Miracle-dz/UniFAR-FTUs huggingface dataset:
High-resolution analysis of human cytomegalovirus-specific T-cell receptor repertoires

The human herpesvirus cytomegalovirus (CMV) is a prevalent pathogen and infects a person for life. After primary infection, CMV latently resides in certain body cells to avoid clearance by the immune system. Primary infection and reactivations from latency usually go unnoticed in persons with an intact immune system. But in immunocompromised persons, such as transplant recipients, CMV can cause severe diseases, because these persons cannot keep the virus in check. Virus-specific CD8+ T cells are the key component of CMV-directed immunity and their presence is associated with protection from overt disease. Several studies have already explored the human T-cell response against the virus. However, the CMV-specific T-cell repertoire is highly complex, and it remains an enigma which CD8+ T cells with which CMV antigen specificity are the most protective and best control the virus. CD8+ T cells recognise antigens using a specialised surface protein, the heterodimeric αβ T-cell receptor (TCR). This receptor is highly variable between T cells and billions of different TCRs can be found on the T cells of a single person. In this PhD project, the CD8+ T-cell repertoire specific for CMV was assessed at high resolution: Virus-specific CD8+ T cells from healthy virus carriers were enriched through in vitro stimulation with short peptides and analysed by TCR mRNA sequencing, primarily of the β-chain. CMV-specific TCRβ sequences were identified by computational analysis via multi-sample comparisons. Subsequently, the magnitude and diversity of interindividual and intraindividual CMV-specific TCRβ repertoires was analysed. The focus was on the TCR repertoire specific for HLA-C--restricted CMV peptides, because presentation of such peptides is least affected by viral immunomodulation. In total, 1809 CMV-specific TCRβ amino acid sequences were identified in this project. The CMV-specific TCR repertoires were generally highly clonal, but repertoire diversity differed between peptides. CMV-specific TCRβ clonotypes, particularly those specific for HLA-C--restricted peptides, were highly frequent in peripheral blood of virus carriers; in 3 of 9 donors, the TCR with the highest frequency in the entire CD8+ T cell repertoire was specific for one CMV peptide. Several TCRβ clonotypes with the same CMV peptide specificity were identical or strikingly similar at the amino acid level and shared by multiple donors. The cumulative frequency of these 162 shared TCRβ clonotypes was significantly higher in CMV-positive than CMV-negative donors in this cohort and a large independent validation cohort. Consequently, CMV infection leaves a specific TCRβ signature in the T-cell repertoires of its human hosts. Signature TCRβ sequences will be valuable in disease monitoring, for instance as markers for the presence of a CMV-specific T-cell response. In addition, such TCRs hold great potential for adoptive T-cell transfer, since they are tolerant to a wide range of HLA-self peptide complexes and are therefore less likely to cause toxicity in the recipient.
Pediatric Sleep Questionnaire Used to Assess Sleep-Related Breathing Disorders in a Western Pennsylvania Private Orthodontic Practice

Sleep related breathing disorders (SRBD) in children have a reported prevalence of 4-11% and manifest as behavioral, physical, and/or academic deficiencies. SRBD in children include snoring, obstructive sleep apnea (OSA), and hypopnea. Unlike adults, OSA incidence in pediatric patients occurs equally in males and females, with the greatest incidence from ages 2-8 years old. The greater incidence during this age range is primarily due to larger pharyngeal lymphatic tissues, which regress as the patient progresses into adolescence. After puberty, the prevalence of OSA increases more in boys than girls, which could be due to testosterone-induced changes. The gold standard for measuring SRBD is an overnight polysomnograph, which is burdensome to both the patient and the parent. For this reason, numerous questionnaires have been created to help identify patients at risk for SRBD. The Pediatric Sleep Questionnaire (PSQ) is a 22-point questionnaire which can be scored quickly and easily. When more than one third of the answers are answered positively, there is an increased likelihood that the patient would have positive signs of SRBD on a polysomnograph. With a specificity of 81% and a sensitivity of 85%, the questionnaire is a powerful tool for identifying patients who may be at a higher risk for SRBD. By looking at 1500 consecutive PSQ given to all patients under the age of 18 as part of the routine medical history, the prevalence of SRDB in pediatric orthodontic patients in a private practice in Western Pennsylvania will be estimated in an effort to describe how common this disorder may be in a common orthodontic environment.
Comparative population structure, abundance and vertical distribution of six copepod species in the North Atlantic: Evidence for intraguild predation?

Abstract The abundance, vertical distribution and stage composition of the copepods Euchaeta norvegica, Metridia lucens and Pleuromamma robusta and the abundance and vertical distribution of Acartia sp. , Oithona spp. and Oncaea sp. were analysed for a period of 4.5 years (1971–1974), based on data previously collected at weather station India in the North Atlantic (59°N, 19°W). The results were compared with previously published results on Calanus finmarchicus during the same study. The factor analysis showed two well-differentiated groups. The cohort development and abundance of C. finmarchicus, E. norvegica and Oncaea were related to successive phytoplankton blooms. On the contrary, the cohort development and abundance of M. lucens, P. robusta, Acartia spp. and Oithona spp. were not related to phytoplankton concentration and showed negative relationships with Calanus abundance. We suggest that C. finmarchicus, which largely dominates the biomass at station India, could play a key role in the structuring of the community: as prey for the carnivorous E. norvegica, vectoring the spring bloom to deep waters through faecal pellet consumption by the coprophagous Oncaea spp. , and through intraguild predation on the early stages of other omnivorous copepods such as Acartia, Oithona, M. lucens and P. robusta.
Molecular analysis of glyphosate and osmotic stress responsive genes

Cross species hybridization can provide a tool for elucidating biological pathways conserved among organisms. Based on sequence conservation among grass species, we selected Affymetrix GeneChip® wheat genome array as a tool to analyze changes in gene expression profiles of three Festuca species in response to varying levels of glyphosate. Differences in transcript expression upon glyphosate application at 5% and 20% of the recommended rate were recorded. Differences highlighted metabolic categories, including photosynthesis, protein synthesis, and stress responses. Expression levels of a larger number of transcripts altered with 20% glyphosate. RT-PCR analysis was conducted for experimental validation. This is the first report to analyze the potential of cross species hybridization in Festuca species and the data help extend our knowledge on the cellular processes affected by glyphosate. Autophagy related gene, Atg8 has been used for monitoring autophagy in various organisms. In this study, Atg8 gene was identified in Brachypodium distachyon (named as BdAtg8) under osmotic stress. Expression profile of BdAtg8 was examined in a variety of tissues of different ages and osmotic stress conditions. Expression level of BdAtg8 elevated with osmotic stress, especially in the roots. BdAtg8 complemented atg8Δ[delta]::kan MX yeast mutants grown under starvation conditions. Monodansylcadaverine was used to observe autophagosomes, and autophagy was shown to be constitutively active in Brachypodium. Autophagy was more active in plants exposed to osmotic stress. BdATG8 protein was expressed in yeast and analyzed with western blotting. In conclusion, under osmotic stress conditions, BdAtg8 gene is required for induction of autophagy in Brachypodium.
Life History Characteristics of Two Introduced Populations of Mysis Relicta

Introduced populations of the opossum shrimp Mysis relicta take 4 yr to reach repro- ductive age in Lake Tahoe, California-Nevada and 1-2 yr in Emerald Bay, an isolated (for Mysis) embayment of Lake Tahoe. Reproduction in both populations occurs in the winter and spring. The duration of embryonic stages in the Emerald Bay population based on field population statistics ranged from 50 d for the egg stage to 6 d for the last embryonic stage. The number of eggs per egg-bearing female in Emerald Bay increased significantly with the total length of the female. Over the entire brooding period, the average number of embryos per female decreased from 13.89 eggs per gravid female to 10.33 stage 5 embryos per female. This decline in brood size with age of the brood was not due to size-related mortality, but probably resulted from embryos falling out of the marsupium. A similar decline in brood size with age of the brood was not observed in Lake Tahoe. The average number of eggs per brood in Lake Tahoe was 10.73 which was significantly less than that observed in Emerald Bay. However, there was no difference in the number of stage 5 embryos per brood in both systems. Differences in generation time and total reproductive output in the Lake Tahoe and Emerald Bay populations were most closely related to differences in the overall production and mean depth of the two systems. In addition, these traits and whether reproduction is seasonal or continuous among other mysid populations are strongly correlated with the total production of the environment. These results suggest that differences in M. relicta life history traits among populations may represent a phenotypic and not an evolutionary life history adaptation.
Assessment of Combined In-Plane and Out-of-Plane Fragility Functions for Adobe Masonry Buildings in the Peruvian Andes

In the city of Cusco and in other parts of Peruvian Andes, adobe masonry is the primary construction material. Adobe continues to be used for the construction of housing because of its low cost, its thermal properties, the use of unskilled labor, and the local traditions of the Peruvian highlands. The Peruvian National Statistics Office estimates that 67% of rural housing in Cusco is made of adobe masonry. Besides, previous seismic events and laboratory tests demonstrated that adobe dwellings without reinforcement are prone to collapse during an earthquake. Therefore, seismic vulnerability assessment of this type of dwellings is necessary aiming at developing proper contingency and mitigation risk policies. Then, fragility curves constitute a key tool when conducting seismic loss assessment because they provide information regarding the probability of exceeding a certain damage limit state as a function of a given engineering demand parameter. This work aims at developing fragility curves, combining in-plane and out-of-plane loading conditions, for typical adobe buildings located in the city of Cusco. Initially, a set of one- and two-story adobe houses were studied to determine the geometrical characteristics of representative local building typologies. Subsequently, 1,000 artificial buildings were generated by means of Monte Carlo simulation based on the information gathered. The structural capacity of each artificial building was represented by simplified bilinear and trilinear capacity curves for in-plane and out-of-plane mechanisms, respectively. In order to represent the characteristics associated with subduction processes, a set of ground motion records was established. The damage state of each building was assessed for each seismic record, and this information was collected into a Probability Damage Matrix (DPM). Finally, fragility curves were fitted for each damage state of the cumulative DPM. Preliminary results show that one- and two-story adobe dwellings have a probability of collapse of 30 and 60%, respectively, when considering a peak ground acceleration of 0.30 g, which corresponds to the expected acceleration related to a return period of 475 years over a soil type 2 according to the Peruvian Standards.
VMAT2 Safeguards β-Cells Against Dopamine Cytotoxicity Under High-Fat Diet–Induced Stress

Vesicular monoamine transporter 2 (VMAT2) uptakes cytoplasmic monoamines into vesicles for storage. VMAT2 plays a role in modulating insulin release by regulating dopamine levels in the pancreas, although the exact mechanism remains elusive. We found that VMAT2 expression in β-cells specifically increases under high blood glucose conditions. The islets isolated from β-cell–specific Vmat2 knockout (βVmat2KO) mice show elevated insulin secretion levels in response to glucose stimulation. Under prolonged high-fat diet feedings, the βVmat2KO mice exhibit impaired glucose and insulin tolerance and progressive β-cell dysfunction. Here we demonstrate VMAT2 uptake of dopamine to protect dopamine from degradation by monoamine oxidase, thereby safeguarding β-cells from excess reactive oxygen species (ROS) exposure. In the context of high demand for insulin secretion, the absence of VMAT2 leads to elevated ROS in β-cells, which accelerates β-cell dedifferentiation and β-cell loss. Therefore, VMAT2 controls the amount of dopamine in β-cells, thereby protecting pancreatic β-cells from excessive oxidative stress.
Persistent Iron Deficiency Anemia in Patients with Celiac Disease Despite a Gluten-Free Diet

Celiac disease (CD) is an autoimmune disorder characterized by intolerance to dietary gluten in genetically predisposed subjects. Iron deficiency anemia (IDA) is a common sign in CD, being the only abnormality in approximately 40% of celiac patients. A multifactorial etiology leads to IDA in CD. The two main causes are the villous atrophy of the mucosa at the site of iron absorption (the duodenum) and the resulting inflammation, which triggers the mechanism that leads to the anemia of chronic disease. Until now, it has been unclear why some patients with CD continue to have IDA despite a careful gluten-free diet (GFD) and the normalization of villous atrophy. Furthermore, some celiac patients are refractory to oral iron supplementation despite the healing of the mucosa, and they thus require periodic intravenous iron administration. The Marsh classification evaluates the degree of inflammation and villous atrophy, but it does not assess the possible persistence of ultrastructural and molecular alterations in enterocytes. The latter was found in CD in remission after adopting a GFD and could be responsible for the persistently reduced absorption of iron and IDA. Even in non-celiac gluten sensitivity, anemia is present in 18.5–22% of patients and appears to be related to ultrastructural and molecular alterations in intestinal microvilli. It is possible that a genetic component may also play a role in IDA. In this review, we evaluate and discuss the main mechanisms of IDA in CD and the possible causes of its persistence after adopting a GFD, as well as their therapeutic implications.
The distribution of free-living nematodes in relation to salinity in the middle and upper reaches of the River Blyth estuary.

The habitat of mud-dwelling estuarine nematodes consists essentially of an extremely complex mixture (Baver 1948) of inorganic and organic particles surrounded by interstitial water. Except when the mud dries out completely the body surface of a nematode in this habitat is continually in contact with the interstitial water. Exposure, salinity changes, and other characteristics of estuaries affect nematodes only in so far as they affect conditions in this water. The ecological factors peculiar to this habitat can be seen to be very different from those affecting nematodes living on rocky shores, intertidal seaweeds or marine beaches. The original work on the marine nematodes of this country is that of Bastian (1865). This was followed by a number of recordings and descriptions of new species made by Southern (1914) during the Clare Island survey. Since then the nematodes of the Plymouth area have been described by Schuurmans-Stekhoven (1935b) and by Wieser (1951, 1952) in two important works. In his latest paper Wieser studied the vertical distribution of nematodes inhabiting intertidal seaweeds, and although the detailed ecology of the species found in this habitat cannot be extrapolated to the present investigation, the species recordings and the general intertidal ecology of the nematodes studied have been useful for comparison. Moore (1931) and Mare (1942) have studied nematodes as a group, without distinguishing the species, during wider investigations on marine benthic communities, and Rees (1940) has dealt generally with intertidal nematodes. The work of Rees dealt with the horizontal and vertical distribution of nematodes found during a wider survey of the ecology of a mud flat in the Bristol Channel, but none was identified. His work has been used as the only available point of departure for the present investigation. The distribution of free-living nematodes in water of varying salinity has been the subject of much research in the Baltic and in certain areas of the Zuiderzee. An extensive literature exists for the Belgian coast, the North Sea coast of Germany and the Dutch coast, which is summarized in Schuurmans-Stekhoven (1935a) and more recently by Wieser (1951). In the Zuiderzee and the Baltic, rates of salinity change are much less rapid than those found in estuaries and the distribution of
Kinetic modeling of runaway-electron dynamics in partially ionized plasmas

An essential result of kinetic plasma physics is the runaway phenomenon, whereby a fraction of an electron population can be accelerated to relativistic energies. Such runaway electrons are formed in astrophysical settings, but are also of great practical relevance to fusion research. In the most developed fusion device, known as the tokamak, runaway electrons have the potential to cause severe damage to the first wall. Runaway-electron mitigation is therefore one of the critical issues in the design of a fusion power plant. In many situations, runaway electrons interact with partially ionized atoms. In particular, the currently envisaged mitigation method for tokamaks is to inject heavy atoms which collisionally dissipate the runaway beam before it can collide with the wall, or prevent it from forming at all. When the atoms are partially ionized, their bound electrons screen out a fraction of the atomic charge, which directly affects the collisional scattering rates. However, accurate expressions for these collisional scattering rates between energetic electrons and partially ionized atoms have not been available previously. In this thesis, we explore kinetic aspects of runaway dynamics in partially ionized plasmas. We derive collisional scattering rates using a quantum-mechanical treatment, and study the interaction between fast electrons and partially ionized atoms. We then apply these results to calculate the threshold field for runaway generation, as well as the production rate of runaway electrons via the avalanche and Dreicer mechanisms. We find that even if material injection increases the dissipation rates, it also enhances avalanche generation which could potentially aggravate the runaway problem. These results contribute to more accurate runaway-electron modeling and can lead to more effective mitigation schemes in the longer term.
The Use of Enterococci as Probiotics in Poultry

Enterococci are members of the lactic acid bacteria family and are responsible for many food spoilage and fermentations. Some strains of this microorganism are used as probiotics in humans and animals to improve host immunity. However, some Enterococci are important pathogens which cause severe infections. Some strains of Enterococci are resistant to common antibiotics. The Enterococcus faecium and Enterococcus faecalis strains are more common probiotics. Such probiotics are used as an alternative to growth promoting antibiotics, which their use has been restricted. In domestic animals, enterococcal probiotics are mostly used to cure or prevent pathogen infections and immune response and growth performance improvement. This review covers the reports on the application of Enterococcus genus as a functional probiotic in poultry. The results suggest that Enterococcus faecium is a safe probiotic and improve the immune system and performance of broiler chickens.
Proximate Composition, Antinutrient Content and Antimicrobial Properties of Cnidoscolus aconitifolius Leaves

Fresh leaves of Cnidoscolus aconitifolius were harvested from area gardens around Mayne Avenue in Calabar. Proximate composition, anti-nutrient content, vitamins content and antimicrobial activity of the extract were determined. The antimicrobial activity using the aqueous extract was also determined. The results of the proximate composition revealed the presence of moisture 86.40%, ash 6.50%, protein 4.38%, fat 1.20%, fibre 2.39% and carbohydrate 85.36%. The antinutrient components detected are within the acceptable limits with phytic acid 60.44mg/100g followed by total oxalate 40.30mg/g and therefore will not cause any adverse health problems. Toxic amino acid and chlorogenic acid were not detected in the plant extract. The vitamin contents range from 0.10mg/100g to 143.20mg/100g. The highest value was found in vitamin A and the least in niacin. The antimicrobial activities of the extract of this plant against the pathogenic test organisms showed zones of inhibition ranging from 20.5 mm for Salmonella typhi to 26 mm for Streptococcus pyogenes at 10 μg/ml. The highest zones of inhibition observed with Original Research Article Lennox and John; AFSJ, 5(4): 1-6, 2018; Article no.AFSJ. 45055 2 the standard antibiotics were gentamycin 19mm at 10 μg/ml against E. coli, ofloxacin 21mm at 5 μg/ml against K. pneumoniae and methicillin 16mm at 10 μg/ml against S. pyogenes, K. pneumonia and E. coli.
Dimensionality reduction, regularization, and generalization in overparameterized regressions

Overparameterization in deep learning is powerful: Very large models fit the training data perfectly and yet generalize well. This realization brought back the study of linear models for regression, including ordinary least squares (OLS), which, like deep learning, shows a "double descent" behavior. This involves two features: (1) The risk (out-of-sample prediction error) can grow arbitrarily when the number of samples $n$ approaches the number of parameters $p$, and (2) the risk decreases with $p$ at $p>n$, sometimes achieving a lower value than the lowest risk at $p<n$. The divergence of the risk for OLS at $p\approx n$ is related to the condition number of the empirical covariance in the feature set. For this reason, it can be avoided with regularization. In this work we show that it can also be avoided with a PCA-based dimensionality reduction. We provide a finite upper bound for the risk of the PCA-based estimator. This result is in contrast to recent work that shows that a different form of dimensionality reduction -- one based on the population covariance instead of the empirical covariance -- does not avoid the divergence. We connect these results to an analysis of adversarial attacks, which become more effective as they raise the condition number of the empirical covariance of the features. We show that OLS is arbitrarily susceptible to data-poisoning attacks in the overparameterized regime -- unlike the underparameterized regime -- and that regularization and dimensionality reduction improve the robustness.