Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro degradability of feed proteins in the rumen: use of non-rumen proteases

Various feed proteins were incubated independently with bacterial protease from Streptomyces griseus (SGP), papain (Corica papaya), and ficin (Ficus glabrata) in a simple laboratory assay to predict ruminal protein degradability. The estimates obtained from in vitro assays were compared with those obtained from an in situ analysis using synthetic fibre bags. The rate and extent of degradation in vitro using proteases from non-rumen sources differed among substrates used. A high correlation coefficient (r2 = 0.99) was observed between N-degradability from the in vitro method using SGP and in situ estimates when soybean meal was the substrate. Soybean meal nitrogen (N) was almost completely hydrolysed (0.99) in vitro. The correlation coefficients were low and variable with assays using other enzymes. The correlation coefficient was also high (r2 = 0.77–0.84) with in vitro methods using either SGP, papain, or ficin when incubated with fish meal. The N disappearance from barley in vitro was slow to moderate. The ‘b’ estimate of barley obtained with the in vitro assay was significantly (P < 0.01) lower than that observed in situ. Slower proteolysis observed in barley may possibly be linked to poor accessibility of structural proteins rather than the degradability of N per se. None of the enzymes could rank barley in the same order as the in situ method.
Ensiling Characteristics of Alfalfa Leaves and Stems

The separate harvesting of alfalfa leaves and stems would provide farmers more flexibility in the harvesting and utilization of alfalfa, but a key issue is storage. In three trials, unwilted alfalfa leaves were ensiled alone or with cell wall degrading enzymes, formic acid or lactic acid bacterial inoculant. Alfalfa stems wilted to 350 g DM/kg were ensiled with the same four treatments. In the two trials where the leaves were above 230 g DM/kg, the leaves ensiled successfully without any additives. Leaves ensiled at 168 g DM/kg eventually underwent a clostridial fermentation with elevated levels of butyric acid and ammonia, regardless of the treatments used. Formic acid could be used to guarantee a good fermentation, but more research is needed to ascertain the addition level as a function of the DM concentration of the leaves. The stems when wilted to approximately 350 g DM/kg ensiled well without additives. The enzyme and inoculant treatments affected fermentation as expected but were not necessary for good preservation by ensiling. Their value to the producer would depend on other factors not measured: improving DM recovery from storage and/or enhancing utilization by livestock or as a biomass feedstock.
Broad- and narrow-sense heritabilities in a South African cloned open-pollinated Eucalyptus grandis breeding population

Genetic variances and heritabilities of a 66-month old cloned Eucalyptus grandis breeding population of families, derived from open-pollinated selections, were estimated. The genetic variance for the growth traits was largely additive genetic variance, whereas the proportion of non-additive genetic variance was notably higher for stem form and disease tolerance. A notably larger proportion of non-additive variance was observed for the growth traits and stem form among the F2 families. This is probably due to the reduction in additive variance through selection for general combining ability for these traits in the previous generations. No selection for disease took place in earlier generations and the proportion of non-additive genetic variance for this trait remains approximately the same for families of different generations.
High copy number plasmid vectors for use in lactic streptococci

A 3.8 kb DNA fragment from plasmid pBD64 which encoded chloramphenicol and kanamycin resistance genes, but had no replication region, was used as a replicator probe to select for the replication region of the cryptic lactic streptococcal plasmid pSH71 using Bacillus subtilis as host. Three of the resultant recombinant plasmids, pCK1, pCK17 and pCK21 are described. They are vectors in Streptococcus lactis and can be used to clone BglII-compatible fragments into their kanamycin resistance gene. All the plasmids have single sites for restriction endonucleases AvaI, BamHI, EcoRI, PvuII and XbaI, while plasmids pCK17 and pCK21 have single sites for ClaI.
Qualidade da carne de novilhos terminados em confinamento e abatidos aos 16 ou 26 meses de idade

It was evaluated in this work the sensorial characteristics of the meat of non-castrate or castrated males feedlot finished and slaughtered at 16 (young steers) or 26 (steers) months old. The diet with 50 roughage: 50concentrate contained 11.8% of crude protein and 2.83 Mcal of digestible energy/kg of dry matter. The highest amplitude of the final pH of the meat was noted on the steers, and the lowest on the young steers. The meat of the non-castrate males, regardless to the age at slaughter, was darker, coarser and showed lower marbling degree than the meat of the castrated animals. Thawing loss was higher for the meat of the castrated animals(8.55 vs 4.99%). There was interaction among categories and sex for cooking loss, palatability and juiciness. Meat of the older non-castrate males showed higher cooking loss, it was less palatable and less juicy regarded to the meat of the older castrated and the younger castrated or non-castrate males. Reduction of slaughtering age from 26 to 16 months old, regardless to sexual condition, improves meat tenderness evaluated by taste panel.
Dry up and survive: the role of antioxidant defences in anhydrobiotic organisms

Although the evolution of life has turned oxygen into a vital chemical for aerobic organisms, this element can also have deleterious effects on living systems through the production of oxidative stress. This is a process resulting from an imbalance between the excessive production of Reactive Oxygen Species (ROS) and the limited action of antioxidant defences. It is a particularly harmful health risk factor, involved in the development of several chronic human pathologies and believed to play a major role in the ageing process. Consequently aerobic metabolism needs a stringent control of ROS. Water too is essential for life, but some organisms widespread throughout nature have the ability to survive complete desiccation by entering an anhydrobiotic state. The loss of water induces changes in metabolism, cell membrane organization, and molecular composition. In the anhydrobiotic state, high temperatures, high humidity, light exposure, and high oxygen partial pressure negatively affect organism survival and directly influence the time required to reactivate the metabolism after a period of desiccation. These abiotic factors induce damages that are accumulated in proportion to the time spent in the desiccated state, potentially leading to organism death. Oxidative stress seems to be one of the most deleterious damages due to water depletion, therefore anhydrobiosis also needs a stringent control of ROS production. Anhydrobiotic organisms seem to apply two main strategies to cope with the danger of oxygen toxicity, namely an increased efficiency of antioxidant defences and a metabolic control of both energy-production and energy-consuming processes. Experimental studies provide evidence that antioxidant defences such as ROS scavenging enzymes ( e.g. peroxidases, catalases, superoxide dismutase, glutathione peroxidases) and other molecules ( e.g. glutathione, carotenoids, vitamins C and E) represent a key group of molecules required for desiccation tolerance in anhydrobiotic organisms. The action of these molecules emphasises the need for redox balancing in anhydrobiotic organisms including tardigrades and chironomid larvae.
Toll-like receptor 3-mediated activation of NF-κB and IRF3 diverges at Toll-IL-1 receptor domain-containing adapter inducing IFN-β

We have previously shown that double-stranded RNA-triggered, Toll-like receptor 3 (TLR3)-mediated signaling is independent of MyD88, IRAK4, and IRAK. Instead, TRAF6, TAK1, and TAB2 are recruited to TLR3 on poly(I·C) stimulation. TRAF6-TAK1-TAB2 are then translocated to the cytosol where TAK1 is phosphorylated and activated, leading to the activation of IκB kinase and NFκB. The present study addressed two important questions: (i) How are TRAF6, TAK1, and TAB2 recruited to TLR3? (ii) Are TRAF6, TAK1, and TAB2 also required for TLR3-mediated IRF3 activation? Recently, a novel Toll-IL-1 receptor (TIR)-containing adapter, TIR domain-containing adapter inducing IFN-β (TRIF), was shown to play a critical role in TLR3-mediated activation of NF-κB and IRF3. We found that TLR3 recruits TRAF6 via adapter TRIF through a TRAF6-binding sequence in TRIF (PEEMSW, amino acids 250-255). Mutation of this TRAF6-binding sequence abolished the interaction of TRIF with TRAF6, but not with TLR3. Interestingly, mutation of the TRAF6-binding site of TRIF only abolished its ability to activate NF-κB but not IRF3, suggesting that TLR3-mediated activation of NF-κB and IRF3 might bifurcate at TRIF. In support of this finding, we showed that DN-TRAF6 and DN-TAK1 blocked poly(I·C)-induced NF-κB but not IRF3 activation. Furthermore, whereas poly(I·C)-induced NF-κB activation is completely abolished inTRAF6-/- MEFs, the signal-induced activation of IRF3 is TRAF6 independent. In conclusion, TRIF recruits TRAF6-TAK1-TAB2 to TLR3 through its TRAF6-binding site, which is required for NF-κB but not IRF3 activation. Therefore, double-stranded RNA-induced TLR3/TRIF-mediated NF-κB and IRF3 activation diverge at TRIF.
Efecto de la pectina sobre la actividad de algunas enzimas digestivas y la digestión de lípidos

Aunque se ha demostrado que la pectina tiene varias funciones fisiologicas beneficas para la salud humana, la informacion disponible sobre los mecanismos mediante los cuales la pectina es capaz de ejercer dichas funciones es limitada. En esta tesis se estudiaron los mecanismos mediante los cuales la pectina es capaz de ejercer sus funciones fisiologicas. Se evaluo el efecto de la pectina sobre la actividad de las principales enzimas digestivas [lipasa pancreatica, alfa-amilasa, fosfatasa alcalina y proteasa (quimotripsina)]. Entre las enzimas estudiadas, la lipasa pancreatica fue la enzima mas susceptible de ser inhibida por la pectina. Se hizo especial enfasis en el efecto de la pectina sobre el destino gastrointestinal de los lipidos, haciendo uso de una emulsion como modelo experimental. Se utilizo un modelo de digestion in vitro que consistio en la simulacion de las fases oral, gastrica e intestinal con el objetivo de evaluar el efecto de la pectina sobre la velocidad y la magnitud del proceso de digestion de lipidos. Las digestiones in vitro mostraron que la velocidad y la magnitud del proceso de digestion fueron inhibidos cuando se aumento la concentracion de pectina. Ademas, se encontro que la pectina de alto grado de metoxilacion (HMP) tuvo mayor capacidad de inhibir el proceso de digestion que la pectina de bajo grado de metoxilacion (LMP). Esto permitio sugerir que los mecanismos fisicoquimicos que pueden explicar la influencia de la pectina sobre la digestion de lipidos son el incremento de la viscosidad de los fluidos gastrointestinales, la floculacion de lipidos y las interacciones existentes entre la pectina y los lipidos, asi como con los componentes gastrointestinales que participan en el proceso de digestion (lipasa pancreatica, sales biliares, CaCl2, y NaCl). Finalmente, se encontro que el aumento de la viscosidad de los fluidos gastrointestinales por efecto de la pectina y las interacciones electrostaticas (atractivas y repulsivas) inhibio la velocidad y la magnitud del proceso de transferencia de masa de los compuestos nutricionales mas importantes (monosacaridos, aminoacidos y lipidos emulsificados). Los resultados obtenidos en esta tesis podrian conllevar a la comprension de la funcionalidad fisiologica de la pectina y como esta funcionalidad puede verse afectada por las caracteristicas estructurales de la pectina.
Biosuppression of Botrytis cinerea in grapes

There is increasing interest in the use of biological control agents (BCAs) and plant resistance stimulants to suppress botrytis bunch rot in grapes, caused by Botrytis cinerea. Numerous different filamentous fungi, bacteria and yeasts have been selected as potential BCAs for control of grey mould based upon demonstrated antagonism towards B. cinerea. Biological suppression of the pathogen arises via competition for nutrients and space, the production of inhibitory metabolites and/or parasitism. Preformed and inducible grapevine defence mechanisms also contribute to disease suppression by preventing or delaying pathogenic infection. Furthermore, various biotic and abiotic agents can stimulate grapevine defence mechanisms and so elevate resistance to B. cinerea infection. Biosuppression of B. cinerea in vineyards, using BCAs and resistance stimulants, has been inconsistent when compared with that observed in controlled glasshouse or laboratory conditions. This may be attributable, in part, to the innate variability of the field environment. Research to improve field efficacy has focused on formulation improvement, the use of BCA mixtures and combinational approaches involving BCAs and plant resistance stimulants with complementary modes of action.
Purification and properties of neutral-cyclodextrin glycosyl-transferase of an alkalophilic Bacillus sp.

Neutral-cyclodextrin glycosyltransferase (EC 3. 2. 1. 19) of alkalophilic Bacillus sp. (ATCC 21783) was purified by starch adsorption, DEAE-cellulose chromatography and Sephadex G-150 gel filtration chromatography followed by preparative polyacrylamide gel electrophoresis. Molecular weight of the purified enzyme was 85, 000_? _88, 000 by SDS-disc gel electrophoresis. The enzyme was most active at pH 7 and 50°C, and stable up to 60°C at pH 7 and in the range of pH 6_? _8 at 60°C by 30min incubation. The apparent Vmax and Km values for α- and β-cyclodextrin at a constant concentration of sucrose were 417, 70 μmoles glucose/min•mg protein and 10, 0.83mM, respectively. About 85_? _90% of amylose, 75_? _80% of potato starch, 65_? _70% of amylopectin, 55_? _60% of glycogen, 45_? _50% of amylopectin β-limit dextrin, 20_? _25% of maltotriose and 10_? _15% of maltose were converted to cyclodextrins with 0. 5_? _1% (w/v) of each substrate. Schardinger β-dextrin was preferentially produced from starch, and α- or γ-dextrin was gradually formed after prolonged incubation. After 20min incubation, about 0.4, 14 and 2.5% of α-, β- and γ-dextrin were formed from starch, respectively.
Escape from pupal predation as a potential cause of outbreaks of the winter moth, Operophtera brumata

The winter moth, Operophtera brumata, shows varying population dynamics in different host plant habitats. Populations in Sitka spruce, Picea sitchensis, plantations and in Scottish moorlands have a tendency to outbreak that is not shown by winter moth in lowland oak woods. Since pupal predators have previously been identified as being important for the regulation of winter moth in a lowland oak wood it was hypothesized that invertebrate pupal predators were failing to control winter moth in outbreak populations. This hypothesis was tested by comparing the abundance of invertebrate predators and patterns of spatially density dependent pupal predation across habitats. Several results supported this hypothesis. Carabid predators of winter moth were one or two orders of magnitude more abundant in oak woods than in moorland or spruce habitats. Staphylinid predators were also more abundant in high winter moth density oak woods than in any other habitat. Beetle predation of tagged cocoons in the field was inversely density dependent in Highland moors in experiments in 1999 and 2000, and in Sitka spruce in 1999. However, in opposition to our hypothesis, pupal predation was also inversely density dependent in oak woods in 2000, although this result may be explained by the low range of winter moth densities in the field that year. These results are discussed in relation to the role of natural enemies in regulating winter moth populations and the differences in life-history of the beetle predators in different habitats.
P781 Patterns of HIV and STI among transgender women in eastern and southern U.S.: interim baseline findings from the LITE cohort

Background Transgender women (TGW) in the U.S. experience a disproportionate burden of HIV and STIs. National HIV/STI surveillance does not report statistics for TGW. We describe the baseline prevalence and characteristics of HIV and STI among a cohort of TGW enrolled across 6 cities in eastern and southern US to-date. Methods Adult TGW, regardless of HIV status, are recruited and enrolled in a baseline screening visit. Participants complete a socio-behavioral survey, oral HIV screening, urine and self-collected anal and vaginal specimens for Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) testing, and serum treponemal syphilis testing and rapid plasma reagin (RPR) testing with quantitative RPR titers. Participants with negative HIV antibody test results at baseline and HIV-related risk behaviors are enrolled into the cohort. Results Enrollment launched in March 2018. As of December 2018, 620 TGW completed baseline. Of these, 30% were identified with HIV at baseline and 63% enrolled into the HIV-uninfected cohort. Forty-percent reported a lifetime diagnosis of any STI. At baseline, 34% of HIV-infected participants and 12% of HIV-uninfected participants had ≥=1 laboratory-confirmed STI. Baseline prevalence among all participants included: 2% rectal GC, 0% urogenital GC, 5% rectal CT, 1% urogenital CT, and 13% active syphilis determined by RPR and treponemal results. None of the 38 participants with self-reported history of vaginoplasty had GC or CT at the neovaginal site. Active syphilis infection was associated with residence in a southern city (aOR: 3.8, 95%CI:1.7–8.6), identification as Black and/or Latinx (aOR: 3.7; 95%CI:1.1–12.7), concern about safety in transit to healthcare (aOR: 1.9; 95%CI:1.1–3.3), and positive baseline HIV antibody test (aOR: 3.1; 95%CI:1.7–5.7). Conclusion TGW in this 6-city baseline cohort have a high prevalence of HIV and STI. Study findings highlight demographic disparities, high HIV/syphilis co-infection, and barriers related to safety that may impede prompt diagnosis and treatment of STI and HIV in American TGW. Disclosure No significant relationships.
Automated processing of coral reef benthic images

We describe an automated computer algorithm for the classification of coral reef benthic organisms and substrates sampled using a typical photographic quadrat survey. The technique compares subsections of a quadrat sample image (blocks) to a library of identified species blocks and computes a distance or probability of identification in a multidimensional hypervolume of discrimination metrics. The discrimination metrics include texture (calculated from a radial sampling of a two‐dimensional discrete cosine transform) and three channels of a normalized color space. A standard multivariate classification technique based on the Mahalanobis distance was unsuccessful in discriminating substrata because of the large morphological variation inherent in reef organisms. An alternative classification scheme based on an exhaustive search through an organism reference library yielded classification maps comparable to those obtained by manual analysis.
Source code analysis on student assignments using machine learning techniques

Abstract. To increase the success in computer programming courses, it is important to understand the learning process and common difficulties faced by students. Although several studies have investigated possible relationships between students performance and self-regulated learning characteristics, little attention has been given the source code produced by students in this regard. Such source code might contain valuable information about their learning process, specially in a context where practical programming assignments are frequent and students write source code constantly during the course. This poses the following research questions: What is the relationship between the characteristics of students source code and their performance in a computer programming course? What is the relationship between source code features and self-regulated learning characteristics (i.e., motivation and learning strategies) in a computer programming course? How the source code and self-regulated features can predict the students' performance? In order to answer these questions, a strategy to support the correlation analysis among students performance, motivation, use of learning strategies, and source code metrics in computer programming courses is proposed. A comprehensive case study is presented to evaluate the strategy. Additionally, an automatic grading tool for programming assignments was used, which facilitated to obtain the source code of the participants for further automatic source code analysis. Moreover, self-regulated learning characteristics were collected using the Motivated Strategies for Learning Questionnaire (MSLQ). Results show that the main features from source code which are significantly related to students performance and self-regulated learning features are: length-related metrics, with mainly positive correlations; and Halstead complexity measures, correlated negatively. In the light of the findings of this study, it is possible to understand better students source code as an artifact that can be used to monitorize several characteristics related to self-regulated learning, course performance, and in general, their learning process. In this way, more research in the area is required to verify if these relationships could give to computing educators new ways to identify and help students with problems.
A new species of Halocnemum M.Bieb. (Amaranthaceae) from southern Turkey

Halocnemum yurdakulolii Yaprak is described as the second species of the previously monotypic genus Halocnemum. The species is endemic to the Goksu Delta in southern Turkey. The main morphological characteristics that separate H. yurdakulolii from H. strobilaceum (Pall.) M.Bieb. are growth form and spike morphology. Apart from these morphological differences, the species show a clear genetic differentiation. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 716–721.
Extremely thermostable amylolytic enzyme from the archaebacterium Pyrococcus furiosus

One of the most thermostable and thermoactive enzymes ever described has been characterized from a hyperthermophilic archaebacterium Pyrococcus furiosus. The enzyme system of this bacterium was capable of hydrolyzing starch forming a mixture of various oligosaccharides. Unlike the amylases from aerobic bacteria this enzyme does not require metal ions for activity or stability. The enzyme is catalytically active over a very broad temperature range, namely between 40°C and 140°C. The half life of this peculiar enzyme during autoclaving at 120°C is 2 h.
Traits that distinguish outbreaking and nonoutbreaking Macrolepidoptera feeding on northern hardwood trees

Life cycle traits of outbreaking and nonoutbreaking species of Macrolepidoptera feeding on hardwoods are compared. Nonoutbreaking and outbreaking species differ in several ways. The majority of outbreaking species either begin feeding in the spring or are gregarious, summer feeders. Diet breadth and fecundity of outbreaking species are greater, and outbreaking species also appear to be better defended against predators