Miracle-dz/UniFAR-FTUs huggingface dataset:
Will earlier treatment lead to drug resistance of the form and prevalence likely to compromise future elimination of HIV

South Africa has the biggest HIV epidemic in the world. Early antiretroviral therapy (ART) is recognised as an effective HIV prevention approach and was introduced to control transmission as well as to delay HIV progression. However, it is unknown whether early treatment will result in suboptimal adherence, poor virological outcomes and emergence of drug resistance, which would hinder HIV elimination. To address this knowledge gap, I undertook a cohort analysis nested within the ANRS-sponsored TasP trial, in which ART was initiated early, to examine adherence in individuals initiating ART at high CD4 counts and quantify virological suppression in those who were ART-naive at trial entry. I also estimated virological suppression at trial entry amongst individuals already ART-experienced at their first trial clinic visit. I examined acquired resistance mutations in individuals with virological failure and estimated prevalence of pre-treatment drug resistance (PDR) in ART-naive individuals and investigated impact of PDR on virological suppression. I found no evidence of a relationship between CD4 count at ART initiation and adherence, but virological suppression was significantly better in individuals who initiated ART at higher CD4 counts, even at the same level of adherence. Most individuals with virological failure had emergent drug resistance, predominantly the M184V mutation associated with lamivudine or emtricitabine resistance. Prevalence of PDR was moderate at nearly 10%, but doubled when low frequency variants were accounted for. This was predominantly the K103N/S mutation which causes high-level resistance to efavirenz and nevirapine. However, PDR was not significantly associated with decreased virological suppression. My results are encouraging over the 12 months’ duration of ART investigated in this study with positive effects amongst patients who started ART at high CD4 counts. However, long-term follow up is required to evaluate the impact of HIV drug resistance on HIV prevention efforts.
Outcomes of surgical treatment for ruptured pericallosal artery aneurysms

The study objectiveis to assess short-term outcomes of surgical treatment in patients with ruptured pericallosal artery aneurysms (PCAA) and to identify factors affecting treatment outcomes.Materials and methods.Patients with ruptured PCAA (n = 61) were admitted to the Department of Emergency Neurosurgery at the N. V. Sklifosovsky Research Institute for Emergency Medicine for examination and surgical treatment between 01.01. 1992 and 31.12. 2015.Results. At the moment of discharge, 33 (54.1 %) patients demonstrated good recovery (Glasgow Outcome Scale (GOS) of 5), 9 (14.7 %) patients had moderate disability (GOS 4), 6 (9.9 %) patients had severe disability (GOS 3), and 13 (21.3 %) patients died (GOS of 1). An outcome was rated as favorable if the GOS was 4 or 5 and unfavorable if the GOS was 1–3. The following risk factors were found to be significant for unfavorable surgical outcome: Hunt and Hess grade 4 and 5, presence of intracerebral hematoma and its volume over 20 cm3, recurrent aneurysm rupture, pronounced angiospasm and intraventricular hemorrhage, early surgery (within 1–3 days). The patient»s age and the volume of intraventricular hemorrhage had no impact on the surgical outcome.Conclusion. The choice of an optimal surgery time should be based on the assessment of hemorrhage severity upon admission. Early surgery is recommended for all patients with Hunt and Hess grade I–II, whereas in patients with Hunt and Hess grade V, the intervention should be postponed until the condition is stabilized, unless the severity is associated with a dislocation syndrome due to intracerebral hematoma or occlusive hydrocephalus. In patients with Hunt and Hess grade III–IV, the decision on surgery time should be made for each individual patient according to existing risk factors.
Molecular phylogenetic analysis of Olea europaea L. subsp. europaea cultivars grown in the Marmara Region, Turkey

DNA markers based on the PCR techniques are being broadly utilized during the past two decades. Randomly Amplified Polymorphic DNA (RAPD) is one of these techniques employed for determining the polymorphisms. In this study, we performed a molecular analysis using DNA markers for some olive (Olea europaea) cultivars grown in the Marmara Region of Turkey. Our goal was to determine the genetic relationships between 12 olive cultivars and ‘Delice’, the outgroup. Seven RAPD primers out of 60 (10 base-pair long) amplified gDNAs with repeatable bands. These primers generated 84 characters / bands in total and 39 out of these were polymorphic. After a Branch-and-Bound analysis and a Neighbour Joining (NJ) analysis via PAUP* software, the smallest genetic distance was found between Gordales and Karamursel Su cultivars as 0.03571 whereas the greatest distances were found between Arbequina and Ascolana, Manzanilla, Hermandos, Gemlik, Verdial and Vegral cultivars as 0.17857, respectively. Maximum parsimony (MP) analysis yielded 8 equally most parsimonious trees with 65 steps. Alternatively, NJ analysis produced one tree mostly congruent with MP tree number one. In conclusion, Turkish olive cultivars grown in the Marmara Region appear to be sister to the Spanish olive cultivars based on the RAPD data.
Advanced Analytics to Predict Survivability of Breast Cancer Patients

: A frequently asked question by cancer patients post-diagnosis is the lifespan they are left with. The oncologist’s response is generally based on past records of cancer patients with similar prognosis or by consulting other physicians and researchers working on comparable cases. Although careful prognosis is vital, it is difficult to predict accurate survival time of patients as survivability is based on many factors. Also, these predictions may not be accurate as the past records are not completely reliable and the prognosis from different oncologists are generally inconsistent. Further, existing repositories of data are not easily accessible and the stored formats are difficult to analyze. We propose an end-to-end process to build a model which predicts survival months of breast cancer patients. The predictive model is trained, tested and validated with different subsets of data. The modeling techniques used in this research are Neural Networks, CHAID, C&RT and an Ensemble of these techniques. The predictive model can also be used as a calculator which predicts survival months of a specific case.
Circumstances and Consequences of Falls in Community-Living Elderly in North Bangalore Karnataka

Background: Falls are one of the causes of injuries and non-communicable diseases associated with old age. Falls lead to 20-30% of mild to severe injuries and are underlying cause of 10-15% of all emergency departments. Knowledge of the circumstances and consequences of falls is important for understanding the etiology and prevention of falls. Material and Methods: A community based cross sectional study was conducted for a period of one year. Complete enumerations of all the elderly were undertaken by house-to-house visit and a sample of 416 elderly was taken by simple random sampling. A pretested semistructured questionnaire was administered. Data was analyzed using SPSS version 17.Results: Prevalence of falls was 29.8 %, about 82.3% of the old had a single episode of fall, 17.7% had recurrent falls in a year. The fall rate was higher 65.7% among old, 26.3% in young old and 20.0% in very old, outdoor falls constituted 57.2%, indoor falls 42.8%. About 81.4% had one or the other form of injury. Injury rate was 82% in females and 80% in males. Statistically significant higher fall rate of 47.8% falls was seen with elderly who had fear of falling than those without fear of fall with 11.8%. Bruises, internal injuries were commonest (48.5%) and (13.8%) of injuries resulted in fractures.18. 4% had difficulty in carrying out activities of daily living, deformity was observed in 12.6%, and residual disability in 10.6% of the elderly. Conclusion: The morbidity due to falls includes injuries, fractures, restricted mobility. The results of this study reflect on the circumstances observed in the indoor and outdoor falls like falls on the footpath, in the bathroom, while using stairs etc. The consequences like bruises and internal injuries followed by sprains, cuts and fractures have been observed. The study suggests possible ways of preventing falls.
MTHFR Gene Polymorphism as a Risk Factor for Silent Brain Infarcts and White Matter Lesions in the Japanese General Population

Background and Purpose— Silent brain infarcts (SBI) and white matter lesions are relatively common neuroimaging findings, especially in the elderly population. The genetic background for SBI and white matter lesions in a large Japanese general population was investigated. Methods— Subjects were recruited from participants in the National Institute for Longevity Sciences, Longitudinal Study of Aging. Genotyping of methylenetetrahydrofolate reductase (MTHFR) C677T gene mutation and brain MRI examination were performed in 1721 subjects free of any history of stroke. SBI and white matter lesions were diagnosed from MRI findings. Results— Of 1721 MRI examinations, SBI was observed in 178 (10.3%). The prevalence of SBI and white matter lesions increased with age. The prevalence of SBI was significantly higher in subjects with the MTHFR TT genotype compared with the TC+CC genotype (14.6% versus 9.5%; 42 of 288 versus 136 of 1433; χ2=6.71; P=0.010). The stage of white matter lesions was not significantly differen.
Predicting 30-days All-cause Hospital Readmissions Considering Discharge-to-alternate-care-facilities

: Hospital discharge is a decision based on several data points including diagnostic, physiological, demographic and caretaker information. Readmissions days after discharge are costly in addition to negative impact on capacity and service quality of hospitals. 30-days readmission (30DRA) literature remains focused on above variables and medical conditions paying little attention to the role of alternate-care-facilities (such as skilled nursing facilities and hospices) on reduction of 30DRA rates. To the best of our knowledge, there is negligible research considering alternate care variables for predicting readmissions even when physicians have actively started considering discharge-to-alternate-care during discharge planning. This paper develops a classification model for predicting patients who are likely to be readmitted within 30 days of discharge-to-alternate-care. Several machine-learning approaches, such as multi-logistic regression, Naïve Bayes, random forest, and neural networks were tested on the model to find the one with highest predictive power. The model was trained and tested on MIMIC-III, a large anonymized electronic health records (EHRs) database from US hospitals. Results suggest discharge-to-alternate-care reduces 30DRA. Moreover, neural networks and logistic regression techniques show better precision and accuracy in identifying the patients likely to be readmitted in 30 days.
Determinants of care efficiency in a group of Polish parents raising children with different developmental disorders: a cross-sectional study

Objectives: Care efficiency of family can be determined by many factors such as mental and physical health status of family members and their socioeconomic situation. Raising children with disabilities is a burdening and stressful situation for their caregivers. This article examines determinants of care efficiency in a group of Polish parents raising children with developmental disorders. Methods: The cross-sectional study was conducted in 9 Polish schools for disabled children located in Cracow. Questionnaire that included the Caregiver Burden Scale and the Scale Efficiency of Care was completed by 213 mothers and 30 fathers. During the data analysis parametric tests (e.g. ANOVA) and nonparametric tests (e.g. a Mann–Whitney U test, Kruskal–Wallis test) were used. Results: Parents’ care efficiency and burden of care were on an average level. Sociodemographic variables such as gender, age, place of residence, education and family structure were not related to the care efficiency. The relationship with housing and material conditions of the respondents was shown. The statistical analysis showed the relationship between the level of parents’ care efficiency and all subscales of Caregiver Burden Scale. Parents who demonstrated a higher level of care efficiency experienced lower level of burden in areas such as General Strain, Isolation, Disappointment, Emotional Involvement and Environment. Conclusions: Disability of a child reduces caring potential of a family. Parents experience more physical and mental fatigue, which aggravates their disappointment. It is important to make precise diagnosis of parents’ care problems and implement an individualized program to help a family.
Acute pancreatitis - Optimizing prevention and prognostication

Background and Aims Post endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis (PEP) is the most prevalent complication after ERCP with an incidence of 3.5% and mortality of 3%. PEP severity is classified according to the consensus or revised Atlanta criteria. The consensus criteria use length of stay as a differentiator, while the revised Atlanta criteria focus on local and systemic adverse events. We question whether length of stay accurately reflects disease severity. In this real-life, international cohort study we investigated which classification is the strongest predictor of PEP-related mortality. Methods We reviewed 13,384 consecutive ERCPs performed between 2012-2017 in 8 hospitals. We reviewed records of PEP patients for evaluation of all pancreatitis-related adverse events and compared the predictive capabilities of both classifications for PEP-related mortality. Furthermore, we investigated the correlation between the two classifications and identified reasons underlying length of stay. Results The total sample consisted of 387 patients. The revised Atlanta criteria have a higher sensitivity (100 vs. 55%), specificity (98 vs. 72%) and positive predictive value (58 vs. 5%). There is a significant difference (p<0.001) between the consensus and revised Atlanta criteria, with 112 (29%) and 19 (5%) severe patients, respectively. In 124 patients (32%), the length of stay was influenced by concomitant diseases. Conclusions The revised Atlanta classification is superior in predicting mortality and better reflects PEP severity. This has important implications for researchers, clinicians and patients. For the diagnosis of post-ERCP pancreatitis, the consensus criteria remain the golden standard. However, the revised Atlanta criteria are the preferable for defining PEP severity.
A rapid methods development workflow for high-throughput quantitative proteomic applications

Recent improvements in the speed and sensitivity of liquid chromatography-mass spectrometry systems have driven significant progress toward system-wide characterization of the proteome of many species. These efforts create large proteomic datasets that provide insight into biological processes and identify diagnostic proteins whose abundance changes significantly under different experimental conditions. Yet, these system-wide experiments are typically the starting point for hypothesis-driven, follow-up experiments to elucidate the extent of the phenomenon or the utility of the diagnostic marker, wherein many samples must be analyzed. Transitioning from a few discovery experiments to quantitative analyses on hundreds of samples requires significant resources both to develop sensitive and specific methods as well as analyze them in a high-throughput manner. To aid these efforts, we developed a workflow using data acquired from discovery proteomic experiments, retention time prediction, and standard-flow chromatography to rapidly develop targeted proteomic assays. We demonstrated this workflow by developing MRM assays to quantify proteins of multiple metabolic pathways from multiple microbes under different experimental conditions. With this workflow, one can also target peptides in scheduled/dynamic acquisition methods from a shotgun proteomic dataset downloaded from online repositories, validate with appropriate control samples or standard peptides, and begin analyzing hundreds of samples in only a few minutes.
A Study of the Association between Dehydroepiandrosterone and Frailty in Elderly

The biological basis for Frailty remains unclear. It is hypothesized that loss of bone mass, decline in protein synthesis, sarcopenia and immune dysfunction influence the onset of frailty. Studies show that low serum DHEA levels are associated with increased rates of morbidity and mortality. Serum levels of DHEA decline with age, and this decline is paralleled by a decrease in muscle and bone mass. Hence we take up this study to test the hypothesis that declining serum DHEA is associated with the frailty phenotype. AIMS & OBJECTIVES: To evaluate the association between Dehydroepiandrosterone (DHEA) and Frailty in the elder population. METHODS: The study group includes elderly subjects > 65 yrs, in the Geriatric ward of Rajiv Gandhi Govt. General Hospital, Chennai, who complied with the inclusion and exclusion criteria. Anthropometric evaluation was done. Fried’s criteria was employed to assess the frailty phenotype. Patients were categorized into 3 groups based on the number of frailty components - FRAIL (≥ 3 characteristics); INTERMEDIATE FRAIL (1-2 characteristics); NON-FRAIL (no characteristic). Blood samples of patients from each group were collected for estimating serum DHEA-s level (using CLIA method) and analysis was performed by appropriate statistical methods. RESULTS: In a study conducted in 100 participants, a significant association between Frailty phenotype and DHEA level was observed (p < 0.0004). Ordinal logistic regression was used to model the relationship between frailty and DHEA, adjusting for age, gender and BMI. A significant DHEA–BMI interaction (OR=1.09; 95% CI; p = 0.0001) suggested that, in general, the relationship between higher levels of frailty decreased relative to higher levels of DHEA, but the magnitude of decrease was larger at lower BMI values and smaller at higher BMI values. A BMI >29 kg/m² attenuated the association between DHEA levels and frailty. CONCLUSION: This study found an inverse association between frailty and DHEA-s levels, similar to other studies that have found associations between DHEA-s and physical function. Whether the inverse association is due to similar conditions resulting in lower DHEA levels and more susceptibility to frailty or whether lower DHEA levels have an impact on increasing frailty cannot be addressed by this cross-sectional
Metabolic Rate, Q10 and Respiratory Quotient (RQ) in Crocodylus porosus, and Some Generalizations about Low RQ in Reptiles

In juvenile Crocodylus porosus, the dependence of oxygen consumption on temperature can be described by the relationship log10 \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage{wasysym} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document}$${\mathrm{Q_{O_{2}}}}$$\end{document} = 0.7221 + 0.0428T C. The Q10 was found to be 2.68 over the temperature range 20-33 C. No trend was observed between body weight and weight-specific oxygen consumption. At Ta (27-33 C) respiratory quotient (RQ) (measured gasometrically) was invariably low (0.32 - 0.74, mean 0.49, 0.13 SD) in animals from freshwater. The low values of gasometric RQ are attributed to incorporation of carbon dioxide in the urine, forming ammonium bicarbonate. Support for this hypothesis is afforded by the similarity of measured values (0.49) to values predicted by the hypothesis (0.51).
A new species of the genus Coleolaelaps (Acari: Laelapidae) associated with larvae of Polyphylla sp. (Coleoptera: Scarabaeidae) in Iran

Coleolaelaps ferdowsi Joharchi sp. n. (Acari: Laelapidae) was collected associated with the larval stage of Polyphylla sp. (Coleoptera: Scarabaeidae) on roots of peach trees in Neishabour, Khorasan Razavi, Iran. This new species is described and illustrations provided.
Addressing obesity in Roma communities: a community readiness approach

Purpose Participation in community programmes by the Roma community is low, whilst this community presents with high risk of poor health and low levels of wellbeing. To improve rates of participation in programmes, compatibility must be achieved between implementation efforts and levels of readiness in the community. The Community Readiness Model (CRM) is a widely used toolkit which provides an indication of how prepared and willing a community is to take action on specific issues. The purpose of this paper is to present findings from a CRM assessment for the Eastern European Roma community in Bradford, UK, on issues related to nutrition and obesity. Design/methodology/approach The authors interviewed key respondents identified as knowledgeable about the Roma community using the CRM. This approach applies a mixed methodology incorporating readiness scores and qualitative data. A mean community readiness score was calculated enabling researchers to place the community in one of nine possible stages of readiness. Interview transcripts were analysed using a qualitative framework analysis to generate the contextual information. Findings An overall score consistent with vague awareness was achieved, which indicates a low level of community readiness. This score suggests that there will be a low likelihood of participation in currently available nutrition and obesity programmes. Originality/value To our knowledge, this is the first study to apply the CRM in the Roma community for any issue. The authors present the findings for each of the six dimensions that make up the CRM together with salient qualitative findings.
An Ancient DNA Study of Four Sympatric Species of Moa (Aves: Dinornithiformes) from Holocene Deposits in North Canterbury, South Island, New Zealand

doi: 10.1098/rspb.2009. 2019 published online 10 March 2010 Proc. R. Soc. B Holdaway, Eske Willerslev and Michael Bunce Alexander Baynes, Joe Dortch, Michael Parker-Pearson, M. Thomas P. Gilbert, Richard N. Camilla Bengtsson, Gifford H. Miller, Jean-Luc Schwenninger, Chris Jacomb, Richard Walter, Charlotte L. Oskam, James Haile, Emma McLay, Paul Rigby, Morten E. Allentoft, Maia E. Olsen, Fossil avian eggshell preserves ancient DNA Supplementary data tml http://rspb.royalsocietypublishing. org/content/suppl/2010/03/09/rspb.2009. 2019.DC1. h "Data Supplement" References ml#ref-list-1 http://rspb.royalsocietypublishing. org/content/early/2010/03/09/rspb.2009. 2019.full. ht This article cites 37 articles, 12 of which can be accessed free P<P Published online 10 March 2010 in advance of the print journal.