Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic diversity of simian immunodeficiency viruses from West African green monkeys: evidence of multiple genotypes within populations from the same geographical locale

High simian immunodeficiency virus (SIV) seroprevalence rates have been reported in the different African green monkey (AGM) subspecies. Genetic diversity of these viruses far exceeds the diversity observed in the other lentivirus-infected human and nonhuman primates and is thought to reflect ancient introduction of SIV in the AGM population. We investigate here genetic diversity of SIVagm in wild-living AGM populations from the same geographical locale (i.e., sympatric population) in Senegal. For 11 new strains, we PCR amplified and sequenced two regions of the genome spanning the first tat exon and part of the transmembrane glycoprotein. Phylogenetic analysis of these sequences shows that viruses found in sympatric populations cluster into distinct lineages, with at least two distinct genotypes in each troop. These data strongly suggest an ancient introduction of these divergent viruses in the AGM population.
Association between physical activity and quality of life in the elderly: a systematic review, 2000-2012.

OBJECTIVE To review information regarding the association of physical activity (PA) with quality of life (QoL) in the elderly and to identify the study designs and measurement instruments most commonly used in its assessment, in the period 2000-2012. METHODS Relevant articles were identified by a search of four electronic databases and cross-reference lists and by contact with the authors of the included manuscripts. Original studies on the association between PA and QoL in individuals aged 60 years or older were examined. The quality of studies as well as the direction and the consistency of the association between PA and QoL were evaluated. RESULTS A total of 10,019 articles were identified as potentially relevant, but only 42 (0.42%) met the inclusion criteria and were retrieved and examined. Most studies demonstrated a positive association between PA and QoL in the elderly. PA had a consistent association with the following QoL domains: functional capacity; general QoL; autonomy; past, present and future activities; death and dying; intimacy; mental health; vitality; and psychological. CONCLUSION PA was positively and consistently associated with some QoL domains among older individuals, supporting the notion that promoting PA in the elderly may have an impact beyond physical health. However, the associations between PA and other QoL domains were moderate to inconsistent and require further investigation.
The soft X-ray/NLR connection: a single photoionized medium?

We present a sample of 8 nearby Seyfert 2 galaxies observed by HST and Chandra . All of the sources present soft X-ray emission which is coincident in extension and overall morphology with the [O iii] emission. The spectral analysis reveals that the soft X-ray emission of all the objects is likely to be dominated by a photoionized gas. This is strongly supported by the 190 ks combined XMM- Newton /RGS spectrum of Mrk 3, which different diagnostic tools confirm as being produced in a gas in photoionization equilibrium with an important contribution from resonant scattering. We tested with the code cloudy a simple scenario where the same gas photoionized by the nuclear continuum produces both the soft X-ray and the [O iii] emission. Solutions satisfying the observed ratio between the two components exist, and require the density to decrease with radius roughly like r -2 , similarly to what often found for the Narrow Line Region.
TS Gene Polymorphisms Are Not Good Markers of Response to 5-FU Therapy in Stage III Colon Cancer Patients

Aim: Although the predictive and prognostic value of thymidylate synthase (TS) expression and gene polymorphism in colon cancer has been widely studied, the results are inconclusive probably because of methodological differences. With this study, we aimed to elucidate the role of TS gene polymorphisms genotyping in therapy response in stage III colon carcinoma patients treated with 5-FU adjuvant chemotherapy. Patients and Methods: 251 patients diagnosed with stage III colon carcinoma treated with surgery followed by 5-FU based adjuvant therapy were selected. The variable number of tandem repeats (VNTR) and the single nucleotide polymorphism (SNP) in the 5′-untranslated region of the TS gene were genotyped. Results: There was a positive association between tumor T stage and the VNTR genotypes (p=0.05). In both univariate and multivariate survival analysis no effects of the studied polymorphisms on survival were found. However, there was an association between both polymorphisms and age. Among patients younger than 60 years, the patients homozygous for 2R seemed to have a better overall survival, whereas among the patients older than 67 this longer survival was seen by the carriers of other genotypes. Conclusion: We conclude that the TS VNTR and SNP do not predict response to 5-FU therapy in patients with stage III colon carcinoma. However, age appears to modify the effects of TS polymorphisms on survival.
MRC OX-22, a monoclonal antibody that labels a new subset of T lymphocytes and reacts with the high molecular weight form of the leukocyte-common antigen

A mouse monoclonal antibody (MRC OX-22) is described that labels rat T cells which mediate graft-versus-host reactions and those responsible for the suppression of antibody synthesis in hosts undergoing these reactions. In contrast, most of the T cells that provide help for B cells are MRC OX-22 negative. These results, taken together with those published previously, demonstrate that the rat contains at least three phenotypically and functionally distinct subsets of T cells. The MRC OX- 22 antibody also labels all B cells, 50% of bone marrow cells, but only 2% of thymocytes. Of these latter cells about half are found at the edge of the medulla and the remainder are randomly distributed throughout the cortex and medulla. These findings lend support to the view that mature thymocytes leave the thymus at the cortico-medullary junction, and also suggest that both cortex and medulla may be sites where thymocytes mature. Biochemical studies showed that the MRC OX-22 antibody reacts with the high molecular weight form of the leukocyte- common antigen (L-CA). Comparison with data on human L-CA suggests that the molecular and antigenic heterogeneity of this set of glycoproteins has been conserved between rat and man.
Laboratory-Modified Argument Driven Inquiry (Lab-Madi) Module: Content Validity Process

This paper aims to determine the validity of the LAB-MADI module using the Content Validity Index (CVI) and Percentage Calculation Method (PCM). The survey was conducted through the evaluation of six experts via purposive sampling. The instrument used for the evaluation was the content validity instrument. Based on the results of the analysis, the mean scores of CVI and PCM of the LAB-MADI module were 0.97 and 87.22%, respectively while the mean scores of CVI and PCM of eight practical activities based on the seven stages of the MADI model were 0.98 and 81.88% respectively. The results of the study indicate that the module has high validity in the six criteria assessed (suitability for target students, feasibility, time allocation and improving the dependent variables under study: argumentation skills, science process skills and concepts of diffusion and osmosis). Therefore, this module has great potential as a good module. This module is therefore recommended to be used and tested for its effectiveness. The module is also a form of alternative teaching method to guide biology teachers so that they can add value to students in terms of argumentation skills, science process skills and Biology concepts through practical work.
Stem cells and neurological disease

A disorder with many names The article by Stone et al (this issue, p 591– 596)1 addresses the natural history of a disorder with many names, none satisfactory. Functional, hysterical, psychogenic, medically unexplained, dissociative, conversion—all the names for this disorder have their faults. Yet the disorder is common, poses a management problem for doctors, and carries a poor prognosis. What is wrong with these patients? What is now clearly known not to be wrong is the occult presence of a neurological disorder. Several follow up studies, this one included, show that the rate of erroneous diagnosis is low; neurological …
On the design and analysis of evolutionary algorithms

: Evolutionary algorithms are problem-independent randomized search heuristics. It is discussed when it is useful to work with such algorithms and it is argued why these search heuristics should be analyzed just as all other deterministic and randomized algorithms. Such an approach is started by analyzing a simple evolutionary algorithm on linear functions, quadratic functions, unimodal functions, and its behavior on plateaus of constant ﬁtness. Furthermore, it is investigated what can be gained and lost by a dynamic variant of this algorithm. Finally, it is proved that crossover can decrease the run time of evolutionary algorithms signiﬁcantly.
Interpreting "altmetrics": viewing acts on social media through the lens of citation and social theories

More than 30 years after Cronin's seminal paper on "the need for a theory of citing" (Cronin, 1981), the metrics community is once again in need of a new theory, this time one for so-called "altmetrics". Altmetrics, short for alternative (to citation) metrics -- and as such a misnomer -- refers to a new group of metrics based (largely) on social media events relating to scholarly communication. As current definitions of altmetrics are shaped and limited by active platforms, technical possibilities, and business models of aggregators such as Altmetric.com, ImpactStory, PLOS, and Plum Analytics, and as such constantly changing, this work refrains from defining an umbrella term for these very heterogeneous new metrics. Instead a framework is presented that describes acts leading to (online) events on which the metrics are based. These activities occur in the context of social media, such as discussing on Twitter or saving to Mendeley, as well as downloading and citing. The framework groups various types of acts into three categories -- accessing, appraising, and applying -- and provides examples of actions that lead to visibility and traceability online. To improve the understanding of the acts, which result in online events from which metrics are collected, select citation and social theories are used to interpret the phenomena being measured. Citation theories are used because the new metrics based on these events are supposed to replace or complement citations as indicators of impact. Social theories, on the other hand, are discussed because there is an inherent social aspect to the measurements.
CO‐EVOLUTIONARY DYNAMICS OF A SOCIAL PARASITE–HOST INTERACTION MODEL: OBLIGATE VERSUS FACULTATIVE SOCIAL PARASITISM

Host–parasite co‐evolution can have profound impacts on a wide range of ecological and evolutionary processes, including population dynamics, the maintenance of genetic diversity, and the evolution of recombination. To examine the co‐evolution of quantitative traits in hosts and parasites, we present and study a co‐evolutionary model of a social parasite–host system that incorporates (i) ecological dynamics that feed back into their co‐evolutionary outcomes; (ii) variation in whether the social parasite is obligate or facultative; and (iii) Holling Type II functional responses between host and social parasite, which are particularly suitable for social parasites that face time costs for host location and its social manipulation. We perform local and global analyses for the co‐evolutionary model and the corresponding ecological model. In the absence of evolution, our ecological model analyses imply that an extremely small value of the death rate for facultative social parasites can drive a host extinct globally under certain conditions, while an extremely large value of the death rate can drive the parasite extinct globally. The facultative parasite system can have one, two, or three coexistence equilibria, while the obligate parasite system can have either one or three coexistence equilibria. Multiple coexistence equilibria result in rich dynamics with multiple attractors. The ecological system, in particular, can exhibit bi‐stability between the facultative parasite‐only equilibrium and the coexistence equilibrium when it has two coexistence equilibria. Our analysis on the co‐evolutionary model provides important insights on how co‐evolution can change the ecological and evolutionary outcomes of host–parasite interactions. Our findings suggest that: (i) The host and parasite can select different strategies that may result in local extinction of host or parasite. These strategies can have convergence stability (CS), but may not be evolutionary stable strategies (ESS); (ii) The host and its facultative (or obligate) parasite can have ESS that drive the host (or the obligate parasite) extinct locally; (iii) The dependence of vital rates on the phenotypic trait plays an important role in the CS of both exclusion and coexistence equilibria, as well as their ESS; and (iv) A small variance in the trait difference that measures parasitism efficiency can destabilize the co‐evolutionary system, and generate evolutionary arms‐race dynamics with different host–parasite fluctuating patterns.
Lost in the Forest, Stuck in the Trees: Dispositional Global/Local Bias Is Resistant to Exposure to High and Low Spatial Frequencies

Visual stimuli can be perceived at a broad, “global” level, or at a more focused, “local” level. While research has shown that many individuals demonstrate a preference for global information, there are large individual differences in the degree of global/local bias, such that some individuals show a large global bias, some show a large local bias, and others show no bias. The main purpose of the current study was to examine whether these dispositional differences in global/local bias could be altered through various manipulations of high/low spatial frequency. Through 5 experiments, we examined various measures of dispositional global/local bias and whether performance on these measures could be altered by manipulating previous exposure to high or low spatial frequency information (with high/low spatial frequency faces, gratings, and Navon letters). Ultimately, there was little evidence of change from pre-to-post manipulation on the dispositional measures, and dispositional global/local bias was highly reliable pre- to post-manipulation. The results provide evidence that individual differences in global/local bias or preference are relatively resistant to exposure to spatial frequency information, and suggest that the processing mechanisms underlying high/low spatial frequency use and global/local bias may be more independent than previously thought.
Activated Signal Transducers and Activators of Transcription 3 Signaling Induces CD46 Expression and Protects Human Cancer Cells from Complement-Dependent Cytotoxicity

CD46 is one of the complement-regulatory proteins expressed on the surface of normal and tumor cells for protection against complement-dependent cytotoxicity. Cancer cells need to access the blood circulation for continued growth and metastasis, thus exposing themselves to destruction by complement system components. Previous studies have established that the signal transducers and activators of transcription 3 (STAT3) transcription factor is persistently activated in a wide variety of human cancer cells and primary tumor tissues compared with their normal counterparts. Using microarray gene expression profiling, we identified the CD46 gene as a target for activated STAT3 signaling in human breast and prostate cancer cells. The CD46 promoter contains two binding sites for activated STAT3 and mutations introduced into the major site abolished STAT3 binding. Chromatin immunoprecipitation confirms binding of STAT3 to the CD46 promoter. CD46 promoter activity is induced by activation of STAT3 and blocked by a dominant-negative form of STAT3 in luciferase reporter assays. CD46 mRNA expression is induced by interleukin-6 and by transient transfection of normal human epithelial cells with a persistently active mutant construct of STAT3, STAT3C. Furthermore, we show that inhibition of STAT3-mediated CD46 cell surface expression sensitizes DU145 prostate cancer cells to cytotoxicity in an in vitro complement lysis assay using rabbit anti-DU145 antiserum and rabbit complement. These results show that activated STAT3 signaling induces the CD46 promoter and protects human cancer cells from complement-dependent cytotoxicity, suggesting a potential mechanism whereby oncogenic signaling contributes to tumor cell evasion of antibody-mediated immunity. (Mol Cancer Res 2007;5(8):823–32)
Comparison of Human Papillomavirus Detection in Urine and Cervical Samples Using High-Risk HPV DNA Testing in Northern Thailand

Objective. To evaluate the performance of high-risk human papillomavirus (HPV) DNA testing in urine samples compared to that of cervical sample testing in Northern Thailand. Methods. Paired urine and cervical samples were collected during the follow-up of women with a previous positive HPV test. HPV testing was performed using the Cobas 4800 HPV Test. Linear Array assay was used for genotyping in selected cases. Results. Paired urine and cervical samples were obtained from 168 women. Of 123 paired samples with valid results, agreement in the detection of high-risk HPV DNA was present in 106 cases (86.2%), with a kappa statistic of 0.65 (substantial agreement). Using the cervical HPV results as a reference, the sensitivity of urine HPV testing was 68.6% (24/35) and the specificity 93.2% (82/88). For the detection of histologic high-grade squamous intraepithelial lesion or worse (HSIL+), the sensitivity of urine HPV testing was 80.0% (4/5) and the specificity 78.0% (92/118). Conclusion. Although urine HPV testing had a rather low sensitivity for HPV detection, its sensitivity for histologic HSIL+ detection was high. For clinical use of urine HPV testing, standardization of specimen collection and processing techniques or application of a more sensitive test, especially in the detection of HPV52 and HPV58, is necessary.
Visual Information Processing From Multiple Displays

Objective: In this study, we examined how effectively people can monitor new stimuli on a peripheral display while carrying out judgments on an adjacent central display. Background: Improved situation awareness is critical for improved operator performance in aviation and many other domains. Given the limited extent of foveal processing, acquiring additional information from peripheral vision offers high potential gains. Method: Participants carried out a sequence of central perceptual judgments while simultaneously monitoring the periphery for new stimuli. Peripheral detection was measured as a function of central-judgment difficulty, the relative timing of the two tasks, and peripheral event rate. Results: Participants accurately detected and located peripheral targets, even at the highest eccentricity explored here (~30°). Peripheral detection was not reduced by increased central-task difficulty but was reduced when peripheral targets arrived later in the processing of central stimuli and when peripheral events were relatively rare. Conclusion: Under favorable conditions—high-contrast stimuli and high event rate—people can successfully monitor peripheral displays for new events while carrying out an unrelated continuous task on an adjacent display. Application: In many fields, such as aviation, existing displays were designed with low-contrast stimuli that provide little opportunity for peripheral vision. With appropriate redesign, operators might successfully monitor multiple displays over a large visual field. Designers need to be aware of nonvisual factors, such as low event rate and relative event timing, that can lead to failures to detect peripheral stimuli.
Towards a unitary Dalitz plot analysis of three-body hadronic B decays

A unitary model of the final state kaon pion interaction amplitudes in the B --> K pi pi decays is constructed. The weak decay penguin amplitudes, derived in QCD factorization, are supplemented by phenomenological contributions. The strange kaon- pion scalar and vector form factors are used to calculate the kaon pion effective mass and helicity angle distributions, branching ratios, CP asymmetries and the phase difference between the B0 and anti B0 decay amplitudes to K*(892) pi. The fit on the phenomenological parameters leads to a good agreement with the experimental data, particularly for the B --> K*(892) pi decays. However, our predicted B+- --> K*0(1430) pi+-, K*0(1430)--> K+-pi-+ branching fraction is smaller than the results of the Belle and BaBar collaborations, obtained from isobar model analyses. A new parameterization of the S-wave kaon- pion effective mass distribution, which can be used in future experimental Dalitz plot analyses, is proposed.
Improving Student Learning about a Threshold Conceptin the IS Discipline

The threshold concepts of a discipline are the portals to a deeper understanding of disciplinary knowledge, form the keys to learning progression, and are typically difficult to explain and learn. The notion of information systems (IS) as social systems is proposed as a threshold concept in the IS discipline. From this perspective IS are considered to be systems of people performing purposeful organizational activity, supported by embedded information technology (IT). Without an understanding of IS as social systems students are unlikely to come to terms with the complex notions underlying the development of IS in business organizations. This paper describes a study that sought to improve undergraduate student learning about IS as social systems. Three learning activities were designed to specifically target key aspects of IS as social systems. Questionnaires were used to categorize 30 students’ understanding before and after participating in the learning activities. A statistically significant improvement in students’ understanding was identified.
Three Weeks of Murine Hindlimb Unloading Induces Shifts from B to T and from Th to Tc Splenic Lymphocytes in Absence of Stress and Differentially Reduces Cell-Specific Mitogenic Responses

Extended space missions are known to induce stress and immune dysregulation. Hindlimb unloading is a ground-based model used to reproduce most spaceflight conditions. The aim of this study was to better characterize the consequences of prolonged exposure to hindlimb unloading on murine splenic lymphocyte sub-populations. To ensure that the observed changes were not due to tail restraint but to the antiorthostatic position, three groups of mice were used: control (C), orthostatic restrained (R) and hindlimb unloaded (HU). After 21 days of exposure, no difference in serum corticosterone levels nor in thymus and spleen weights were observed between HU mice and their counterparts, revealing a low state of stress. Interestingly, flow cytometric analyses showed that B cells were drastically reduced in HU mouse spleens by 59% and, while the T cells number did not change, the Th/Tc ratio was decreased. Finally, the use of a fluorescent dye monitoring lymphoproliferation demonstrated that lymphocyte response to mitogen was reduced in Th and Tc populations and to a greater extent in B cells. Thus, we showed for the first time that, even if restraint has its own effects on the animals and their splenic lymphocytes, the prolonged antiorthostatic position leads, despite the absence of stress, to an inversion of the B/T ratio in the spleen. Furthermore, the lymphoproliferative response was impaired with a strong impact on B cells. Altogether, these results suggest that B cells are more affected by hindlimb unloading than T cells which may explain the high susceptibility to pathogens, such as gram-negative bacteria, described in animal models and astronauts.