Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular differentiation and pathogenicity of Aviadenoviruses isolated during an outbreak of inclusion body hepatitis in South Africa.

Fowl adenovirus (FAdV) is a member of the genus Aviadenovirus and causes a number of economically important poultry diseases. One of these diseases, inclusion body hepatitis (IBH), has a worldwide distribution and is characterised by acute mortality (5% - 20%) in production chickens. The disease was first described in the United States of America in 1963 and has also been reported in Canada, the United Kingdom, Australia, France and Ireland, but until now, not in South Africa. Adenoviruses isolated from the first outbreak of IBH in South Africa were able to reproduce the disease in chicken embryo livers. The aim of the present study was to characterise the viruses and determine the pathogenicity of the FAdV strains responsible for the first reported case of IBH in South Africa. Polymerase chain reaction (PCR) amplification of the L1 loop region of the fowl adenovirus hexon gene using degenerate primer pair hexon A/B was used to identify the viruses that were isolated. Restriction fragment length polymorphism (RFLP) of the amplification products was used for the differentiation of 14 isolates of fowl adenovirus. Sequencing of the PCR products followed by amino acid comparison and phylogenetic analysis using the L1 loop region of the hexon protein was done to determine the identity of the isolates. Amino acid sequences of the hexon genes of all the South African isolates were compared with those of reference strains representing FAdV species. Amino acid comparison of 12 South Africa field isolates to FAdV reference strains revealed a high sequence identity (> 93.33%) with reference strains T8-A and 764. Two of the isolates had high sequence identity (93.40%) with reference strains P7-A, C2B and SR48. Phylogenetic analysis of the L1 loop region of the hexon protein of all 14 South African isolates was consistent with their RFLP clusters. The mortality rates of embryos challenged with 106 egg infective doses (EID50) FAdV 2 were 80% - 87% and mortality rates for embryos challenged with 105.95 (EID50) FAdV 8b were 65% - 80%.
Langevin Dynamics with Continuous Tempering for Training Deep Neural Networks

Minimizing non-convex and high-dimensional objective functions is challenging, especially when training modern deep neural networks. In this paper, a novel approach is proposed which divides the training process into two consecutive phases to obtain better generalization performance: Bayesian sampling and stochastic optimization. The first phase is to explore the energy landscape and to capture the `fat'' modes; and the second one is to fine-tune the parameter learned from the first phase. In the Bayesian learning phase, we apply continuous tempering and stochastic approximation into the Langevin dynamics to create an efficient and effective sampler, in which the temperature is adjusted automatically according to the designed ``temperature dynamics''. These strategies can overcome the challenge of early trapping into bad local minima and have achieved remarkable improvements in various types of neural networks as shown in our theoretical analysis and empirical experiments.
Effects of neuropeptide Y (NPY) at the sympathetic neuroeffector junction. Can pre- and postjunctional receptors be distinguished?

Neuropeptide Y (NPY) is widely distributed in central and peripheral neurons. In sympathetic postganglionic neurons, NPY coexists with noradrenaline. NPY and its structural relative peptide YY (PYY) appear to exert three principally different effects at the sympathetic neuroeffector junction. Firstly, NPY has a direct postjunctional effect; this effect is manifested as a vasoconstriction when studied on the guinea pig iliac vein. Secondly, NPY has an indirect postjunctional effect in that it potentiates the response to various vasoconstrictors; this was studied on the rabbit femoral artery and vein, using noradrenaline and histamine, respectively, as vasoconstrictors. Thirdly, NPY acts prejunctionally in that it suppresses the release of noradrenaline from sympathetic nerve terminals; this was studied in the rat vas deferens. The aim of the investigation was to examine whether the three effects of NPY were mediated by the same type of receptor. For this purpose, we examined the effects of a series of NPY-related peptides, namely NPY, PYY, desamido-NPY, and five C-terminal fragments (NPY 19-36, NPY 24-36, PYY 13-36, PYY 24-36 and PYY 27-36). NPY and PYY were active in all three assay systems. The C-terminal amide appears to be crucial for maintaining the biological activity, since desamido-NPY was inactive in the three test systems. Interestingly, PYY 13-36 was almost as active as NPY and PYY in suppressing the electrically evoked contractions of the vas deferens; PYY 13-36 was inactive in the two other test systems. None of the shorter fragments had any biological activity. (ABSTRACT TRUNCATED AT 250 WORDS)
Factor VIII delivered by haematopoietic stem cell-derived B cells corrects the phenotype of haemophilia A mice

Summary The main impediments to clinical application of haematopoietic stem cell (HSC) gene therapy for treatment of haemophilia A are the bone marrow transplant-related risks and the potential for insertional muta-genesis caused by retroviral vectors. To circumvent these limitations, we have adapted a non-myeloablative conditioning regimen and directed factor VIII (FVIII) protein synthesis to B lineage cells using an insulated lentiviral vector containing an immunoglobulin heavy chain enhancer-promoter. Transplantation of lentiviral vector-modified HSCs resulted in therapeutic levels of FVIII in the circulation of all transplanted mice for the duration of the study (six months). Immunostaining of spleen cells showed that the majority of FVIII was synthesised by B220+ B cells and CD138+ plasma cells. Subsequent challenge with recombinant FVIII elicited at most a minor anti-FVIII antibody response, demonstrating in-duction of immune hyporesponsiveness. All transplant recipients exhibited clot formation and survived tail clipping, indicating correction of their haemophilic phenotype. Therapeutic levels of FVIII could be transferred to secondary recipients by bone marrow transplantation, confirming gene transfer into long-term repopulating HSCs. Moreover, short-term therapeutic FVIII levels could also be achieved in secondary recipients by adoptive transfer of HSC-derived splenic B cells. Our findings support pursuit of B cell-directed protein delivery as a potential clinical approach to treat haemophilia A and other disorders correctable by systemically distributed proteins.
Analysis of MIMO with Zero Forcing Successive Interference Cancellation Equalizer

— This paper contain some advanced application of MIMO systems and some main notes in their implementations, which started by MIMO with ZF technique that investigate the effects of phase noise in centralized and distributed narrowband MIMO systems, and discuss the feasibility of phase and frequency synchronization problem. An equalizer, called successive interference cancellation zero-forcing equalizer (SIC-ZFE) is proposed. The proposed equalizer provides ISI-free communications over the ISI MIMO channels without a long guard period. The simulated results with the 2×2 MIMO system with zero forcing equalizer showed matching results as obtained in for a 1×1 system for BPSK modulation in Rayleigh channel. In this paper, we will try to improve the bit error rate performance by trying out Successive Interference Cancellation (SIC). We will assume that the channel is a flat fading Rayleigh multipath channel and the modulation is BPSK. Simulation results show that even with only one selected antenna at the receiver, performances in terms of BER still satisfactory. Nevertheless, when more antennas are selected, better BER values are achieved thanks to receive diversity.
Applications of Gluco-oligosaccharide Oxidase

The nascent study of carbohydrate-active enzymes is now influencing a variety of industries at the commercial scale, particularly in processing lignocellulosic biomass for the production of fuels, materials, and other commodities. These enzymes are highly specific and can modify sugars with selectivity unmatched by chemical processes. Our group has worked extensively with gluco-oligosaccharide oxidase (GOOX), and feel the enzyme’s oxidative activity would prove desirable in many new and existing applications where other commercialized carbohydrate oxidases are employed. The work presented here has demonstrated the improved characteristics of an immobilized fusion enzyme, CtCBM22A_GOOX-Y300A, on insoluble polysaccharide fibre, with potential applications in food additives, protein purification, and aldonic acid production. A second study has successfully employed GOOX oxidation as part of a synthetic pathway to generate a clickable monomer from glucuronoxylan capable of forming a carbohydratebased polytriazole polymer; a process which could be extended to include neutral hemicelluloses such as galactoglucomannan.
Assessing the impact of adjusting for maturity in weight status classification in a cross-sectional sample of UK children

Objectives To compare the weight categorisation of a cohort of UK children using standard procedures (ie, comparing body mass index (BMI) centiles to age-matched UK reference data) versus an approach adjusted for maturation status (ie, matching relative to biological age). Design Analysis of data collected from an observational study of UK primary school children. Setting Schools in South West England. Participants Four hundred and seven 9–11 year-old children (98% white British). Main outcome measures Weight status was classified using BMI centiles using (1) sex and chronological age-matched referents and (2) sex and biological age-matched referents (based on % of predicted adult stature) relative to UK 1990 reference growth charts. For both approaches, children were classified as a normal weight if >2nd centile and <85thcentile, overweight if 85th and <95thcentiles, and obese if ≥95thcentile. Results Fifty-one children (12.5%) were overweight, and a further 51 obese (12.5%) according to standard chronological age-matched classifications. Adjustment for maturity resulted in 32% of overweight girls, and 15% of overweight boys being reclassified as a normal weight, and 11% and 8% of obese girls and boys, respectively, being reclassified as overweight. Early maturing children were 4.9 times more likely to be reclassified from overweight to normal weight than ‘on-time’ maturers (OR 95% CI 1.3 to 19). Conclusions Incorporating assessments of maturational status into weight classification resulted in significant changes to the classification of early-maturing adolescents. Further research exploring the implications for objective health risk and well-being is needed.
Feed contaminated with classical swine fever vaccine virus (lom strain) can induce antibodies to the virus in pigs

In November 2004, antibodies to classical swine fever virus (csfv) were detected in finishing pigs during the annual serological surveillance in Jeju Province, Korea. In addition, csf vaccine viruses (lom strain) had recently been isolated from pigs raised on farms known to have csfv antibody-positive pigs. In contrast with mainland Korea, Jeju Province had been csf free and its pigs had not been vaccinated against csf for more than five years. An epidemiological investigation team from the National Veterinary Research and Quarantine Service investigated the current status of csf prevention on the Korean mainland and in Jeju Province to determine possible routes of introduction of the virus into the province. It was concluded that improperly processed blood meals, manufactured on mainland Korea, had been contaminated with the csf vaccine lom strain, and that the lom strain had been transmitted to pigs fed feed or feedstuffs containing the contaminated meal.
Neurogenesis and identification of developing layers in the visual cortex of the wallaby (Macropus eugenii)

Birthdates of the neurons that comprise the layers of the mature visual cortex in the wallaby (Macropus eugenii) have been determined with the aid of tritiated thymidine autoradiography. The laminar positions of cells, identified by their birthdates, have then been followed at early stages during development and compared with previously published data on the distribution of thalamocortical afferents and corticothalamic projecting cells (Sheng et al. [1991] J. Comp. Neurol. 307:17–38). Neurons are born in a deep to superficial sequence typical of other mammals. The loosely packed zone of cells, which develops at the base of the thin compact zone of cells at the superficial margin of the cortical plate early in development, was identified as being part of the cortical plate. Afferents did not wait below this zone but grew into the developing cortical layers immediately after the cells that form these layers began accumulating in the loosely packed zone, starting with layer 6 on postnatal day 22 (P22). The genesis of layer 4 did not begin until P32, and these cells reached the superficial cortical plate at P54 and entered the loosely packed zone by P65. Cells of layers 5 and 6 formed the initial projection to the thalamus. Despite the protracted development of the wallaby and the large discrepancy between the time of thalamic ingrowth and genesis of layer 4, there was no extended waiting period for afferents in the subplate. J. Comp. Neurol. 416:131–142, 2000. © 2000 Wiley‐Liss, Inc.
Ultrastructural Alterations in Thyrocytes of Zebrafish (Danio rerio) after Exposure to Propylthiouracil and Perchlorate

Histopathology is a widely used approach to evaluate effects of endocrine-active chemicals in the thyroid. However, effects at an ultrastructural level have hardly been examined in fish thyroids. In the present study, zebrafish was exposed to sublethal concentrations of propylthiouracil (PTU; 0–50 mg/L) and perchlorate (PER; 0–5,000 µg/L) for 5 weeks in a modified early life–stage test. None of the treatments caused significant mortality (no observed effect concentrations for survival ≥50 mg/L [PTU] and ≥5,000 µg/L [PER]). PTU induced dose-dependent alterations in the rough endoplasmic reticulum (rER) in all exposure groups, whereas only the 2 highest PER exposure groups (500 and 5,000 µg/L) resulted in alterations of the rER. Both substances caused an increase in the numbers of lysosomes and mitochondria, with mitochondria displaying distorted cristae. Increased mitochondrial diameters were only observed in the PTU treatment. PER-exposed samples displayed an increase in apical microvilli. The highest PTU concentration (50 mg/L) showed first signs of cellular degeneration. Ultrastructural changes in zebrafish thyrocytes thus appear specific for different chemicals, most likely depending on their specific modes of action. Additional knowledge of subcellular changes in thyrocytes can help to better understand and interpret existing histological data in the future.
Assessment of ovarian reserve

Purpose of review Various methods have been proposed and are currently used in the assessment of ovarian reserve in order to predict the outcome in assisted reproduction. This review focuses on the current information regarding the ovarian reserve markers and tests, an active area of research. Recent findings Female age alone is a rough parameter for assessing ovarian reserve. The basal follicle stimulating hormone level is not adequately sensitive to predict poor outcome and the same is true for other basal parameters, including basal estradiol, the follicle stimulating hormone/luteinizing hormone ratio, and inhibin-B levels. The clomiphene citrate challenge test has a low sensitivity but this sensitivity is greater than that of basal follicle stimulating hormone. The value of other hormonal dynamic tests remains to be determined. Among the ultrasound markers the total antral follicle count seems to be promising. Ovarian biopsy in this assessment is controversial. History of poor response to ovarian stimulation is a strong indicator for declining ovarian function. Summary There is currently no clinically useful predictive test sufficiently accurate and distinct in time from controlled ovarian stimulation to assess ovarian reserve accurately. Further research is warranted to validate the ovarian reserve tests in the general population and in populations with different causes of infertility.
Species‐related differences in inotropic effects of angiotensin II in mammalian ventricular muscle: receptors, subtypes and phosphoinositide hydrolysis

1 Experiments were carried out to clarify the mechanisms responsible for variations in the positive inotropic effect (PIE) of angiotensin II (AII) on ventricular muscles from various mammals. We examined the density of All receptors, the relative proportions of receptor subtypes and the acceleration of the hydrolysis of phosphoinositide that was induced by AII, as well as the PIE of AII in ventricular muscles from the rabbit, dog, rat and ferret. 2 In the rabbit, AII (1 μm) in the presence of bupranolol (0.3 μm) and prazosin (0.1 μm) elicited a concentration‐dependent PIE, which was antagonized by a selective AT1 subtype antagonist, losartan, but not by an AT2 antagonist, PD123319. AII did not have any inotropic effects in ventricular muscles from the dog, rat and ferret. 3 Specific high‐affinity binding of [125I]‐AII, with a similar Kd value in each case (1–2 nm), was observed with membrane fractions derived from ventricular muscle of all four species tested. 4 In the rabbit, losartan and PD123319 each displaced approximately 50% of [125I]‐AII specific binding having high affinity for the receptors, and indicating that AT1 and AT2 subtypes were present in equal numbers. In the other species the AT1 subtype of receptors was predominant. 5 In all four species AII caused a concentration‐dependent acceleration of the hydrolysis of phosphoinositide in ventricular slices that had been prelabelled with myo‐[3H]‐inositol. 6 The results indicate that the signal‐transduction process distal to acceleration of the hydrolysis of phosphoinositide may be responsible for the wide range of species variations in the inotropic action of AII on mammalian ventricular myocardium.
Absence of Poly(ADP-Ribose) Polymerase 1 Delays the Onset of Salmonella enterica Serovar Typhimurium-Induced Gut Inflammation

ABSTRACT The immune system comprises an innate and an adaptive immune response to combat pathogenic agents. The human enteropathogen Salmonella enterica serovar Typhimurium invades the intestinal mucosa and triggers an early innate proinflammatory host gene response, which results in diarrheal disease. Several host factors, including transcription factors and transcription coregulators, are involved in the acute early response to Salmonella infection. We found in a mouse model of enterocolitis induced by S. Typhimurium that the absence of the nuclear protein poly(ADP-ribose) polymerase 1 (PARP1), a previously described cofactor for NF-κB-mediated proinflammatory gene expression, is associated with a delayed proinflammatory immune response after Salmonella infection. Our data reveal that PARP1 is expressed in the proliferative zone of cecum crypts, where it is required for the efficient expression of proinflammatory genes, many of which are related to interferon signaling. Consequently, animals lacking PARP1 show impaired infiltration of immune cells into the gut, with severely delayed inflammation.
Distribution and function of tenascin during cranial neural crest development in the chick

Tenascin is a glycoprotein associated with the extra‐cellular matrix and the surface of some cell types. Here, the distribution and possible function of tenascin have been examined along the pathways followed by cranial neural crest cells. During early stages of neural crest migration, tenascin was observed in a dense matrix surrounding premigratory cranial neural crest cells. Along the neural tube, tenascin immunoreactivity was observed in a dorsoventral gradient and was also noted under the ectoderm and around the notochord. During advanced neural crest migration, tenascin immunoreactivity colocalized with and appeared to be on the surface of migrating neural crest cells. At later stages, tenascin was present around the otic vesicles, retina, lens, and in an interstitial matrix in the region of the branchial arches. At the level of the occipital somites, tenascin immunoreactivity was observed around the neural tube, notochord, dermamyotome, and on the basal surface of the ectoderm. Tenascin was also observed in an interstitial matrix within the sclerotome. At early stages of vagal neural crest migration, immunoreactivity was uniform within the sclerotome, whereas at later stages tenascin colocalized with vagal neural crest cells within the rostral half of each sclerotome. The possible function of tenascin was tested by injecting antitenascin antibodies lateral to the mesencephalic neural tube. Two predominant defects were noted in injected embryos: (1) ectopic aggregates of cranial neural crest cells external to the neural tube and sometimes located on the apical side of the ectoderm; and (2) open and deformed neural tubes. Both the distribution and results of the perturbation experiment suggest that tenascin is required for proper cranial neural crest migration.
Identification of Domains within the V-ATPase Accessory Subunit Ac45 Involved in V-ATPase Transport and Ca2+-dependent Exocytosis

Background: Accessory subunit Ac45 is an important regulator of the V-ATPase pump. Results: Ac45 deletion mutants (involving its proteolytic cleavage site or luminal/cytoplasmic domains) affected Ac45 transport through the secretory pathway, V-ATPase trafficking, and Ca2+-dependent secretion. Conclusion: Proper V-ATPase functioning requires Ac45 processing, and N- and C-terminal domains of Ac45. Significance: Elucidation of structural requirements for Ac45 to act as V-ATPase regulator. The vacuolar (H+)-ATPase (V-ATPase) is crucial for maintenance of the acidic microenvironment in intracellular organelles, whereas its membrane-bound V0-sector is involved in Ca2+-dependent membrane fusion. In the secretory pathway, the V-ATPase is regulated by its type I transmembrane and V0-associated accessory subunit Ac45. To execute its function, the intact-Ac45 protein is proteolytically processed to cleaved-Ac45 thereby releasing its N-terminal domain. Here, we searched for the functional domains within Ac45 by analyzing a set of deletion mutants close to the in vivo situation, namely in transgenic Xenopus intermediate pituitary melanotrope cells. Intact-Ac45 was poorly processed and accumulated in the endoplasmic reticulum of the transgenic melanotrope cells. In contrast, cleaved-Ac45 was efficiently transported through the secretory pathway, caused an accumulation of the V-ATPase at the plasma membrane and reduced dopaminergic inhibition of Ca2+-dependent peptide secretion. Surprisingly, removal of the C-tail from intact-Ac45 caused cellular phenotypes also found for cleaved-Ac45, whereas C-tail removal from cleaved-Ac45 still allowed its transport to the plasma membrane, but abolished V-ATPase recruitment into the secretory pathway and left dopaminergic inhibition of the cells unaffected. We conclude that domains located in the N- and C-terminal portions of the Ac45 protein direct its trafficking, V-ATPase recruitment and Ca2+-dependent-regulated exocytosis.