Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of allelic heterogeneity on the power of the transmission disequilibrium test

Due in part to an influential paper by Risch and Merikangas [(1996) Science 273:1516–1517], which suggested that disequilibrium tests would have greater power to detect genes of small effect than would linkage tests, interest in the use of the Transmission Disequilibrium Test (TDT) as an analysis tool for genomewide studies is steadily growing. However, the paper by Risch and Merikangas made several simplifying assumptions. One such assumption was that the underlying gene showed allelic homogeneity, and another was that the allele being measured was the actual susceptibility allele. Here we investigate the effect of allelic heterogeneity on the power of the TDT using multiplicative, additive, dominant, and recessive modes of inheritances in the context of a genomewide study. We further distinguish two cases: first, that the marker alleles are the actual susceptibility alleles, and second, that alleles are measured at a marker linked to the disease gene with zero recombination. We consider two family structures, either a single affected offspring (SAO) and two parents, or an affected sib‐pair (ASP) and two parents. We find that, as expected, the power of the TDT declines as the number of susceptibility alleles at the locus being tested increases and the effect on power can be substantial. When a linked marker is measured rather than a susceptibility allele itself, sample sizes reach unattainable levels when as few as two susceptibility alleles are present. Across all the models we consider, the required number of families for a TDT with ASP sampling varies from 19 to over a million families. Thus, the TDT may not be an optimal test in the context of genomic screens under more biologically realistic assumptions. Genet. Epidemiol. 18:143–156, 2000. © 2000 Wiley‐Liss, Inc.
On the Differential Privacy of Bayesian Inference

We study how to communicate findings of Bayesian inference to third parties, while preserving the strong guarantee of differential privacy. Our main contributions are four different algorithms for private Bayesian inference on probabilistic graphical models. These include two mechanisms for adding noise to the Bayesian updates, either directly to the posterior parameters, or to their Fourier transform so as to preserve update consistency. We also utilise a recently introduced posterior sampling mechanism, for which we prove bounds for the specific but general case of discrete Bayesian networks; and we introduce a maximum-a-posteriori private mechanism. Our analysis includes utility and privacy bounds, with a novel focus on the influence of graph structure on privacy. Worked examples and experiments with Bayesian naive Bayes and Bayesian linear regression illustrate the application of our mechanisms.
The Effect of Using Scientific Stories on Teaching Science and on the Academic Achievement of the Students

Bugunlerde cogu arastirmaci ogrencilerin ogrenmelerinden sorumlu olan sinif ortami uzerinde durmaktadir. Cagdas egitimin en onemli konusu ogrenme ortamini istenilen duzeye cikarmaktir. Bu baglamda bu calismanin da ana konusu bilimsel hikayelerle yapilan bir egitim yonteminin ogrencilerin akademik basarilarina etkisini incelemektir. Bu amacla calisma da on test-son test gruplu yari deneysel desen kullanilmistir. Calisma 7. Sinif ogrencilerinden rastgele belirlenmis bir deney ve bir kontrol grubu uzerinde gerceklestirilmistir. Veri toplama araclari olarak kisa cevap gerektiren 24 soruluk basari testi ve katilimcilarin arastirma sureci boyunca goruslerini kaydettikleri jurnaller kullanilmistir. Elde edilen bulgular daha sonra dokuman ve icerik analizi kullanilarak incelenmistir. Calismada elde edilen bulgulardan bilimsel hikayelerin kullanildigi deney grubundaki ogrencilerin lehine olmak uzere, akademik basarilarinin kontrol grubundaki ogrencilere gore istatistiksel olarak anlamli bir farklilik gosterdigi sonucuna ulasilmistir
Living in nonbreeding groups: an alternative strategy for maturing gorillas

The one‐male reproductive strategy implies that maturing males are temporarily excluded from reproduction. In gorillas, these excluded males live either solitarily or in nonbreeding groups (NBGs) that are devoid of adult females. The dynamics of NBGs are not well known. In this study, which was conducted on a gorilla population (Gorilla gorilla gorilla) of 377 individuals that visited the Lokoué clearing in the Republic of Congo, we detail how the NBGs formed, and analyze their dynamics according to age‐sex classes, the relatedness of members, and the origin and destination of transferring individuals. We discuss the potential benefits gained by individuals living in these groups. The NBGs included mainly immature males, most of which appeared to have migrated voluntarily from their natal groups. Some individuals (including juvenile females) came from disbanded breeding groups (BGs). Migrants preferentially joined NBGs that included a silverback male. Their dispersal patterns were not determined by their degree of relatedness, but they tended to associate with related silverbacks. In this way, the migrants could enhance their protection against predators and gain experience with different environmental conditions. By tolerating and protecting offspring, aging silverbacks could enhance their inclusive fitness. Finally, young and healthy silverbacks could increase their likelihood of forming a future BG when unrelated females joined them. Am. J. Primatol. 68:275–291, 2006. © 2006 Wiley‐Liss, Inc.
The Role of Mechanical Force and ROS in Integrin-Dependent Signals

Cells are exposed to several types of integrin stimuli, which generate responses generally referred to as “integrin signals”, but the specific responses to different integrin stimuli are poorly defined. In this study, signals induced by integrin ligation during cell attachment, mechanical force from intracellular contraction, or cell stretching by external force were compared. The elevated phosphorylation levels of several proteins during the early phase of cell attachment and spreading of fibroblast cell lines were not affected by inhibition of ROCK and myosin II activity, i.e. the reactions occurred independently of intracellular contractile force acting on the adhesion sites. The contraction-independent phosphorylation sites included ERK1/2 T202/Y204, AKT S473, p130CAS Y410, and cofilin S3. In contrast to cell attachment, cyclic stretching of the adherent cells induced a robust phosphorylation only of ERK1/2 and the phosphorylation levels of the other investigated proteins were not or only moderately affected by stretching. No major differences between signaling via α5β1 or αvβ3 integrins were detected. The importance of mitochondrial ROS for the integrin-induced signaling pathways was investigated using rotenone, a specific inhibitor of complex I in the respiratory chain. While rotenone only moderately reduced ATP levels and hardly affected the signals induced by cyclic cell stretching, it abolished the activation of AKT and reduced the actin polymerization rate in response to attachment in both cell lines. In contrast, scavenging of extracellular ROS with catalase or the vitamin C analog Asc-2P did not significantly influence the attachment-derived signaling, but caused a selective and pronounced enhancement of ERK1/2 phosphorylation in response to stretching. In conclusion, the results showed that “integrin signals” are composed of separate sets of reactions triggered by different types of integrin stimulation. Mitochondrial ROS and extracellular ROS had specific and distinct effects on the integrin signals induced by cell attachment and mechanical stretching.
Teacher Candidates with Learning Disabilities: Effective and Ethical Accommodations

The number of teacher candidates with learning disabilities (LD) has grown over the past several years. Teacher education programs are accountable to produce quality teachers while providing reasonable accommodations that facilitate completion of a degree program. This study investigated accommodations provided to teacher candidates with LD in teacher education programs. Accommodations at the knowledge level were considered acceptable, while accommodations in field experiences were less common and more likely to raise ethical concerns. For some accommodations, a wide disparity of opinions was evident, indicating poor consistency across teacher education programs. Findings indicated that programs were willing to provide accommodations that maintain the standards of the program and require candidates to demonstrate competence in essential skills of being a teacher.
Pruning phantom detections from multiview foreground intersection

Homography mapping and fusion of foreground regions from multiple camera views is an effective technique for moving object detection. However, the intersections of non-corresponding foreground regions frequently cause phantom detections. In this paper, an algorithm using colour template matching is proposed to identify such phantoms from the multiview foreground intersection. Experiments on real-world video sequences have been carried out.
Object marking in isiZulu

Abstract I examine object marking in the Nguni language isiZulu, focusing specifically on those properties that are subject to micro-parametric variation within the Bantu family. This includes the occurrence of object markers in object relative clauses and in double object constructions, and the correlation between object marking and dislocation. I also address the extent to which my findings support either a pronoun- or an object agreement-analysis of object markers. My results provide support for the idea that object markers in isiZulu are in the process of changing from pronominal clitics into agreement markers.
Delayed antibiotic prescribing and associated antibiotic consumption in adults with acute cough.

BACKGROUND Delayed antibiotic prescribing is promoted as a strategy to reduce antibiotic consumption, but its use and its effect on antibiotic consumption in routine care is poorly described. AIM To quantify delayed antibiotic prescribing in adults presenting in primary care with acute cough/lower respiratory tract infection (LRTI), duration of advised delay, consumption of delayed antibiotics, and factors associated with consumption. DESIGN AND SETTING Prospective observational cohort in general practices in 14 primary care networks in 13 European countries. METHOD GPs recorded clinical features and antibiotic prescribing for adults presenting with an acute infective illness with cough as the dominant symptom. Patients recorded their consumption of antibiotics from any source during the 28-day follow up. RESULTS Two hundred and ten (6.3%) of 3368 patients with usable consultation data were prescribed delayed antibiotics. The median recommended delay period was 3 days. Seventy-five (44.4%) of the 169 with consumption data consumed the antibiotic course and a further 18 (10.7%) took another antibiotic during the study period. 50 (29.6%) started their delayed course on the day of prescription. Clinician diagnosis of upper respiratory tract/viral infection and clinician's perception of patient's wanting antibiotics were associated with less consumption of the delayed prescription. Patient's wanting antibiotics was associated with greater consumption. CONCLUSION Delayed antibiotic prescribing was used infrequently for adults presenting in general practice with acute cough/LRTI. When used, the effect on antibiotic consumption was less than found in most trials. There are opportunities for standardising the intervention and promoting wider uptake.
Impact of vitamin E on plasma asymmetric dimethylarginine (ADMA) in chronic kidney disease (CKD): a pilot study.

BACKGROUND Asymmetric dimethylarginine (ADMA), an endogenous inhibitor of endothelial nitric oxide synthase and a proposed cardiovascular risk factor, is elevated in chronic kidney disease (CKD). Pharmacological strategies that lower plasma concentration of ADMA may be expected to increase nitric oxide (NO.) bioavailability and potentially limit atherosclerosis. We hypothesized that the antioxidant alpha-tocopherol (vitamin E) reduces ADMA levels in CKD. METHODS An open-label pilot interventional study using 800 IU of vitamin E was undertaken in eight stable out-patients with non-diabetic CKD (creatinine clearance <30 ml/min/1.73 m(2)) and six healthy controls, with the objective of measuring plasma ADMA levels at baseline and after 8 weeks of treatment. Plasma ADMA, symmetric dimethylarginine (SDMA) and alpha-tocopherol concentrations were determined at study entry and exit using high-performance liquid chromatography, while plasma total F2-isoprostanes, an index of oxidative stress, were measured using a commercially available enzyme-linked immunosorbent assay kit. RESULTS ADMA and SDMA concentrations were significantly higher in the plasma of patients compared with that of controls (P </= 0.001). After treatment with vitamin E, ADMA decreased by 23% in six of eight patients (P <0.001). The remaining two patients showed either an increase or no change (overall, P = 0.16). There was no significant change in plasma F2-isoprostanes with vitamin E treatment for 8 weeks. CONCLUSIONS Antioxidant therapy with vitamin E has the potential to lower ADMA levels in CKD patients, implying increased NO. availability. This strategy merits further exploration in the setting of CKD prior to renal replacement.
A STUDY OF THE PEDAGOGICAL STRATEGIES USED IN SUPPORT OF STUDENTS WITH LEARNING DISABILITIES AND ATTITUDES HELD BY ENGINEERING FACULTY

This study used an anonymous online survey instrument to explore the educational preparation as well as the pedagogical and assessment methods used in support of students with learning disabilities (LD) by engineering faculty members from undergraduate engineering programs of four southern California educational institutions. This work also sought to determine whether engineering faculty members utilized pedagogy that encouraged student development of metacognitive skills. Further, engineering faculty attitudes toward students with LD and faculty willingness to provide accommodations for students with LD were examined through the survey instrument. Although participant responses (n=30) offered evidence of positive attitudes and willingness to support students with LD, results indicated that more faculty development regarding the needs of students with LD and of alternative pedagogical and assessment methods was warranted for college-level engineering faculty.
Ethane-beta-Sultam Modifies the Activation of the Innate Immune System Induced by Intermittent Ethanol Administration in Female Adolescent Rats

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Psychopathy and recidivism: A review

Psychopathy is defined by a constellation of interpersonal, affective and behavioural characteristics that should, in principle, be strongly related to risk for recidivism and violence. We reviewed the literature on The Hare Psychopathy Checklist-Revised scales (PCL-R; Hare, 1980, 1991) and recidivism. We found that the PCL-R consistently was an important predictor across inmate samples and was consistently among the best predictors of recidivism. Average correlations between the PCL-R and recidivism, weighted by their degrees of freedom, were . 27 for general recidivism, . 27 for violent recidivism, and . 23 for sexual recidivism. Relative risk statistics at one year indicated that psychopaths were approximately three times more likely to recidivate—or four times more likely to violently recidivate—than were non-psychopaths. The correlation between general recidivism and PCL-R Factor 2 (a measure of the social deviance facet of psychopathy) was stronger than the correlation between general recidivism and PCL-R Factor 1 (a measure of the interpersonal/affective facet of psychopathy). Both PCL-R factors contributed equally to the prediction of violent recidivism. The PCL-R routinely made a significant contribution towards predicting recidivism beyond that made by key demographic variables, criminal history, and personality disorder diagnoses. Across studies, PCL-R scores were as strongly associated with general recidivism, and were more strongly associated with violent recidivism, than were actuarial risk scales designed specifically to predict reoffending. Taken together, these findings indicate that the PCL-R should be considered a primary instrument for guiding clinical assessments of risk for criminal recidivism and dangerousness.
Human Immunodeficiency Virus and Leishmaniasis

The Leishmaniases are a group of diseases transmitted to humans by the bite of a sandfly, caused by protozoan parasites of the genus Leishmania. Various Leishmania species infect humans, producing a spectrum of clinical manifestations. It is estimated that 350 million people are at risk, with a global yearly incidence of 1-1.5 million for cutaneous and 500,000 for visceral Leishmaniasis (VL). VL is a major cause of morbidity and mortality in East Africa, Brazil and the Indian subcontinent. Co-infection with human immunodeficiency virus (HIV) alters the immune response to the disease. Here we review the immune response to Leishmania in the setting of HIV co-infection. Improved understanding of the immunology involved in co-infections may help in designing prophylactic and therapeutic strategies against Leishmaniasis.
Remove or Reform? a Case for (Restructuring) Chiefdom Governance in Post-Conflict Sierra Leone

Recent analyses of Sierra Leone's eleven-year civil war have argued that the conflict was fuelled by a crisis within chiefdom authority, with emphasis on increasing tensions between rural youth and their elders. However, a counter-argument has also emerged, emphasising that customary authority is still highly regarded in post-conflict Sierra Leone and that chiefs act as an influential barrier against bureaucratic abuses of power. This article draws on fieldwork from three districts in Sierra Leone to argue that chiefdom authority indeed continues to have considerable support. In particular, section chiefs and headmen are seen as being particularly important for settling small disputes, especially in the rural areas where contact between villagers and chiefs is most apparent.
Rumor Cascades

Online social networks provide a rich substrate for rumor propagation. Information received via friends tends to be trusted, and online social networks allow individuals to transmit information to many friends at once. By referencing known rumors from Snopes.com, a popular website documenting memes and urban legends, we track the propagation of thousands of rumors appearing on Facebook. From this sample we infer the rates at which rumors from different categories and of varying truth value are uploaded and reshared. We find that rumor cascades run deeper in the social network than reshare cascades in general. We then examine the effect of individual reshares receiving a comment containing a link to a Snopes article on the evolution of the cascade. We find that receiving such a comment increases the likelihood that a reshare of a rumor will be deleted. Furthermore, large cascades are able to accumulate hundreds of Snopes comments while continuing to propagate. Finally, using a dataset of rumors copied and pasted from one status update to another, we show that rumors change over time and that different variants tend to dominate different bursts in popularity.
Detectability Counts when Assessing Populations for Biodiversity Targets

Efficient, practical and accurate estimates of population parameters are a necessary basis for effective conservation action to meet biodiversity targets. The brown hare is representative of many European farmland species: historically widespread and abundant but having undergone rapid declines as a result of agricultural intensification. As a priority species in the UK Biodiversity Action Plan, it has national targets for population increase that are part of wider national environmental indicators. Previous research has indicated that brown hare declines have been greatest in pastural landscapes and that gains might be made by focussing conservation effort there. We therefore used hares in pastural landscapes to examine how basic changes in survey methodology can affect the precision of population density estimates and related these to national targets for biodiversity conservation in the UK. Line transects for hares carried out at night resulted in higher numbers of detections, had better-fitting detection functions and provided more robust density estimates with lower effort than those during the day, due primarily to the increased probability of detection of hares at night and the nature of hare responses to the observer. Hare spring densities varied widely within a single region, with a pooled mean of 20.6 hares km−2, significantly higher than the reported national average of hares in pastures of 3.3 hares km−2. The high number of encounters allowed us to resolve hare densities at site, season and year scales. We demonstrate how survey conduct can impact on data quantity and quality with implications for setting and monitoring biodiversity targets. Our case study of the brown hare provides evidence that for wildlife species with low detectability, large scale volunteer-based monitoring programmes, either species specific or generalist, might be more successfully and efficiently carried out by a small number of trained personnel able to employ methods that maximise detectability.
Finding the target sites of RNA-binding proteins

RNA–protein interactions differ from DNA–protein interactions because of the central role of RNA secondary structure. Some RNA‐binding domains (RBDs) recognize their target sites mainly by their shape and geometry and others are sequence‐specific but are sensitive to secondary structure context. A number of small‐ and large‐scale experimental approaches have been developed to measure RNAs associated in vitro and in vivo with RNA‐binding proteins (RBPs). Generalizing outside of the experimental conditions tested by these assays requires computational motif finding. Often RBP motif finding is done by adapting DNA motif finding methods; but modeling secondary structure context leads to better recovery of RBP‐binding preferences. Genome‐wide assessment of mRNA secondary structure has recently become possible, but these data must be combined with computational predictions of secondary structure before they add value in predicting in vivo binding. There are two main approaches to incorporating structural information into motif models: supplementing primary sequence motif models with preferred secondary structure contexts (e.g., MEMERIS and RNAcontext) and directly modeling secondary structure recognized by the RBP using stochastic context‐free grammars (e.g., CMfinder and RNApromo). The former better reconstruct known binding preferences for sequence‐specific RBPs but are not suitable for modeling RBPs that recognize shape and geometry of RNAs. Future work in RBP motif finding should incorporate interactions between multiple RBDs and multiple RBPs in binding to RNA. WIREs RNA 2014, 5:111–130. doi: 10.1002/wrna.1201