Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating Inbreeding Rates in Natural Populations: Addressing the Problem of Incomplete Pedigrees

Understanding and estimating inbreeding is essential for managing threatened and endangered wildlife populations. However, determination of inbreeding rates in natural populations is confounded by incomplete parentage information. We present an approach for quantifying inbreeding rates for populations with incomplete parentage information. The approach exploits knowledge of pedigree configurations that lead to inbreeding coefficients of F = 0.25 and F = 0.125, allowing for quantification of Pr(I|k): the probability of observing pedigree I given the fraction of known parents (k). We developed analytical expressions under simplifying assumptions that define properties and behavior of inbreeding rate estimators for varying values of k. We demonstrated that inbreeding is overestimated if Pr(I|k) is not taken into consideration and that bias is primarily influenced by k. By contrast, our new estimator, incorporating Pr(I|k), is unbiased over a wide range of values of k that may be observed in empirical studies. Stochastic computer simulations that allowed complex inter- and intragenerational inbreeding produced similar results. We illustrate the effects that accounting for Pr(I|k) can have in empirical data by revisiting published analyses of Arabian oryx (Oryx leucoryx) and Red deer (Cervus elaphus). Our results demonstrate that incomplete pedigrees are not barriers for quantifying inbreeding in wild populations. Application of our approach will permit a better understanding of the role that inbreeding plays in the dynamics of populations of threatened and endangered species and may help refine our understanding of inbreeding avoidance mechanisms in the wild.
Effects of Sample Size and Full Sibs on Genetic Diversity Characterization: A Case Study of Three Syntopic Iberian Pond-Breeding Amphibians

Accurate characterization of genetic diversity is essential for understanding population demography, predicting future trends and implementing efficient conservation policies. For that purpose, molecular markers are routinely developed for nonmodel species, but key questions regarding sampling design, such as calculation of minimum sample sizes or the effect of relatives in the sample, are often neglected. We used accumulation curves and sibship analyses to explore how these 2 factors affect marker performance in the characterization of genetic diversity. We illustrate this approach with the analysis of an empirical dataset including newly optimized microsatellite sets for 3 Iberian amphibian species: Hyla molleri, Epidalea calamita, and Pelophylax perezi. We studied 17-21 populations per species (total n = 547, 652, and 516 individuals, respectively), including a reference locality in which the effect of sample size was explored using larger samples (77-96 individuals). As expected, FIS and tests for Hardy-Weinberg equilibrium and linkage disequilibrium were affected by the presence of full sibs, and most initially inferred disequilibria were no longer statistically significant when full siblings were removed from the sample. We estimated that to obtain reliable estimates, the minimum sample size (potentially including full sibs) was close to 20 for expected heterozygosity, and between 50 and 80 for allelic richness. Our pilot study based on a reference population provided a rigorous assessment of marker properties and the effects of sample size and presence of full sibs in the sample. These examples illustrate the advantages of this approach to produce robust and reliable results for downstream analyses.
Acknowledging a Dual Heritage for Qualitative Evidence Synthesis: Harnessing the Qualitative Research and Systematic Review Research Traditions

Qualitative evidence synthesis, an umbrella term that includes all forms of secondary qualitative synthesis and analysis including qualitative systematic review, has emerged from the confluence of conventional systematic review methods with methods for primary qualitative research. With such a mixed heritage, and the juxtaposition of quite different epistemological positions, it is inevitable that the resultant tensions have generated considerable creative energy and significant methodological frictions. These tensions have created an environment within which I have sought to make a contribution. Working with colleagues within the School of Health and Related Research (ScHARR), University of Sheffield, and collaborators at other institutions, including fellow co-convenors of the Cochrane Collaboration Qualitative Methods Group, I have examined the state of qualitative synthesis methods (Paper M1). I have traced and examined the respective contributions of the two components of the mixed heritage through five methodological papers that examine the stages of the systematic review process; searching (Paper M2), quality assessment (Paper M3), framework and thematic synthesis (Paper M4) and exploring heterogeneity (Paper M5) through to consideration of reporting standards (Papers M1-M3). This Thesis explores these issues through five case studies (Case Studies 1-5) to which I have contributed as lead methodologist. While, initially at least, the legacy of conventional systematic review methods could be seen to enjoy dominance, an emerging imperative to review systematically different types of evidence to explore different review questions, coupled with reduced time and resource envelopes within which to address time-critical questions from policy and practice, has opened up a more versatile and pragmatic toolkit. The Thesis concludes by identifying key methodological issues that require further investigation. I contend that many outstanding methodological challenges may derive their most productive insights from a more detailed consideration of corresponding solutions from primary qualitative research. The five papers in this body of work, therefore, make an original contribution to knowledge by establishing and demonstrating methodological principles by which flexible and context sensitive application of the versatile systematic review model can be used to meet the pragmatic demands of health services research and technology assessment.
Transcutaneous electrical nerve stimulation (TENS) versus placebo for chronic low-back pain.

BACKGROUND Transcutaneous electrical nerve stimulation (TENS) was introduced more than 30 years ago as a therapeutic adjunct to the pharmacological management of pain. However, despite widespread use, its effectiveness in chronic low-back pain (LBP) is still controversial. OBJECTIVES To determine whether TENS is more effective than placebo for the management of chronic LBP. SEARCH STRATEGY The Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, PEDro and CINAHL were searched up to July 19, 2007. SELECTION CRITERIA Only randomized controlled clinical trials (RCTs) comparing TENS to placebo in patients with chronic LBP were included. DATA COLLECTION AND ANALYSIS Two review authors independently selected the trials, assessed their methodological quality and extracted relevant data. If quantitative meta-analysis was not possible, a qualitative synthesis was performed, taking into consideration 5 levels of evidence as recommended by the Cochrane Collaboration Back Review Group. MAIN RESULTS Four high-quality RCTs (585 patients) met the selection criteria. Clinical heterogeneity prevented the use of meta-analysis. Therefore, a qualitative synthesis was completed. There was conflicting evidence about whether TENS was beneficial in reducing back pain intensity and consistent evidence in two trials (410 patients) that it did not improve back-specific functional status. There was moderate evidence that work status and the use of medical services did not change with treatment. Conflicting results were obtained from two studies regarding generic health status, with one study showing no improvement on the modified Sickness Impact Profile and another study showing significant improvements on several, but not all subsections of the SF-36 questionnaire. Multiple physical outcome measures lacked statistically significant improvement relative to placebo. In general, patients treated with acupuncture-like TENS responded similarly to those treated with conventional TENS. However, in two of the trials, an inadequate stimulation intensity was used for acupuncture-like TENS, given that muscle twitching was not induced. Optimal treatment schedules could not be reliably determined based on the available data. Adverse effects included minor skin irritation at the site of electrode placement. AUTHORS' CONCLUSIONS At this time, the evidence from the small number of placebo-controlled trials does not support the use of TENS in the routine management of chronic LBP. Further research is encouraged.
Probiotics for treating acute infectious diarrhoea

ABSTRACT BACKGROUND: Probiotics may offer a safe intervention in acute infectious diarrhoea to reduce the duration and severity of the illness. OBJECTIVES: To assess the effects of probiotics in proven or presumed acute infectious diarrhoea. SEARCH STRATEGY: We searched the Cochrane Infectious Diseases Group's trials register (July 2010), the Cochrane Controlled Trials Register (The Cochrane Library Issue 2, 2010), MEDLINE (1966 to July 2010), EMBASE (1988 to July 2010), and reference lists from studies and reviews. We also contacted organizations and individuals working in the field, and pharmaceutical companies manufacturing probiotic agents. SELECTION CRITERIA: Randomized and quasi-randomized controlled trials comparing a specified probiotic agent with a placebo or no probiotic in people with acute diarrhoea that is proven or presumed to be caused by an infectious agent. DATA COLLECTION AND ANALYSIS: Two reviewers independently assessed the methodological quality of the trial and extracted data. Primary outcomes were the mean duration of diarrhoea, stool frequency on day 2 after intervention and ongoing diarrhoea on day 4. A random-effects model was used. MAIN RESULTS: Sixty-three studies met the inclusion criteria with a total of 8014 participants. Of these, 56 trials recruited infants and young children. The trials varied in the definition used for acute diarrhoea and the end of the diarrhoeal illness, as well as in the risk of bias. The trials were undertaken in a wide range of different settings and also varied greatly in organisms tested, dosage, and participants’ characteristics. No adverse events were attributed to the probiotic intervention. Probiotics reduced the duration of diarrhoea, although the size of the effect varied considerably between studies. The average of the effect was significant for mean duration of diarrhoea (mean difference 24.76 hours; 95% confidence interval 15.9 to 33.6 hours; n = 4555, trials = 35) diarrhoea lasting ≥ 4 days (risk ratio 0.41; 0.32 to 0.53; n = 2853, trials = 29) and stool frequency on day 2 (mean difference 0.80; 0.45 to 1.14; n = 2751, trials = 20). The differences in effect size between studies was not explained by study quality, probiotic strain, the number of different strains, the viability of the organisms, dosage of organisms, the causes of diarrhoea, or the severity of the diarrhoea, or whether the studies were done in developed or developing countries. AUTHORS’ CONCLUSIONS: Used alongside rehydration therapy, probiotics appear to be safe and have clear beneficial effects in shortening the duration and reducing stool frequency in acute infectious diarrhoea. However, more research is needed to guide the use of particular probiotic regimens in specific patient groups.
Migraine genetics and prospects for pharmacotherapy

Migraine is a common complex neurological disorder with a well‐known but poorly characterized genetic liability. The search for migraine susceptibility genes has been the focus of intense research. It is now believed that common migraine is not a single gene disorder, but attributable to several potentially interacting genetic variants. These variants may differ in each sufferer and interact with environmental factors to set the individual migraine threshold. This genetic liability may play an important role in the clinical heterogeneity seen in migraine and also in the variability of treatment response. This review will look at genetic loci implicated in migraine to date and consider their current or prospective role in migraine therapy. To elucidate the complex nature of migraine genetic liability, approaches that consider detailed endophenotypic profiles that encompass treatment response may provide much more relevant information than simple end diagnosis. Drug Dev Res 68:282–293, 2007. © 2007 Wiley‐Liss, Inc.
The Comparison of Four Types of Everyday Interdependencies

Actor behavior is compared theoretically and experimentally in four well-known everyday interdependence situations; (i) the market, (ii) the tragedy of the commons or resource dilemma, (iii) the public good problem, and (iv) the household. It is shown that the four situations can be studied within one general framework of exchange networks with externalities. Core theory is generalized to exchange networks with externalities and applied to derive predictions concerning differences in behavior in the four situations. The experiments corroborate the prediction that competition is most fierce in the resource dilemma, fierce in the market, and absent in the public good problem and household.
Vaginal prostaglandin (PGE2 and PGF2a) for induction of labour at term.

BACKGROUND Prostaglandins have been used for induction of labour since the 1960s. Initial work focused on prostaglandin F2a as prostaglandin E2 was considered unsuitable for a number of reasons. With the development of alternative routes of administration, comparisons were made between various formulations of vaginal prostaglandins. OBJECTIVES To determine the effects of vaginal prostaglandins E2 and F2a for third trimester cervical ripening or induction of labour in comparison with placebo/no treatment or other vaginal prostaglandins (except misoprostol). SEARCH STRATEGY We searched the Cochrane Pregnancy and Childbirth Group's Trials Register (May 2009) and bibliographies of relevant papers. SELECTION CRITERIA Clinical trials comparing vaginal prostaglandins used for third trimester cervical ripening or labour induction with placebo/no treatment or other methods listed above it on a predefined list of labour induction methods. DATA COLLECTION AND ANALYSIS We assessed studies and extracted data independently. MAIN RESULTS Sixty-three (10,441 women) have been included.Vaginal prostaglandin E2 compared with placebo or no treatment reduced the likelihood of vaginal delivery not being achieved within 24 hours (18.1% versus 98.9%, risk ratio (RR) 0.19, 95% confidence interval (CI) 0.14 to 0.25, two trials, 384 women). The risk of the cervix remaining unfavourable or unchanged was reduced (21.6% versus 40.3%, RR 0.46, 95% CI 0.35 to 0.62, five trials, 467 women); and the risk of oxytocin augmentation reduced (35.1% versus 43.8%, RR 0.83, 95% CI 0.73 to 0.94, 12 trials, 1321 women) when PGE2 was compared to placebo. There was no evidence of a difference between caesarean section rates, although the risk of uterine hyperstimulation with fetal heart rate changes was increased (4.4% versus 0.49%, RR 4.14, 95% CI 1.93 to 8.90, 14 trials, 1259 women). PGE2 tablet, gel and pessary appear to be as efficacious as each other and the use of sustained release PGE2 inserts appear to be associated with a reduction in instrumental vaginal delivery rates (9.9 % versus 19.5%, RR 0.51, 95% CI 0.35 to 0.76, NNT 10 (6.7 to 24.0), five trials, 661 women) when compared to vaginal PGE2 gel or tablet. AUTHORS' CONCLUSIONS PGE2 increases successful vaginal delivery rates in 24 hours and cervical favourability with no increase in operative delivery rates. Sustained release vaginal PGE2 is superior to vaginal PGE2 gel with respect to some outcomes studied.Further research is needed to assess the best vehicle for delivering vaginal prostaglandins and this should, where possible, include some examination of the cost-analysis.
Secretory carcinoma of the breast and its histopathological mimics: value of markers for differential diagnosis

Secretory carcinoma (SC) is a rare histological type of breast cancer, and ETV6–NTRK3 gene fusion is highly specific to it. The differential diagnoses of SC include acinic cell carcinoma (ACCA) and cystic hypersecretory carcinoma (CHC), as well as invasive ductal carcinoma (IDC). For patients with these rare but distinctive histological subtypes, SC and its histopathological mimics should be differentiated from each other. However, differential markers have not yet been assessed systematically, and we aimed to identify and evaluate novel and existing markers.
1551The Patient-Centered Medical Home: A Reality for HIV Care in Nigeria

Objective: HIV care delivery in resource-limited settings (RLS) may serve as a paradigm for chronic disease care, but comprehensive measurement frameworks are lacking. Our objective was to adapt the patient-centered medical home (PCMH) framework for use in RLS, and evaluate the performance of HIV treatment programs within this framework. Design and setting: Cross-sectional survey administered within the AIDS Prevention Initiative in Nigeria (APIN) network. Participants: Medical directors at APIN clinics. Main outcome measures: We adapted the 2011 US National Committee on Quality Assurance’s PCMH standard to develop a survey measuring five domains of HIV care: (i) enhancing access and continuity, (ii) identifying and managing patient populations, (iii) planning and managing care, (iv) promoting self-care and support and (v) measuring and improving performance. Results: Thirty-three of 36 clinics completed the survey. Most were public (73%) and urban/semi-urban (64%); 52% had >500 patients in care. On a 0–100 scale, clinics scored highest in self-care and support, 91% (63–100%); managing patient populations, 80% (72–81%) and improving performance, 72% (44–78%). Clinics scored lowest with the most variability in planning/managing care, 65% (22–89%), and access and continuity, 61% (33–80%). Average score across all domains was 72% (58–81%). Conclusions: Our findings suggest that the modified PCMH tool is feasible, and likely has sufficient performance variation to discriminate among clinics. Consistent with extant literature, clinics showed greatest room for improvement on access and continuity, supporting the tool’s face validity. The modified PCMH tool may provide a powerful framework for evaluating chronic HIV care in RLS.
An evaluation of antibiotic prescribing patterns in adult intensive care units in a private hospital in KwaZulu-Natal

The emergence of resistant microorganisms and its association with antimicrobial use is widely recognised as a global concern. Therefore, rational and regulated antimicrobial use is essential in both the public and private healthcare sectors in South Africa. A retrospective chart review was conducted of patients who were prescribed antibiotics over a two-month period. Prescriptions were assessed for adherence to the guidelines, either local or international, and/or to drug registration information, as a measure of rational prescribing practice. Accuracy of dose, and the frequency and duration of administration were evaluated, as were microbiologically informed treatment and de-escalation. 28.8% of patients (n = 226) received antibiotics during their intensive care unit (ICU) admission. A clear indication for antibiotic therapy was noted in 58.5% (n = 131) of the patients, of whom 70.2% were prescribed treatment consistent with the guidelines or drug registration information. Doses were deemed to be correct for 91.1% of the sample, microbiological investigations were evident for 61.2% of patients and de-escalation was noted in only 13.1% of the 70.8% of cases where de-escalation was indicated. Antibiotic prescription rates were relatively lower than those described in the international literature on antibiotic use in the ICU. Antibiotic prescription in the absence of indication in 41.1% of patients, the lack of microbiological verification in 38.8% of patients, inaccurate drug choice in 29.8% of the subset for whom antibiotics were indicated and incorrect dosing in 8.9% of the subset necessitates microbiologically informed therapy and compliance with the treatment guidelines.
Introduction to Occupational Therapy

Section 1: Occupational Therapy: The Profession 1. Introductory Questions 2. Looking Back: A History of Occupational Therapy 3. Philosophical Principles and Values in Occupational Therapy 4. Current Issues and Emerging Practice Areas Section 2: Occupational Therapy: The Practitioner 5. From Student to Practitioner: Educational Preparation and Certification 6. Professional Organizations 7. The Occupational Therapy Practitioner: Roles, Responsibilities, and Relationships 8. Practicing Legally and Ethically Section 3: The Practice of Occupational Therapy 9. Occupational Therapy Practice Framework: Domain and Process 10. Occupational Therapy Across the Lifespan 11. Treatment Settings and Areas of Practice 12. Occupational Therapy Process: Evaluation, Intervention, and Outcomes 13. Service Management Functions 14. Models of Practice and Frames of Reference 15. Intervention Modalities 16. Therapeutic Relationships 17. Clinical Reasoning Appendices
Progesterone for premenstrual syndrome.

BACKGROUND About 5% of women experience severe symptoms called premenstrual syndrome (PMS), only in the two weeks before their menstrual periods. Treatment with progesterone may restore a deficiency, balance menstrual hormone levels or reduce effects of falling progesterone levels on the brain or on electrolytes in the blood. OBJECTIVES The objectives were to determine if progesterone has been found to be an effective treatment for all or some premenstrual symptoms and if adverse events associated with this treatment have been reported. SEARCH STRATEGY We searched the Cochrane Menstrual Disorders and Subfertility Group's Trials Register, the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library, Issue 1, 2005), MEDLINE (1966 to 2005) and EMBASE (1980 to 2005) in March 2005, and PsycINFO (1806 to 2006) in April 2006. We contacted pharmaceutical companies for information about unpublished trials.The Trials Search Co-ordinator searched MEDLINE, EMBASE and PsycLIT on October 16 2000. MEDLINE and EMBASE were searched again on March 1 2005 and all again on March 3 2008. CINAHL was searched on March 3 2008. The search strings are in Appendix 2. SELECTION CRITERIA We included randomised double-blind, placebo-controlled trials of progesterone on women with PMS diagnosed by at least two prospective cycles, without current psychiatric disorder. DATA COLLECTION AND ANALYSIS Two reviewers (BM and OF) extracted data independently and decided which trials to include. OF wrote to trial investigators for missing data. MAIN RESULTS From 17 studies, only two met our inclusion criteria. Together they had 280 participants aged between 18 and 45 years. One hundred and fifteen yielded analysable results. Both studies measured symptom severity using subjective scales. Differing in design, participants, dose of progesterone and how delivered, the studies could not be combined in meta-analysis.Adverse events which may or may not have been side effects of the treatment were described as mild.Both trials had defects. They intended to exclude women whose symptoms continued after their periods. When data from ineligible women were excluded from analysis in one trial, the other women were found to have benefited more from progesterone than placebo. The smaller study found no statistically significant difference between oral progesterone, vaginally absorbed progesterone and placebo, but reported outcomes incompletely. AUTHORS' CONCLUSIONS The trials did not show that progesterone is an effective treatment for PMS nor that it is not. Neither trial distinguished a subgroup of women who benefited, nor examined claimed success with high doses.