Miracle-dz/UniFAR-FTUs huggingface dataset:
ConsensusDriver improves upon individual algorithms for predicting driver alterations in different cancer types and individual patients – a toolbox for precision oncology

Background In recent years, several large-scale cancer genomics studies have helped generate detailed molecular profiling datasets for many cancer types and thousands of patients. These datasets provide a unique resource for studying cancer driver prediction methods and their utility for precision oncology, both to predict driver genetic alterations in patient subgroups (e.g. defined by histology or clinical phenotype) or even individual patients. Methods We performed the most comprehensive assessment to date of 18 driver gene prediction methods, on more than 3,400 tumour samples, from 15 cancer types, to determine their suitability in guiding precision medicine efforts. These methods have diverse approaches, which can be classified into five categories: functional impact on proteins in general (FI) or specific to cancer (FIC), cohort-based analysis for recurrent mutations (CBA), mutations with expression correlation (MEC) and methods that use gene interaction network-based analysis (INA). Results The performance of driver prediction methods varies considerably, with concordance with a gold-standard varying from 9% to 68%. FI methods show relatively poor performance (concordance <22%) while CBA methods provide conservative results, but require large sample sizes for high sensitivity. INA methods, through the integration of genomic and transcriptomic data, and FIC methods, by training cancer-specific models, provide the best trade-off between sensitivity and specificity. As the methods were found to predict different subsets of drivers, we propose a novel consensus-based approach, ConsensusDriver, which significantly improves the quality of predictions (20% increase in sensitivity). This tool can be applied to predict driver alterations in patient subgroups (e.g. defined by histology or clinical phenotype) or even individual patients. Conclusion Existing cancer driver prediction methods are based on very different assumptions and each of them can only detect a particular subset of driver events. Consensus-based methods, like ConsensusDriver, are thus a promising approach to harness the strengths of different driver prediction paradigms.
Production of volatile metabolites in model fermentations and in raw sausages by Lactobacillus sakei

Different strains of Lactobacillus sakei , used as starter cultures for the fermentation of raw sausages, showed a similar metabolism in the production of volatile compounds in model fermentations as well as in raw sausages and they could be differentiated from other starter cultures, e.g. Staphylococcus carnosus. The addition of α-keto acids to the model fermentations led to an enhanced production of carboxylic acids and ketones by the L. sakei strains. Used as starter culture in raw sausages showed that the L. sakei strains are different assertive towards other Lactobacillus-species. The cultivation under salt stress led to a reduced cell size and a reduction of produced volatile compounds, while nitrite- and salt-stress had a positive effect towards the production of metabolites.
Chemical Composition and Antibacterial Effect of Medicinal Plants against Some Food-Borne Pathogen

Corresponding Author: Hasan Habibi Assistant’s professor of Agriculture and Natural Resources College, Persian Gulf University, Bushehr, Iran. Phone: +98-9173034921 E-mail: h.habibi@pgu.ac. ir Abstract Background: Pulicaria gnaphalodes, Ducrosia anethifolia, Trachyspermum copticum, Foeniculum vulgare Mill and Majorana hortensis Minch are widely used as herbal plants in traditional medicine and they have been reported to have a variety of therapeutic effects. This study was carried out to evaluate the antimicrobial effects of essential oils (EOs) extracted from these medicinal herbs against six species of food-borne microorganisms. Materials and Methods: The EOs were analyzed by gas chromatography mass spectrometry (GC/MS). The detection of inhibitory effect of the EOs on the tested bacteria was carried out by agar disk-diffusion method and then MIC (Minimum Inhibitory Concentration) and MBC (Minimum Bactericidal Concentration) of the EOs against six bacteria were determined. Results: The analysis of the components of the essential oils (EOs) extracted by gas chromatography spectrometry allowed the identification of 63 compounds of the five tested EOs. All of these five tested EOs indicated an antimicrobial effect against strains of Bacillus sp and Listeria Monocytogenes ATCC1297. Essential oils from T. copticum, M. hortensis and F. vulgare possessed a wide spectrum of antibacterial activity against the growth of the six bacteria with zone diameter of inhibition (ZDI) between 14-32 mm, depending on the susceptibility of the tested organism. Conclusion: Antibacterial efficacy shown by these plants provides a scientific basis and thus validates their use as medicinal remedies. Isolation and purification of different phytochemicals may further yield significant antibacterial agents.
Implications of historical interactions between herbivory and fire for rangeland management in African savannas

Herbivory and fire are important drivers of ecosystem processes within African rangelands. We explore whether mid-Holocene African savannas were dominated by herbivory as a means of cycling nutrients, and whether fire perhaps played a lesser role than today. Evidence from savanna ecology, paleoecology, and historical literature indicates higher herbivore densities in mid-Holocene and pre-colonial times compared to present. While fire may increase or decrease forage availability for herbivores, depending on the nutrient status of the environment, herbivory tends to decrease fire intensity and frequency by decreasing fuel loads. Given this competitive relationship between fire and herbivory and the higher herbivore densities of the past, we suggest that some fire-dominated present-day savannas are the product of anthropogenic alterations in herbivore and fire regimes, including the increasing use of fire as a tool for managing ecosystems. We discuss whether managing for an alternative stable state dominated by herbivory could stimulate ecosystem processes such as nutrient cycling and production, and whether this will achieve the same management objectives traditionally satisfied by fire. Management implications may include the adaptive manipulation of herbivore densities over time and space to maintain an appropriate carrying capacity for the rainfall and soil nutrient status of the area, occasional use of fire, and including a diversity of herbivore functional guilds.
Glucose level associated with behavior of diabetic children

♦ McDonnell CM, et al. Diabetes Care. 2007;30:2211 -2215. [OpenUrl][1][Abstract/FREE Full Text][2] High blood glucose levels in children with type 1 diabetes were associated with an increase in behavior problems such as aggression and hyperactivity, according to a study of 42 children ages 5 to 10
Avaliação do processo de imunização de murganhos vacinados com virus-like particles (VLPs) contendo candidatos antigénicos de Trypanosoma cruzi

x 1. Introdução . 1 1.1 Doenças Tropicais Negligenciadas . 1 1.2 O parasita . 2 1.2. 1 Trypanosoma cruzi . 2 1.2. 2 O ciclo de vida . 5 1.2. 3 Transmissão de Trypanosoma cruzi . 7 1.2. 4 Vetores de Trypanosoma cruzi . 7 1.3 Doença de Chagas . 9 1.3. 1 Epidemiologia . 9 1.3. 2 Apresentação clínica da doença de Chagas . 10 1.3. 3 Aspetos imunológicos da doença de Chagas . 11 1.3. 4 Diagnóstico laboratorial da doença de Chagas . 16 1.3. 5 Opções terapêuticas para o tratamento da doença de Chagas . 17 1.3. 6 Medidas de controlo e prevenção da doença de Chagas . 19 1.4 História do desenvolvimento de vacinas contra Trypanosoma cruzi . 20 1.4. 1 Heat-shock Protein 70 (HSP70) como candidato antigénico para vacina contra T. cruzi . 23 1.5 Virus-like particles (VLPs) . 24 1.6 Triatoma virus e a produção de virus-like particles . 29 2. Objetivos . 33 3. Materiais e métodos . 35
Comparing soluble to controlled-release nitrogen fertilizers: storage cabbage yield, profit margins, and N use efficiency1

Abstract: Optimizing N fertilizer applications involves maximizing N use efficiency (NUE) while minimizing losses but depends on complex interactions of crop, soil, weather, and management practices. One approach may be to use controlled-release fertilizer that synchronizes N availability with plant demand. A field experiment at two Ontario locations from 2007 to 2009 compared split-applied ammonium nitrate (ANs) to preplant-applied poly-coated urea (PCU) and soluble N at a ratio of 75:25 at five N rates on late-season storage cabbage (Brassica oleracea L. var. capitata). Maximum yield and profit margins were obtained at an average of 286 and >300 kg N ha-1, but few differences among sources were observed. Compared with ANs, PCU did not affect plant N content, nor did PCU reduce soil nitrate or NUE, which indicates little differences in risk of environmental N losses between N sources. Dissolution from mesh bags indicated 5%–25% of various PCU formulations remained by harvest but 5%–10% remained by spring, which suggests conservation over the winter, a need to synchronize N release with crop uptake, and partially explains the lack of treatment differences. From agronomic, economic, and environmental perspectives, the tested PCU treatments for cabbage production in a humid, temperate climate were equivalent to the standard practice.
Pembuatan Pakan Terapung Terfermentasi Saccharomyces cerevisiae Melalui Proses Non-ekstrusi

ASRI LINDASARI. Making The Floating Feed Fermented Saccharomyces cerevisiae by Non-extrusion Process. Supervised by YULI RETNANI and SURYAHADI. This study aimed to make a floating feed fermented Saccharomyces cerevisiae through non-extrusion process to a floating feed based on density, floating ability, solubility, hardness, and pellet durability index. This research was designed by a Completely Randomized Design with three treatments and four replication. The treatments were P1: feed fermented, P2: fermented feed with a drying oven 60C, P3: fermented feed draining by deep frying. The data were analyzed using ANOVA. The parameters observed were density, floating ability, solubility, hardness, and pellet durability index. The result showed that the treatments were significally effected (p <0.05) on feed's density, floating ability, water stability and hardness. The best treatment was the treatment of fermentation by draining deep frying with low density, approximately 6 hours of floating ability, and has the best solubility, hardness and durability index.
Introduction to “Space Oddity: Recent Advances Incorporating Spatial Processes in the Fishery Stock Assessment and Management Interface”1

Journal: Canadian Journal of Fisheries and Aquatic Sciences Manuscript ID cjfas-2017-0296 Manuscript Type: Article Date Submitted by the Author: 19-Jul-2017 Complete List of Authors: Berger, Aaron; NOAA-NMFS, FRAM Goethel, Daniel; Southeast Fisheries Science Center, Lynch, Patrick; NOAA Fisheries, Office of Science and Technology Is the invited manuscript for consideration in a Special Issue? : AFS Spatial Processes
Effects of metabolizable protein on intake and milk production of dairy cows independent of effects on ruminal digestion

The role of protein in food intake regulation is complex in ruminants. Previous research has shown that a deficiency in degradable nitrogen (N) could affect microbial activity and decrease intake. On the other hand, an increase in metabolizable protein content of the diet seems to stimulate food intake in lactating dairy cows. The aim of this experiment was to determine whether metabolizable protein supply plays a direct role in the stimulation of food intake. Treatments comprised two infusions of soya protein isolate (800 g/day) either into the rumen (RP) or into the duodenum (DP), which were compared with two iso-energy infusions of glucose (880 g/day) either into the rumen (RG) or into the duodenum (DG). Four ruminally and duodenally cannulated cows producing 36·5 kg/day of milk were assigned to a 4 ✕ 4 Latin-square design with periods of 4 weeks. Duodenal infusions of protein (DP) significantly increased (P 0·05) on the apparent digestibility of dry matter, organic matter, neutral-detergent fibre or acid-detergent fibre and also no or only small effects on ruminal fermentation variables. Plasma concentrations of most of the essential amino acids increased significantly with the duodenal infusion of protein, whereas ruminal infusion of protein had no significant effect. It is concluded that direct supply of metabolizable protein stimulates intake independently of ruminal digestion effects.
Origins and nature of vessels in monocotyledons. 10. Boryaceae: xeromorphic xylem structure in a resurrection plant

Boryaceae are unusual in having xylem with an abundance of thick-walled tracheids, combined with relatively few vessel elements with scalariform perforation plates that have very slender bars. These features are relevant to the resurrection plant habit of Borya. The abundance of thick-walled tracheids provide sites for maintenance of water columns during hot dry months, whereas the perforation plates offer minimal impedance to flow during wet periods. This combination is unusual in monocotyledons. Root xylem is like stem xylem in the two species studied. Borya sphaerocephala occurs in the Mediterranean-type climate of south west Western Australia, whereas Borya subulata grows in a tropical summer-monsoon area, the Kimberley plateau of northern Western Australia. Despite differences in climatic regimes of the two species, survival of the dry season appears to be the primary factor in design of the xylem of both, and explains their similarity. Boryaceae are now placed in Asparagales, near Asteliaceae, Blandfordiaceae, Hypoxidaceae, and Orchidaceae. Xylem structure does not parallel the phylogenetic interconnections among these families, in which moist habitats, succulent habits, and other modifications seem to mitigate the effect of ecology in patterning xylem structure.
Improved MRO Inventory Management System in Oil and Gas Company: Increased Service Level and Reduced Average Inventory Investment

This study proposes a methodology for the oil and gas businesses to keep their production plant productive with a minimum investment in carrying maintenance, repair, and operating inventory planning. The goal is to assist the exploration and production companies in minimizing the investment in keeping maintenance, repair, and operating (MRO) inventory for improving production plant uptime. The MRO inventory is the most expensive asset and it requires substantial investment. It helps in keeping the oil and gas production plant productive by performing planned and unplanned maintenance activities. A (Q, r) model with a stock-out and backorder cost approach is combined with a continuous inventory review policy for the analysis of class A items of oil and gas production plant MRO inventory. The class A items are identified through popular ABC analysis based on annual dollar volume. The demand for the inventory is modeled through Poisson distribution with consideration of constant lead time. The (Q, r) model in both stock-out cost and backorder cost approaches assigned higher order frequency and lower service level to low annual demand and highly expensive items. The stock-out cost approach shows an 8.88% increase in the average service level and a 56.9% decrease in the company average inventory investment. The backorder cost approach results in a 7.77% increase in average service level and a 57% decrease in average inventory investment in contrast to the company’s existing inventory management system. The results have a direct impact on increasing plant uptime and productivity and reducing company maintenance cost through properly managing maintenance stock. The analysis is carried out on the oil and gas production plant’s MRO inventory data, but it can be applied to other companies’ inventory data as well. All the results reflected in this research are based on the inventory ordering policy of two orders per year. The inventory ordering frequency per year may be other than two orders per year depending on the type of organization.
Illuminating Actionable Biology in Breast Cancer: Novel Predictive and Prognostic Biomarkers

Assessing hormone receptors (the estrogen and progesterone receptors) and the human epidermal growth factor receptor 2 (HER2) to guide clinical decision making revolutionized treatment for breast cancer patients. However, in the years since these biomarkers were first incorporated into routine clinical care, only a few others have been validated as clinically useful in guiding adjuvant chemotherapy decisions and are recommended by the American Society of Clinical Oncology (ASCO) for patients with hormone-positive breast cancer. For patients with triple-negative breast cancer (TNBC), which lacks hormone and HER2 receptors, not any of these biomarkers are recommended by ASCO due to insufficient evidence that they meaningfully improve clinical outcomes. Breast cancer is the second-leading cause of cancer-related death among women in the US, indicating an unmet need to improve treatments, which can be accomplished in part by identifying and validating novel predictive and prognostic biomarkers that yield actionable information about the clinical course of breast cancers, especially TNBCs. A major obstacle to improving outcomes for breast cancer patients is intratumor heterogeneity (ITH), which can be extensive in breast cancer and drives treatment resistance and relapse. I envision that assaying drivers of ITH can inform clinicians about which breast tumors may be intrinsically more aggressive and carry a greater risk of breast cancer-related morbidity and mortality. My research, presented here, primarily focuses on testing the impact of drivers of ITH (namely, centrosome amplification [CA], the clustering protein KIFC1, and mitotic propensity and its drivers) on clinical outcomes in breast cancer in multivariable models as well as the correlates of in vitro efficacy of centrosome declustering drugs (which can selectively eliminate cancer cells with CA). Collectively, these studies reveal gene signatures and immunohistochemical biomarkers that are independent predictors of aggressive breast cancer course and rational strategies to optimize targeted therapy to combat cancer cells exhibiting CA, thereby contributing to the literature on the development of precision medicine for breast cancer patients, including TNBC patients. INDEX WORDS: Chromosomal instability, proliferation, Ki67, HSET, HER3, EGFR, RARA, racial disparity ILLUMINATING ACTIONABLE BIOLOGY IN BREAST CANCER: NOVEL PREDICTIVE AND PROGNOSTIC BIOMARKERS
The role of epidermal growth factor in psoriasis

Psoriasis is a chronic skin disease characterized by benign proliferation of epidermal cells. The most important seems to be: excessive divisions of keratinocytes in the basal-cell layer, its abnormal maturation and increase of angiogenesis. Epidermal growth factor (EGF) is regarded as a factor playing probably the major role in pathogenesis of psoriasis. It regulates cell growth, and stimulates proliferation and differentiation through binding with the EGF receptor (EGFR). In active psoriatic lesions regular increase of EGFR expression in all layers of the epidermis is observed. Blockage of EGFR with monoclonal antibodies inhibits proliferation of keratinocytes. In this review article we present data on the importance of EGF in pathogenesis of human skin diseases, indicating the need for further studies on its role in the pathogenesis of psoriasis. SŁOWA KLUCZOWE: łuszczyca, czynniki wzrostu, EGF, EGFR.
Breeding Behavior of Northern Saw-Whet Owls in Oregon

Abstract We know little about the breeding behavior of most nocturnal raptors. Nest attendance and prey delivery rates can be used as indices of relative habitat quality or extent of parental care. We used video cameras to document and observe prey delivery rates, nest attendance and bout durations at two northern saw-whet owl (Aegolius acadicus) nests in two artificial nest boxes in north-central Oregon. We collected 858 hours of video surveillance between 21 March and 01 June 2014. The number of prey deliveries per night increased as the nesting season progressed: 1.25 during laying, 1.33 during incubation, and 4.0 during the nestling phase. Prey was delivered most often between 2100 and 2200. Nest attendance by females was high during pre-laying (97.8%), laying (97.9%) and incubation (98.2%), but decreased during the nestling phase (55.7%). Nest attendance was higher during diurnal hours than nocturnal hours across all nesting phases. Duration of off bouts (recesses) was similar during pre-laying and laying (26 min), decreased during incubation (19 min), then increased during the nestling phase (55 min). One of the nesting attempts was successful and the female abandoned the other clutch 22 days after initiation. The incubation and nestling periods were 30 days each.
MODELOS DE REGRESSÃO ALEATÓRIA PARA CARACTERÍSTICA DE CRESCIMENTO EM BOVINOS DA RAÇA GUZERÁ

The aim of this study was to estimate (co)variance components and genetic parameters from birth to yearling weight (550 days of age) in Guzera cattle, using random regression models. Data set from animals (male and female) born between 1993 and 2011 belonging to ten farms in seven Brazilian States were used. The best-fit model considering direct and maternal genetic effect and permanent environmental animal effect were adjusted by fourth, third, and second order, respectively, using orthogonal polynomials of Legendre. The higher estimated values of direct heritability were observed in birth (0.88) and yearling weight (0.70). The genetic correlations were moderate to high magnitude, remaining up even with the increase in the ages gap.
Do parents listen to their children? Begging does not go unanswered in European Starlings (Sturnus vulgaris)

ABSTRACT Begging by nestling passerines is an important way to communicate their state of hunger to parents. We examined whether experimentally increased nestling begging vocalizations can quickly alter parental provisioning rates in European Starlings (Sturnus vulgaris). We predicted that an increase in begging volume heard by parents during the experimental treatment would result in a significantly higher number of provisioning visits compared to the pre-playback control of natural begging levels. Total number of parental provisioning visits during 1 h control and experimental trials were compared for 23 broods of 14-day-old nestlings. Begging calls of each brood were recorded when nestlings were 13 days old; the loudest calls from each brood were made into a 3 min loop and projected continuously the next day during the experimental trial. As predicted, parents provisioned at a significantly higher rate during the experimental trials than the control trials. European starlings are sensitive to begging calls made by their offspring and respond quickly to any changes in their begging vocalizations.
Population Structure, Connectivity, and Phylogeography of Two Balistidae with High Potential for Larval Dispersal: Balistes capriscus and Balistes vetula

ii ACKNOWLEDGMENTS . iv DEDICATION . vi LIST OF TABLES . xii LIST OF ILLUSTRATIONS . xiv CHAPTER I INTRODUCTION . 1 1.1 Experimental Approaches to Study Connectivity . 4 1.2 Genetic Approaches to Study Population Structure and Gene Flow . 5 1.3 Molecular Approaches to Characterize Gene Flow . 10 1.4 Considerations on Sampling Designs . 13 1.5 Model Species Chosen . 14 1.6 Research Objectives . 14 CHAPTER II – DEVELOPMENT OF HOMOLOGOUS MICROSATELLITE MARKERS FOR GRAY TRIGGERFISH . 17 2.