Miracle-dz/UniFAR-FTUs huggingface dataset:
A Human Endogenous Retrovirus Suppresses Translation of an Associated Fusion Transcript, PLA2L

ABSTRACT Human endogenous retroviruses (HERVs) are repetitive, noninfectious chromosomal elements degenerated from exogenous retroviruses. The HERV-H family is composed of approximately 1,000 elements which are dispersed throughout the human genome. We have shown previously that an HERV-H element splices into a downstream locus, termed PLA2L, which has a large open reading frame (ORF) containing two domains with phospholipase A2 homology. Over half of the putative 5′ untranslated region (5′ UTR) of the resulting fusion transcript is derived from HERV-H long-terminal-repeat and internal sequences. As 5′ UTRs are known to modulate translation initiation, we tested for possible effects upon gene expression at the translation level due to the 5′ fusion with HERV-H sequences. No PLA2L protein was detected in teratocarcinoma cell lines in which PLA2L mRNA is abundantly expressed. In addition, despite a high level of transcription, no protein synthesis was detected when the full-length PLA2L cDNA was expressed in COS cells. Upon removal of the 5′-terminal HERV-H sequences, PLA2L protein was seen in transfectants. The 5′ UTR contains both small ORFs and a strong predicted RNA secondary structure, both of which have been shown to contribute to translation suppression. The HERV-H sequences, combined with a unique PLA2L 5′ UTR sequence, form a predicted RNA stem-loop that has a stability greater than that proposed to negatively affect translation. Interestingly, this stem-loop is abolished when the HERV-H sequences are removed. We hypothesize that the PLA2L 5′ HERV-H sequences function as an abnormally long and complex 5′ UTR, resulting in suppression of translation in both teratocarcinoma cell lines and full-length cDNA transfectants. This is the first known example of a endogenous retrovirus integration affecting expression of a heterologous human gene at the translational level.
The Role of Plasma Membrane Aquaporins in Regulating the Bundle Sheath-Mesophyll Continuum and Leaf Hydraulics1[C][W][OPEN]

Silencing aquaporins of the xylem bundle sheath cells reduces leaf hydraulic conductance and affects the water permeability of adjacent mesophyll cells, suggesting a bundle sheath-mesophyll feed-forward hydraulic control. Our understanding of the cellular role of aquaporins (AQPs) in the regulation of whole-plant hydraulics, in general, and extravascular, radial hydraulic conductance in leaves (Kleaf), in particular, is still fairly limited. We hypothesized that the AQPs of the vascular bundle sheath (BS) cells regulate Kleaf. To examine this hypothesis, AQP genes were silenced using artificial microRNAs that were expressed constitutively or specifically targeted to the BS. MicroRNA sequences were designed to target all five AQP genes from the PLASMA MEMBRANE-INTRINSIC PROTEIN1 (PIP1) subfamily. Our results show that the constitutively silenced PIP1 (35S promoter) plants had decreased PIP1 transcript and protein levels and decreased mesophyll and BS osmotic water permeability (Pf), mesophyll conductance of CO2, photosynthesis, Kleaf, transpiration, and shoot biomass. Plants in which the PIP1 subfamily was silenced only in the BS (SCARECROW:microRNA plants) exhibited decreased mesophyll and BS Pf and decreased Kleaf but no decreases in the rest of the parameters listed above, with the net result of increased shoot biomass. We excluded the possibility of SCARECROW promoter activity in the mesophyll. Hence, the fact that SCARECROW:microRNA mesophyll exhibited reduced Pf, but not reduced mesophyll conductance of CO2, suggests that the BS-mesophyll hydraulic continuum acts as a feed-forward control signal. The role of AQPs in the hierarchy of the hydraulic signal pathway controlling leaf water status under normal and limited-water conditions is discussed.
“I feel like half a woman all the time”: The impacts of coerced and forced sterilisations on HIV-positive women in South Africa

abstract HIV-positive women are entitled to sexual and reproductive health rights, including access to contraceptives of their choice. One such option is sterilisation. Given its permanency, a woman's decision to sterilise should be voluntary and fully informed. However, there have been multiple reports that HIV-positive women are being sterilised without their informed consent, and sometimes without their knowledge, in southern Africa and elsewhere. The Article explores the socio-cultural, physical and emotional/psychological impacts of coerced and forced sterilisations on HIV-positive women. It is part of a larger qualitative study, conducted in South Africa, which explored the experiences of 22 HIV-positive women who reported being sterilised without their informed consent. Involuntary sterilisation has devastating impacts on women, affecting them mentally and physically, and impacting on their relationships with their partners, families and the wider community. Many interviewees reported that being sterilised profoundly affected their perceptions of themselves as women. Involuntary sterilisations have grave social and emotional implications for already marginalised HIV-positive women. Therefore efforts should be made to address human rights violations in South African healthcare settings and to prevent further gender-based abuses.
Enhancing Software Quality by an SPL Testing based Software Testing

Software testing is a process of providing information that a software application or program meets the business and technical requirements that guided its design and development; and works as expected. Regardless of the environment (i.e. Structured or Object Oriented), software testing can also identifies important defects, flaws, or errors in the application code that must be fixed. Quality control involves the maintenance of quality in a product, particularly by comparing the performance of a product with a set of specifications. This paper introduces some basic knowledge regarding to software testing. The paper provides some new model that could improve quality of software testing as a mean to increase the overall quality of the product.
Using Lod Scores to Detect Sex Differences in Male-Female Recombination Fractions

Human recombination fraction (RF) can differ between males and females, but investigators do not always know which disease genes are located in genomic areas of large RF sex differences. Knowledge of RF sex differences contributes to our understanding of basic biology and can increase the power of a linkage study, improve gene localization, and provide clues to possible imprinting. One way to detect these differences is to use lod scores. In this study we focused on detecting RF sex differences and answered the following questions, in both phase-known and phase-unknown matings: (1) How large a sample size is needed to detect a RF sex difference? (2) What are ‘optimal’ proportions of paternally vs. maternally informative matings? (3) Does ascertaining nonoptimal proportions of paternally or maternally informative matings lead to ascertainment bias? Our results were as follows: (1) We calculated expected lod scores (ELODs) under two different conditions: ‘unconstrained,’ allowing sex-specific RF parameters (Θ♀, Θ♂); and ‘constrained,’ requiring Θ♀ = Θ♂. We then examined the ΔELOD (≡ difference between maximized constrained and unconstrained ELODs) and calculated minimum sample sizes required to achieve statistically significant ΔELODs. For large RF sex differences, samples as small as 10 to 20 fully informative matings can achieve statistical significance. We give general sample size guidelines for detecting RF differences in informative phase-known and phase-unknown matings. (2) We defined p as the proportion of paternally informative matings in the dataset; and the optimal proportion pcirc; as that value of p that maximizes ΔELOD. We determined that, surprisingly, pcirc; does not necessarily equal ½, although it does fall between approximately 0.4 and 0.6 in most situations. (3) We showed that if p in a sample deviates from its optimal value, no bias is introduced (asymptotically) to the maximum likelihood estimates of Θ♀ and Θ♂, even though ELOD is reduced (see point 2). This fact is important because often investigators cannot control the proportions of paternally and maternally informative families. In conclusion, it is possible to reliably detect sex differences in recombination fraction.
Nicotinic alteration of functional thalamocortical topography

The thalamocortical pathways form highly topographic connections from the primary sensory thalamic nuclei to the primary cortical areas. The synaptic properties of these thalamocortical connections are modifiable by activation from various neuromodulators, such as acetylcholine. Cholinergic activation can alter functional properties in both the developing and the mature nervous system. Moreover, environmental factors, such as nicotine, can activate these receptors, although the circuit-level alterations resulting from such nicotinic activation of sensory neural circuits remain largely unexplored. Therefore, we examined alterations to the functional topography of thalamocortical circuits in the developing sensory pathways of the mouse. Photostimulation by uncaging of glutamate was used to map these functional thalamocortical alterations in response to nicotinic receptor activation. As a result, we found that activation of forebrain nicotinic acetylcholine receptors results in an expansion and enhancement of functional thalamocortical topographies as assessed in brain slice preparations using laser-scanning photostimulation by uncaging of glutamate. These physiological changes were correlated with the neuroanatomical expression of nicotinic acetylcholine receptor subtypes (&agr;7 and &bgr;2). These circuit-level alterations may provide a neural substrate underlying the plastic development and reshaping of thalamocortical circuitry in response to nicotinic receptor activation.
Learning of Chunking Sequences in Cognition and Behavior

We often learn and recall long sequences in smaller segments, such as a phone number 858 534 22 30 memorized as four segments. Behavioral experiments suggest that humans and some animals employ this strategy of breaking down cognitive or behavioral sequences into chunks in a wide variety of tasks, but the dynamical principles of how this is achieved remains unknown. Here, we study the temporal dynamics of chunking for learning cognitive sequences in a chunking representation using a dynamical model of competing modes arranged to evoke hierarchical Winnerless Competition (WLC) dynamics. Sequential memory is represented as trajectories along a chain of metastable fixed points at each level of the hierarchy, and bistable Hebbian dynamics enables the learning of such trajectories in an unsupervised fashion. Using computer simulations, we demonstrate the learning of a chunking representation of sequences and their robust recall. During learning, the dynamics associates a set of modes to each information-carrying item in the sequence and encodes their relative order. During recall, hierarchical WLC guarantees the robustness of the sequence order when the sequence is not too long. The resulting patterns of activities share several features observed in behavioral experiments, such as the pauses between boundaries of chunks, their size and their duration. Failures in learning chunking sequences provide new insights into the dynamical causes of neurological disorders such as Parkinson’s disease and Schizophrenia.
Efficient Evaluation of Continuous Text Search Queries

Consider a text filtering server that monitors a stream of incoming documents for a set of users, who register their interests in the form of continuous text search queries. The task of the server is to constantly maintain for each query a ranked result list, comprising the recent documents (drawn from a sliding window) with the highest similarity to the query. Such a system underlies many text monitoring applications that need to cope with heavy document traffic, such as news and email monitoring. In this paper, we propose the first solution for processing continuous text queries efficiently. Our objective is to support a large number of user queries while sustaining high document arrival rates. Our solution indexes the streamed documents in main memory with a structure based on the principles of the inverted file, and processes document arrival and expiration events with an incremental threshold-based method. We distinguish between two versions of the monitoring algorithm, an eager and a lazy one, which differ in how aggressively they manage the thresholds on the inverted index. Using benchmark queries over a stream of real documents, we experimentally verify the efficiency of our methodology; both its versions are at least an order of magnitude faster than a competitor constructed from existing techniques, with lazy being the best approach overall.
Improving folksonomies quality by syntactic tag variations grouping

Folksonomies offer an easy method to organize information in the current Web. This fact and their collaborative features have derived in an extensive involvement in many Social Web projects. However they present important drawbacks regarding their limited exploring and searching capabilities, in contrast with other methods as taxonomies, thesauruses and ontologies. One of these drawbacks is an effect of its flexibility for tagging, producing frequently multiple variations of a same tag. In this paper we propose a method to group syntactic variations of tags using pattern matching techniques. We propose the utilization of a fuzzy similarity measure and we conclude that this technique offers better results than other classic techniques after comparing them on a large real dataset.
Physiological and proteomic analyses on artificially aged Brassica napus seed

Plant seeds lose their viability when they are exposed to long term storage or controlled deterioration treatments, by a process known as seed aging. Based on previous studies, artificially aging treatments have been developed to accelerate the process of seed aging in order to understand its underlying mechanisms. In this study, we used Brassica napus seeds to investigate the mechanisms of aging initiation. B. napus seeds were exposed to artificially aging treatment (40°C and 90% relative humidity) and their physio-biochemical characteristics were analyzed. Although the treatment delayed germination, it did not increase the concentration of cellular reactive oxygen species (ROS). Comparative proteomic analysis was conducted among the control and treated seeds at different stages of germination. The proteins responded to the treatment were mainly involved in metabolism, protein modification and destination, stress response, development, and miscellaneous enzymes. Except for peroxiredoxin, no changes were observed in the accumulation of other antioxidant enzymes in the artificially aged seeds. Increased content of abscisic acid (ABA) was observed in the artificially treated seeds which might be involved in the inhibition of germination. Taken together, our results highlight the involvement of ABA in the initiation of seed aging in addition to the ROS which was previously reported to mediate the seed aging process.
Robust satisfiability of constraint satisfaction problems

An algorithm for a constraint satisfaction problem is called robust if it outputs an assignment satisfying at least (1-g(ε))-fraction of the constraints given a (1-ε)-satisfiable instance, where g(ε) -> 0 as ε -> 0, $g(0)=0. Guruswami and Zhou conjectured a characterization of constraint languages for which the corresponding constraint satisfaction problem admits an efficient robust algorithm. This paper confirms their conjecture.
Affects of ionizing radiation on T-cell population lymphocyte: A risk factor of Irritable Bowel Syndrome

Irritable bowel syndrome is observed mostly in Ukrainian children and may be related to adverse health effects as a result of the Chernobyl disaster. The aim of this study was to determine status of T-cell population lymphocytes in children with clinical symptom of irritable bowel syndrome. The test population consisted of 95 participants: 75 rural patients aged 4 to 18 who lived in a contaminated area exposed to natural environmental radiation with clinical symptom of irritable bowel syndrome (categorized in three groups) and 20 healthy urban participants from Kiev aged 5 to 15 as control group. Internal radiation activity has been measured by γ-ray spectrometry. Peripheral blood leukocytes were analyzed for T-lymphocytes subset such as T-lymphocytes (CD3+), T-helper (CD4+) and T-cytotoxic (CD8+) and then CD4/CD8 ratio was calculated. Percentage of CD3+ and CD4+ in all study groups decreased significantly in comparison to control group (p < 0.001). Percentage of CD8+ increased significantly in all study groups in comparison to control group (p < 0.05). The CD4/CD8 ratio decreased significantly all study groups in comparison to control group (p < 0.001). Cellular immune status of study groups that are residing in a contaminated area has changed. Our data have demonstrated that this change may be related to a higher incidence of children with irritable bowel syndrome.
A Testing Based Extraction Algorithm for Identifying Significant Communities in Networks

A common and important problem arising in the study of networks is how to divide the vertices of a given network into one or more groups, called communities, in such a way that vertices of the same community are more interconnected than vertices belonging to different ones. We propose and investigate a testing based community detection procedure called Extraction of Statistically Significant Communities (ESSC). The ESSC procedure is based on p-values for the strength of connection between a single vertex and a set of vertices under a reference distribution derived from a conditional configuration network model. The procedure automatically selects both the number of communities in the network and their size. Moreover, ESSC can handle overlapping communities and, unlike the majority of existing methods, identifies “background” vertices that do not belong to a well-defined community. The method has only one parameter, which controls the stringency of the hypothesis tests. We investigate the performance and potential use of ESSC and compare it with a number of existing methods, through a validation study using four real network data sets. In addition, we carry out a simulation study to assess the effectiveness of ESSC in networks with various types of community structure, including networks with overlapping communities and those with background vertices. These results suggest that ESSC is an effective exploratory tool for the discovery of relevant community structure in complex network systems. Data and software are available at http://www.unc. edu/~jameswd/research.html.
Familial Resemblance for Serum Metabolite Concentrations

Metabolomics is the comprehensive study of metabolites, which are the substrates, intermediate, and end products of cellular metabolism. The heritability of the concentrations of circulating metabolites bears relevance for evaluating their suitability as biomarkers for disease. We report aspects of familial resemblance for the concentrations in human serum of more than 100 metabolites, measured using a targeted metabolomics platform. Age- and sex-corrected monozygotic twin correlations, midparent–offspring regression coefficients, and spouse correlations in subjects from two independent cohorts (Netherlands Twin Register and Leiden Longevity Study) were estimated for each metabolite. In the Netherlands Twin Register subjects, who were largely fasting, we found significant monozygotic twin correlations for 121 out of 123 metabolites. Heritability was confirmed by midparent–offspring regression. For most detected metabolites, the correlations between spouses were considerably lower than those between twins, indicating a contribution of genetic effects to familial resemblance. Remarkably high heritability was observed for free carnitine (monozygotic twin correlation 0.66), for the amino acids serine (monozygotic twin correlation 0.77) and threonine (monozygotic twin correlation 0.64), and for phosphatidylcholine acyl-alkyl C40:3 (monozygotic twin correlation 0.77). For octenoylcarnitine, a consistent point estimate of approximately 0.50 was found for the spouse correlations in the two cohorts as well as for the monozygotic twin correlation, suggesting that familiality for this metabolite is explained by shared environment. We conclude that for the majority of metabolites targeted by the used metabolomics platform, the familial resemblance of serum concentrations is largely genetic. Our results contribute to the knowledge of the heritability of fasting serum metabolite concentrations, which is relevant for biomarker research.
Binding and regulation of thrombopoietin to human megakaryocytes

Thrombopoietin (TPO, c‐Mpl ligand) is considered to play an important role in the regulation of megakaryocytopoiesis and platelet production by activating the cytokine receptor c‐Mpl. We have examined the binding of 125I‐TPO to the human megakaryocytic cell line, CMK, and to primary human megakaryocytes. Scatchard analysis of TPO binding to its cognate receptor in megakaryocytic cells suggested the existence of a single class of c‐Mpl receptors. CMK cells exhibited 1223 receptors per cell with a dissociation constant (Kd) of Kd = 223 p M, whereas primary human megakaryocytes exhibited 12 140 receptors per cell and a dissociation constant of Kd = 749 p M. The pretreatment of CMK cells and primary bone marrow megakaryocytes with TPO resulted in a decreased binding of TPO to the c‐Mpl receptors. This down‐regulation was observed within 3 h and was not inhibited by cycloheximide. Phorbol ester, an activator of protein kinase C, also inhibited TPO binding to the c‐Mpl receptors by reducing the number of these receptors. The pretreatment of CMK cells with IL‐3, IL‐6 and DMSO, all of which induced the differentiation of CMK cells, did not affect the binding of TPO to the c‐Mpl receptors. These results suggest an additional mechanism, where protein kinase C may help to regulate the binding of TPO to these cells.