Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling the impact on the HIV epidemic of treating discordant couples with antiretrovirals to prevent transmission

Background:The HPTN 052 study demonstrated a 96% reduction in HIV transmission in discordant couples using antiretroviral therapy (ART). Objective:To predict the epidemic impact of treating HIV-discordant couples to prevent transmission. Design:Mathematical modeling to predict incidence reduction and the number of infections prevented. Methods:Demographic and epidemiological data from Ghana, Lesotho, Malawi and Rwanda were used to parameterize the model. ART was assumed to be 96% effective in preventing transmission. Results:Our results show there would be a fairly large reduction in incidence and a substantial number of infections prevented in Malawi. However, in Ghana a large number of infections would be prevented, but only a small reduction in incidence. Notably, the predicted number of infections prevented would be similar (and low) in Lesotho and Rwanda, but incidence reduction would be substantially greater in Lesotho than Rwanda. The higher the proportion of the population in stable partnerships (whether concordant or discordant), the greater the effect of a discordant couple's intervention on HIV epidemics. Conclusion:The effectiveness of a discordant couples intervention in reducing incidence will vary among countries due to differences in HIV prevalence and the percentage of couples that are discordant (i.e. degree of discordancy). The number of infections prevented within a country, as a result of an intervention, will depend upon a complex interaction among three factors: population size, HIV prevalence and degree of discordancy. Our model provides a quantitative framework for identifying countries most likely to benefit from treating discordant couples to prevent transmission.
Multiple roles of the coding sequence 5′ end in gene expression regulation

The codon composition of the coding sequence's (ORF) 5′ end first few dozen codons is known to be distinct to that of the rest of the ORF. Various explanations for the unusual codon distribution in this region have been proposed in recent years, and include, among others, novel regulatory mechanisms of translation initiation and elongation. However, due to the fact that many overlapping regulatory signals are suggested to be associated with this relatively short region, its research is challenging. Here, we review the currently known signals that appear in this region, the theories related to the way they regulate translation and affect the organismal fitness, and the debates they provoke.
Experience Report: Error Distribution in Safety-Critical Software and Software Risk Analysis Based on Unit Tests

Systematic verification and validation measures are of essential importance in particular for safety-critical software. After a short introduction into the test environment and error categories, the paper presents the results of a unit test performed on a C++ software package for the European Space Agency in the ARC Seibersdorf research test lab. The authors analyse the error distribution and relations between software metrics and software faults and recommend guidelines for a less error-prone design of safety-critical software.
Comparative analysis of dopamine and tyrosine hydroxylase immunoreactivities in the brain of two amphibians, the anuran Rana ridibunda and the urodele Pleurodeles waltlii

To gain more insight into the dopaminergic system of amphibians and the evolution of catecholaminergic systems in vertebrates in general, the distribution of dopamine and tyrosine hydroxylase immunoreactivity was studied in the brains of the anuran Rana ridibunda and the urodele Pleurodeles waltlii. In both species, dopamine‐immunoreactive (DAi) cell bodies were observed in the olfactory bulb, the preoptic area, the suprachiasmatic nucleus, the nucleus of the periventricular organ and its accompanying cells, the nucleus of the posterior tubercle, the pretectal area, the midbrain tegmentum, around the solitary tract, in the ependymal and subependymal layers along the midline of the caudal rhombencephalon, and ventral to the central canal of the spinal cord. Tyrosine hydroxylase (TH) immunohistochemistry revealed a similar pattern, although some differences were noted. For example, with the TH antibodies, additional cell bodies were stained in the internal granular layer of the olfactory bulb and in the isthmal region, whereas the same antibodies failed to stain the liquor contacting cells in the nucleus of the periventricular organ.
Alcohol surveys with high and low coverage rate: a comparative analysis of survey strategies in the alcohol field.

Two Swedish alcohol surveys were compared in a search for a reasonable explanation of the large difference in their coverage rates, namely 75% and 28%. In many respects both surveys conducted in the late 1980s by large, well-known institutes, are of a similar type with rather large samples of Swedes. The technique used in the survey with a very high coverage rate (Survey A) takes into consideration the actual drinking pattern of the population studied (i.e., the concentration of drinking on weekends). By dividing a "normal week's consumption" into four units (Monday-Thursday, Friday, Saturday and Sunday), the technique allows one to average periods with varying drinking habits. In the survey with a low coverage rate (Survey B) a "normal week's consumption" was not so divided. A test of internal validity within Survey A underlined the general finding that its higher coverage rate was due to this division. A test of the external validity at aggregate level did not support assumptions about "telescoping" effects in A. Both A and B had a normal week as a basis of measurement for investigating typical drinking habits. The literature concerning differences in coverage rates focuses on the measurement of modal habits versus mean habits. The main explanation of differences is that methods that focus on modal habits (i.e., the Quantity-Frequency Scale) generate a lower coverage rate than do methods that elicit the arithmetic mean (i.e., the last-week recall). Since A and B both belong to the former type of scale, this does not explain our results.
Psycholinguistics cannot escape prosody

Once, sentence processing research set aside prosody in order to focus on syntactic and semantic processing. Experimental sentences were mostly presented visually, often without prosodic markers such as commas. Now that we have made some progress by this ‘divide and conquer’ approach, and now that the technology for working on speech has improved, it may be time to integrate prosody into processing models. I argue here that we have no choice but to do so, because current evidence shows that even in silent reading, prosody is projected onto written sentences, and can influence the course of syntactic processing. 1. Why try to escape?
Correlations between anxiety and the stress responses of electrogastrography (EGG) induced by the mirror drawing test (MDT)

Electrogastrograms (EGGs) were recorded at 16 locations on the thoraco-abdominal surface at rest and then both during and after the acute stress of performing the mirror drawing test (MDT). A significant linear correlation with a negative slope was found between the anxiety scores and the ratio of the power content during MDT to the power content at rest (r) (MDTr–1) of the 3 cpm component from the epigastric channel 2 recording. In contrast, significant linear correlations with positive slopes were found between the anxiety scores and MDTr–1 of the 6 cpm component of the recordings from the infraumbilical channels (channels 13, 15, and 16). The epigastric 3-cpm EGG activity reflects gastric myoelectric activity, while the infraumbilical 3- and 6-cpm activity reflects that of the colon. Therefore, these results seem to further support the previous report of the inhibition of gastric EGG by stress and the stress-mediated facilitation of colonic EGG (Homma S, J Smooth Muscle Res. 2012; 48(2–3): 47–57).
Surface roughness of denture base acrylic resins after processing and after polishing.

PURPOSE Circumstances exist in which the need to adjust denture base acrylic resins is necessary. This process obviously alters the surface of the polished denture base. The purpose of this study was to compare the effects of three chairside polishing kits and conventional polishing on four denture acrylic resins. MATERIALS AND METHODS Twenty-four 30 x 30 x 2 mm acrylic resin specimens were fabricated with each of four acrylic resins: autopolymerizing, heat processed, injection molded, and microwaveable. One side was polished conventionally with pumice and polishing compound. The other side was polished with one of three chairside polishing kits: Axis, Brasseler, and Shofu. Each side was evaluated by a Dektak 8 Programmable Stylus Profiler to determine the surface roughness (Ra). RESULTS One-way analysis of variance (ANOVA) revealed that: (1) There was no significant difference in the time it took to polish the specimens with the chairside polishing kits (F=2.118, p=0.14). (2) There was a significant difference in surface roughness between the acrylic resins before any polishing, with the injection-molded and heat-processed being less rough than the autopolymerizing (F=4.588, p=0.005). (3) There was a significant difference in surface roughness between the acrylic resins when conventionally polished, with the injection-molded and microwavable being less rough than the autopolymerizing (F=4.503, p=0.005). Factorial ANOVA revealed that: (1) There was no significant difference in the surface roughness among the chairside polishing kits (F=1.209, p=0.30). (2) There was a significant difference between the acrylic resins, with the heat-processed, injection-molded, and microwaveable being significantly less rough than the autopolymerizing (F=6.610, p=0.0001). (3) There was no significant interaction between the acrylic resins and the chairside polishing kit in the amount of surface roughness (F=1.728, p=0.12). An independent t-test revealed that conventional polishing was significantly smoother than polishing with the chairside polishing kits (t=3.847, p=0.0001). CONCLUSIONS It was concluded that time was not a factor in using any of the chairside polishing kits. It is recommended that conventional polishing be used after adjustments to the cameo surface of denture acrylic resin.
Environmental heterogeneity leads to higher plasticity in dry‐edge populations of a semi‐arid Chilean shrub: insights into climate change responses

Interannual variability in climatic conditions should be taken into account in climate change studies in semi‐arid ecosystems. It may determine differentiation in phenotypic plasticity among populations, with populations experiencing higher environmental heterogeneity showing higher levels of plasticity. The ability of populations to evolve key functional traits and plasticity may determine the survival of plant populations under the drier and more variable climate expected for semi‐arid ecosystems. Working with populations of the semi‐arid Chilean shrub Senna candolleana along its entire distribution range, we assessed inter‐ and intra‐population variation in functional traits as well as in their plasticity in response to water availability. We measured morphological and physiological traits related to drought resistance in both field conditions and in a greenhouse experiment, where drought response was evaluated under two water availability treatments. All populations responded plastically, but higher precipitation heterogeneity in dry‐edge populations seemed to have selected for more plastic genotypes compared to populations growing at mesic sites and with more homogeneous environmental conditions. Synthesis. Our results suggest adaptive plasticity since higher levels of phenotypic plasticity were positively associated with plant performance. However, we did not find evidence for genetic variation for plasticity within populations. To the extent that phenotypic plasticity may play a key role in future persistence, populations at mesic sites may be more vulnerable to climate change due to their lower plasticity and their current limitations to evolve novel norms of reaction. Conversely, although Senna candolleana populations at the dry edge are exposed to higher levels of stress, they may be less susceptible to climate change in view of their greater plasticity. We highlight the need to consider population differentiation in both mean traits and their plasticity to model realistic scenarios of species distribution under climate change.
Overexpression of urokinase receptor and cell surface urokinase-type plasminogen activator in the human vessel wall with different types of atherosclerotic lesions

Urokinase-type plasminogen activator (UPA) has been implicated in a broad spectrum of pathogenic processes involved in the formation and disruption of atherosclerotic lesions. Up to now, there is no consensus on the contribution of membrane-bound UPA and its receptor CD87 (UPAR) to the development of atherosclerosis. In this study, we determined comparatively the levels of UPAR and UPAR-bound UPA in segments of human coronary and aortic vessels with different degrees of atherosclerotic lesions (macroscopically normal areas, early atherosclerotic lesions, fibrous and calcified plaques). The UPAR content increased progressively with the severity of atherosclerosis. In aortic segments, in which intima and media layers were analyzed separately, the content of UPAR in the intima significantly exceeded the levels measured in the media. Using a detergent-phase separation method with a Triton X-114-containing buffer, we could demonstrate that the levels of membrane (glycosylphosphatidylinositol)-anchored UPAR were significantly higher in the intima of early atherosclerotic lesions as well as in the cap areas of fibrous plaques compared with macroscopically normal areas. However, only 20–25% of the intimal and 30–50% of the medial glycosylphosphatidylinositol-UPAR was occupied by UPA as determined on a molar basis. These data confirm that the overexpression of UPAR in advanced atherosclerotic lesions contributes to lesion development. Whether UPAR's excess over cell surface UPA provides an additional role for this receptor in atherogenesis besides UPA-mediated proteolysis remains to be elucidated.
CD8+ T Cell Responses against TAP-Inhibited Cells Are Readily Detected in the Human Population

Target cell recognition by CTLs depends on the presentation of peptides by HLA class I molecules. Tumors and herpes viruses have adopted strategies to greatly hamper this peptide presentation at the important bottleneck, the peptide transporter TAP. Previously, we described the existence of a CD8+ CTL subpopulation that selectively recognizes such TAP-deficient cells in mouse models. In this study, we show that the human counterpart of this CTL subset is readily detectable in healthy subjects. Autologous PBMC cultures were initiated with dendritic cells rendered TAP-impaired by gene transfer of the viral evasion molecule UL49.5. Strikingly, specific reactivity to B-LCLs expressing one of the other viral TAP-inhibitors (US6, ICP47, or BNLF2a) was already observed after three rounds of stimulation. These short-term T cell cultures and isolated CD8+ CTL clones derived thereof did not recognize the normal B-LCL, indicating that the cognate peptide-epitopes emerge at the cell surface upon an inhibition in the MHC class I processing pathway. A diverse set of TCRs was used by the clones, and the cellular reactivity was TCR-dependent and HLA class I-restricted, implying the involvement of a broad antigenic peptide repertoire. Our data indicate that the human CD8+ T cell pool comprises a diverse reactivity to target cells with impairments in the intracellular processing pathway, and these might be exploited for cancers that are associated with such defects and for infections with immune-evading herpes viruses.
Soundness and Completeness Theorems for Three Formalizations of Action

Instead of trying to compare methodologies for reasoning about action on the basis of specific examples, we focus here on a general class of problems, expressible in a declarative language A. We propose three translations, P, R and B from A, representing respectively the first order methods of reasoning about action proposed by Pednault and Reiter and the circumscriptive approach of Baker. We then prove the soundness and completeness of these translations relative to the semantics of A. This lets us compare these three methods in a mathematically precise fashion. Moreover, we apply the methods of Baker in a general setting and prove a theorem which shows that if the domain of interest can be expressed in A, circumscription yields results which are intuitively expected.
Differences in procrastination and motivation between undergraduate and graduate students

Procrastination became increasingly prevalent among students in recent years. However, little research was found that directly compares academic procrastination across different academic grade levels. The present study used a self-regulated learning perspective to compare procrastination types and associated motivation between undergraduate and graduate students. Sixty-six undergraduate and sixty-eight graduate students responded to a packet of questionnaires concerning their experience in an educational psychology class. The results show that students’ beliefs about the usefulness of procrastination were a better predictor of academic procrastination than self-efficacy beliefs and achievement goal orientations. Student age was related to procrastination types. Among the undergraduate procrastinators, the younger students were more likely to engage in active procrastination while the older students tended to engage in passive procrastination. Implications and future research directions are discussed.
De novo direct tandem duplication of a small segment of the short arm of chromosome 7 (p21.22→22.1)

We report a boy with duplication of a small segment of the short arm of chromosome 7 (46, XY, dir dup (7) (p21.2→22.1). The boy presented with supravalvular pulmonary stenosis, atrial septum defect and mental retardation. The origin of the additional material from chromosome 7 was confirmed by fluorescence in situ hybridization. This technique in combination with the use of single‐copy DNA probes may in future help to delineate the phenotype/karyotype correlation.
Differential Activation and Trafficking of μ-Opioid Receptors in Brain Slices

The activation of G protein-coupled receptors results in a cascade of events that include acute signaling, desensitization, and internalization, and it is thought that not all agonists affect each process to the same extent. The early steps in opioid receptor signaling, including desensitization, have been characterized electrophysiologically using brain slice preparations, whereas most previous studies of opioid receptor trafficking have been conducted in heterologous cell models. This study used transgenic mice that express an epitope-tagged (FLAG) μ-opioid receptor (FLAGMOR) targeted to catecholamine neurons by regulatory elements from the tyrosine hydroxylase gene. Brain slices from these mice were used to study tagged MOR receptors in neurons of the locus ceruleus. Activation of the FLAGMOR with [Met5]enkephalin (ME) produced a hyperpolarization that desensitized acutely to the same extent as native MOR in slices from wild-type mice. A series of opioid agonists were then used to study desensitization and receptor trafficking in brain slices, which was monitored with a monoclonal antibody against the FLAG epitope (M1) conjugated to Alexa 594. Three patterns of receptor trafficking and desensitization were observed: 1) ME, etorphine, and methadone resulted in both receptor desensitization and internalization; 2) morphine and oxymorphone caused significant desensitization without evidence for internalization; and 3) oxycodone was ineffective in both processes. These results show that two distinct forms of signaling were differentially engaged depending on the agonist used to activate the receptor, and they support the hypothesis that ligand-specific regulation of opioid receptors occurs in neurons maintained in brain slices from adult animals.
Real-Time Robot Path Planning via a Distance-Propagating Dynamic System with Obstacle Clearance

An efficient grid-based distance-propagating dynamic system is proposed for real-time robot path planning in dynamic environments, which incorporates safety margins around obstacles using local penalty functions. The path through which the robot travels minimizes the sum of the current known distance to a target and the cumulative local penalty functions along the path. The algorithm is similar to but does not maintain a sorted queue of points to update. The resulting gain in computational speed is offset by the need to update all points in turn. Consequently, in situations where many obstacles and targets are moving at substantial distances from the current robot location, this algorithm is more efficient than . The properties of the algorithm are demonstrated through a number of simulations. A sufficient condition for capture of a target is provided.
(Un-)Covering Equivalent Mutants

Mutation testing measures the adequacy of a test suite by seeding artificial defects (mutations) into a program. If a test suite fails to detect a mutation, it may also fail to detect real defects-and hence should be improved. However, there also are mutations which keep the program semantics unchanged and thus cannot be detected by any test suite. Such equivalent mutants must be weeded out manually, which is a tedious task. In this paper, we examine whether changes in coverage can be used to detect non-equivalent mutants: If a mutant changes the coverage of a run, it is more likely to be non-equivalent. Ina sample of 140 manually classified mutations of seven Java programs with 5,000to 100,000 lines of code, we found that: (a) the problem is serious and widespread-about 45% of all undetected mutants turned out to be equivalent;(b) manual classification takes time-about 15 minutes per mutation; (c)coverage is a simple, efficient, and effective means to identify equivalent mutants-with a classification precision of 75% and a recall of 56%; and (d)coverage as an equivalence detector is superior to the state of the art, in particular violations of dynamic invariants. Our detectors have been released as part of the open source Javalanche framework; the data set is publicly available for replication and extension of experiments.
FBF and Its Dual Control of gld-1 Expression in the Caenorhabditis elegans Germline

FBF, a PUF RNA-binding protein, is a key regulator of the mitosis/meiosis decision in the Caenorhabditis elegans germline. Genetically, FBF has a dual role in this decision: it maintains germ cells in mitosis, but it also facilitates entry into meiosis. In this article, we explore the molecular basis of that dual role. Previous work showed that FBF downregulates gld-1 expression to promote mitosis and that the GLD-2 poly(A) polymerase upregulates gld-1 expression to reinforce the decision to enter meiosis. Here we ask whether FBF can act as both a negative regulator and a positive regulator of gld-1 expression and also investigate its molecular mechanisms of control. We first show that FBF co-immunoprecipitates with gld-1 mRNA, a result that complements previous evidence that FBF directly controls gld-1 mRNA. Then we show that FBF represses gld-1 expression, that FBF physically interacts with the CCF-1/Pop2p deadenylase and can stimulate deadenylation in vitro, and that CCF-1 is partially responsible for maintaining low GLD-1 in the mitotic region. Finally, we show that FBF can elevate gld-1 expression, that FBF physically interacts with the GLD-2 poly(A) polymerase, and that FBF can enhance GLD-2 poly(A) polymerase activity in vitro. We propose that FBF can affect polyadenylation either negatively by its CCF-1 interaction or positively by its GLD-2 interaction.