Miracle-dz/UniFAR-FTUs huggingface dataset:
Nuclear magnetic resonance spectroscopy as a new approach for improvement of early diagnosis and risk stratification of prostate cancer

Prostate cancer (PCa) is the second most common male cancer worldwide and the fifth leading cause of death from cancer in men. Early detection and risk stratification is the most effective way to improve the survival of PCa patients. Current PCa biomarkers lack sufficient sensitivity and specificity to cancer. Metabolite biomarkers are evolving as a new diagnostic tool. This review is aimed to evaluate the potential of metabolite biomarkers for early detection, risk assessment, and monitoring of PCa. Of the 154 identified publications, 27 and 38 were original papers on urine and serum metabolomics, respectively. Nuclear magnetic resonance (NMR) is a promising method for measuring concentrations of metabolites in complex samples with good reproducibility, high sensitivity, and simple sample processing. Especially urine-based NMR metabolomics has the potential to be a cost-efficient method for the early detection of PCa, risk stratification, and monitoring treatment efficacy. 概 要前列腺癌 (PCA) 是全球第二个最常见的男性癌症, 同时也是男性癌症死亡的第五大原因。 早期发现和危险度分级是提高前列腺癌患者生存率 最有效的方法。 目前前列腺癌的生物标志物缺乏足够的敏感性和特异性, 而代谢产物作为生物标 志物可以作为一种新的提高早期诊断的工具。 我们检索了 154 篇出版物, 其中 27 篇和 38 篇是分别关于尿液和血清代谢组学分析的原研论文, 提示了核磁共振波谱分析是一种很有前景的检测方法, 可用于测量复杂的样本中代谢物的浓度, 具有良好的重现性、 高灵敏度和样本处理的便捷性。 特别是基于核磁共振的代谢组学检测尿液已成为检测前列腺癌的早期潜在的危险度分级和监测治疗效果的有效的方法。
BatScope manages acoustic recordings, analyses calls, and classifies bat species automatically

BatScope is a free application for processing acoustic high-frequency recordings of bats. It can import data, including meta-data information, from recorders such as Batlogger. The resulting content can be filtered visually as spectrograms or according to data fields and can be displayed. Automated processing includes detecting and extracting of echolocation calls, filtering noise, and measuring statistical parameters. Calls are classified to species by statistically matching to a reference database. A weighted list of classifiers helps to assign the most likely species per call. Classifiers were trained on 19 636 echolocation calls of 27 European bat species. When classifiers all agree on a species (76.4% of all cases), the mean correct classification rate reaches 95.7%. A sequence’s summary statistic indicates the most likely species occurring therein. Classifications can be verified visually, by filtering, and by acoustic comparison with reference calls. Procedures are available for, e.g., excluding dubious cutouts from the statistics and for accepting or overriding the proposed species assignment. Acoustic recordings can be exported and exchanged with other users. Finally, the verified results can be exported to spreadsheets for further analyses and reporting. We currently reprogram BatScope using Java, PostgreSQL, and R to reach a unified and portable software architecture.
Effects of negative pressure on boar semen quality during liquid storage at 17°C

This study aimed to investigate the influence of negative pressure on boar semen quality during liquid preservation at 17°C. Semen samples from ten large white boars were collected and pooled, divided into four equal parts, and diluted with Modena containing 0.4% (w/v) of bovine serum albumin. The semen samples were placed in a closed container with valve, and a negative pressure was applied for 2–5 minutes using a vacuum pump with a barometer. The control group had no treatment, the P200 group was treated at 200 mbar, the P400 group at 400 mbar, and the P800 group at 800 mbar. During liquid preservation, sperm motility, total antioxidant capacity, and semen H2O2 content were analyzed every 24 h. The effective survival time of boar semen during preservation was evaluated. The results indicated that a suitable negative pressure decreased the effects on reactive oxygen species on boar sperm quality during liquid preservation compared with the control group. Among all the groups, the 400 mbar negative pressure group had the highest sperm motility, total antioxidant capacity, and the percentage of spermatozoa with high mitochondrial membrane potential. The P400 group also had semen H2O2 content than the other groups. A suitable negative pressure improves sperm quality by reducing oxidative stress and the respiratory metabolism of sperm, and the optimum negative pressure is 400 mbar.
Pediatric reference intervals of free thyroxine and thyroid stimulating hormone in three different hospitals

Abstract Objective Using data retrieved from three different hospitals, we established indirect reference intervals of free thyroxine (FT4) and thyroid stimulating hormone (TSH) for the Centaur XP or the Immulite 2000 instruments, in separate reference limits at each subset. Methods We categorized children into seven age groups: 4–7 days, 8–15 days, 16–23 days, 24–61 days, 3–6 months, 7–36 months and 4–6 years. After a Box-Cox transformation was employed, we followed the Horn algorithm to eliminate the extreme values. Results The remaining FT4 (11,230) and TSH (11,274) tests were statistically analyzed. We determined separate reference limits at each subset with their own 2.5th and 97.5th percentiles. The interaction effect of both hospital and age grouping on FT4 was meaningful, but there was no interaction effect on TSH. Conclusions Pediatric FT4 and TSH test results should be interpreted via narrowed age groups, especially in the first 3 weeks of neonatal period. Our reference limits may be recommended in pediatric follow-ups, considering the conditions of prematurity, birth-weight or multiple births. Preanalytical and analytical variations related with complex molecular structure of FT4 should be taken into consideration to ensure the validity of the result.
Seasonal variation in physiological responses, stress and metabolic-related hormones, and oxidative status of Murrah buffaloes

Abstract Harsh environmental conditions adversely affect the health and productivity of buffaloes. The present study was conducted to investigate the effect of seasonal thermal stress on the physiological responses, oxidative stress and some related hormones in Murrah buffaloes. A significant (p < 0.05) rise was observed in the rectal temperature, respiration rate, pulse rate and superoxide dismutase (SOD) during hot-humid (HH) and hot-dry (HD) seasons compared to thermoneutral (TN) season. Plasma cortisol and malondialdehyde (MDA) levels were low during TN season, intermediate in HD and highest during HH season. Although the levels of plasma triiodothyronine and thyroxine were high during TN season, their levels declined notably during HD and HH seasons. The temperature humidity index had a positive correlation (p < 0.01) with physiological responses, SOD, MDA and plasma cortisol levels. However, it was negatively correlated (p < 0.01) with the concentration of plasma thyroid hormones. The results reveal that buffaloes could cope efficiently with heat stress by reducing the levels of metabolic heat production-related hormones and releasing more antioxidant (SOD). However, they were still showing signs of stress which were reflected by higher levels of cortisol, lipid peroxidation (MDA) and physiological responses. Therefore, promoting health and productivity of buffaloes requires suitable management strategies to alleviate heat stress and provide comfort to them during extreme seasons.
Global measurements of human transcription factor occupancy: Insights into development and genome evolution

Global measurements of human transcription factor occupancy: Insights into development and genome evolution Andrew Ben Stergachis Chair of the Supervisory Committee: Associate Professor John A. Stamatoyannopoulos Department of Genome Sciences Transcription factors (TFs) are a class of proteins that interact with the genome, dictating which parts of the genome are utilized by a given cell. Despite the central role TFs play in regulating the genome, technologies available to date have not permitted global measurement of TF occupancy within the cell. Consequently, our understanding of how TFs model cellular development and genome evolution has been limited. To address this, I focused my graduate studies on the development of genomic and proteomic tools that facilitates global measurements of TF occupancy within a cell, including the development of: (i) targeted proteomic assays to quantify TF protein abundances within the nucleus; (ii) a protein-centric method to map TF protein occupancy in functionally distinct chromatin microenvironments; (iii) a genome-wide DNaseI footprinting method that enables construction of global maps of TF occupancy along the genome and core human regulatory networks; and (iv) a method for mapping the in vivo affinity of a TF genome-wide. Using a combination of these techniques, I have identified the sequence and chromatin features that direct TF occupancy within a cell and have characterized the mechanisms underlying TF occupancy dynamics during development and oncogenesis. These global TF occupancy maps have revealed novel insights into how TF occupancy shapes the evolution of both non-coding and coding genomic sequence. Specifically, it appears that TF affinity, not occupancy, plays the dominant role in shaping the evolution of TF binding elements. In addition, coding TF binding elements significantly contribute to protein evolution and codon usage biases in mammals. Together, these results depict the sequence, chromatin, developmental and evolutionary forces that shape TF occupancy within a cell—revealing unforeseen evolutionary constraints on the human genome.
Comparison of transient and asymptotic perturbation analyses of three epiphytic orchid species growing in coffee plantations in Mexico: effect on conservation decisions

ABSTRACT Background: Epiphyte removal forms part of routine management in shade coffee plantations. Aims: Assess the current status of three population orchids growing in Mexican shaded coffee plantations and evaluate the effect of perturbing the transient behaviour of different life stages. Methods: We modelled the short-term response of eliminating I) non-reproductive juveniles, or II) reproductive adult plants from coffee bushes, on populations of Oncidium poikilostalix, Lepanthes acuminata and Telipogon helleri (Orchidaceae). First, we calculated the transient dynamics per se and second, we made a perturbation analysis on population inertia. Finally, we made a comparison with a traditional sensitivity analysis. Results: All three species showed different positive asymptotic growth rate: O. poikilostalix (λmax = 1.106), L. acuminata (λmax = 1.209), and T. helleri (λmax = 1.012). The effect of eliminating the major part of the juvenile or adult orchids gave population inertia in relation to steady state, respectively, (+19%, -24%) for O. poikilostalix, (+17%, -28%) for T. helleri and (+57%, -35%) for L. acuminata. Conclusions: Eliminating juveniles or adults affects in different ways the short-term dynamics due to differential impact on size stages that have the non-linear effects associated with important disturbances that currently affect orchids growing in coffee plantations.
Investigation of the population structure of barley landraces (Hordeum vulgare L.) from different eco-geographical environments in Syria

The population structure o f accessions o f barley landraces (BLR) (Hordeum vulgare L ssp. vulgare) from Syria was investigated using genetic markers. Barley landraces are old, diverse cultivars of barley which have evolved under cultivation without much directed selection. BLRs have been shown to outperform modern cultivars under low input conditions in Syria due to the level of local adaptation and population buffering (i.e. the ability to compensate the failure o f a component by a genetically different component o f the same population) based on a high level of diversity within landraces. The purpose o f the present study was to identify suitable genetic markers, to use these to characterise the population structure and diversity of barley landraces, and to investigate how population structure is influenced by environmental conditions. Results were compared with those achieved for accessions o f wild barley (Hordeum vulgare ssp. spontaneum C. Koch) and modern cultivars in order to investigate the influence of domestication and cultivation on mating system and population structure. Implications o f the results for breeding strategies in low input agriculture and for conservation strategies were investigated. Two recent accessions o f wild barley and 15 recent accessions o f BLRs were available from Syria, where landraces are still under cultivation. Seven earlier accessions o f the same landraces from Syria were available from gene banks. Modern cultivars and progeny of known pedigree were available from barley breeders. Genetic indices of accessions were analysed using three contrasting types o f genetic markers, morphological, isoenzyme and molecular markers, respectively. Standard methods of population genetics were used to analyse the population structure o f accessions. Environmental conditions o f the sampling sites were analysed using the geographical information system ArcView. Results showed that BLRs are predominantly inbreeding populations with a low outcrossing rate o f 1.7%. The same outcrossing rate has been reported for wild barley,
Effect of substrate change on macrozoobenthos structure

The aim of the study was to determine the impact of the increase in the organic matter content in the bottom sediments on the benthic fauna structure. The research was carried out in a strongly rheolimnic the Wloclawek Dam Reservoir (Poland). The samples were taken on eight dates from March 1988 to February 1989. The sampling sites were located at the following depths: 1 m, 2 m, 5 m, 8 m and 10 m. The organic matter content in the bottom sediments increased with depth from 0.6% at a depth of 1 m to 13.2% at a 10 m depth. To a depth of 8 m, the bottom fauna was relatively rich in quality. The significant decline in the diversity and, above all, the number of taxa of the macrozoobenthos groups, only at a depth of 10 m were found. In turn, the abundance (density and biomass) of the bottom fauna increased with depth of the site. The analysis of the increase in Oligochaeta abundance with depth suggests that at the level of about 4% of the organic matter content in the bottom sediments, the food conditions are no longer a factor limiting the Oligochaeta occurrence.
Age, growth and maturity of tub gurnard (Chelidonichthys lucerna Linnaeus 1758: Triglidae) in the inshore coastal waters of Northwest Wales, UK

10.5-41.0 cm (males) and 10.4-57.5 cm (females). The majority of the female fish were 31 between 20-30cm TL (60.2%) and the majority of the male fish between 20-30cm TL 32 (58.3%) respectively. TL/weight (W) relations for male and female fish were similar and 33 the combined data was described by W = 0.0067 TL 3.10 . Age of fish ranged between 1-7 34 years old for female fish and 1-5 years old for male fish respectively with the majority of 35 female fish 3 years old (40%) and the majority of male fish 3 years old (37%). The age 36 structures of female and male tub gurnards were not significantly different with the older 37 age classes consisting predominantly of female fish. Both males and females exhibited 38 similar asymptotic growth patterns and the combined von Bertalanffy growth function 39 was TL t = 51.6 (1-e [-0.25(t + 0.41)] ). Instantaneous rates of total mortality were calculated as 40 1.04 year -1 for males and 1.11 year -1 for females. The size ( L 50 ) and age at first maturity 41 ( A 50 ) were estimated to be 29.1 cm TL and 2.8 years for males, 27.7 cm TL and 2.7 years 42 for females and 28.0 cm TL and 2.8 years for both sexes combined. The results of this 43 study provide the first information on the biology and population dynamics of C. lucerna 44 in the Irish Sea, the first data collected in the northeast Atlantic since 1985 and the most 45 northerly population studied to date.
Myeloid p38 MAPK signaling in intestinal homeostasis, inflammation and tumorigenesis = Señalización por la MAPK p38 de células mieloides en la homeostasis, inflamación y tumorogénesis intestinal

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Macrorefugia for North American trees and songbirds: Climatic limiting factors and multi‐scale topographic influences

Results: End-of-century macrorefugia for both trees and songbirds were concentrated in western mountains and, to a lesser extent, in north-eastern coastal regions. For the highest-value refugia, precipitation was generally most limiting in the north, and warm temperatures and moisture availability were limiting in the south. Tree refugia were more limited by precipitation and moisture, while songbird refugia were more limited by temperature. Upper-percentile refugia, but not median values, were well explained by topographic conditions. Songbird refugia were strongly associated with elevation, while coastal proximity and landform composition (particularly headwaters) were important for both groups. There was a general lack of concordance between patterns of current species richness and future climate refugia.
The current status of species in Diaporthe

In this paper we give an account of species in the genus Diaporthe. Since morphological characters are inadequate to define species in this genus, DNA sequence data are essential to differentiate them. We therefore focus this paper on the 171 species for which ex-type/exepitype/ex-isotype/ex-neotype isolates and corresponding molecular data are available and these species are listed alphabetically. Sexual or asexual morph are noted under each species, detailed descriptions of type materials, host records and geographic distribution are provided. Available DNA sequence data from ex-type cultures are listed in Table 1. Phylogenetic relationships of the species are given in a multi-locus phylogenetic tree based on combined ITS, tef1-α, β-tubulin and CAL sequences.
Lycopene: a natural antioxidant for prevention of heat-induced oxidative stress in poultry

Heat stress is one of the most important physiological factors challenging poultry production throughout the world especially in tropical and sub-tropical countries. Oxidative stress induced by heat stress not only compromises productivity and performance but also results in morbidity and mortality losses leading to the economic burden for poultry producers. It reduces the shelf life of poultry product in addition to poor meat and egg quality. Recently, a trend towards using phytochemicals derived from natural sources with potential antioxidant activities has increased. Lycopene is a predominant carotenoid pigment which is universally found in fruits and vegetables, with tomatoes and their products being key sources. Several in vivo and in vitro studies have suggested that lycopene is a powerful antioxidant compared to other carotenoids. Supplementation of tomato (Solanum lycopersicum) derived lycopene revealed numerous health promoting activities in poultry birds, such as anti-oxidant, anti-inflammatory, immunomodulation, improved performance and better meat as well as egg quality. Lycopene maintains oxidative balance in birds through various ways including serving as a free radical scavenger, inhibiting signalling pathways and activating host antioxidant enzymes, such as superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) and catalase (CAT). The aims of this current review are to summarise mechanisms of action through which lycopene quench reactive species and maintain oxidative balance, highlight the potential role of lycopene as a natural antioxidant agent for poultry industry and examine the benefits to poultry producers when using this natural antioxidant on commercial basis in poultry diets to alleviate the adverse effects of heat stress.
Invasion pathway switching of plasmodium falciparum reveals post-transcriptional regulation of merozoite proteins

The clinical symptoms of the parasitic disease malaria are caused by the intraerythrocytic stage of the Plasmodium spp life cycle. The invasive form of the malarial parasite for erythrocytes is the merozoite. Erythrocyte invasion is a multistep process and proteins required for this event are transcribed during the schizont stage and subsequently expressed at the merozoite stage. The merozoite is able to invade erythrocytes using a wide range of invasion pathways. Invasion pathways are determined by erythrocyte and merozoite properties. Erythrocyte characteristics and availability of erythrocyte receptors are crucial criteria for successful invasion. Each parasite clone possesses unique invasion properties: firstly the parasite clone does not necessarily express all homologues of the invasion protein family; secondly, the amount of a particular protein being expressed may vary; and thirdly some proteins are predominantly expressed over others. The Plasmodium falciparum clone W2mef is able to switch from a sialic aciddependent to independent (W2mef/NM) invasion pathway when selected in the presence of neuraminidase-treated erythrocytes. Neuraminidase cleaves sialic acid from erythrocyte surface proteins thus limiting the availability of erythrocyte receptors. Some aspects of the molecular mechanism underlying this switch has been determined by Stubbs et al., (2005) and Gaur et al., (2006) by transcriptional assessment of the schizont stage and subsequent expression analysis of identified candidate molecules. Recent studies have though shown that invasion molecules may not only be regulated at the transcriptional stage, but also during protein expression. By using a novel ̂ quantitative proteomic approach (iTRAQ) this present study investigates merozoite protein expression profiles and reveals differences in protein expression between W2mef and W2mef/NM. Of the 600 proteins that were quantitatively analysed 88 proteins show differential expression in W2mef/NM versus W2mef. Furthermore, this study exploits the ability of the W2mef clone to switch between invasion pathways as a tool to uncover the gene regulation mechanism by directly comparing gene transcription during the schizont stage and protein expression at the merozoite stage. Post-transcriptional regulation appears to i ATTENTION: The Singapore Copyright Act applies to the use of this document. Nanyang Technological University Library