Miracle-dz/UniFAR-FTUs huggingface dataset:
Presence of mismatches between diagnostic PCR assays and coronavirus SARS-CoV-2 genome

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; initially named as 2019-nCoV) is responsible for the recent COVID-19 pandemic and polymerase chain reaction (PCR) is the current standard method for its diagnosis from patient samples. This study conducted a reassessment of published diagnostic PCR assays, including those recommended by the World Health Organization (WHO), through the evaluation of mismatches with publicly available viral sequences. An exhaustive evaluation of the sequence variability within the primer/probe target regions of the viral genome was performed using more than 17 000 viral sequences from around the world. The analysis showed the presence of mutations/mismatches in primer/probe binding regions of 7 assays out of 27 assays studied. A comprehensive bioinformatics approach for in silico inclusivity evaluation of PCR diagnostic assays of SARS-CoV-2 was validated using freely available software programs that can be applied to any diagnostic assay of choice. These findings provide potentially important information for clinicians, laboratory professionals and policy-makers.
OSlihc: An Online Prognostic Biomarker Analysis Tool for Hepatocellular Carcinoma

Liver hepatocellular carcinoma (LIHC) is one of the most common malignant tumors in the world with an increasing number of fatalities. Identification of novel prognosis biomarker for LIHC may improve treatment and therefore patient outcomes. The availability of public gene expression profiling data offers the opportunity to discover prognosis biomarkers for LIHC. We developed an online consensus survival analysis tool named OSlihc using gene expression profiling and long-term follow-up data to identify new prognosis biomarkers. OSlihc consists of 637 cases from four independent cohorts. As a risk assessment tool, OSlihc generates the Kaplan–Meier survival plot with hazard ratio (HR) and p value to evaluate the prognostic value of a gene of interest. To test the reliability of OSlihc, we analyzed 65 previous reported prognostic biomarkers in OSlihc and showed that all of which have significant prognostic values. Furthermore, we identified four novel potential prognostic biomarkers (ATG9A, WIPI1, CXCL1, and CSNK2A2) for LIHC, the elevated expression of which predict the unfavorable survival outcomes. These genes (ATG9A, WIPI1, CXCL1, and CSNK2A2) may be potentially new biomarkers to identify at-risk LIHC patients when further validated. By OSlihc, users can evaluate the prognostic abilities of genes of their interest, which provides a platform for researchers to identify prognostic biomarkers to further develop targeted therapy strategies for LIHC patients. OSlihc is public and free to the users at http://bioinfo.henu. edu.cn/LIHC/LIHCList.jsp.
Generation Z and Y – are they different, when it comes to trust in robots?

Readiness is still a hot topic in the 21st century, but it is not about modern ICT technology any more, but about artificial intelligence (AI) and robots in specific. Robots are the new industrial revolution. They can extend human sensory, psychomotor, and cognitive capabilities, and for this, they are feared, or even abhorred by some. The new generations, however, seem to be much more eager to engage with them. Present paper intends to analyse international literature about young generations’ attitudes towards AI and robots and presents a primary research about Hungarian young people’s attitude towards robots. The aim of the paper is to test the statements of international literature against a suitable sample of Y and Z generation people, to figure out, whether there are real significant differences between the two generations, when it comes to robots and trust in them. On the basis of the data presented in the paper generation Z is much more willing to engage with robots, than generation Y. However, this attitude is not generated by their "loneliness", but originates from their need for personal contact. Hence, the research did not only succeed in identifying differences between the two generations under scrutiny, but pinpointed a difference that is rather neglected, or misinterpreted in international literature.
The skull of Cteniogenys, a choristodere (Reptilia: Archosauromorpha, from the Middle Jurassic of Oxfordshire

The genus Ctemogenys was originally described as a lizard on the basis of isolated jaw fragments from the Upper Jurassic deposits of Como Bluff, Wyoming. The discovery of new material from a Middle Jurassic locality at Kirtlington, Oxfordshire, showed that Cteniogenys was not a lizard, but an early choristodere. The skull is represented by a collection of isolated bones, associated on the basis of fit and dermal sculpture pattern. The bones are here described and compared with those of the Late Cretaceous and Palaeocene choristoderes Champsosaurus and Simoedosaurus. Allowing for the much smaller size of the Middle Jurassic form, there is a close correspondence between the isolated bones of the three genera. Comparison with known choristoderes, based on an analysis of 53 derived character states, suggests that Ctemogenys is the most primitive of known genera. In general, the character states shared by all choristoderes support recent analyses which conclude that choristoderes arc derived from archosauromorph diapsids, not lepidosauromorphs as once thought. At Kirtlington, Cteniogenys forms part of a diverse microvertebrate assemblage including amiids, sharks, frogs, salamanders, lizards, mammals, crocodiles, pterosaurs, turtles and small dinosaurs.
Anticipating Parenthood Among Lesbian, Gay, Bisexual, and Heterosexual Young Adults Without Children in Portugal: Predictors and Profiles

Parenthood is a highly valued life goal, independent of one’s sexual orientation. However, the majority of studies exploring young adults’ parenthood plans have relied exclusively on samples of heterosexual individuals. This study aimed (i) to explore differences in parenthood intentions as a function of sexual orientation, (ii) to investigate to what extent sociodemographic and psychological characteristics predict parenthood intentions of lesbian, gay, bisexual (LGB), and heterosexual individuals, (iii) to test the mediating effect of stigma between sexual orientation and parenthood intentions, and (iv) to identify and characterize profiles of prospective parenthood (through cluster analysis). Data were gathered using an online survey from 375 self-identified LGB and heterosexual young adults without children in Portugal, with a mean age of 25.83 years old (SD = 4.49). Findings indicated that LGB individuals were less likely to intend to have children than heterosexual individuals; furthermore, among LGB individuals, lesbian women expressed stronger intentions to have children than did gay men. Similarities between heterosexual and LGB young adults were observed concerning the psychological determinants of parenthood intentions. Four distinctive profiles of prospective parenthood were identified: aspiring parents not anticipating stigma, aspiring parents anticipating stigma, childfree intent, and childfree ambivalent. Lesbian and bisexual women mostly populated the childfree ambivalent cluster; in contrast, the aspiring parents anticipating stigma cluster contained an overrepresentation of men, including sexual minority men. Professionals may want to attend to communalities and specificities of prospective parenthood as a function of sexual orientation, in order to provide unbiased and culturally competent support to sexual minority individuals.
IR-Level Dynamic Data Dependence Using Abstract Interpretation Towards Speculative Parallelization

Recently, with the wide usage of multicore architectures, automatic parallelization has become a pressing issue. Speculative parallelization, one of the most popular automatic parallelization techniques, depends on estimating probably-parallelized code parts. This in turn motivates the employment of data dependence detection techniques for these code parts to report whether they contain dependence or not in order to be parallelized. In this paper, we propose a runtime data-dependence detection technique that is based on abstract interpretation at the intermediate representation (IR) level. We apply our proposed approach on the most frequently visited blocks of the code, hot loops. Unlike most existing approaches in which data analysis occurs at compile time, our proposed method conducts the analysis immediately while interpreting the code, which in turn saves the analysis time for potentially parallelized loops. Specifically, the proposed technique depends on the concept of abstract interpretation to analyze the hot loops at runtime. This process is done by firstly computing the abstract domain for each hot loop program points. Each abstract domain is incrementally computed, till a fixpoint is achieved for all program points, and correspondingly the analysis terminates in order to consecutively detect the existence of data dependence. Once the analysis result reports a parallelization possibility for the finished hot loop, the interpreter invokes the compiler to resume the execution in a parallel fashion as recommended by our proposed approach. The proposed technique is implemented on LLVM compiler, then used to test the dependence detection for a set of kernels on the Polybench framework, and the data dependence analysis required for each kernel is studied in terms of the computation overhead.
GATA Binding Protein 3 Is a Direct Target of Kruppel-Like Transcription Factor 7 and Inhibits Chicken Adipogenesis

Kruppel-like transcription factor 7 (KLF7) is a negative regulator of adipogenesis, however, its precise mechanism is poorly understood. Our previous KLF7 ChIP-seq analysis showed that one of the KLF7 binding peaks was present upstream of GATA binding protein 3 (GATA3) in chicken preadipocytes. In the present study, we identified GATA3 as a target of KLF7. Overexpression analysis showed KLF7 markedly enhanced the endogenous expression of GATA3 in the immortalized chicken preadipcyte cell line (ICP2), and the luciferase reporter assay showed that KLF7 overexpression increased the reporter gene activity of the cloned upstream region (-5285/-4336 relative to the translation initiation codon ATG) of GATA3 in ICP2 and DF1 cells, and mutation of the putative KLF7 binding site abolished the promotive effect of KLF7 overexpression on the reporter gene activity of the cloned GATA3 upstream region. ChIP-qPCR further demonstrated that KLF7 directly bound to the GATA3 upstream region. Gene expression analysis showed that GATA3 mRNA expression in abdominal adipose tissue was significantly higher in lean chicken line than in the fat line at 2, 3, and 6 weeks of age. In addition, GATA3 mRNA expression markedly decreased during the preadipocyte differentiation. Furthermore, a functional study showed that GATA3 overexpression inhibited the differentiation of the ICP2 cells. Taken together, our results demonstrated that KLF7 inhibits chicken adipogenesis, at least in part through direct upregulation of GATA3.
Malolactic fermentation in wine – beyond deacidification

Malolactic fermentation (MLF) in wine is a secondary fermentation that usually occurs at the end of alcoholic fermentation by yeasts, although it sometimes occurs earlier. It is practically a biological process of wine deacidification in which the dicarboxylic L-malic acid (malate) is converted to the monocarboxylic L-lactic acid (lactate) and carbon dioxide (Davis et al. 1985). Deacidification is particularly desirable for high-acid wine produced in cool-climate regions, such as New Zealand and Canada. This process is normally carried out by lactic acid bacteria (LAB) isolated from wine, including Oenococcus oeni (formerly Leuconostoc oenos; Dicks et al. 1995), Lactobacillus spp. and Pediococcus spp. (Wibowo et al. 1985). Various technologies, such as bioreactors with high-density cells and immobilized cells or enzymes, have been developed to facilitate wine deacidification (Maicas 2001). Oenococcus oeni is the preferred species used to conduct MLF due to its acid tolerance and flavour profile produced. In addition to its occurrence in wine, MLF occurs in other fermented beverages, such as cider (Carr 1987; Jarvis et al. 1995). Numerous reviews on MLF have been published since the 1960s, covering the history of research on MLF, taxonomy, ecology, genetics and physiology of wine LAB and the oenological significance of MLF (Bartowsky and Henschke 1995; Kunkee 1967, 1974, 1991; Lafon-Lafourcade 1983; Davis et al. 1985; Wibowo et al. 1985; Henick-Kling 1988, 1993, 1995; Henschke 1993; van Vuuren and Dicks 1993; Lonvaud-Funel 1995, 1999; Versari et al. 1999). However, a review that is specifically focused on the metabolic capacity of wine LAB and its impact on wine quality is still lacking. Furthermore, new information on the metabolism of wine LAB has emerged since the publication of these reviews. It is now accepted that the role of MLF is more than just a deacidification process, although deacidification via MLF is still a primary objective in wine fermentation in cool-climate regions. The complexity and diversity of the metabolic activity of LAB suggest that MLF may affect wine quality both positively and negatively. Knowledge of the metabolism of wine LAB is necessary to assess the impact of MLF on wine quality. The primary focus of this review is to evaluate the current knowledge of the metabolism of wine LAB (predominantly oenococci) with a view to stimulating further research in this area. The author also aims to assess the potential impact of MLF on wine flavour, mouthfeel/body and human health in relation to the metabolism of wine LAB. References are made with respect to the metabolism of LAB from other fermented beverages and foods, such as cider and cheese.
Effect of mechanical removal of water hyacinth (Eichhornia crassipes) on the water quality and biological communities in a Mexican reservoir

The Valsequillo reservoir, located near the city of Puebla, Mexico, is a hard-water eutrophic subtropical system, with minimum temperatures in winter (November–December), and marked dry-rain seasons with fluctuating depth. The reservoir has been infested with water hyacinth for over three decades. A management program involving the use of triturating machines was applied from December 1996 to February 1997. After trituration, remains were allowed to settle to the bottom. The purpose of this study was to monitor the changes in the water quality and the biological communities before and after physical control of weeds. A monthly sampling of surface water was performed at four stations one year before the treatment. After trituration, one year sampling was also carried out. Variables measured included temperature, Secchi disk transparency, depth, pH, dissolved oxygen, oxygen saturation, hardness, nitrate content, nitrite content, ammonia, orthophosphates, and numerical abundance of phytoplankton, zooplankton, and nekton. Weed control affected changes in all variables measured, as a result of residual decomposition of triturated matter. Secchi transparency and oxygen levels decreased and pH became slightly more alkaline. More important changes occurred for nutrients. Orthophosphate concentration increased, for nitrate and nitrite, increase was about 320% and 450% respectively. Ammonia reached lethal values for at least four months after trituration. As a result, phytoplankton decreased initially, and when it flourished again, the Bacillariophyta were replaced by Cyanophyta. Euglenophyta were important in both years. Of zooplankton, calanoids decreased, but cyclopoids and cladocerans maintained similar numbers, although the latter group changed in composition in that Ceriodaphnia was replaced by Moina. Fish disappeared from the system after weed trituration. In the second year a small recovery of water quality occurred, but water hyacinth also started to develop again. At present, Valsequillo is again covered by water hyacinth.
The reproduction of lake trout in southern Lake Superior

Abstract The principal spawning grounds of lake trout (Salvelinus namaycush namaycush) in United States waters of southern Lake Superior are on rocky shoals at depths of less than 20 fathoms. Most spawning occurs in October and early November. Of the mature fish collected on or near the spawning grounds, 60 to 69 percent were males. Among mature fish the average length of females was greater than that of males; few males less than 24 inches or females less than 26 inches in total length were caught. Recoveries of lake trout tagged on the spawning grounds showed that some males remained in the immediate area for a period of several weeks during the spawning season. Marked fish showed a tendency to return during later years to spawning grounds on which they had been tagged, even though many of them ranged long distances between spawning seasons. The percentage of the total weight composed by gonads of maturing females collected in 1950 was 5.0 percent on August 11–30 and 12.3 percent on October 6–9, but thi.
Effects of Fin‐Clipping on the Foraging Behavior and Growth of Age‐0 Muskellunge

Abstract We evaluated the effects of fin-clipping on the foraging behavior and growth of age-0 muskellunge Esox masquinongy. Fish were subjected to one of six fin-clipping treatments (one or both pectoral and pelvic fins, all paired fins, and a nonclipped control) and allowed to forage on golden shiners Notemigonus crysoleucas in laboratory pools (1.7 m in diameter). Observations of foraging behavior showed that muskellunge required a similar number of stalks, follows, and strikes to capture prey regardless of fin clip. Capture efficiencies (56%) were also similar among treatments. In outdoor pools (1.5 m in diameter), the growth and food conversion efficiency of fin-clipped muskellunge feeding on golden shiners over a 1-month period did not differ from those of unclipped controls. Fin removal did not compromise foraging behaviors and growth for juvenile muskellunge foraging on moderately evasive prey, and fish showed immediate behavioral compensation.
Assessment of crop farmers coping strategies to pastoralism/nomad activities in Nigeria

Abstract This study examined the coping strategies of crop farmers to pastoralist activities in Odo-Otin Local Government Area of Osun State, Nigeria. A multistage sampling technique was used to select 120 farmers. The data were collected using a well-structured questionnaire and interview and were analysed using descriptive and inferential statistical tools. The result revealed various levels of damage caused to food security by the pastoralist as follows: compaction of soil (84%), damage and eating of the crops on the field (79%), indiscriminate bush burning leading to fire outbreak on farms (73%), stealing of farm produce by herders (73%), pollution of water points (54%), killing of farmers (13%) and others. The result further revealed the coping strategies used by crop farmers: praying for peace (98%), early harvesting (95%), early planting (92%), multiple farm plots (91%), group farming (90%), relocating farm (77%), police intervention (60%), government intervention (9%), NGO intervention (9%) and insurance (4.2%). The results of Chi-square analysis showed that there is a significant relationship between the educational status (X2 = 13.06, P = 0.01) and coping strategies used against pastoralist activities. Therefore, it is recommended that the government should formulate a policy that will stimulate peace among crop farmers and pastoralist to sustain food security and reduce poverty among rural dwellers, thereby transforming the rural environment into an attractive centre.
The Effect of Ammonia on Magnesium Metabolism in Sheep

Zusammenfassung Der Einflus einer erhohten Ammoniakkonzentration im Pansen auf den Magnesium-Stoffwechsel beim Schaf Am gewaschenen und vorubergehend isolierten Pansen von Schafen wurde der Einflus einer akut erhohten Ammoniakkonzentration in der Pansenflussigkeit auf die Magnesiumabsorption gepruft. Um akute und chronische Wirkungen erhohter NH4-Konzentrationen in der Pansenflussigkeit auf den Mg-Haushalt zu untersuchen, wurden Bilanzversuche an Schafen mit Pansenkanulen durchgefuhrt. In einem weiteren Versuch wurde der Effekt einer erhohten Ammoniakkonzentration im Blut auf die Mg-Ausscheidung im Urin uberpruft. Es ergaben sich folgende Beobachtungen: 1 NH4 (40 mmol/1) in der Pansenflussigkeit reduzierte die ruminale Mg Absorption um 30% im Vergleich mit einer NH4 freien Flussigkeit. 2 Eine intraruminale Harnstoffinfusion fuhrte zu einem Konzentrationsanstieg von NH4 in der Pansenflussigkeit von 4,81 auf 47,9 mmol/1. Wahrend des akuten Anstiegs der Ammoniakkonzentration in der Pansenflussigkeit verringerte sich vorubergehend (2–3 Tage) die Mg Ausscheidung im Urin. Bei langer anhaltender hoher NH4 Konzentration in der Pansenflussigkeit wurden keine signifikanten Einflusse auf Nettoresorption, Retention, Urinexkretion und Plasmakonzentration von Magnesium festgestellt. 3 Eine intravenose Infusion von NH4 fuhrte zu einer erhohten Plasmakonzentration von NH4, aber beeinfluste nicht die Plasmakonzentration von Mg und die Mg-Ausscheidung mit dem Urin. Aus den Beobachtungen wurde geschlossen, das ein schneller und starker Anstieg der NH4-Konzentration im Pansensaft die Mg-Absorption aus dem Pansen vorubergehend vermindert. Bei langer bestehender erhohter NH4-Konzentration in der Pansenflussigkeit scheint sich das Epithel adaptieren und damit den depressiven Effekt des NH4 auf die Mg-Absorption ausgleichen zu konnen.