Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural analysis of cytokine signaling modulators

The N-linked glycans attached to cytokine receptors modulate signal transduction by interacting with galectin-3 and generating a cell surface lattice. This opposes constitutive endocytosis and reduces the thresholds for cytokine signaling. The preferred ligands for galectin-3 are the poly-N-acetyl lactosaminylated tetra-antennary glycans which are synthesized by Mgat 5 and are present at high levels in tumor cells. A null mutation in Mgat 5 inhibits lattice formation and cancer progression in cells with an oncogenic background. GlcNAc feeding reestablishes lattice formation, cytokine signaling and tumorigenesis. A MALDI-TOF analysis was employed to identify the N-glycans involved in modulating signal transduction in wild type and null Mgat 5 cells grown with different GlcNAc supplements. Native N-glycan profiling showed alterations in N glycosylation generated by GlcNAc supplements through stimulation of hexosamine pathway. After methylation the tetra-antennary and poly-N-acetyl lactosaminylated glycans were identified only in Mgat 5 wild type cells either supplemented or not with GlcNAc. These structures were absent from the signaling deficient Mgat 5 null cells. Although lattice formation and tumor progression are reestablished after GlcNAc feeding, the preferred galectin-3 ligands were absent from Mgat 5 null cells. Collision Induced Dissociation in a MALDI-IT-TOF instrument was used for N-glycan structural determination. For monitoring the alterations in N-glycosylation, null and wild type Mgat 5 cells were grown in medium supplemented with increasing GlcNAc concentrations. The N-glycans were extracted and subjected to neuraminic acid release to facilitate quantitative estimation. Oligosaccharide profiles for the Mgat 5 wild type cells showed little variation in the high mannose glycan series and a slight increase in the relative abundances of complex type glycans. In the Mgat 5 null cells the increments in GlcNAc concentration determine increasing levels of biand triantennary glycans and decreasing levels of high mannose glycans. These suggest that present in a higher number the glycans with lower LacNAc multiplicity are able to establish lattice interactions with adequate avidity to stimulate cytokine signaling and tumor progression in a Mgat 5 null background.
AN ABSTRACT OF THE THESIS OF Christian Unoermann for the degree of Master of Science in Biochemistry and Biophysics presented on May 4, 1993. Title: Protein-Protein Interactions of the Bacteriophaoe T4-coded dCTPase-

approved: C ristopher K. Mathews, Ph.D. The bacteriophage T4 forms a deoxynucleoside triphosphate (dNTP) synthesizing complex in its host Escherichia coli (E.coli) during the infection cycle. This complex provides dNTPs to the replication machinery and consists of at least ten proteins, including enzymes encoded by the host cell genome. The enzyme deoxycytidine triphosphatase-deoxyuridine triphosphatase (dCTPase-dUTPase), which is encoded by gene 56 of the bacteriophage, was purified from an overexpressing strain of E.coli. The enzyme was immobilized on an affinity column and used for affinity chromatography. The specifically retained proteins belong to the dNTP synthetase complex and, furthermore, to the replication machinery. Purified protein was injected in rabbits to generate polyclonal antisera. The purified antibodies were tested, and then again injected in rabbits to raise antiidiotypic antibodies. The antiidiotypic antibodies had specificity for deoxynucleoside monophosphokinase. Native gel electrophoresis with dCTPase-dUTPase was applied to study protein-protein interactions in a native environment. In this in vitro approach, the enzyme dCMP deaminase was shown to interact with dCTPase-dUTPase and dCMP hydroxymethylase. In a second project, the purification of the dNTP synthetase complex was Redacted for privacy attempted in a novel approach. An affinity tag consisting of six consecutive histidines was added to the Nand the C-terminus of the enzyme dCMP hydroxymethyiase, one of the constituent enzymes of the complex. This tag interacts specifically with a Ni2+-column. The modified enzyme displays approximately the same activity as the wild-type form. I attempted the purification of complex by infecting the overexpressing bacteria with a T4-strain deficient in dCMP hydroxymethylase and applying the lysate to the Ni2+-column. However, the copurification of the dNTP synthetase complex failed. Protein-Protein Interactions in the Bacteriophage T4-coded dCTPase-dUTPase
A Proposal of Statement Fill-in-blank Problem Using Program Dependence Graph in Java Programming Learning Assistant System

To assist Java educations, we have developed a Web-based Java Programming Learning Assistant System (JPLAS), that provides the element fill-in-blank problem and the code writing problem. The former problem is designed for novice students to study the grammar and coding style of Java by filling in correct words to the blanks in a given Java code which are marked automatically through checking for coincidences of correct ones. The latter problem is for students to study writing Java codes for given specifications described in natural language that are automatically verified using the test-driven development (TDD) method. Unfortunately, rough transition exists due to different difficulties found between the two problems. In this paper, we propose the statement fill-in-blank problem in JPLAS by asking students to fill in the gap and write one whole statement in a code where the correctness is verified by the TDD method. The blank statement is selected by generating the Program Dependence Graph (PDG) of the code and finding the statement that has the largest dependence in PDG. We verify the effectiveness through applications of the Java programming course in our department.
Preparation and Characterization of Antioxidant Peptides from Carrot Seed Protein

Carrot is a very popular vegetable and used for culinary and cosmetic purposes. Carrot seeds can be used for treatment of hangovers and stimulating menstruation. In the present study, the carrot seed protein (CSP) extracted from carrot seed (Daucus carota L.) was hydrolysed by four proteases (papain, trypsin, neutrase, and alcalase). Alcalase hydrolysate exhibited the strongest DPPH radical-scavenging activity (DRSA). The optimum hydrolysis condition for the antioxidant peptide production from CSP was obtained using response surface methodology (RSM). The optimum condition was as follows: hydrolysis time of 3.50 h, substrate concentration of 52.8 g/L, and protease dosage of 419.36 U/g, under which DRSA of 82.46% at 2 mg/mL was obtained. The carrot seed protein hydrolysates (CSPHs) were separated using size exclusion chromatography in order to obtain peptides with stronger antioxidant activity. The hydrolysates were fractionated into four peaks, and fractions F3 and F4 with smaller molecular weight showed stronger antioxidant activity. These findings indicated that the success of RSM in optimizing the hydrolysis conditions and the further work in separation of antioxidant peptides in CSPH is feasible. The CSPH exhibites good antioxidant properties and can be used as useful ingredient in foods.
- 1-Numerical simulation of liquid water and gas flow in a channel and a simplified gas diffusion layer model of polymer electrolyte membrane fuel cells using the lattice Boltzmann method

Numerical simulations using the lattice Boltzmann method (LBM) are developed to elucidate the dynamic behavior of condensed water and gas flow in a polymer electrolyte membrane (PEM) fuel cell. Here, the calculation process of the LBM simulation is improved to extend the simulation to a porous medium like a gas diffusion layer (GDL), and a stable and reliable simulation of two-phase flow with large density differences in the porous medium is established. It is shown that dynamic capillary fingering can be simulated at low migration speeds of liquid water in a modified GDL, and the LBM simulation reported here, which considers the actual physical properties of the system, has significant advantages in evaluating phenomena affected by the interaction between liquid water and air flows. Two-phase flows with the interaction of the phases in the two-dimensional simulations are demonstrated. The simulation of water behavior in a gas flow channel with air flow and a simplified GDL shows that the wettability of the channel has a strong effect on the two-phase flow. The simulation of the porous separator also indicates the possibility of controlling two-phase distribution for better oxygen supply to the catalyst layer by gradient wettability design of the porous separator.
Susceptibility of Malassezia pachydermatis to azole antifungal agents evaluated by a new broth microdilution method

Malassezia pachydermatis is considered an opportunistic pathogen of the outer ear duct in dogs and cats. This yeast can also be found in the skin, rectum, anal sacks and vagina. Eighty-two samples of this yeast isolated from dogs with the symptoms of external otitis from the Porto Alegre region were tested for their susceptibility to antifungal agents using the Broth Microdilution Method. The testing antifungal agents were Ketoconazole, Fluconazole and Itraconazole. Experimental essays determined that Sabouraud dextrose broth supplemented with 1% Tween 80 was the most appropriate medium for culture, for a ten-fold dilutions for the inocula, and 48 hours as the interval of readings. The ranges of the Minimal Inhibitory Concentrations (MICs) for the 82 samples were (a) Ketoconazole, from 0.015 to 0.25 mg/mL (mean of 0.08 mg/mL), (b) Fluconazole, from 1 to 32 mg/mL (mean of 9.22 mg/mL), and (c) Itraconazole, from 0.007 to 0.125 mg/mL (mean of 0.05 mg/mL). The isolates of M. pachydermatis showed an excellent level of susceptibility to antifungal azole agents, with all strains being susceptible to Itraconazole, and with only 2.4 % and 3.7% being resistant to Fluconazole and Kketoconazole, respectively . The use of the broth microdilution method allows the assessment of the susceptibility of large numbers of samples from M. pachydermatis isolates to the most common antifungal agents. The proposed procedure is easy to perform and considerably inexpensive compared with other existing tests, which makes this a method of choice for laboratorial use. A standardization of procedures currently used in veterinary mycology laboratories is required. Consistent results among laboratories could greatly benefit the establishment of proper comparisons between studies on antifungal susceptibility and therapeutic trials.
Acute and chronic inflammatory responses induced by smoking in individuals susceptible and non-susceptible to development of COPD: from specific disease phenotyping towards novel therapy. Protocol of a cross-sectional study

Introduction Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease with pulmonary and extra-pulmonary manifestations. Although COPD is a complex disease, diagnosis and staging are still based on simple spirometry measurements. Different COPD phenotypes exist based on clinical, physiological, immunological and radiological observations. Cigarette smoking is the most important risk factor for COPD, but only 15–20% of smokers develop the disease, suggesting a genetic predisposition. Unfortunately, little is known about the pathogenesis of COPD, and even less on the very first steps that are associated with an aberrant response to smoke exposure. This study aims to investigate the underlying local and systemic inflammation of different clinical COPD phenotypes, and acute effects of cigarette smoke exposure in individuals susceptible and non-susceptible for the development of COPD. Furthermore, we will investigate mechanisms associated with corticosteroid insensitivity. Our study will provide valuable information regarding the pathogenetic mechanisms underlying the natural course of COPD. Methods and analysis This cross-sectional study will include young and old individuals susceptible or non-susceptible to develop COPD. At a young age (18–40 years) 60 ‘party smokers’ will be included who are called susceptible or non-susceptible based on COPD prevalence in smoking family members. In addition, 30 healthy smokers (age 40–75 years) and 110 COPD patients will be included. Measurements will include questionnaires, pulmonary function, low-dose CT scanning of the lung, body composition, 6 min walking distance and biomarkers in peripheral blood, sputum, urine, exhaled breath condensate, epithelial lining fluid, bronchial brushes and biopsies. Non-biased approaches such as proteomics will be performed in blood and epithelial lining fluid. Ethics and dissemination This multicentre study was approved by the medical ethical committees of UMC Groningen and Utrecht, the Netherlands. The study findings will be presented at conferences and will be reported in peer-reviewed journals. Trial registration ClinicalTrials.gov, NCT00807469 (study 1) and NCT00850863 (study 2).
The Impact of Cognitive Fatigue on Age-related Differences in Neuromuscular Function

Fatigue is a multifactorial phenomenon including both cognitive and physical components. While age-related changes in neuromuscular function due to physical fatigue are well investigated, the effects of cognitive fatigue on neuromuscular function in older adults are unclear. The purpose of this study is to describe the methodology to examine the influence of cognitive fatigue on age-related changes in neuromuscular function and associated prefrontal cortex (PFC) activity. 4 younger and 1 older females underwent a 60-minute quiet session (control) and 60-minute cognitive fatigue session prior to a moderate intensity fatiguing handgrip exercise. An integrated neuroergonomic approach for collecting brain and muscle activity, cardiovascular responses and fatigue-related self-reports are described. Expected outcomes from this neuroergonomic investigation will provide the rationale for developing training and rehabilitative interventions for promoting both brain and body health to improve physical competencies in older adults.
Children’s perceptions of their right to quality healthcare in Uganda: Critical gaps in programme and policy development

In 1989, Article 24 of the Convention on the Rights of the Child (UNCRC) stipulated good quality healthcare, the best healthcare possible, as a human right for every child. This qualitative study in Uganda examined children’s awareness of and access to timely, quality healthcare as part of a broader study examining whether institutions established for children in Africa are raising awareness about children’s rights amongst children and engaging with children in decision-making and planning. To establish whether children possessed knowledge of their rights and could inform decisions at a community level. Using action research approaches, the team conducted focus group discussions (FGD), drawing, key informant interviews(KII), dialogue meetings (DM), and observations in one village in a rural and another in aperi-urban district, with 72 participants (21 children aged 10–15 and 51 adult stakeholders at community, district and national levels). Children were aware of their right to quality health services. In FGDs and drawing, children described their dissatisfaction with and difficulties in accessing healthcare services. These were confirmed with the adult stakeholders in the KIIs and DMs, the DMs also including children who presented their FGD results to community stakeholders. The findings suggested a lack of clear guidelines in schools or health facilities to support children needing medical attention. There was limited stakeholder capacity to involve children meaningfully in programme plans and decisions directly affecting them. Recommendations included the development of explicit policies with specific strong linkages between educational, health and other service institutions to promote, protect and respect children’s rights and also training to elicit children’s perspectives in decisions that affect them.
On the formation history of Galactic double neutron stars

Double neutron stars (DNSs) have been observed as Galactic radio pulsars, and the recent discovery of gravitational waves from the DNS merger GW170817 adds to the known DNS population. We perform rapid population synthesis of massive binary stars and discuss model predictions, including DNS formation rates, mass distributions, and delay time distributions. We vary assumptions and parameters of physical processes such as mass transfer stability criteria, supernova natal kick distributions, remnant mass prescriptions, and common-envelope energetics.We compute the likelihood of observing the orbital period-eccentricity distribution of the Galactic DNS population under each of our population synthesis models, allowing us to quantitatively compare the models.We find that mass transfer from a stripped post-heliumburning secondary (case BB) on to a neutron star is most likely dynamically stable. We also find that a natal kick distribution composed of both low (Maxwellian σ = 30 km s-1) and high (σ = 265 km s-1) components is preferred over a single high-kick component. We conclude that the observed DNS mass distribution can place strong constraints on model assumptions.
GMRT DISCOVERY OF PSR J1544+4937: AN ECLIPSING BLACK-WIDOW PULSAR IDENTIFIED WITH A FERMI-LAT SOURCE

Using the Giant Metrewave Radio Telescope, we performed deep observations to search for radio pulsations in the directions of unidentified Fermi-Large Area Telescope γ-ray sources. We report the discovery of an eclipsing black-widow millisecond pulsar, PSR J1544+4937, identified with the uncataloged γ-ray source Fermi J1544.2+4941. This 2.16 ms pulsar is in a 2.9 hr compact circular orbit with a very low mass companion (Mc > 0.017M☉). At 322 MHz this pulsar is found to be eclipsing for 13% of its orbit, whereas at 607 MHz the pulsar is detected throughout the low-frequency eclipse phase. Variations in the eclipse ingress phase are observed, indicating a clumpy and variable eclipsing medium. Moreover, additional short-duration absorption events are observed around the eclipse boundaries. Using the radio timing ephemeris we were able to detect γ-ray pulsations from this pulsar, confirming it as the source powering the γ-ray emission.
Laws of large numbers for mesoscopic stochastic models of reacting and diffusing particles

We study the asymptotic behaviour of some mesoscopic stochastic models for systems of reacting and diffusing particles (also known as density-dependent population processes) as the number of particles goes to infinity. Our approach is related to the variational approach to solving the parabolic partial differential equations that arise as limit dynamics. We first present a result for a model that converges to a classical system of reaction-diffusion equations. In addition, we discuss two models with nonlinear diffusion that give rise to quasilinear parabolic equations in the limit.
Consumption Smoothing and the Structure of Risk and Time Preferences:Theory and Evidence from Village India

This paper investigates the extent to which rural households in developing countries are able to smooth consumption, using a theoretical model of full risk sharing, in which participating households have di®erent risk and time preferences. A resulting rule of resource allocation is characterized in an intuitive way, clarifying the e®ects of diverse preferences. Empirical models are applied to a household panel data collected from rural India. Estimation results strongly support the heterogeneity in risk preferences. In contrast, little evidence is found in favor of the intertemporal resource allocation across households according to di®erences in time preferences.
Real Time PCR: the Use of Reference Genes and Essential Rules Required to Obtain Normalisation Data Reliable to Quantitative Gene Expression

Quantitative Real-time Polymerase Chain Reaction (qPCR) is an important tool for molecular biology and biotechnology research, widely used to determine the expression levels of mRNA. Two main methods to performing qPCR are largely used: The absolute quantification, in which the mRNA levels are determined by using a standard curve and the relative method, which is based on the use of reference genes. Reference genes are widely expressed in cells of animal and plant tissues and their expression pattern are theoretically unchanged within several situations, which makes them an excellent choice to normalize mRNA quantification data in relative qPCR studies. However, several reports are increasingly showing that the use of only one reference gene in relative qPCR studies should be avoided, because in the real world their expression levels can significantly change from tissue to tissue. Several softwares, such as geNorm, BestKeeper and NormFinder, have been developed to perform data normalisation, and these programs may assist in choosing the most stable reference genes. The aim of this review was to describe the current normalisation strategies used in qPCR assay, as well as to establish essential rules to perform reliable mRNA quantification. Finally, this review show some innovations in the advances on qPCR.
The Effect of Diffrent Factors on X- and Y Bearing Sperm in Bull Semen

Background: Newborn gender ratio is one of the most important factors in livestock industry. This ratio has affected on economic condition and controls sex-linked genetically transferred diseases. Offspring sex ratio is affected by such various factors. One of these factors is the Y to X bearing sperm ratio in normal semen that is called primary sex ratio, season and individual differences are important factors that can have an effect on primary sex ratio. OBJECTIVES: The objective of this study was to investigate two main effective factors, Individual difference and season, on proportion of sperms containing Y-chromosomes to sperms containing X-chromosomes in bull semen. METHODS: Semens were collected from 16 bulls during summer (Jul-Aug) and winter (Dec. to Jun). After sperm analysis, DNAs were extracted and Real-time PCR performed using three sets of primers to study SRY (Y-chromosome specific sequence), PLP (X-chromosome specific sequence) and PAR (Housekeeping) genes. RESULTS: The results showed that the sex ratio of sperms in normal ejaculation was not equal in different bulls. Moreover, season can affect primary sex ratio. Y-bearing sperm increase in summer. CONCLUSIONS: We concluded that the primary sex ratio is affected by individual differences and season. We also suggested using Northern blotting on PCR products to confirm results.
Temporal and Spatial Variation of the Fish Assemblage Around a Gas Platform in the Northern Adriatic Sea, Italy

The "Barbara NW" platform, located in the northern Adriatic Sea 56 km offshore and at 68.5 m depth, was monitored for investigating the temporal and the horizontally spatial extent to which the gas platform attracted different fish species during the three years after its deployment (2000-2002). Fish were sampled with a trammel net both at the rig and at an open-sea control site placed at a distance of about 1.8 km, on the same type of seabed. At each survey, the catch obtained around the platform was subdivided based on the distance from the jacket (submerged part of the platform). Six strata, each 34 m wide, were identified up to 204 m horizontally from the rig. The platform showed its aggregation effect within the first year after installation. Catch rates significantly declined at increasing distances from the rig. The value recorded inside a 34 m radius from the structure was significantly higher than those obtained at distances greater than 140 m and at the control site. Reef-dwelling benthic fish, partially reef-dwelling pelagic and nekto-benthic species dominated inside the stratum closest to the rig, whilst the organisms which had no affinity towards hard substrates prevailed in the farther strata and at control site.