linked to obstetricians and gynaecologists (O&Gs) to identify factors in clinical practice associated with claims, for the purposes of guiding future research and risk management solutions. METHODS This was a retrospective, observational study of private sector O&Gs' medicolegal case histories. All incidents declared to a prominent local professional indemnity insurer were categorised in terms of medicolegal case type, as well as clinical parameters. To allow for risk-adjusted calculations of case incidence, year of entry into private practice was estimated for all practitioners. RESULTS Steep increases in medicolegal investigations and demands were demonstrated for both obstetrics- and gynaecology-related cases from about 2003 to 2012. Whereas the total numbers of claims, regulatory complaints and requests for records were similar for obstetrics and gynaecology in recent years (accounting for 52% v. 48% of known cases, respectively), a significantly greater percentage of demands and paid settlements related to gynaecology rather than obstetrics (58% and 76% v. 42% and 24% of cases, respectively). In obstetrics, about half of all cases on record with a paid settlement were in the context of severe neonatal birth-related neurological injury (n=9). For gynaecology, procedure-related complications accounted for 92% of settlements, of which at least 41% were for intraoperative injuries to internal organs and vessels. Laparoscopic procedures were most frequently associated with such intraoperative injuries, followed by vaginal and abdominal hysterectomies/oophorectomies and caesarean sections. For O&Gs in private practice for >2 years, 50/458 (11%) accounted for 138/228 (61%) of demands over a 10-year period. CONCLUSIONS The higher number of gynaecological demands and settlements in comparison with obstetric cases was unexpected and is contrary to international experiences and public sector findings, calling for more research to identify reasons for this finding. Other than further exploring surgical outcomes in private sector gynaecological patients, aspects of surgical training and accreditation standards in gynaecology may need review. Regarding birth-related injuries, the contribution of system failures needs quantification and further interrogation. The high contribution towards the medicolegal burden by a small group of practitioners suggests a need for doctor-focused interventions, including strengthening of peer review and regulatory oversight.
Burden on caregivers of schizophrenia outpatients in Brazil: Relationship to symptomatology and functioning

Background: To investigate the objective and subjective burden on caregivers of schizophrenia outpatients and their associations with sociodemographic factors, symptomatology, and functioning. Methods: This study included 60 schizophrenic outpatients aged 18 to 65 years who were clinically stable for at least 6 months, and 60 caregivers aged 18 to 80 years who were in contact with the patient for ⩾30 hours/week. The patients were assessed using a sociodemographic questionnaire, the Clinical Global Impression Scale for Schizophrenia (CGI-SCH), and the Personal and Social Performance scale (PSP). The caregivers were assessed using a sociodemographic questionnaire and the Family Burden Interview Schedule, Brazilian version (FBIS-BR). Results: The objective burden was positively correlated with CGI-SCH cognitive symptom scores (p = .032) and number of hours spent weekly with the patient (p = .028), and negatively correlated with PSP score (r = −.346, p = .007). The subjective burden showed a negative correlation with age of disease onset (r = −.338, p = .08). The independent variables included in the regression model were family income (p = .005), PSP score (p = .009), patient marital status (p = .012), patient gender (p = .046), and reception of financial benefit (p = .027) for objective burden; and disease duration (p = .045) and father/mother or sibling relationship (p = .001) for subjective burden. The coefficient of determination (R2) of the linear regression model for objective burden was 39.4%; subjective burden, 21.6%. Conclusion: Caring for female, single patients with longer disease duration, more severe cognitive symptoms, impaired functioning, and more caregiving time required per week were associated with higher caregiver burden levels.
FOUR-SITE SKINFOLDS THICKNESS PERCENTILES of SCHOOLCHILDREN and ADOLESCENTS in TURKEY.

OBJECTIVE The primary purpose of this study was to establish Turkish smoothed centile charts and LMS tables for four-site skinfold thickness based on a population-based sample and secondary purpose was to elaborate a reference for the percentage of body fat. DESIGN A cross-sectional and descriptive study was conducted between January and May 2017. Triceps, biceps and subscapular, suprailiac skinfold thickness were measured using Holtain skinfold caliper. Age and gender specific percentile values were determined with the LMS method, and body fat percentage was calculated using the Westrate and Deurenberg equation. SETTING Afyonkarahisar province in Turkey. PARTICIPANTS This study was conducted on 4565, 6-18 years old students. RESULTS The triceps, biceps, and subscapular skinfolds of the girls were higher than the boys. From the age of seven, the sum of four skinfold thicknesses of the girls was more than those of the boys. This difference became more evident after the age of 12. Although fat percentages of girls showed a fluctuating change, it decreased with the age in boys. Westrate and Deurenberg equation fat percentages of girls until adolescence were lower than boys, but increased after 12 years of age and exceeded that of boys. CONCLUSIONS This study has provided sex and age specific reference values for skinfold thickness, and has shown that obesity in girls is higher than in boys in schoolchildren in Afyonkarahisar. This study has also shown that skinfold thickness measurements are a valuable tool for screening obesity in children.