Miracle-dz/UniFAR-FTUs huggingface dataset:
Plant community patterns in unburned and burned blackbrush (Coleogyne ramosissima) shrublands in the Mojave Desert

-The blackbrush vegetation type is dominated by Coleogyne ramossisinUl, which is thought to preclude the coexistence of many other plant species. Fire can remove blackbrush cover and possibly increase plant species richness and evenness. Fire also may increase the frequency and cover of alien annual grasses, thereby intensifying landscape flammability. We tested these predictions in unburned and burned (6---14 years postflre) blackbrush at 3 sites spanning the range of this vegetation type in the Mojave Desert. Species richness in unburned blackbrush was similar to published values for other vegetation types in western North America, but riclmess varied significantly among the 3 sites and 4 spatial scales (1, 10, 100, and 1000 m2). Richness values declined in order from annual forbs, woody perennials, herbaceous perennials, annual grasses, cacti, to perennial grasses. Fire reduced Coleogyll€ cover, thus boosting species evenness. In contrast, species richness decreased after burning, although the results varied among spatial scales. Total cover was unaffected by fire because cover of woody perennials decreased, while cover of annual forbs, annual grasses, herbaceous perennials, and perennial grasses increased. N'ative species richness and cover decreased, whereas alien richness and cover increased after burning, especially where the alien forb Erodillln cicutarillln was present. Fire had no effect on frequency and variable effects on cover of alien annual grasses. These results indicate that in blackbrush species richness can vary among sites and local spatial scales, and effects of fire can vary among plant Iife-fonns and between natives and aliens.
An overview on cytogenetics of the genus Astragalus subgenus Hypoglottis (Fabaceae)

This study reports the chromosome number and meiotic behavior of 24 populations belonging to 16 species of Astragalus sect. Malacothrix from Iran. Thirteen populations showed the diploid chromosome number 2n = 2x = 16; consistent with the proposed base number of x = 8 from ICPN. However, tri-, tetra- and hexaploids were also observed in the rest of the taxa. Although the species displayed regular bivalent pairing and chromosome segregation at meiosis, non-oriented bivalents, laggard chromosomes, precocious migration of chromosomes to the poles, micronuclei, multipolar meiocytes, desynapsis, chromosome stickiness, bridges, asynchronism and cytomixis were also determined as meiotic abnormalities. Evolution in chromosome numbers in taxa belonging to A. sect. Malacothrix along with six other sections which have been classified under A. subgen. Hypoglottis is also discussed.
Induction of Oral Tolerance in TGF-β1 Null Mice

Previous studies have suggested that oral tolerance induction by low doses of Ag is mediated by inhibitory cytokines, particularly TGF-β1. To examine the roles of TGF-β1 and other inhibitory cytokines in the induction of oral tolerance, TGF-β1 null mice and controls were gavaged with 10 to 20 mg (high dose) or 1 mg (low dose) of OVA for 3 days. After immunization with OVA, the in vitro proliferative response of OVA-specific popliteal lymph node cells was assessed. Lymphocytes from all TGF-β1 null mice fed high doses of OVA exhibited highly significant suppression compared with controls. A weaker, but still significant, suppression was observed in lymphocytes from the majority of TGF-β1 null mice fed low doses of OVA. In addition, supernatants from these lymphocytes exhibited lower levels of IL-4, IL-10, and IFN-γ than those from water-fed control animals. These results indicate that while TGF-β1 may play a role in suppression, inhibitory cytokines are not the exclusive mechanism by which low dose oral tolerance is induced.
Modeling of Total Fertility Rate (TFR) in East Java Province using Mixed Semiparametric Regression Spline Truncated and Kernel Approach

: The problem of population growth in Indonesia year by year is relatively very high. Based on data from Indonesia Demographic and Health Survey (SDKI), there is a very high increase of TFR and uncontrollable increase of population in Indonesia. TFR in East Java is very high in 2012 reached 20%. The behavior of TFR patterns is associated with the variables that are suspected to affect the Unmet Need, the Age Specific Fertility Rates (ASFR), the Human Development Index (HDI) and the Infant Mortality Rate (IMR) has a very special pattern. The relationship pattern between TFR and Unmet Need tends to be linear. While the pattern of relationship between TFR with ASFR and HDI, in contrast to the Unmet Need that tends to be nonlinear especially change as the increase or decrease value of these variables. The pattern of relationship between TFR and IMR appears not to follow a certain pattern. Taking into account this description, this study modeled using mixed semiparametric regression spline truncated and kernel spline models. The best model is a mixed semiparametric regression spline truncated and kernel model with a combination of knots that has the smallest GCV of 0.003964 and the coefficient of determination of 97.04%.
Photosynthetic productivity of the epilithic lichen Lecanora muralis: Long-term field monitoring of CO2 exchange and its physiological interpretation. I. dependence of photosynthesis on water content, light, temperature, and CO2 concentration from laboratory measurements

Summary CO 2 exchange of the epilithic, green algal lichen Lecanora muralis was monitored continuously for 15 months by means of an automatic cuvette in its natural habitat in the Botanical Garden, Wurzburg (Bavaria, Germany). As a first stage in the interpretation of the results, identically treated parallel samples were used, under controlled laboratory conditions, to determine the dependence of net photosynthesis (NP) and dark respiration (DR) on light, CO 2 concentration, thallus hydration and temperature. Results of these measurements are communicated in the present, first part of a series of publications. The lichen showed an extremely large and extended suprasaturation depression of its CO 2 assimilation. NP at high hydration was reduced almost to the compensation point. Maximal NP was only possible in a very small window of thallus water content (WC). Thallus water relations dominated the lichen’s responses to the other environmental factors and the combination of ‘optimal’ moisture and light conditions was a rare event and lasted only for short times under natural conditions. Light response curves showed typical saturation kinetics with ‘sun-plant’ characteristics. Maximal NP, light saturation, maximal quantum use efficiency, and light compensation point were highly dependent on WC. Temperature optimum of NP was about 22°C. But, at 2°C, NP was still 60% of maximal NP. Under optimal WC, NP became saturated at c 1000 ppm external CO 2 and, at natural, ambient CO 2 , NP was 62% of maximal NP with a CO 2 compensation point of 16 ppm. Suprasaturation depression of NP was not completely removed by 5000 ppm external CO 2 . Seasonal changes in photosynthetic capacity and other photosynthetic parameters were extremely small. However, dark respiratory capacity showed a clear adaptation to low winter temperatures. This resulted in a higher light compensation point for CO 2 exchange in winter than in summer. The daily and seasonal courses of CO 2 exchange of L. muralis under natural conditions will be reported in further communications. The field performance of the lichen will be interpreted and analysed by means of the data presented here.
Computational discovery of animal small RNA genes and targets

Though recently discovered, small RNAs appear to play a wealth of regulatory roles, being involved in degradation of target mRNAs, translation silencing of target genes, chromatin remodeling and transposon silencing. Presented here are the computational tools that I developed to annotate and characterize small RNA genes and to identify their targets. One of these tools is oligomap, a novel software for fast and exhaustive identi�cation of nearly-perfect matches of small RNAs in sequence databases. Oligomap is part of an automated annotation pipeline used in our laboratory to annotate small RNA sequences. The application of these tools to samples of small RNAs obtained from mouse and human germ cells together with subsequent computational analyses lead to the discovery of a new class of small RNAs which are now called piRNAs. The computational analysis revealed that piRNAs have a strong uridine preference at their 5' end, that unlike miRNAs, piRNAs are not excised from fold-back precursors but rather from long primary transcripts, and that the genome organization of their genes is conserved between human and mouse even though piRNAs on the sequence level are poorly conserved. In vertebrates, the most studied class of small regulatory RNAs are the miRNAs which bind to mRNAs and block translation. A computational framework is introduced to identify miRNA targets in mammals, ies, worms and �sh. The method uses extensive cross species conservation information to predict miRNA binding sites that are under evolutionary pressure. A downstream analysis of predicted miRNA targets revealed novel properties of miRNA target sites, one of which is a positional bias of miRNA target sites in long mammalian 3' untranslated regions. Intersection of our predictions with biochemical pathway annotation data suggested novel functions for some of the miRNAs. To gain further insights into the mechanism of miRNA targeting, I studied microarray data obtained in siRNA experiments. SiRNAs have been shown to produce o�- targets that resemble miRNA targets. This analysis suggests the presence of additional determinants of miRNA target site functionality (beyond complementarity between the miRNA 5' end and the target) in the close vicinity (about 150 nucleotides) of the miRNA-complementary site. Finally, as part of a study aiming to reduce siRNA o�-target e�ects by introducing chemical modi�cations in the siRNA, I performed microarray data analysis of siRNA transfection experiments. Presented are the methods used to quantify o�- target activity of siRNAs carrying di�erent types of chemical modi�cations. The analysis revealed that o�-targets caused by the passenger strand of the siRNA can be reduced by 5'-O-methylation.
Monitoring species abundance and distribution at the landscape scale

Summary 1. The abundance and distribution of a species are affected by processes which operate at multiple scales. Large-scale dynamics are increasingly recognized in conservation responses such as metapopulation management, transfrontier protected areas and softening the agricultural matrix. Landscape-scale monitoring is needed both to inform and judge their efficacy. In this Special Profile we address some of the challenges presented by monitoring at the landscape scale, how models of species distribution can be used to inform policy, and we discuss how monitoring at the global-scale could be approached. 2. Collecting data over a large area is inherently costly, so methods which can provide robust information at low-cost are particularly valuable. We present two papers which test low-cost approaches against more data-hungry methods (indices of abundance vs. direct density estimates, and species distribution models built from presence-only vs. presence/absence data). 3. Occupancy modelling is a useful approach for landscape-scale monitoring due to the relatively low-cost of collecting detection/non-detection data. We discuss challenges, such as non-random sampling locations and periodical unavailability for detection, in using detection/non-detection data for monitoring species distribution. Such data can also provide estimates of abundance and we show how existing models have been modified to allow the abundance of multiple species to be estimated simultaneously. 4. Models of species distribution can be used to project likely future scenarios and thus inform conservation planning where distributions are likely to change because of climate change or changing disturbance patterns. We also discuss how an optimization framework can be used to make efficient management decisions for invasive species management in the light of imperfect information. 5. Synthesis and applications. Monitoring is needed for many purposes including auditing past management decisions and informing future choices. Much monitoring data are collected at the site scale, although management authorities increasingly recognize landscape-scale dynamics. Recent global targets for conservation require monitoring which can report trends at the global-scale. Integrating data collected at a variety of scales to draw robust inference at the scale required is a challenge which deserves more attention from applied ecologists.
Evolution of indefinite generation lengths

Intrinsic mortality at relatively advanced age results from natural selection favouring early reproduction. When individuals produce many and early offspring, costs are incurred due to the accumulation of pleiotropic mutations with adverse effects late in life, which make senescence an inevitable result of evolution. However, a few organisms exist with seemingly indefinite generation lengths. This paper identifies conditions of life history and ecology under which natural selection favours continually reducing intrinsic mortality. The analysis considers the particular case of populations held at carrying capacity by density dependence suppressing net fertility, acting either on fecundity equally across fecund ages or on juvenile mortality up to the first fecund age. This broad category of density dependence increases the susceptibility of populations to invasion by mutations that extend net fertility into later life. Whether a population then evolves longer generation times depends on the relative timing of period benefit to onset of senescent cost amongst antagonistic pleiotropisms that arise to confront the selection process. Simulations show that if the onset of senescent costs either precedes the benefit, is concurrent with it, or is postponed by a fixed interval, then natural selection will favour those pleiotropisms that increase generation length. The selection on generation-lengthening pleiotropisms continues indefinitely and regardless of current generation length, for as long as the environment remains constant. The wide range of life histories encompassed by these conditions leads to the conclusion that many species may have evolved generation lengths considerably longer than the minimum set by developmental constraints.
Perforin-Deficient CD8+ T Cells Provide Immunity to Listeria monocytogenes by a Mechanism That Is Independent of CD95 and IFN-γ but Requires TNF-α

CD8+ T cells are effective mediators of immunity against Listeria monocytogenes, but the mechanisms by which they provide antilisterial immunity are poorly understood. CD8+ T cells efficiently lyse target cells in vitro by at least two independent pathways. To test the hypothesis that CD8+ T cell-mediated immunity to L. monocytogenes is dependent on perforin or CD95 (Fas, Apo-1), we used C57Bl/6 (B6) and perforin-deficient (PO) mice to generate CD8+ T cell lines specific for the L. monocytogenes-encoded Ag listeriolysin O (LLO). Both lines specifically produce IFN-γ and TNF-α, and mediate target cell lysis in vitro. Cytolysis mediated by the PO-derived CD8+ T cell line is delayed relative to the B6-derived line and is completely inhibited by anti-CD95 Abs. In vivo, PO-derived CD8+ T cells provide specific antilisterial immunity in B6 hosts, CD95-deficient hosts, and IFN-γ-depleted hosts. However, PO-derived CD8+ T cells fail to provide antilisterial immunity in hosts depleted of TNF-α. These results indicate that single Ag-specific CD8+ T cells derived from PO mice can mediate antilisterial immunity by a mechanism that is independent of CD95 or IFN-γ, but requires TNF-α.
Effect of the missense mutation Asp298Asn in MC4R on growth and fatness traits in commercial pig crosses in the Czech Republic

The current knowledge of factors regulating voluntary feed intake in pigs is quite limited. The objective of this study was to test the influence of the missense mutation p.Asp298Asn (AF087937:c.746G>A) of the MC4R gene on selected production traits in pig crosses. These crosses are commonly used on com - mercial farms in the Czech Republic. The allele frequencies of c.746G>A were as follows: G allele - 0.59 and A allele - 0.41. We detected statistically significant differences in the content of intramuscular fat in the musculus longissimus lumborum et thoracis, and a similar trend was observed in shoulder and neck. A allele correlated with higher values of fatness and G allele with a higher percentage of lean meat. However, we did not find any significant influence on either feed intake or growth rate in this study. For another muta -
REDOX REGULATION OF PROTEIN TRANSLATION IN EUKARYOTES

Gene expression may be controlled at multiple levels, e.g., through genomic architecture, transcription and translation. In the current work, we focused on regulation of protein synthesis. Historically, the investigation of the regulation of gene expression at the level of translation lagged behind the transcriptional control because of the lack of accessible high-throughput methods. Our research has begun with the finding of the use of alternative non-AUG start codon in thioredoxin-glutathione reductase (TGR), a selenoprotein involved in redox control during male reproduction. The use of this codon, CUG, relies on the Kozak consensus sequence and ribosomal scanning mechanism. However, the CUG serves as an inefficient start codon that allows downstream in-frame initiation, generating two isoforms of the enzyme in vivo and in vitro from the same mRNA. These findings were extended with the use of systemic, proteome-wide approaches, that supported targeted discovery of initiation start sites. For this purpose, a new technology, ribosomal profiling, was employed. It embraced high-throughput sequencing and offered analyses of ribosome occupancy along the mRNA at a single nucleotide resolution. We applied this technique to examine the interplay between transcription and translation under conditions of hydrogen peroxide treatment in Saccharomyces cerevisiae. Oxidative stress elicited by hydrogen peroxide led to a massive and rapid increase in ribosome occupancy of short upstream open reading frames (uORFs), including those with non-AUG translational starts, and N-terminal regions of ORFs that preceded the transcriptional response. In addition, this treatment induced the synthesis of N-terminally extended proteins and elevated stop codon read-through and frameshift events. It also increased ribosome occupancy at the beginning of ORFs and potentially duration of the elongation step. We identified proteins whose synthesis was rapidly regulated by hydrogen peroxide post-transcriptionally; however, for the majority of genes increased protein synthesis followed transcriptional regulation. Nevertheless, a number of proteins were regulated post-transcriptionally even at the 5 min time point. These data defined the landscape of genome-wide regulation of translation in response to hydrogen peroxide and suggested that "potentiation" (co-regulation of the transcript level and translation) is a feature of oxidative stress. Finally, we expanded this research to better define conditions for ribosome profiling, which are broadly applicable for studies on regulation of translation. ACKNOWLEDGEMENTS I would like to express my deepest gratitude to my advisor, Dr. Vadim Gladyshev, for giving me the opportunity to work in his lab, as well as for his support and continuous guidance during my years as …
STUDIES ON THE IMMUNOMODULATORY AND THERAPEUTIC EFFICACY OF NEEM (AZADIRACHTA INDICA) ON ENDOMETRITIS IN REPEAT BREEDING CROSSBRED COWS

An experiment was designed to investigate the imunomodulatory and therapeutic efficacy of neem on endometritis in repeat breeding crossbred cows. Twenty four cows were selected on the basis of history, breeding records, transrectal examination, white side test and randomly divided into 3 groups (Group A: 30 ml normal saline; Group B: 30 ml hydro-alcoholic neem bark; Group C: 30 ml hydro-acetonic neem bark). Treatments were given intrauterine beginning on the day of estrus for seven days in each group. Cervical mucus samples were collected on the day of estrus before treatment and at subsequent estrus after treatment and tested for appearance, pH, white side test and bacterial load. Blood samples were collected on the day of treatment and 24 hr after treatment and analyzed for glucose, Hb, PCV, TLC and DLC to know health status of the experimental animals. Uterine flushings were collected on the day of estrus before treatment and again on eighth day of first collection i.e. 24 hr after last treatment. These flushings were used for the estimation of total protein, immunoglobulin, TLC and polymorphonuclear cells (PMNs). At subsequent standing estrus following treatment, all cows were artificially inseminated twice using frozen semen 12 hours apart. Pregnancy was confirmed transrectally 45-60 days after insemination. Significant (p<0.05) decline in pH and bacterial load was observed in cervical mucus of the groups after treatment. Hemoglobin, neutrophils, lymphocytes and WBC were increased significantly (p<0.05) in both hydro-alcoholic and hydro-acetonic extract treated groups. Moreover, RBCs and glucose were increased in hydroalcoholic extract treated group. Significant (p<0.05) rise was found in TLC, PMN and immunoglobulin concentration in both the treated groups. Although both the extracts led to improved clinical recovery and conception rates, the hydro-alcoholic extract was more effective. Based on these results, it may be concluded that hydro-alcoholic extract of the neem has a better antibacterial and immuno-modulation and can be used as a therapy for endometritis in repeat breeding crossbred cows.
The Mediating Role of Metacognitive Self-Regulation on Student Procrastination and Academic Performance

: The current study intends to investigate the link between procrastination, academic performance, and metacognitive self-regulation, as well as the mediation role of metacognitive self-regulation between procrastination and academic performance. There were 199 undergraduate students of psychology participated in this study. They were administered metacognitive self-regulation scale, pure procrastination scale, and also reported their recent Grade Point Average (GPA). Results indicate that procrastination correlated significantly and negatively with metacognitive self-regulation. In line with that, metacognitive self-regulation has a positive and significant association with GPA. Furthermore, metacognitive self-regulation fully mediated the link between procrastination and GPA.