Miracle-dz/UniFAR-FTUs huggingface dataset:
Immune responses and pathogenesis of SARS‐CoV‐2 during an outbreak in Iran: Comparison with SARS and MERS

The beginning of 2020 has seen the emergence of COVID‐19, an outbreak caused by a novel coronavirus, SARS‐CoV‐2, an important pathogen for humans. There is an urgent need to better understand this new virus and to develop ways to control its spread. In Iran, the first case of the COVID‐19 was reported after spread from China and other countries. Fever, cough, and fatigue were the most common symptoms of this virus. In worldwide, the incubation period of COVID‐19 was 3 to 7 days and approximately 80% of infections are mild or asymptomatic, 15% are severe, requiring oxygen, and 5% are critical infections, requiring ventilation. To mount an antiviral response, the innate immune system recognizes molecular structures that are produced by the invasion of the virus. COVID‐19 infection induces IgG antibodies against N protein that can be detected by serum as early as day 4 after the onset of disease and with most patients seroconverting by day 14. Laboratory evidence of clinical patients showed that a specific T‐cell response against SARS‐CoV‐2 is important for the recognition and killing of infected cells, particularly in the lungs of infected individuals. At present, there is no specific antiviral therapy for COVID‐19 and the main treatments are supportive. In this review, we investigated the innate and acquired immune responses in patients who recovered from COVID‐19, which could inform the design of prophylactic vaccines and immunotherapy for the future.
Presence of asymptomatic CMV and EBV DNA in blood of persons with HIV starting antiretroviral therapy are associated with non-AIDS clinical events.

BACKGROUND Even with antiretroviral therapy (ART), persons with HIV (PWH) experience increased morbidity/mortality. Cytomegalovirus (CMV) and Epstein-Barr-Virus (EBV) co-infections likely exacerbate inflammatory-related diseases. OBJECTIVE To determine if presence of detectable CMV or EBV DNA in peripheral blood mononuclear cells (PBMC) is associated with non-AIDS events among PWH receiving modern ART. DESIGN We performed a case-control study of PWH starting ART and HIV-suppressed at year 1 and thereafter, 140 cases who experienced non-AIDS events and 305 matched controls. Events included myocardial infarction, stroke, malignancy, serious bacterial infection or death. METHODS Blood samples were studied pre-ART, 1-year post-ART and pre-event. Controls had an event-free follow-up equal or greater than cases. CMV and EBV levels were measured in PBMC. Conditional logistic regression analysis assessed associations and adjusted for relevant covariates; Spearman's correlations compared CMV and EBV levels with other biomarkers. RESULTS CMV was detected in PBMC of 25% of participants, EBV was detected in > 90%. Higher EBV levels were associated with increased risk of events at all time points (odds ratio (OR) per one IQR = 1.5-1.7, all p < 0.009). At year 1, detectable CMV was associated with increased risk of events in most adjusted models (OR = 1.4-1.8, p-values ranging 0.03-0.17). Higher levels of CMV and EBV correlated with multiple inflammatory markers and lower CD4/CD8 ratio. CONCLUSIONS In PWH starting ART, CMV and EBV in PBMC were associated with development of non-AIDS events. Clinical trials will be needed to understand causal mechanisms and ways to interrupt them.
Variación estructural del bosque de oyamel (Abies hickelii Flous & Gaussen) en relación con factores ambientales en el pico de Orizaba, México

Este trabajo se llevo a cabo cerca del ejido de Jacal, municipio de Calcahualco, Veracruz, en los oyametales que forman parte del parque naciona Pico de Orizaba. Se estudiaron los cambios estructurales del bosque de oyamel a lo largo de un gradiente altitudinal, en relacion con factores del ambiente (relieve, suelo y temperatura). Para ello, por medio de recorridos de campo se reconocieron cuarto variantes fisonomicas; en cada fisonomia se tomaron datos de vegetacion (densidad y area basal) por medio del metodo de los cuadrantes centrados en un punto, muesrtas de suelo y temperatura. Esta informacion fue procesada por medio del programa de ordenacion CANOCO (Canonical Community Ordination). Los cambios estructurales en el oyametal estan asociados a un gradiente complejo, que presenta cambios en altitud, temperatura, profundidad de suelo y diferentes caracteristicas quimicas del mismo.
Anaemia and transfusion triggers in critically ill patients – What we have learnt thus far

Anaemia is a common finding in critically ill patients, the cause of which is multi-factorial including: sepsis, haemolysis (and disseminated intravascular coagulation), iatrogenic blood loss secondary to laboratory sampling, post-operative anaemia, bone marrow suppression/failure, decreased production of erythropoietin, anaemia secondary to drugs/toxins, overt or occult blood loss, functional iron deficiency, poor nutrition and haemodilution. Anaemia is associated with deleterious outcomes including increased risk of cardiac-related morbidity and mortality and decrease in oxygen-carrying capacity in the face of increased metabolic demands. There is a growing body of evidence, which demonstrates that packed red blood cell transfusions are associated with poorer outcomes. Clinicians therefore need to weigh the potential benefit of treating anaemia against the desire to avoid unnecessary transfusions. We explored current literature regarding transfusion triggers and morbidity and mortality associated with packed red blood cell transfusions transfusion, concentrating on studies that have been conducted in critical care patients. In addition, we reflected on trials which considered the viability of iron transfusion and erythropoietin in critically unwell patients.
An investigation of NADPH oxidase in normal and diseased skeletal muscle

Oxidative stress has been implicated in various progressive degenerative conditions, such as skeletal muscle wasting and therefore this study sought to determine a role for the superoxide generating NADPH oxidase and antioxidant enzyme systems in conditions of skeletal muscle wasting. The results of these studies indicated changes in the gene expression of important components of NADPH oxidase in animal models of age-associated sarcopenia, cancer-induced cachexia and a model of antioxidant superoxide dismutase overexpression. Also observed were changes in superoxide dismutase that appeared to contribute significantly to alterations in cellular reactive oxygen species and contribute to skeletal muscle wasting in these conditions. While these oxidative and antioxidative systems demonstrated complex changes in these models, NADPH oxidase is indeed altered in response to aging, cancer and superoxide dismutase overexpression, which appear to be involved in complex redox-sensitive signaling that essentially regulates skeletal muscle atrophy and hypertrophy pathways.
Deficit Irrigation Analysis of Red Pepper (Capsicum annum L.) Using the Mathematical Optimisation Method

The objectives of this study were to analyse deficit irrigation with the mathematical optimisation method using the water-yield relationship and cost functions of red pepper, and to determine alternative deficit irrigation water levels. For this purpose, the effect of 5 different irrigation levels (I 1 , I 2 , I 3 , I 4 , and I 5 ) on dry yield (DY) was determined using a line source sprinkler irrigation system in KahramanmaraŞ, Turkey in 1999 and 2000. The average water amounts applied with I 1 (non-water stress treatment) and I 5 (water stress treatment) for the 2 years were 913 and 296 mm, and I 2 , I 3 , and I 4 varied between these extremes. The quadratic production and cost functions were established between the average irrigation water and DY, and between water and total costs, respectively. Maximum irrigation water (W m ), economically optimum level of irrigation water for land-limiting (W I ) and water-limiting (W W ), and equivalent deficit level for land-limiting (W el ) and water-limiting (W ew ) for red pepper yield were calculated as 1026, 815, 752, 603, and 551 mm, respectively. The most economical irrigation levels, in terms of both net income from per unit of land and water, were 815 mm and 752 mm, respectively. At W ew level, field irrigation was 1.86 times greater than at the W m level, without reducing net farm income. The findings of this study suggested that water resources should be distributed over the entire farm, rather than concentrated to maximise yields on particular parts of the farm.
Clinical characteristics of 161 cases of corona virus disease 2019 (COVID-19) in Changsha.

OBJECTIVE In December 2019, a new type of coronavirus-infected pneumonia broke out in Wuhan and spread rapidly to other parts of the country. The purpose of this study was to investigate the clinical features of coronavirus disease 2019 (COVID-19). MATERIALS AND METHODS A retrospective analysis was performed on the confirmed cases of COVID-19, who were admitted to the North Hospital of Changsha first Hospital (Changsha Public Health treatment Center) from January 17 to February 7, 2020. RESULTS The median age of COVID-19 patients was 45 years (range 33.5-57). The male patients accounted for 49.7%, 64.6% of the patients had a history of exposure in Wuhan, and 31.7% had family aggregation. The median days of onset were six, and the incidence of severe illness was 18.6%. Compared with the non-severe group, the severe group showed statistical significance in older age, hypertension, bilateral lung plaque shadow, decrease in lymphocyte count, increase in C-reactive protein (CRP), aspartate aminotransferase (AST), lactate dehydrogenase, and creatine kinase. CONCLUSIONS Age, combined hypertension, oxygenation index, double lung patch, decreased lymphocyte count, and elevated levels of C-reactive protein, aspartate aminotransferase, lactate dehydrogenase, and creatine kinase can be used as predictors of the disease severity.
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Different methods have been developed to model tearing prediction, as e.g., the combination between the cohesive principle and the finite element method. Unfortunately, this method has some well known issues that can be fixed by recourse to discontinuous Galerkin formulation. Such a formulation allows to insert very easily an extrinsic cohesive element at onset of fracture without any mesh modification. This promising technique has been recently developed by the authors for linear shell. Although promising numerical results were obtained, it is difficult to compare the method with experiments due to the large plastic deformation present in material before the fracture apparition. Thus, the method is extent herein to elasto-plastic finite deformations. The simulations of some benchmarks prove the ability of this new framework to model accurately the continuum part of the deformation and the crack propagation.
Oncology and functional prognosis are both vital in the surgical treatment of RGCTs around the knee joint.

AIMS To explore and provide reasonable surgical options for recurrent giant cell tumors of bone (RGCTs) around the knee joint and compare the pros and cons of extended curettage (EC) and segmental resection (SR). MATERIALS AND METHODS A retrospective analysis was performed of 22 patients (11 male, 11 female; mean age, 34.1 years) with RGCT around the knee joint treated in our hospital between June 2007 and June 2017. Average recurrence time was 14.2 ± 4.7 months. Basic clinical data, including Campanacci grade, lesion location, filler materials, pathological fracture, were recorded. Based on different reoperation methods, patients were divided into the EC and SR groups. Patients were regularly followed up; and recurrence, metastasis, local complications such as osteoarthritis, infection, prosthesis loosening, were recorded. Patient function and surgical efficacy were evaluated using the musculoskeletal tumor society (MSTS) score and Mankin score, respectively. RESULTS Postoperative recurrence occurred in one patient in both groups, and no difference in the prognosis of oncology was observed between the groups. In the EC group, seven patients developed postoperative complications, but required no surgical treatment, whereas in the SR group, five patients developed postoperative complications and surgical treatment was performed on two patients. There were significant differences in the functional prognosis and surgical efficacy between the two groups; however, the EC group showed more satisfactory results. CONCLUSION The oncological and functional prognosis of patients with RGCT around the knee joint is vital. EC should be considered as the first-line treatment, unless the tumors severely invade the surrounding soft tissues or are accompanied by complex fractures with significant displacement leading to no surgical curettage boundary.
Efficacy and immunological mechanisms of type 1 interferon gene therapy in murine cytomegalovirus

This thesis presents a comparative analysis of the type I Interferon (IFN) subtypes and an evaluation of their potential as DNA vaccines in a model of murine cytomegalovirus (MCMV) infection and disease. MCMV induces acute and chronic phases of myocarditis, a heart disease characterised by an inflammatory cell infiltrate, in susceptible BALB/c mice. The type I IFNs comprise 14 IFN alpha genes in the human and >10 IFN alpha genes in the mouse with a single IFN beta gene in both species, however, the purpose of their multiplicity has remained unclear to date. An extensive panel of murine type I IFN subtype genes, including IFNA1, A2, A4, A5, A6, A9 and B, were sub-cloned into the mammalian expression vector pkCMVint (Vical, Inc.) for expression in BALB/c mice. These DNA constructs express biologically active IFN both in vitro and in vivo with systemic, low level expression persisting in the mouse for up to 4 weeks. The individual type I IFN subtypes differentially affect the immune response to MCMV challenge. IFNA6 proved most efficacious, reducing viral replication and inflammation in the acute and chronic phase of disease. Data suggests this occurs via induction of a Th1-like cytokine and antibody response. Furthermore, IFNA6 inoculation after the acute phase was shown to protect mice from the onset of chronic myocarditis. Characterisation of the immune cell response in IFN-treated, MCMV-infected mice demonstrated that type I IFN subtypes modulate the type of immune cells infiltrating the myocardium during myocarditis. Notably, reduced CD8+ and CD4+ T cells and B cell numbers in the heart was associated with reduced chronic myocarditis. Finally, coadministration of type I IFNs, in particular, IFNA6 and IFNB, synergistically improved immunotherapy against MCMV infection and myocarditis. The findings detailed here highlight the potential for the type I IFNs as DNA vaccines and most importantly, demonstrate that the type I IFNs have differential antiviral and immunomodulatory efficacies in the MCMV model of infection and myocarditis.
Food and feeding habits of the spotted seer, Scomberomorus guttatus (Bloch and Schneider), in the Gulf of Mannar and Palk Bay

The spotted seer, essentially a surfaa feeder, feeds on a limited number of about five species, of which the sardinea are the most important and the whitehits the next The ration per active feeding (R) in 1968-69 declined by 50% of the 196748 level.owing to shortage of food. The shift from whitebaits which constitute the exclusive diet of the young, to sardines which form the major food of the adult, takes place at about 315 mm, about 114 the asymptotic length. The fish is far less aggressive than the kingseer or the streaked seer as evident from ih inability to compete ably in times of food shortage, the much larger size at which it shifts to feeding on larger forage species and the orientation of 68.4% of the forage fish in its stomach in its reverse axis. The spotted seer is numerically more abundant, but gravimetrically less abundant than the kingseer, and thenfore, its poor catch by weight must be seen more as a function of its small size than as a function of competence or competitiveness.
The earliest known crown-Testudo tortoise from the late Miocene (Vallesian, 9 Ma) of Greece

We here report on fossil remains of the earliest known crown-Testudo, an extant clade of Mediterranean testudinid tortoises from the late Miocene (Vallesian, MN 10) from the hominoid locality Ravin de la Pluie (RPl) in Greece. The material studied is a small, nearly complete carapace with a clearly distinct hypo-xiphiplastral hinge. This supports the sensu stricto generic assignment. This new terrestrial testudinid specimen is characterized by a possible tectiform, narrow, elongated shell with a pentagonal pygal and a long, posteriorly elevated, lenticular and rounded dorsal epiplastral lip. These unique features differ from those of other known Mediterranean hinged forms and allow the erection of the new species Testudo hellenica sp. nov. This taxon is phylogenetically close to two Greek species, the extant T. marginata and the fossil T. marmorum (Turolian, around 7.3 Ma). This record provides evidence for the first appearance of the genus Testudo sensu stricto at a minimum age of 9 Ma.
Effect Of Carvacrol-Loaded Nanoemulsions On A Bioluminescent Strain Of Escherichia Coli O157:H7

Vasquez Mejia, Clara M. M.S., Purdue University, May 2014. Effect of carvacrol-loaded nanoemulsions on a bioluminescent strain of Escherichia coli O157:H7. Major Professors: Maria Fernanda San Martin-Gonzalez and Bruce M. Applegate. Nanoemulsions have been shown to be effective delivery vehicles for natural antimicrobials that are poorly soluble in water. In this study the antimicrobial activity of carvacrol (5-isopropyl-2-methylphenol) nanoemulsions against a bioluminescent Escherichia coli O157:H7 was investigated using light emission as an indicator of cell viability. Different emulsifiers (Ultralec Lecithin and Tween 20), oils (Palm stearin and Coconut oil) and various carvacrol concentrations (0, 1, 2 and 2.5%) were evaluated. Bioluminescence was monitored in situ using a Hamamatsu (photo multiplier tube) sensor module integrated with a Programmable Logic Controller interfaced with a PC for data acquisition. Bioluminescence decreased rapidly with the addition of emulsions containing increasing concentrations of carvacrol (250ppm-1000ppm). However when cells were assayed for viability, plate counts showed there was not a correlation of bioluminescence to cell inactivation. Bioluminescence was able to recover after the removal of carvacrol from the surrounding media. The same bioluminescent pattern was also observed with sub-lethal doses of the oxidative uncoupler 2,4-dinitrophenol and the supplementary addition of the luciferase reaction substrate recovered the light emission in presence of carvacrol.
Effect of pulsed electric fields and high pressure on improved recovery of high-added-value compounds from olive pomace.

Olive pomace is considered a solid by-product and a rich source of valuable compounds such as polyphenols, flavonoids with antioxidant properties, and proteins. Nonthermal technologies, which cause alterations to cell permeability, are being explored to assist conventional recovery techniques. The aim of this study was to assess the effect of pulsed electric fields (PEF) and high pressure (HP) on improved recovery yield of the high-added-value compounds or to shorten the extraction time of these compounds. Olive pomace (Tsounati cv) was pretreated with PEF (1.0 to 6.5 kV/cm, 0.9 to 51.1 kJ/kg, and 15 µs pulse width) or HP (200 to 600 MPa and 0 to 40 min). Evaluation of the intracellular compounds extracted via solid-liquid extraction (50% ethanol-water solution) was performed. More intense PEF and HP conditions resulted in a significant increase of the phenolic concentration up to 91.6% and 71.8%, respectively. The increased antioxidant capacity of each extract was correlated to phenolic compound concentration. The protein concentration that was achieved with PEF pretreatment was doubled; however, HP-pretreated extracts reached 88.1% higher yield than untreated for pressures up to 200 MPa. HP and PEF pretreatment decreased extraction completion time t98 (needed time to recover the equal amount of phenolics and proteins of untreated after 60 min of conventional extraction) to 12 min and lower than 1 min, respectively. To conclude, both pretreatments are effective in improving the conventional extraction process for increased yield recovery of high-added-value compounds from olive pomace.
Insights on repetitive DNA behavior in two species of Ctenus Walckenaer, 1805 and Guasuctenus Polotow and Brescovit, 2019 (Araneae, Ctenidae): Evolutionary profile of H3 histone, 18S rRNA genes and heterochromatin distribution

Ctenidae represents one of the most representative spider families in the tropical forests of Brazil. Its largest genus, Ctenus, has approximately 220 species out of the more than 520 Ctenidae species described, and several authors consider it polyphyletic. Chromosomal data are only available for four species of Ctenus, representing a large gap in the cytogenetic knowledge about the group. This study provided cytogenetic data on two Ctenus species and one Guasuctenus (previously described as Ctenus). All showed 2n♂ = 28 (26+X1X20). Guasuctenus longipes presented two chromosome pairs containing 18S rDNA genes and C. medius, however C. ornatus showed only one chromosome pair with the 18S rDNA gene. Hybridization data using histone H3 probe indicated specific profiles: histone H3 genes were found in one chromosome pair in G. longipes, in three pairs in C. medius, and in four pairs in C. ornatus. Furthermore, supernumerary chromosomes were identified in C. ornatus presenting a meiotic behavior similar to that of sex chromosomes; and a trivalent was found in C. medius, formed by the association of one sex chromosome and an autosomal bivalent, indicating the importance of these events for the diversification of sex chromosomes in spiders. The C-banding pattern was similar between C. medius and C. ornatus with regard to the number and locations of heterochromatic bands, suggesting that heterochromatin amplification and dispersion, affect karyotypic evolution in the genus. Cytogenetic data showed similarity between C. medius and C. ornatus, and differentiation of G. longipes congruent with morphological data. Moreover, although more comparative analyses are needed to specify composition of the dispersed heterochromatin in Ctenus, the mapping of heterochromatic bands provided insights about the evolution of the karyotypes in this genus.