Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection and Genetic Characterization of Enteroviruses Circulating among Wild Populations of Chimpanzees in Cameroon: Relationship with Human and Simian Enteroviruses

ABSTRACT Enteroviruses (EVs), members of the family Picornaviridae, are a genetically and antigenically diverse range of viruses causing acute infections in humans and several Old World monkey (OWM) species. Despite their known wide distribution in primates, nothing is currently known about the occurrence, frequency, and genetic diversity of enteroviruses infecting apes. To investigate this, 27 chimpanzee and 27 gorilla fecal samples collected from undisturbed jungle areas with minimal human contact in Cameroon were screened for EVs. Four chimpanzee samples were positive, but none of the gorilla samples were positive. Genetic characterization of the VP1, VP4, and partial VP2 genes, the 5′ untranslated region, and partial 3Dpol sequences enabled chimpanzee-derived EVs to be identified as (i) the species A type, EV76, (ii) a new species D type assigned as EV111, along with a human isolate from the Democratic Republic of Congo previously described by the International Committee on the Taxonomy of Viruses, and (iii) a new species B type (assigned as EV110) most closely related to, although a distinct type from, the SA5 isolate recovered from a vervet monkey. The identification of EVs infecting chimpanzees related to those circulating in human and OWM populations provides evidence for cross-species transmission of EVs between primates. However, the direction of transfer and the existence of primate sources of zoonotic enterovirus infections in humans require further investigation of population exposure and more extensive characterization of EVs circulating in wild ape populations.
Subgenotypes of hepatitis B virus genotype D (D1, D2, D3 and D5) in India: differential pattern of mutations, liver injury and occult HBV infection

Summary. Hepatitis B genotype D (HBV/D) is the most widespread genotype and exists as at least five subgenotypes (HBV/D1–D5). However, little is known about the association of virological characteristics with clinical differences among HBV/D subgenotypes. To investigate the virological characteristics of these subgenotypes and their clinical implications, we selected a cohort of 109 genotype D infected individuals from the state of West Bengal, India, including 68 HBsAg positive patients and 41 with occult HBV infection. Among the HBsAg positive subjects 28 had chronic hepatitis B virus infection, 40 were asymptomatic carriers based on clinical examination, liver function test and ultrasonograph results. Overall, HBV/D1 was found in 17%, HBV/D2 in 29%, HBV/D3 in 34% and HBV/D5 in 20% of the cases. HBV/D1 was significantly associated with chronic liver disease (P = 0.01), and in this subgenotype A1896 (PreC mutations) were most common. Although BCP mutations (A/C1753 and T1762/A1764) were found to be frequently associated with HBV/D2 (33% and 33%) and D5 (47% and 59%), no apparent clinical correlation was observed. On the other hand, occult HBV infection was significantly associated with HBV/D3 infection, along with low level of BCP and PreC mutations and several non‐synonymous substitutions in the catalytic reverse transcriptase (RT) domain of polymerase gene. Similar nucleotide substitutions in the surface (S) gene region were observed from both northern and eastern Indian HBV/D3 isolates. In conclusion, HBV/D subgenotypes differ in their mutational patterns in the S, polymerase and the BCP/PreC regions that may influence their clinical outcomes.
Binding of human SLBP on the 3′-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring

In metazoans, cell-cycle-dependent histones are produced from poly(A)-lacking mRNAs. The 3′ end of histone mRNAs is formed by an endonucleolytic cleavage of longer precursors between a conserved stem–loop structure and a purine-rich histone downstream element (HDE). The cleavage requires at least two trans-acting factors: the stem–loop binding protein (SLBP), which binds to the stem–loop and the U7 snRNP, which anchors to histone pre-mRNAs by annealing to the HDE. Using RNA structure-probing techniques, we determined the secondary structure of the 3′-untranslated region (3′-UTR) of mouse histone pre-mRNAs H4–12, H1t and H2a–614. Surprisingly, the HDE is embedded in hairpin structures and is therefore not easily accessible for U7 snRNP anchoring. Probing of the 3′-UTR in complex with SLBP revealed structural rearrangements leading to an overall opening of the structure especially at the level of the HDE. Electrophoretic mobility shift assays demonstrated that the SLBP-induced opening of HDE actually facilitates U7 snRNA anchoring on the histone H4–12 pre-mRNAs 3′ end. These results suggest that initial binding of the SLBP functions in making the HDE more accessible for U7 snRNA anchoring.
Investigation of Adaptive Optics Imaging Biomarkers for Detecting Pathological Changes of the Cone Mosaic in Patients with Type 1 Diabetes Mellitus

Purpose To investigate a set of adaptive optics (AO) imaging biomarkers for the assessment of changes of the cone mosaic spatial arrangement in patients with type 1 diabetes mellitus (DM1). Methods 16 patients with ≥20/20 visual acuity and a diagnosis of DM1 in the past 8 years to 37 years and 20 age-matched healthy volunteers were recruited in this study. Cone density, cone spacing and Voronoi diagrams were calculated on 160x160 μm images of the cone mosaic acquired with an AO flood illumination retinal camera at 1.5 degrees eccentricity from the fovea along all retinal meridians. From the cone spacing measures and Voronoi diagrams, the linear dispersion index (LDi) and the heterogeneity packing index (HPi) were computed respectively. Logistic regression analysis was conducted to discriminate DM1 patients without diabetic retinopathy from controls using the cone metrics as predictors. Results Of the 16 DM1 patients, eight had no signs of diabetic retinopathy (noDR) and eight had mild nonproliferative diabetic retinopathy (NPDR) on fundoscopy. On average, cone density, LDi and HPi values were significantly different (P<0.05) between noDR or NPDR eyes and controls, with these differences increasing with duration of diabetes. However, each cone metric alone was not sufficiently sensitive to discriminate entirely between membership of noDR cases and controls. The complementary use of all the three cone metrics in the logistic regression model gained 100% accuracy to identify noDR cases with respect to controls. Conclusion The present set of AO imaging biomarkers identified reliably abnormalities in the spatial arrangement of the parafoveal cones in DM1 patients, even when no signs of diabetic retinopathy were seen on fundoscopy.
Recovery Guarantee of Non-negative Matrix Factorization via Alternating Updates

Non-negative matrix factorization is a popular tool for decomposing data into feature and weight matrices under non-negativity constraints. It enjoys practical success but is poorly understood theoretically. This paper proposes an algorithm that alternates between decoding the weights and updating the features, and shows that assuming a generative model of the data, it provably recovers the ground-truth under fairly mild conditions. In particular, its only essential requirement on features is linear independence. Furthermore, the algorithm uses ReLU to exploit the non-negativity for decoding the weights, and thus can tolerate adversarial noise that can potentially be as large as the signal, and can tolerate unbiased noise much larger than the signal. The analysis relies on a carefully designed coupling between two potential functions, which we believe is of independent interest.
Genetic variation in APOJ, LPL, and TNFRSF10B affects plasma fatty acid distribution in Alaskan Eskimos.

BACKGROUND Alterations in plasma fatty acid distribution are linked to metabolic abnormalities related to type 2 diabetes and cardiovascular disease. OBJECTIVE The aim of this study was to investigate genetic factors influencing plasma fatty acid distribution in Alaskan Eskimos from the Genetics of Coronary Artery Disease in Alaska Natives (GOCADAN) study. DESIGN Fatty acids in plasma were measured by gas chromatography in 761 related individuals (>35 y of age). RESULTS Quantitative genetic analyses showed that fatty acid distribution is significantly heritable (P < 0.001), with heritabilities ranging from 0.33 to 0.55. A genome-wide scan for plasma fatty acids identified a 20-cM region on chromosome 8 (p12-p21) with a quantitative trait locus for monounsaturated fatty acids (logarithm of odds score = 3.8). The same region had a quantitative trait locus for polyunsaturated fatty acids (logarithm of odds score = 2.6). We genotyped single nucleotide polymorphisms (SNPs) in candidate genes in 8p12-p21 and found a significant association between fatty acids and SNPs in apolipoprotein J (APOJ), lipoprotein lipase (LPL), macrophage scavenger receptor 1 (MSR1), and tumor necrosis factor receptor superfamily member 10b (TNFRSF10B). A Bayesian quantitative trait nucleotide analysis based on a measured genotype model showed that SNPs in LPL, TNFRSF10B, and APOJ had strong statistical evidence of a functional effect (posterior probability > or =75%) on plasma fatty acid distribution. CONCLUSIONS The results indicate that there is strong genetic influence on plasma fatty acid distribution and that genetic variation in APOJ, LPL, and TNFRSF10B may play a role. The GOCADAN study was registered at www.clinicaltrials. gov as NCT00006192.
Influences on Creativity in Technical Communication: Invention, Motivation, and Constraints

ABSTRACT Interviews with 14 technical communicators reveal that skills in rhetorical invention help them creatively address communication problems. They define creativity in relation to four interrelated exigencies of invention: thinking like a user, reinvigorating dry content, inventing visual ideas, and alternating between heuristic and algorithmic processes. They recognize intrinsic factors such as curiosity and sympathy as motivations for their creativity, while being conscious of the external factors (people, money, and time) that may restrain creativity.
Linking the Salt Transcriptome with Physiological Responses of a Salt-Resistant Populus Species as a Strategy to Identify Genes Important for Stress Acclimation1[W][OA]

To investigate early salt acclimation mechanisms in a salt-tolerant poplar species (Populus euphratica), the kinetics of molecular, metabolic, and physiological changes during a 24-h salt exposure were measured. Three distinct phases of salt stress were identified by analyses of the osmotic pressure and the shoot water potential: dehydration, salt accumulation, and osmotic restoration associated with ionic stress. The duration and intensity of these phases differed between leaves and roots. Transcriptome analysis using P. euphratica-specific microarrays revealed clusters of coexpressed genes in these phases, with only 3% overlapping salt-responsive genes in leaves and roots. Acclimation of cellular metabolism to high salt concentrations involved remodeling of amino acid and protein biosynthesis and increased expression of molecular chaperones (dehydrins, osmotin). Leaves suffered initially from dehydration, which resulted in changes in transcript levels of mitochondrial and photosynthetic genes, indicating adjustment of energy metabolism. Initially, decreases in stress-related genes were found, whereas increases occurred only when leaves had restored the osmotic balance by salt accumulation. Comparative in silico analysis of the poplar stress regulon with Arabidopsis (Arabidopsis thaliana) orthologs was used as a strategy to reduce the number of candidate genes for functional analysis. Analysis of Arabidopsis knockout lines identified a lipocalin-like gene (AtTIL) and a gene encoding a protein with previously unknown functions (AtSIS) to play roles in salt tolerance. In conclusion, by dissecting the stress transcriptome of tolerant species, novel genes important for salt endurance can be identified.
Dependence of Halo Properties on Interaction History, Environment, and Cosmology

I present results from numerical N-body simulations regarding the effect of merging events on the angular momentum distribution of galactic halos, as well as a comparison of halo growth in Press-Schechter versus N-body methods. A total of six simulations are used, spanning three cosmologies: a standard flat Ω0 = 1 model, an open Ω0 = 0.3 model, and a "tilted" flat Ω0 = 1 model with spectral index n = 0.8. In each model, one run was conducted using a spatially uniform grid of particles and one using a refined grid in a large void. In all three models and all environments tested, the mean angular momentum of merger remnants (halo interaction products with mass ratios 3 : 1 or less) is greater than nonmerger remnants. Furthermore, the dispersion in the merger-remnant angular momentum distribution is smaller than the dispersion of the nonmerger distribution. The interpretation most consistent with the data is that the orbital angular momentum of the interactors is important in establishing the final angular momentum of the merger product. I give the angular momentum distribution, which describes the merger remnant population. I trace the most massive progenitor of L* galactic-mass halos (uniform grid) and 1011 M☉ halos (refined void) from z = 0 back to z = 5. Monte Carlo mass histories match simulations reasonably well for the latter sample. I find that for halos of mass 1012 ≲ M ≲ 1014 M☉, this method can underestimate the mass of progenitors by 20%, hence yielding improper formation redshifts of halos. With this caveat, however, the general shapes of halo mass histories and formation time distributions are preserved.
Description and evaluation of the Earth System Regional Climate Model (Reg CM‐ES)

We describe a new, state‐of‐the‐art, Earth System Regional Climate Model (RegCM‐ES), which includes the coupling between the atmosphere, ocean, and land surface, as well as a hydrological and ocean biogeochemistry model, with the capability of using a variety of physical parameterizations. The regional coupled model has been implemented and tested over some of the COordinated Regional climate Downscaling Experiment (CORDEX) domains and more regional settings featuring climatically important coupled phenomena. Regional coupled ocean‐atmosphere models can be especially useful tools to provide information on the mechanisms of air‐sea interactions and feedbacks occurring at fine spatial and temporal scales. RegCM‐ES shows a good representation of precipitation and SST fields over the domains tested, as well as realistic simulations of coupled air‐sea processes and interactions. The RegCM‐ES model, which can be easily implemented over any regional domain of interest, is open source, making it suitable for usage by the broad scientific community.
Selective Inhibition of iNOS by Benzyl‐ and Dibenzyl Derivatives of N‐(3‐Aminobenzyl)acetamidine

Nitric oxide (NO), one of the smallest known bioactive products of mammalian cells, can be produced by almost all cells. In mammals, NO is synthesized by a family of three NO synthases (NOS): neuronal nNOS, inducible iNOS and endothelial eNOS, that are products of three genes: NOS1, NOS2, and NOS3, respectively. The three isoforms generate NO by the conversion of l-arginine to l-citrulline; they differ in both structure and function but share about 50 % sequence homology and are differentially regulated making the catalytic activity distinct for each isoform. nNOS and eNOS are constitutive and primarily expressed in neurons and endothelial cells, respectively. These isoforms are calcium/calmodulin dependent and generate low levels of NO for short periods of time in a pulsative manner. iNOS was first identified and characterized in cytokine-activated murine macrophages. This isoform is not dependent upon calcium/calmodulin for its enzymatic action and is expressed in a wide array of cells and tissues, for example, macrophages, hepatocytes, neutrophils, pulmonary epithelium, colonic epithelium, and vasculature. After induction, iNOS continuously produces NO until the enzyme is degraded. The overproduction of NO by iNOS may have detrimental consequences, and this activity seems to be involved in the pathophysiology of several human diseases, such as asthma, arthritis, multiple sclerosis, colitis, psoriasis, neurodegenerative diseases, tumor development, transplant rejection, and septic shock. In recent years, considerable effort has been directed toward the selective inhibition of iNOS as a strategy for the prevention of excessive NO production, while maintaining the basal formation of NO from constitutive NOS that is required for normal physiological function. The first approach to NOS inhibitors included analogues of the natural substrate l-arginine that act competitively at the substrate binding site; however, these compounds are not selective enough over the eNOS and nNOS isoforms, which limits their application in vivo. More recent studies have focused on the design and synthesis of non-amino acid analogues, such as amino heterocycles, amidines, guanidines, isoquinolinamines, and isothioureas. We previously reported the synthesis, biological evaluation, and docking studies of a series of N-substituted acetamidines, structurally related to the leading scaffold W1400 (1), a potent and selective iNOS inhibitor. Starting from docking results previously obtained, and with the aim of extending the study of possible ligand–enzyme interactions, we have now evaluated the effect of the introduction of several substituents in ortho, meta or para positions of the leading scaffolds 2 and 3, differing from 1 by the amino substitution at the 3-aminomethyl group with one or two benzylic groups.
Games, deception, and Jones' Lemma

Deception is pervasive in adversarial situations. Here we present a formulation of deception using a two-player game setting. One of the two players deploys a sensor network to gather information on the opponent who in turn can employ deception tactics. We solve the resulting general game using linear programs. We pose an illustrative example and develop closed form solutions for special cases. Finally, we show how our solutions capture the well-known "Jones' Lemma" from the deception literature.
Graduation: What Happens to the Retarded Child When He Grows Up?

Interviews were held with parents or guardians of 120 graduates of classes for the moderately (trainable) retarded in a large southern California metropolitan school district in the years 1968, 1969, and 1970. Information was gathered to assess the quality of community life experienced by these moderately retarded adults after graduation from school. Recommendation is made for (a) new criteria for evaluation of community adjustment of the moderately retarded which emphasizes comprehensive postschool programing to meet the recreational and social needs of the retarded as well as to provide occupational and vocational training and (b) community based residential facilities to provide such programing as an alternative to the parent care model and the permanent parent-child relationship it reinforces.
When are intergroup attitudes based on perceived consensus information?

Two studies examined the extent to which individuals' attitudes toward familiar and unfamiliar social groups are differentially related to perceptions of the attitudes held by other people about those groups. In Study 1, participants indicated their own attitudes, as well as their perceptions of the attitudes of relevant ingroup members, toward nine familiar and nine unfamiliar groups. The relationship between participants' perceptions of their own attitudes and the attitudes of others was stronger for groups that were unfamiliar to them than for groups that were familiar to them. In Study 2, we manipulated perceived group familiarity and again found that individuals were more likely to desire and use consensus information about unfamiliar than familiar groups. We also found that individuals were more confident in their intergroup attitudes after receiving consensus information and that attitude confidence mediated the relationship between group familiarity and the effects of consensus on intergroup attitudes. Implications of the research for the stability and change of intergroup attitudes, as well as for the processes of social influence more generally, are discussed.
ASSESSING IMPACT OF AFFECT RECOGNITION ON THERAPEUTIC RELATIONSHIP

OF THESIS ASSESSING IMPACT OF AFFECT RECOGNITION ON THERAPEUTIC RELATIONSHIP Therapeutic alliance and its relationship to client nonverbal behavior, specifically facial expressions, were examined. Therapist interpretation of the client nonverbal behavior, or affect, influences the therapeutic alliance and process. Based on a sample of clients from a graduate school therapy training facility, results suggest therapist training in facial expressions, and how they relate to client emotion, improve the therapeutic alliance between therapist and client. After a micro-expression training for therapists, clients reported higher life functioning on the Outcome Rating Scale (ORS) and an improved therapeutic alliance on the Session Rating Scale (SRS). Overall, these findings support the benefit of incorporating micro-expression training into therapy instruction.
Accountability, contextualisation and the standard of judicial review of affirmative action : Solidarity obo Barnard v South African Police Services : notes

The decision in Solidarity obo Barnard v South African Police Services (2010) 31 ILJ 742 (LC) (‘Barnard’) has, once again, raised the issue of the proper standard of review of affirmative action measures. The Labour Court ruled that under s 6 of the Employment Equity Act 55 of 1998 (‘EEA’) the respondent bears the onus of proving the fairness of its decision not to appoint the applicant, a white female. This approach contradicts the Constitutional Court’s leading judgment on the test for affirmative action under s 9(2) of the Constitution. In Minister of Finance v Van Heerden 2004 (6) SA 121 (CC) (‘Van Heerden’), the court held that affirmative action measures falling within the ambit of s 9(2) are not subject to the presumption of unfairness in terms of s 9(5) of the Constitution. Given the obvious importance of s 9 of the Constitution for the interpretation of the EEA, the contradictory judicial approaches set out above deserve closer scrutiny. This note compares the judgments by examining their implications with reference to two issues of fundamental constitutional importance. The first issue concerns how the standard of judicial review affects the degree of public accountability expected of the state for actions which limit rights. Judicial review institutionalises the degree of public accountability through the imposition of a particular burden of justification. It will be argued that the burden of justification required in terms of the rationality-based standard of review adopted in Van Heerden is too deferential to be able realise the degree of accountability required of state action which impacts on equality rights. The fairness standard applied in Barnard is better suited to meet the constitutional expectations in this respect. Secondly, judicial standards of review also determine the factors which constitute the scope of the contextual framework for the adjudication of rights disputes. Therefore, the choice of a standard of review is vital in respect of the deliberative or discursive inclusivity of the adjudicative process. Again, it will be contended that the Barnard standard of review is preferable and an ideal way of resolving constitutional disputes in an inclusive and integrated manner.