Miracle-dz/UniFAR-FTUs huggingface dataset:
Disease processes may be reflected by correlations among tissue kallikrein proteases but not with proteolytic factors uPA and PAI-1 in primary ovarian carcinoma

Abstract In epithelial ovarian cancer, the high mortality rate is usually ascribed to late diagnosis, since these tumors commonly lack early-warning symptoms, but tumor-associated biomarkers useful for prognosis or therapy response prediction are in short supply. However, members of the tissue kallikrein serine protease family, the serine protease uPA and its inhibitor PAI-1, are associated with tumor progression of ovarian cancer. Therefore, we used ELISA to determine uPA, PAI-1, and tissue kallikreins hK5–8, 10, 11, and 13 in extracts of 142 primary tumor tissue specimens from ovarian cancer patients and studied the strength of association between protein expression levels of these tumor tissue-associated factors. uPA, PAI-1, hk5, and hk8 were related to FIGO stage; hK5 expression was higher in FIGO III/IV than in FIGO I/II patient tissues. PAI-1 and hk5 differed significantly according to nuclear grading; expression of hK5 was higher in G3 than in G1/2 tumors. Associations between uPA, PAI-1, and the tissue kallikreins were weak. There were strong pairwise correlations within the cluster of tissue kallikreins hK5, 6, 7, 8, 10, and 11, but their bivariate distributions depended on nuclear grading. These results support the notion that several tissue kallikreins are co-expressed in ovarian cancer patients, substantiating the existence of a steroid hormone-driven tissue kallikrein cascade in this disease.
Sex Ratios of Nestling and Fledgling Red-Cockaded Woodpeckers (Picoides borealis) Favor Males

Red-cockaded woodpeckers breeding in coastal South Carolina produce nestling and fledgling sex ratios dominated by males. Differences in the costs of daughters versus sons in terms of the growth of nestlings, an earlier death of sons, or local resource competition between parents and daughters are not evident. However, local resource enhancement is a possible source of the theoretically reduced costs of sons. Because red-cockaded woodpeckers breed in clans consisting of pairs alone and pairs assisted by adult male helpers, we hypothesized that progeny sex depends on the presence or absence of helpers. We found no strong support for this notion; nestling sex, however, depends on the tenure class of breeding females, suggesting that sex-ratio variation may be facultative (in the sense of Williams 1979) and related to kinship asymmetries among the clan types in this species.
The habenula clock regulates response to a stressor

The lateral habenula, a regulator of neuromodulators that is activated by aversive stimuli, contains a molecular clock whose significance is unknown. Here, using zebrafish, we test the hypothesis that the habenula clock affects the switch in internal state that is triggered by an aversive stimulus. Consistent with the expression of clock genes, habenula neural activity varies in a circadian manner. Disruption of clock function, by expression of a truncated clock gene specifically in the habenula, did not affect acute responses to the alarm pheromone Schreckstoff. However, behaviours elicited by transient exposure to Schreckstoff, namely freezing in a novel environment and dark avoidance, were reduced. Behaviours that are regulated by the pineal clock and not triggered by stressors were unaffected. These findings establish that the habenula clock independently influences the stress response induced by an aversive stimulus, indicating that this clock underlies circadian variation in response to a stressor.
Genome-Wide Mutagenesis Identifies Factors Involved in Enterococcus faecalis Vaginal Adherence and Persistence

Enterococcus faecalis is a Gram-positive commensal bacterium native to the gastrointestinal tract and an opportunistic pathogen of increasing clinical concern. E. faecalis also colonizes the female reproductive tract, and reports suggest vaginal colonization increases following antibiotic treatment or in patients with aerobic vaginitis. Currently, little is known about specific factors that promote E. faecalis vaginal colonization and subsequent infection. ABSTRACT Enterococcus faecalis is a Gram-positive commensal bacterium native to the gastrointestinal tract and an opportunistic pathogen of increasing clinical concern. E. faecalis also colonizes the female reproductive tract, and reports suggest vaginal colonization increases following antibiotic treatment or in patients with aerobic vaginitis. Currently, little is known about specific factors that promote E. faecalis vaginal colonization and subsequent infection. We modified an established mouse vaginal colonization model to explore E. faecalis vaginal carriage and demonstrate that both vancomycin-resistant and -sensitive strains colonize the murine vaginal tract. Following vaginal colonization, we observed E. faecalis in vaginal, cervical, and uterine tissue. A mutant lacking endocarditis- and biofilm-associated pili (Ebp) exhibited a decreased ability to associate with human vaginal and cervical cells in vitro but did not contribute to colonization in vivo. Thus, we screened a low-complexity transposon (Tn) mutant library to identify novel genes important for E. faecalis colonization and persistence in the vaginal tract. This screen revealed 383 mutants that were underrepresented during vaginal colonization at 1, 5, and 8 days postinoculation compared to growth in culture medium. We confirmed that mutants deficient in ethanolamine catabolism or in the type VII secretion system were attenuated in persisting during vaginal colonization. These results reveal the complex nature of vaginal colonization and suggest that multiple factors contribute to E. faecalis persistence in the reproductive tract.
Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana

Advanced transcriptome sequencing has uncovered that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Here we reveal, in the plant model Arabidopsis thaliana, that the PIN7 gene, which encodes a polarly localized transporter for the phytohormone auxin, produces two evolutionary-conserved transcripts. These isoforms PIN7a and PIN7b, differing in a 4 amino acid motif, are present at nearly equal levels in most cells. Although both variants do not differ in the subcellular localization and transport auxin with similar capacity, they closely associate and mutually influence their stability within the plasma membrane. Phenotypic complementation tests reveal that the functional contribution of PIN7b per se is minor but it markedly attenuates the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. These results establish alternative splicing of the PIN family as a conserved, functionally-relevant mechanism, unveiling an additional regulatory level of auxin-mediated plant development.
Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6)

All-atom simulations reveal the molecular mechanisms of inositol hexakisphosphate binding to HIV capsids. Inositol hexakisphosphates (IP6) are cellular cofactors that promote the assembly of mature capsids of HIV. These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP6 increases the stable lifetimes of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP6. We find that capsid hexamers and pentamers have differential binding modes for IP6. Ligand density calculations show three sites of interaction with IP6 including at a known capsid inhibitor binding pocket. Free energy calculations demonstrate that IP6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly. These results elucidate the molecular role of IP6 in stabilizing and assembling the retroviral capsid.
Cdon mutation and fetal alcohol converge on Nodal signaling in a mouse model of holoprosencephaly

Holoprosencephaly (HPE), a defect in midline patterning of the forebrain and midface, arises ~1 in 250 conceptions. It is associated with predisposing mutations in the Nodal and Hedgehog (HH) pathways, with penetrance and expressivity graded by genetic and environmental modifiers, via poorly understood mechanisms. CDON is a multifunctional co-receptor, including for the HH pathway. In mice, Cdon mutation synergizes with fetal alcohol exposure, producing HPE phenotypes closely resembling those seen in humans. We report here that, unexpectedly, Nodal, not HH, signaling is the point of synergistic interaction between Cdon mutation and fetal alcohol. Window-of-sensitivity, genetic, and in vitro findings are consistent with a model whereby brief exposure of Cdon mutant embryos to ethanol during gastrulation transiently and partially inhibits Nodal pathway activity, with consequent effects on downstream HH signaling during midline patterning. These results illuminate mechanisms of gene-environment interaction in a multifactorial model of a common birth defect.
The predatory strategy, natural diet, and life cycle of Cyrba algerina, an araneophagic jumping spider (Salticidae: Spartaeinae) from Azerbaijan

Abstract The life cycle and natural diet of Cyrba algerina (Lucas) in the Apsheron Peninsula (Azerbaijan) was determined by sampling at frequent intervals throughout the year. Early‐instar juveniles emerged in late July, grew to about half of adult size by winter, over‐wintered and then, in the spring of the following year, grew to adult size and reached maturity. The primary mating season was in May, after which the number of adults in the population declined sharply. Ten arthropod orders were represented in the prey records from nature. Six of these were insects and four were arachnids. Spiders (order Araneae) were the dominant prey, accounting for 56% of the records. Half of these spiders were from one family, Oecobiidae. In laboratory prey‐choice tests, C. algerina selected spiders in preference to insects and selected oecobiids in preference to other spiders. Video taping under infrared light confirmed that the Azerbaijan C. algerina captures prey in complete darkness.
Cell-based approaches in drug development – a concise review

Abstract In vitro models represent an alternative technique to in vivo or ex vivo studies in the drug development process. Cell-based assays are used to measure the level of proliferation and toxicity, as well as activation of signalling pathways and changes in morphology in cultivated cells. The studies conducted in vitro are aimed to estimate the newly synthesised drugs’ ability to permeate biological barriers and exert their therapeutic or cytotoxic effects. However, more than half of all studied drugs fail in the second or third phase of clinical trials due to a lack of confirmed efficacy. About a third of drugs fail because of safety issues, such as unacceptable levels of toxicity. To reduce attrition level in drug development, it is crucial to consider the implementation of translational phenotypic assays as well as to decipher various molecular mechanisms of action for new molecular entities. In this review, we summarise the existing cell-based methods most frequently used in the studies on drugs, taking into account their advantages and drawbacks. Running title: Cell-based approaches in drug development
Efeito do período de coleta de urina, dos níveis de concentrado e de fontes protéicas sobre a excreção de creatinina, de uréia e de derivados de purina e a produção microbiana em bovinos Nelore

The effects of collection days on urinary excretion of creatinine and purine derivatives (PD), absorbed purines and microbial N synthesis (Nmic) were evaluated in different categories of Nellore cattle: heifers, steers, bulls and lactating cows. Yield of Nmic estimated from spot urine samples was compared to that obtained by total urine collection. Sixteen feedlot Nellore animals were assigned to a completely randomized design in a split plot scheme with treatments (two levels of concentrate [25 or 50%] and four categories [heifers, steers, bulls and lactating cows] included in the plots (2 x 4 factorial arrangement) and collection days (six days) in the sub-plots. No significant interactions among concentrate levels, animal categories and collection days were observed. In addition, urinary volume was not affected by concentrate levels and collection days, although a significant effect was observed for cows. Neither treatments nor collection days significantly affected urinary excretion of creatinine that averaged 27.1 mg/kg0.75. Similar results were observed for absorbed purines and Nmic production. Production of Nmic estimated by spot urine sample did not differ from that obtained by total collection. The estimation of Nmic also was not affected by concentrate levels and animal category. It was concluded that 24-h urinary collection period is recommended for Nellore cattle and that was independent of animal category (heifers, steers, bulls and lactating cows). Therefore, spot urine samples can be used to estimate microbial protein synthesis.
How is phenology of grassland species influenced by climate warming across a range of species richness

We imposed two different global changes, climate warming and declining species richness, to synthesized grassland ecosystems, in order to determine both their single-factor effect as well as their possible interactions on plant phenology. Twelve climate-controlled chambers were therefore exposed to two temperature treatments (0 °C and 3 °C above ambient air temperature) and three species richness treatments (1,3 and 9 species). Measurements consisted of visual phenological observations of the appearance of flower buds until flowering and of autumn senescence stages, as well as of readings of the leaf chlorophyll content. In spring, chlorophyll concentrations increased under warming (9.7%) and decreasing species richness (39.4%). Warming also induced an earlier spring start (4 days) and enhanced flower production, whereas decreasing species richness likewise enhanced flower production but delayed the start of spring (16 days). In autumn, leaf senescence started simultaneously at the two temperature treatme.
Aortocoronary conduits may show a different inflammatory response - comparative study at transcript level

Abstract Coronary artery bypass grafting (CABG), together with percutaneous coronary intervention (PCI), are both still the most efficient procedures for myocardial revascularization to treat advanced coronary artery disease (CAD). Donor blood vessels used in CABG are usually the internal thoracic artery (ITA) and saphenous vein (SV). The importance of inflammation and inflammatory pathways in graft patency is well established. Nevertheless, not all molecular mechanisms underlying the inflammatory process appear to be clear. Employing the expressive microarray approach to analyze the transcriptome of both venous and arterial grafts, five GO BP terms has been selected: “cellular response to interferon-gamma”, “inflammatory response”, “interferon-gamma-mediated signaling pathway”, “response to interferon-gamma” and “positive regulation of inflammatory response”. This study aimed to evaluate potential molecular factors that could be characteristic markers for both SV and ITA conduits. Running title: Aortocoronary conduits may show a different inflammatory response
First record of a rare sand whiting, Sillago caudicula (Perciformes: Sillaginidae), from Madagascar

Abstract Seven specimens (106–180 mm in standard length) of the sand whiting Sillago caudicula Kaga, Imamura & Nakaya, 2010 previously known only from the type specimens from Oman, were collected from the southeast coast of Madagascar. These new specimens represent the first record of the species from Madagascar and the southern hemisphere. Comparisons in meristic and morphometric characters with the four type specimens from Oman, as well as with the five other species in the subgenus Sillago, allowed their clear identification using the following combination of characters: small head (28.6–30.1% SL), 35–36 total vertebrae, fused or narrowly separated first and second hypurals, fused third and fourth hypurals, and 9–11 dusky spots on midline of body.
High order modified differential equation of the Beam–Warming method, I. The dispersive features

Abstract The analysis of the modified partial differential equation (MDE) of the constant wind speed advection equation explicit difference scheme up to the eighth order with respect to both space and time derivatives is presented. So far, in majority of publications this modified equation has been derived mainly as a fourth-order equation. The MDE is presented in the so-called Π-form of the first differential approximation. This form includes only the space derivatives of higher order p and their coefficients μ(p). Analysis of these coefficients provides indications of the nature of the dissipative and dispersive errors. A fragment of the stencil for determining the modified differential equation up to the eighth-order MDE for the second-order Beam–Warming scheme is included. The derived coefficients μ(p) as well as the analysis of the phase shift errors, the phase and group velocities and dispersive features on the basis of these coefficients have not been published so far. The dissipative features of this method we present in [33].
Browsed Betula pubescens trees are not carbon-limited

Summary 1Slower growth after repetitive browsing of young trees has been attributed to a carbon (C) limitation, but data from long-term studies are lacking. To determine if repeated summer browsing causes a C (source) limitation in trees in the long-term, we analysed the non-structural carbohydrate (NSC) and nitrogen (N) concentrations and pools of Betula pubescens saplings subjected to different clipping treatments (unclipped, 33% and 66% shoot removal) for 7 years. 2The short-term effect of browsing on C allocation was assessed by clipping trees with different browsing histories and analyzing their C and N responses within the same growing season. 3Long-term repetitive summer browsing significantly decreased sapling growth and soluble sugar (SS) concentrations in fine roots. However, trees subjected to different browsing histories did not change their C partitioning into starch. Although trees with a different browsing history showed differences in the NSC concentrations and pools of leaves, these differences were not maintained through time. 4Simulated browsing had no significant short-term effect on root C and N pools of birch trees, but it decreased all C pools in leaves, 1-year and current-year stems and the starch and total NSC pools in main stems. 5We conclude that although browsing may cause a temporary decrease in C pools, B. pubescens trees are able to compensate for such losses and hence are not C-limited in the long-term.
Environmental Worldview: A Case Study of Young People from Kosovo

Abstract Understanding attitudes towards the environment is important because they often determine behaviour that either increases or decreases environmental quality. In this article we investigate the environmental worldview of the young people from Kosovo. The New Revised Environmental Paradigm Scale or New Ecological Paradigm Scale, known as NEP Scale (Dunlap et al., 2000) was used. The study involved 330 young people age 18-20. 150 young people are from secondary schools, and other (180) are from some different faculties at the State University in Mitrovica. The mean score for the full NEP scale in this study was 3.48, which indicates a low endorsement of the NEP among the sample of Kosovo young people. The averages of the sub-dimensions varied between 3.08 (“Limits to growth”) and 3.73 (“Eco-crisis”). Like as others non-industrialized societies, young people from Kosovo tend to believe in the profound connection between humanity and nature, or there are no clear differences between pro-NEP and pro-DSP views. This study confirms the thesis that environmental worldviews differ across cultures. The mean value of the NEP Scale can be feasibly associated with various variables concerning general environmental attitudes. In order to discover the factors that create a pro-ecological orientation of young people in this country, additional researches are needed.
Numerical Investigations of Stress Concentration in Reinforcement Steel Structure by Composite Overlays

Abstract The stress concentration observed in the vicinity of cut-outs and holes in structural elements significantly influences the fatigue endurance of machines subjected to cyclic loads. Numerous studies have been made so far to improve this situation and increase the structure lifetime. Several design recommendations have also been worked out to avoid the problem of premature failure. The proposed article illustrates the influence of the composite overlays applied around the cut-outs made in flat steel constructional elements subjected to axial tension. The detailed study concerns the reinforcement made from the FRP (fibre reinforcement polymer) composite applied around the notches. Two types of composite materials were used, namely: TVR 380 M12/R-glass (glass fibres embedded in epoxy resin matrix) and AS4D/9310 (carbon fibres embedded in epoxy resin matrix). In the first step, the detailed numerical studies (finite element analysis) were performed for the steel samples (with no overlays added) with cut-outs made in the form of circle, square and triangle hole (the last two with rounded corners). The results of these studies were compared with the existing analytical solutions with respect to the stress concentration factors (SCF) estimation. The relatively good conformity was observed when using dense meshes of finite elements placed around the void vicinity. In the next step, the composite overlays were applied around cut-outs and their influence on the stress concentration was investigated. The influence of the fibre orientation, numbers of layers, sizes of the composite overlay used were considered. It was proved that the application of composite overlays evidently decreases the stress concentration around the notches.
Nest scrape design and clutch heat loss in Pectoral Sandpipers (Calidris melanotos)

Summary 1. The reasons why birds construct nest scrapes, and the extent to which scrape designs reflect functional optima, are poorly understood. Working on Pectoral Sandpipers (Calidris melanotos, Vieillot), we investigated whether scrapes function to insulate clutches and are efficiently designed to reduce heat loss rates. 2. Excavating a scrape and using lining material reduced the rate at which an object positioned within a scrape lost heat by 9% and 25%, respectively, suggesting that lined scrapes insulate clutches. 3. The rate of heat loss from an object within a scrape increased with scrape depth and decreased non-linearly with lining depth. The extent to which wind increased forced convective heat loss decreased with scrape depth. 4. On average, Pectoral Sandpipers used the minimum lining depth that approximately minimized heat loss through the lining. Mean scrape depth approximately minimized convective cooling in windy conditions while minimizing heat loss to the ground. Pectoral Sandpiper scrapes therefore efficiently reduced heat loss given conflicting environmental thermal pressures. 5. Available lining materials differed in insulative quality when both damp and dry. Pectoral Sandpipers used lining materials that insulated relatively well when damp more than expected given random collection of locally available materials. Linings therefore insulated efficiently given the damp nesting environment.