Miracle-dz/UniFAR-FTUs huggingface dataset:
Candidate gene analysis for loci affecting litter size and ovulation rate in swine.

A candidate gene approach was used to determine whether specific loci explain responses in ovulation rate (OR) and number of fully formed (FF), live (NBA), stillborn, and mummified pigs at birth observed in two lines selected for ovulation rate and litter size compared with a randomly selected control line. Line IOL was selected for an index of OR and embryonic survival for eight generations, followed by eight generations of two-stage selection for OR and litter size. Line C was selected at random for 16 generations. Line COL, derived from line C at Generation 8, underwent eight generations of two-stage selection. Lines IOL and C differed in mean EBV by 6.1 ova and 4.7 FF, whereas lines COL and C differed by 2.2 ova and 2.9 FF. Pigs of Generation 7 of two-stage selection lines were genotyped for the retinol binding protein 4 (RBP4, n = 190) and epidermal growth factor (EGF, n = 189) loci, whereas pigs of Generations 7 and 8 were genotyped for the estrogen receptor (ESR, n = 523), prolactin receptor (PRLR, n = 524), follicle-stimulating hormone beta (FSHbeta, n = 520), and prostaglandin-endoperoxide synthase 2 (PTGS2, n = 523) loci. Based on chi-square analysis for homogeneity of genotypic frequencies, distributions for PRLR, FSHbeta, and PTGS2 were different among lines (P < 0.005). Differences in gene frequencies between IOL vs C and COL vs C were 0.33 +/- 0.25 and 0.16 +/- 0.26 for PRLR, 0.35 +/- 0.20 and 0.15 +/- 0.24 for FSHbeta, and 0.16 +/- 0.16 and 0.08 +/- 0.18 for PTGS2. Although these differences are consistent with a model of selection acting on these loci, estimates of additive and dominance effects at these loci did not differ from zero (P > 0.05), and several of them had signs inconsistent with the changes in allele frequencies. We were not able to find significant associations between the polymorphic markers and phenotypes studied; however, we cannot rule out that other genetic variation within these candidate genes has an effect on the traits studied.
Characterization of plasma proteins in children of different Mycobacterium tuberculosis infection status using label-free quantitative proteomics

Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is an infectious disease found worldwide. Children infected with MTB are more likely to progress to active TB (ATB); however, the molecular mechanism behind this process has long been a mystery. We employed the label-free quantitative proteomic technology to identify and characterize differences in plasma proteins between ATB and latent TB infection (LTBI) in children. To detect differences that are indicative of MTB infection, we first selected proteins whose expressions were markedly different between the ATB and LTBI groups and the control groups (inflammatory disease control (IDC) and healthy control (HC) groups). A total of 521 proteins differed (> 1.5-fold or < 0.6-fold) in the LTBI group, and 318 proteins in the ATB group when compared with the control groups. Of these, 49 overlapping proteins were differentially expressed between LTBI and ATB. Gene Ontology (GO) analysis revealed most proteins had a cellular and organelle distribution. The MTB infection status was mainly related to differences in binding, cellular and metabolic processes. XRCC4, PCF11, SEMA4A and ATP11A were selected and further verified by qPCR and western blot. At the mRNA level, the expression of XRCC4, PCF11and SEMA4A presented an increased trend in ATB group compare with LTBI. At the protein level, the expression of all these proteins by western blot in ATB/LTBI was consistent with the trends from proteomic detection. Our results provide important data for future mechanism studies and biomarker selection for MTB infection in children.
Effects of nerve growth factor ( NGF ) on blood vessels area and expression of the angiogenic factors VEGF and TGFbeta 1 in the rat ovary

Background: Angiogenesis is a crucial process in follicular development and luteogenesis. The nerve growth factor (NGF) promotes angiogenesis in various tissues. An impaired production of this neurotrophin has been associated with delayed wound healing. A variety of ovarian functions are regulated by NGF, but its effects on ovarian angiogenesis remain unknown. The aim of this study was to elucidate if NGF modulates 1) the amount of follicular blood vessels and 2) ovarian expression of two angiogenic factors: vascular endothelial growth factor (VEGF) and transforming growth factor beta 1 (TGFbeta1), in the rat ovary. Results: In cultured neonatal rat ovaries, NGF increased VEGF mRNA and protein levels, whereas TGFbeta1 expression did not change. Sectioning of the superior ovarian nerve, which increases ovarian NGF protein content, augmented VEGF immunoreactivity and the area of capillary vessels in ovaries of prepubertal rats compared to control ovaries. Conclusion: Results indicate that NGF may be important in the maintenance of the follicular and luteal vasculature in adult rodents, either indirectly, by increasing the expression of VEGF in the ovary, or directly via promoting the proliferation of vascular cells. This data suggests that a disruption on NGF regulation could be a component in ovarian disorders related with impaired angiogenesis. Background Angiogenesis is an essential process in follicular development and luteogenesis [1,2]. Once the proliferation of new blood vessels is complete, a rapid capillary regression takes place in the non-fertile cycle which suggests a delicate coordination between angiogenesis inducers and inhibitors [3]. The intervention of ovarian vascularization has an adverse effect on the growth of the dominant follicle, the ovulation and the functioning of the corpus luteum and its ability to secrete progesterone [1,4]. The regulation of cyclic angiogenesis in the ovary is commanded by a variety of growth factors; vascular endothelial growth factor (VEGF) playing a major role by Published: 10 November 2006 Reproductive Biology and Endocrinology 2006, 4:57 doi:10.1186/1477-7827-4-57 Received: 26 September 2006 Accepted: 10 November 2006 This article is available from: http://www.rbej. com/content/4/1/57 © 2006 Julio-Pieper et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Bioaccumulation of Copper, Lead and Zinc by Taraxacum Officinale Agg : Growing on Urban Soils of Different Land-Use Types

Common dandelion Taraxacum officinale agg. (T. officinale F.H. Wigg) is a plant species commonly found on urban areas. It is characterised by low habitat requirements and proven bioindication properties. The aim of this study was to assess the possibility of using T. officinale agg. for monitoring of the urban soils in the City of Kielce with regard to selected heavy metal concentrations, i.e. Pb, Cu and Zn. Twenty-one soil and dandelion samples (roots and leaves) were collected from the area of Kielce. The study areas were designated with regard to land-use types, i.e. industrial areas, urban parks and forests, urban green areas, and urban allotment gardens. The total heavy metal concentrations were determined in the soil and plant material by the ICP-AES (inductively coupled plasma atomic emission spectroscopy) method, after mineralisation of the samples in a mixture of HCl-HNO3 (3:1). Moreover, the soil samples were analysed in terms of pH values. The concentrations of heavy metals in the analysed soils were oscillating at: 16.5-290 mg/kg d.m. for Pb; 7.1141mg/kg d.m. for Cu; 55.7-338 mg/kg d.m. for Zn In the case of dandelion leaves, the concentration range was recorded at: 1.07-3.11 mg/kg d.m. for Pb; 3.11-14.1 mg/kg d.m. for Cu; 19.7-121 mg/kg d.m. for Zn. Regarding the dandelion roots, the concentration range was as follows: 0.54-2.09 mg/kg d.m. for Pb; 2.89-8.11 mg/kg d.m. for Cu; 15.8-67.1 mg/kg d.m. for Zn. The study indicated that the concentrations of analysed heavy metals adopted the sequence of soil>leaves>root. The above relationship may Anna Świercz, Ewelina Zajęcka 1374 indicate a significant impact of heavy metals contained in the air on their concentrations in the upper parts of plants. The pH of analysed soils were oscillating at 3.99-7.92 and was not correlated with the concentrations of heavy metals in the soils. Heavy metal concentrations were not significantly affected by the land-use types, which may indicate that urban pollution emission zones are not limited only to industrial and transportation areas.
SOIL HEALTH IN SMALLHOLDER COLOMBIAN COFFEE SYSTEMS AND ITS SOCIO-ECONOMIC IMPLICATIONS

Coffee is a high value commodity in developing countries that is second in total commercial value only to petroleum. Understanding its agronomic characteristics including soil health (SH) is crucial for the environmental and socio-economic sustainability of coffee production. In this multidisciplinary study, SH and associated farmers’ perceptions were explained by farmers’ geodemographic traits. Results revealed that female and co-op member-farmers have higher SH than their counterparts, correct SH perception is associated with farm SH conditions, and biological indicators are most related to farmers’ perceptions. In the second chapter, the scoring framework created for assessing the Colombian soil samples was compared to other regional scoring frameworks. Results showed agreement in scoring SH indicators with disagreements arising from the contrasting inherent soil properties of the different localities. In the third chapter, the relationship between coffee quality and SH was assessed. Results showed that coffee quality is negatively correlated with key SH indicators.
Mortality from infections and malignancies in patients treated with renal replacement therapy: data from the ERA-EDTA registry.

BACKGROUND Infections and malignancies are the most common non-cardiovascular causes of death in patients on chronic renal replacement therapy (RRT). Here, we aimed to quantify the mortality risk attributed to infections and malignancies in dialysis patients and kidney transplant recipients when compared with the general population by age group and sex. METHODS We followed 168 156 patients included in the ERA-EDTA registry who started RRT in 1993-2007 until 1 January 2012. Age- and cause-specific mortality rates per 1000 person-years (py) and mortality rate ratios (MRRs) compared with the European general population (WHO) were calculated. To identify risk factors, we used Cox regression. RESULTS Infection-related mortality was increased 82-fold in dialysis patients and 32-fold in transplant recipients compared with the general population. Female sex, diabetes, cancer and multisystem disease were associated with an increased risk of infection-related mortality. The sex difference was most pronounced for dialysis patients aged 0-39 years, with women having a 32% (adjusted HR 1.32 95% CI 1.09-1.60) higher risk of infection-related mortality than men. Mortality from malignancies was 2.9 times higher in dialysis patients and 1.7 times higher in transplant recipients than in the general population. Cancer and multisystem disease as primary causes of end-stage renal disease were associated with higher mortality from malignancies. CONCLUSION Infection-related mortality is highly increased in dialysis and kidney transplant patients, while the risk of malignancy-related death is moderately increased. Young women on dialysis may deserve special attention because of their high excess risk of infection-related mortality. Further research into the mechanisms, prevention and optimal treatment of infections in this vulnerable population is required.
Bacterial populations in samples of bioleached copper ore as revealed by analysis of DNA obtained before and after cultivation

The composition of bacterial populations in copper bioleaching systems was investigated by analysis of DNA obtained either directly from ores or leaching solutions or after laboratory cultures. This analysis consisted of the characterization of the spacer regions between the 16 and 23S genes in the bacterial rRNA genetic loci after PCR amplification. The sizes of the spacer regions, amplified from DNAs obtained from samples, were compared with the sizes of those obtained from cultures of the main bacterial species isolated from bioleaching systems. This allowed a preliminary assessment of the bacterial species present in the samples. Identification of the bacteria was achieved by partial sequencing of the 16S rRNA genes adjacent to the spacer regions. The spacer regions observed in DNA from columns leached at different iron concentrations indicated the presence of a mixture of different bacteria. The spacer region corresponding to Thiobacillus ferrooxidans was the main product observed at high ferrous iron concentration. At low ferrous iron concentration, spacer regions of different lengths, corresponding to Thiobacillus thiooxidans and "Leptospirillum ferrooxidans" were observed. However, T. ferrooxidans appeared to predominate after culture of these samples in medium containing ferrous iron as energy source. Although some of these strains contained singular spacer regions, they belonged within previously described groups of T. ferrooxidans according to the nucleotide sequence of the neighbor 16S rRNA. These results illustrate the bacterial diversity in bioleaching systems and the selective pressure generated by different growth conditions.
Transport and Localization Elements in Myelin Basic Protein mRNA

Myelin basic protein (MBP) mRNA is localized to myelin produced by oligodendrocytes of the central nervous system. MBP mRNA microinjected into oligodendrocytes in primary culture is assembled into granules in the perikaryon, transported along the processes, and localized to the myelin compartment. In this work, microinjection of various deleted and chimeric RNAs was used to delineate regions in MBP mRNA that are required for transport and localization in oligodendrocytes. The results indicate that transport requires a 21-nucleotide sequence, termed the RNA transport signal (RTS), in the 3′ UTR of MBP mRNA. Homologous sequences are present in several other localized mRNAs, suggesting that the RTS represents a general transport signal in a variety of different cell types. Insertion of the RTS from MBP mRNA into nontransported mRNAs, causes the RNA to be transported to the oligodendrocyte processes. Localization of mRNA to the myelin compartment requires an additional element, termed the RNA localization region (RLR), contained between nucleotide 1,130 and 1,473 in the 3′ UTR of MBP mRNA. Computer analysis predicts that this region contains a stable secondary structure. If the coding region of the mRNA is deleted, the RLR is no longer required for localization, and the region between nucleotide 667 and 953, containing the RTS, is sufficient for both RNA transport and localization. Thus, localization of coding RNA is RLR dependent, and localization of noncoding RNA is RLR independent, suggesting that they are localized by different pathways.
Floating Point or LNS: Choosing the Right Arithmetic on an Aapplication Basis

For applications requiring a large dynamic range, real numbers may be represented either in floating-point (FP), or in the logarithm number system (LNS). Which system is best for a given application is difficult to know in advance, because the cost and performance of LNS operators depend on the target accuracy in a highly non linear way. In doubt, designers would choose floating-point. This article demonstrates a methodology for a better informed choice thanks to FPLibrary, a freely available, dual FP/LNS arithmetic operator library. FPLibrary may be used in the prototype phase of an application to obtain, with low design effort, accurate measures of performance, cost and accuracy of both LNS and FP approaches. Two case studies demonstrate the benefits of this methodology
The Potential of Antimicrobial Peptides as Biocides

Antimicrobial peptides constitute a diverse class of naturally occurring antimicrobial molecules which have activity against a wide range of pathogenic microorganisms. Antimicrobial peptides are exciting leads in the development of novel biocidal agents at a time when classical antibiotics are under intense pressure from emerging resistance, and the global industry in antibiotic research and development stagnates. This review will examine the potential of antimicrobial peptides, both natural and synthetic, as novel biocidal agents in the battle against multi-drug resistant pathogen infections.
A Randomized, Double-Blind, Placebo-Controlled, Dose-Ranging Study of Oral Sildenafil Citrate in Treatment-Naive Children With Pulmonary Arterial Hypertension

Background— Safe, effective therapy is needed for pediatric pulmonary arterial hypertension. Methods and Results— Children (n=235; weight ≥8 kg) were randomized to low-, medium-, or high-dose sildenafil or placebo orally 3 times daily for 16 weeks in the Sildenafil in Treatment-Naive Children, Aged 1–17 Years, With Pulmonary Arterial Hypertension (STARTS-1) study. The primary comparison was percent change from baseline in peak oxygen consumption (PV[Combining Dot Above]O2) for the 3 sildenafil doses combined versus placebo. Exercise testing was performed in 115 children able to exercise reliably; the study was powered for this population. Secondary end points (assessed in all patients) included hemodynamics and functional class. The estimated mean±SE percent change in PV[Combining Dot Above]O2 for the 3 doses combined versus placebo was 7.7±4.0% (95% confidence interval, −0.2% to 15.6%; P=0.056). PV[Combining Dot Above]O2, functional class, and hemodynamics improved with medium and high doses versus placebo; low-dose sildenafil was ineffective. Most adverse events were mild to moderate in severity. STARTS-1 completers could enter the STARTS-2 extension study; patients who received sildenafil in STARTS-1 continued the same dose, whereas placebo-treated patients were randomized to low-, medium-, or high-dose sildenafil. In STARTS-2 (ongoing), increased mortality was observed with higher doses. Conclusions— Sixteen-week sildenafil monotherapy is well tolerated in pediatric pulmonary arterial hypertension. Percent change in PV[Combining Dot Above]O2 for the 3 sildenafil doses combined was only marginally significant; however, PV[Combining Dot Above]O2, functional class, and hemodynamic improvements with medium and high doses suggest efficacy with these doses. Combined with STARTS-2 data, the overall profile favors the medium dose. Further investigation is warranted to determine optimal dosing based on age and weight. Clinical Trial Registration— http://www.clinicaltrials. gov. Unique identifier: NCT00159913.
A Language Modeling Approach to Tracking News Events

This paper presents the TNO tracking system for the 2000 Topic Detection and Tracking evaluation project (TDT2000). The objective of the TDT tracking task is to track events of interest over time. Being a first year participant to the TDT project, our original goal for this year was to build a baseline tracking system based on a language modeling approach. This approach had proved to be powerful for the TREC adaptive filtering task and several other IR tasks. Whereas the focus of adapative filtering lies on individual threshold adaptation based on feedback, tracking requires a uniform decision threshold. The assumption that test document-topic scores are approximately normally distributed turned out to be a key ingredient. The results on the tracking task of TDT2000 surpassed our expectations: our baseline system was ranked second for both the basic required and the alternate challenge conditions.
Empathy and Mental Health Literacy

Background: There is growing literature on mental health literacy (MHL), but few studies have conducted research on anything more than demographic predictors of MHL. We believe that those who are more empathic would be more interested in and more knowledgeable about mental illnesses. Objective: This study was concerned to establish whether people who were more empathic would have higher MHL. Methods: The 129 volunteer, university panel, participants completed the Interpersonal Reactivity Index and were presented with 15 vignettes describing people with various mental disorders. Questions assessed participants' identification of the disorders and their perception of the life adjustment of each person. Key Results: The results showed that 3 of the 4 empathy subscales correlated with the MHL score. Results from correlation and regression analyses suggest that people who are more empathic, have studied psychology, and have had personal experience of mental illness demonstrate better MHL. Conclusions: As predicted, people with greater MHL had greater empathy, but this cross-sectional correlational study could not ascertain causal patterns. [Health Literacy Research and Practice. 2017;1(2):e31–e40. ] Plain Language Summary: This study addressed whether people who are more empathic tend to be better informed about mental health issues because of their care for, interest in, and sympathy toward those with a range of mental illnesses. This was a questionnaire study and we did indeed find the relationship we thought may occur. However, we cannot be certain which caused which—do those who know more about mental illnesses and how common they are become more empathic or do those with greater empathy learn more about all aspects of mental illness?
Using serious games to teach business process modeling and simulation

Serious game and virtual-based environments have recently been used in business contexts to promote training of business related competences as is the case of business process modeling. Due to its characteristics modern BPM methods rely heavily on computers, since they are used as a tool for model, simulate and analyze a process and its effects on the organizations. Several authors argue that these approaches offer several limitations with respect to the modeling processes namely, they typically offer a low degree of collaboration between users, the simulations are simplistic and do not take into account the possible interaction of users during the simulation process and the interfaces are many time complex and abstract requiring an extensive training in order to use those tools. Serious games and virtual environments are mentioned as a promising approach for teaching and simulating BPM since due to their characteristics they can solve or minimize many of those limitations. In this paper we describe a serious game named ImPROVE for teaching business process modeling in a realworld context, the Manchester triage system. The simulation layer of the game was based on Time-based Activity-based Costing which also provides feedback information related to costing of activities in a business process.