Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiological and Clinical Features of the Preterms Followed-Up at Our Clinic in Turkey: A Study about 458 Infants

Purpose: We aimed to evaluate 458 infants, who were followed up due to retinopathy of prematurity (ROP), demographically and epidemiologically. Methods: 458 infants with ROP, who were referred from our hospital’s neonatal intensive care unit and from other health centers to our clinic for the staging and treatment between February 2016 and December 2017, were studied retrospectively. Design: Retrospective-observational study. Results: Of the 458 infants, 243 infants (53.06%) did not have ROP and they were at a mean of 32nd (26 - 35) gestational week, weighing a mean of 1700 (820 - 2830) gr. The remaining 215 (46.94%) infants were diagnosed with ROP at various stages and they were at a mean of 29th (23 - 35) gestational week, weighing a mean of 1180 (490 - 2850) gr. Of the infants without ROP, 116 (47.7%) were females and 127 (52.3%) were males. The mean duration of stay at the incubator was a mean of 16.5 (0 - 120) days and the mean duration of follow-up was a mean of 43 (40 - 56) weeks. 103 (40.2%) of them were breastfed only. Of the infants with ROP at various stages, 95 (44.2%) were females, and 120 (55.8%) were males. The mean duration of stay at the incubator was 42 (6 - 195) days, and the mean duration of follow-up was 48 (40 - 73) weeks. 43 (20.0%) of them were breastfed only. 32 (13.2%) infants without ROP were born of multi-fetal pregnancies. Only 1 of them was born as one of the triplets. Of the babies with ROP; 56 (26.04%) were born of multi-fetal pregnancies, 5 of them being triplets. The numerical values of the gestational week at birth and the birth weight, and the rates of breastfeeding were lower in infants with ROP compared to the ones without it (p 0.05, <0.001). Conclusions: This study showed that the gestational age, birth weight, breastfeeding rates, birth history and follow-up periods of multiple fetal pregnancies were different in ROP infants compared to non-ROP infants.
Partial characterization and tissue-specific expression profile of immunoglobulin M heavy chain gene in rohu, Labeo rohita (Hamilton, 1822)

The present study was aimed to characterize the immunoglobulin M (IgM) heavy chain gene in rohu, Labeo rohita, and its tissue-specific expression. A 451 bp segment of IgM heavy chain gene of rohu spanning the variable region was amplified and sequenced. The partial nucleotide sequence of the rohu IgM heavy chain gene showed 91, 90 and 87%homology with IgM of Cyprinus carpio, Danio rerio and Ctenopharyngodon idella respectively. The deduced aminoacid sequence of the partial rohu IgM heavy chain gene was 85, 82 and 79% identical to that of C. carpio, C. idella and D. rerio, respectively. Quantitative real-time PCR analysis of the IgM heavy chain gene expression in various tissues revealed that the highest expression was in the lymphoid tissues, namely kidney and spleen followed by heart, intestine, gill, liver and muscle. It was also observed that the IgM heavy chain gene expression increased with age, i.e. 6-monthold fish showed higher levels than 4-month-old and 2-month-old fishes.
Plaice (Pleuronectes platessa L.) nursery habitat on the Forth Estuary and the Firth of Forth

The nursery function of the Forth estuary and Firth of Forth for juvenile plaice was investigated using several methods. Growth rates of juvenile plaice in the estuary were compared with growth rates of juvenile plaice in the Firth of Forth. Growth was estimated for comparisons between sites because growth is expected to indicate the quality of a particular habitat as a nursery. Growth was estimated at four sites in 2005 using two methods and in 2006 using a single method: 1) Tracking changes in length - frequency distributions of newly - settled plaice over time was used in both years and 2) Plaice were aged to the day using otolith microstructure in 2005 only, and the ages were regressed against length to estimate growth rates as a 'ground - truthing' of method 1). The growth rates of plaice were found to be similar between estuarine and outer firth sites, but lower at all four sites in 2006 than 2005. A temperature - dependent model was used to compare maximum growth rates with estimated growth rates to determine if plaice were growing optimally, and growth was less than optimal at all four sites in both years, with some evidence of density - dependence. A push net was used to sample plaice for length measurements at each site on each sampling date, and efficiencies of the net were estimated to determine actual densities of plaice and whether the net was length selective. No length selectivities were found, however, the efficiency of the net was less than 100 % and lower on muddy sites than on sandy sites. The effect of salinity on growth of juvenile plaice was assessed in a laboratory experiment. Plaice were found to grow faster at salinity 25, next fastest at salinity 30 and lowest at salinity. Assessment of consumption rates showed that the differences were likely to be caused by the effects of salinity on physiological performance of fish. A new method of inferring contribution of juvenile plaice from each habitat to adult recruitment, using stable isotopic composition of plaice otoliths was assessed. Plaice from the estuary could not be distinguished from outer firth plaice on the basis of otolith isotopic composition on the small scale used here, however, the work provides a baseline for this area in larger scale studies. Sediment isotopic composition showed differences between the estuary and outer firth, with differences between sediment types and a detectable influence of marine photosynthesis.
Breeding, survival, movements and foraging of tawny owls strix aluco in a managed spruce forest: a spatial approach

In 1996-98,1 studied the spatial ecology of the tawny owl Strix aluco (L.) in Kielder, a managed spruce forest in Northumberland, northern England. I employed radio tracking in an individual-based approach, estimating densities of field voles Microtus agrestis, the owl's main prey in Kielder Forest, using a calibrated sign index. In both 1996, a low vole year, and 1997, an increasing vole year, juvenile mortality was high, and largely due to starvation and predation. 55.4% of the variation in the mean number of days survived post-fledging per brood was explained by a model comprising the variables mean clutch hatch date, brood size, and voles per hectare at the clear-cuts nearest natal nest boxes in the spring of breeding. Nine percent of non radio tagged juveniles were recruited in 1997-98, in comparison with none of the radio marked individuals. Post onset of dispersal, vole abundance explained 25.7% of the variation in the time that juveniles spent in different areas. Juveniles did not become more sedentary over time nor avoided roosting in occupied territories. Adult home ranges contained more grassy areas than expected from their abundance in the study area, but not from their abundance at watershed level. The absolute areas of grassy habitat and lengths of habitat edge that were included in home ranges varied widely. Range area was correlated with distance to the nearest clear-cut, but not with variation in estimated vole abundance. Nocturnal activity centred on clear-cuts, other grassy areas, and mature forestry plantations. Field voles constituted 59% of prey deliveries to two nest boxes. The time that owls spent at clear-cuts was not correlated with estimated vole abundance there. Tawny owls are generalist predators, but their spatial ecology was strongly influenced by the abundance of their main prey species and the distribution of habitats that supported it.
THREE PERSPECTIVES ON SOCIAL PATHOLOGY

The issue of social pathology is a multilayered topic which goes through a series of disciplines. It can be perceived mainly as a sociological topic. The paper presents the contexts of other disciplines which define the issue such as social deviations, respectively from the viewpoint of psychology and pedagogy as risk behaviour. The paper points to three possible views on social pathology. The first view is social pathology as a set of phenomena which are perceived as problematic by the society (deviating from the behaviour according to the norms of the society). The second view is social pathology as a field of study preparing graduates for the prophylaxis and treatment of pathologically social phenomena. The third view is social pathology as a study subject concerning not only the students of socially oriented fields but mainly the students who are to become teachers. They often tend to be important sources of social support and possible actors in the process of searching for and elimination of pathological phenomena in the period of childhood and adolescence.
DE NOVO EXPRESSION AND FUNCTION OF THE EPITHELIAL MUCIN MUC1 ON T CELLS

MUC1 has conventionally been studied as an epithelial cell surface molecule. Its glycosylation and expression change when those cells are transformed into adenocarcinomas. These changes have led to focus on MUC1 as a tumor antigen and also its role in adhesion to blood vessels and signaling within the tumor cell. The recent discovery that T cells also express MUC1 on their surface extends the physiological role of MUC1, with the possibility that functions observed in tumors may be reproduced on T cells. Expression of MUC1 on T cells was first characterized in terms of timing, location and structure. T cells activated both in vivo and in vitro express MUC1. Expression in vitro is maintained over long time periods as the T cell population acquires the memory phenotype. Activated T cells induced to polarize by inflammatory conditions focus MUC1 expression to their leading edge, the sensory compartment of polarized T cells. Reactivity with glycosylation-sensitive antibodies and induction of glycosyltransferases indicates that the glycosylation of MUC1 on T cells is similar to that on normal epithelial cells. A MUC1-negative T cell line was transfected with MUC1 cDNA and used as a model to investigate consequences of MUC1 expression on the T cell surface. Interaction of MUC1+ T cells with resting or activated endothelial cells revealed that MUC1 aids in adhesion under both normal and inflammatory conditions. Analysis of interactions with individual adhesion molecules demonstrated MUC1 specific enhancement of binding to ICAM-1 but inhibition of binding to E-selectin. Phosphorylation of the MUC1 intracytoplasmic tail is constitutive but decreases upon interaction with activated endothelium. MUC1 expression on T cells is also associated with differential phosphorylation of proteins in the molecular weight ranges of 39 kDa, ~80 kDa and 190 kDa, with the ~80 kDa band identified as beta-catenin. While human T cells express MUC1 on their surface upon activation, this does not appear to be a characteristic of mouse T cells from the human MUC1 transgenic mouse model. However, as recent work indicates that mouse T cells express mouse Muc-1 after activation, human and mouse T cells may similarly depend on MUC1 for normal functioning.
Overview of Deep Learning Models in Biomedical Domain with the Help of R Statistical Software

Abstract With the increase in volume of data and presence of structured and unstructured data in the biomedical filed, there is a need for building models which can handle complex & non-linear relations in the data and also predict and classify outcomes with higher accuracy. Deep learning models are one of such models which can handle complex and nonlinear data and are being increasingly used in the biomedical filed in the recent years. Deep learning methodology evolved from artificial neural networks which process the input data through multiple hidden layers with higher level of abstraction. Deep Learning networks are used in various fields such as image processing, speech recognition, fraud deduction, classification and prediction. Objectives of this paper is to provide an overview of Deep Learning Models and its application in the biomedical domain using R Statistical software Deep Learning concepts are illustrated by using the R statistical software package. X-ray Images from NIH datasets used to explain the prediction accuracy of the deep learning models. Deep Learning models helped to classify the outcomes under study with 91% accuracy. The paper provided an overview of Deep Learning Models, its types, its application in biomedical domain. - is paper has shown the effect of deep learning network in classifying images into normal and disease with 91% accuracy with help of the R statistical package.
Effects of Curcumin on Vascular Endothelial Growth Factor Expression on Rattus norvegicus Cervical Cancer Xenograft Model

Objective: To analyze the effect of curcumin in VEGF expression on Rattus norvegicus cervical cancer cell xenograft model.Methods: An experimental study with randomized post test only control group design. The subjects were Rattus norvegicus (Sprague Dawley), inoculated with He-la cervical cancer cells from American Type Culture Collection (ATCC) processed in stem cell laboratory Institute of Tropical Disease (ITD) Airlangga University. 5x106 of He-La cells were injected subcutaneously in dorsal flank area of Rattus norvegicus. After 30 days of observation we performed histopathological examination of xenograft tissue and randomized into 2 groups which were given curcumin orally 1000 mg/kg (curcumin group) vs. no therapy (control group). After another 30 days the xenograft tissue was dissected and underwent immunochemistry examination for VEGF expression.Results: 32 samples of Rattus norvegicus were divided into 2 groups, In curcumin group the VEGF median expression was 2,2 (0,3-7,6) and in control group the VEGF median expression was 6,6 (1,2-12). There was a statistically significant difference with p value =0,009 with Mann Whitney test (p<0,05). Conclusion: VEGF expression in Rattus norvegicus xenograft model of cervical cancer was suppressed by giving Curcumin 1000 mg/kgBB orally.
Microbiological study of methicillin-resistant Staphylococcus aureus isolated from wound samples at a tertiary care hospital, Central India

Staphylococcus aureus is a major pathogen associated with serious community-and hospital-acquired infections. It is commonly found in air, dust, water, and as normal flora on skin and in the respiratory tracts of humans. The most common mode of transmission is by skin-to-skin contact from an infected host. S. aureus is one of the most harmful species of staphylococci encountered. It is the leading cause of bacteremia, pneumonia, myocarditis, acute endocarditis, pericarditis, osteomyelitis, encephalitis, meningitis, chorioamnionitis, mastitis, and scalded skin syndrome. [1]
Crystallin proteolysis in lens during aging and cataract formation

approved: Larry L. David The major purpose of this research was to characterize partially degraded proteins appearing in the ocular lens during aging and cataract, and to identif' the responsible proteolytic activities. This research is significant, because increased protein degradation is associated with lens opacification and cataract. Determining the sites where lens proteins become truncated and identification of the responsible proteases is important because this information could be used to develop anticataract agents, such as new protease inhibitors. The methods used in this research include the application of several techniques employed in the field of proteomics. Two-dimensional electrophoresis (2-DE) was used to separate crystallins, the major proteins of the lens, and the modifications to these proteins were then determined by electrospray ionization mass spectrometry (ESI-MS). Lenses from mice of increasing age were used for these studies. Lp82 and m-calpain, the proteases hypothesized to cause the observed truncation of mouse crystallins, were purified from fetal calf lenses or expressed recombinantly, and their enzymatic properties compared. The cleavage sites produced in a-crystallin by Lp82 and m-calpain in vitro were then compared to truncated a-crystallins from normal rat lens, and rat lens with selenite-induced cataract. The results included data showing that crystallins in mouse lenses underwent extensive truncation after 6-weeks of age that was associated with their insolubilization. Characteristics of purified Lp82 included: a lower calcium requirement for activation, a decreased sensitivity to the endogenous inhibitor calpastatin, and a greater resistance to autolysis than m-calpain. Analysis of truncated Redacted for Privacy a-crystallins isolated from both normal and cataractous rat lens indicated that Lp82 was more active in young rat lens than was m-calpain. Lp82 specifically removed 5 residues from the C-terminus of aA-crystallin. This aA degradation product was far more abundant in the lenses of young rats than was the m-calpain specific aA product missing 11 residues from its C-terminus. In conclusion, this study showed that insolubilization of crystallins and cataract may result in animal lenses from uncontrolled crystallin degradation by the protease Lp82. This has led to a fundamental change in our view of experimental cataract formation, since activation of the protease m-calpain was previously believed to cause cataract. Crystallin Proteolysis in Lens during Aging and Cataract Formation
Genetic Diversity and Genetic Relatives Analysis of Tobacco Germplasm Based on Inter-Simple Sequence Repeat (ISSR)

Objective In order to provide theoretical information for tobacco breeding,this study was to probe the relationship and genetic diversity of the tobacco germplasms.MethodNinety-six accessions,including ninety-one lines of cultivated tobacco (Nicotiana tabacum L.) and five other Nicotiana species were used to detect the intra-and inter-specific genetic variation by inter-simple sequence repeat (ISSR) analysis. ResultThree hundred and fourteen DNA fragments were amplified,using eighteen primers screened from 90 ISSR primers,among which 299 DNA bands were polymorphic (PPB= 95.20%). The genetic similarity (GS) among ninety-six accessions ranged from 0.28 to 0.97,with a GS range of 0.28-0.58 for five other Nicotiana species and N. tabacum,and 0.62-0.98 among cultivated tobacco lines. This analysis showed that a greater amount of genetic polymorphism exists among species of Nicotiana than among cultivated forms. The cluster analysis for 91 tobacco cultivars presented that some accessions with the same geographical origin were clustered into one group,and a few domestic cultivars were categorized with foreign lines owing to their close genetic relationship. Moreover,a very few groups contained only one cultivar suggesting that it had a special genetic base.Conclusion The study showed that ISSR is a valuable marker system. The findings of this research would be favorable for the further practices,such as tobacco breeding,the molecular genetic linkage mapping and the DNA fingerprint building of tobacco germplasms.
Germinao in vitro de embries zigticos de murmuru (Astrocaryum ulei)

Com o presente trabalho objetivou-se avaliar a influencia de concentracoes de sacarose e a idade fisiologica da semente na germinacao in vitro de embrioes zigoticos de murmuru. Frutos em dois estagios de desenvolvimento coletados de plantas do campo tiveram os embrioes excisados, desinfestados e inoculados em meio de cultura de MS com 75% das concentracoes de sais, suplementado com 2,5 g.L-1 de acido giberelico e diferentes concentracoes de sacarose: 15, 30 e 45 g.L-1. Em sala de crescimento, o material foi mantido por 30 dias no escuro, sendo transferido em seguida para condicoes luminosas de 30 me.m-2.s-1, temperatura de 25±2oC e fotoperiodo de 16 horas para completo desenvolvimento. O delineamento estatistico utilizado foi inteiramente casualizado em arranjo fatorial 2 x 3, com seis repeticoes e cinco embrioes por parcela. Apos 30 dias foi avaliada a porcentagem de germinacao e altura das plântulas. Verificou-se que embrioes provenientes de frutos imaturos apresentaram maior porcentagem de germinacao, sendo a concentracao de 30 g.L-1 de sacarosea que proporcionou os melhores resultados dentre as demais testadas. Embrioes provenientes de frutos maduros apresentaram altura de plântulas significativamente maior aos imaturos e tambem para essa variavel, a concentracao de 30 g.L-1 de sacarose foi a que proporcionou os melhores resultados.
Detection of Fetal Copy Number Aberrations by Shallow Sequencing of Maternal Blood Samples

Motivation: Numerous genetic disorders can be detected in prenatal diagnosis using Chorionic Villus Sampling. As this brings a 1:100 chance for miscarriage, this method is only applied when the fetus is suspected to have an increased chance at having an aberration. It is known that a small percentage of DNA in maternal plasma is of fetal origin and with the upswing of Next Generation Sequencing (NGS) it is now possible to diagnose trisomy 21 cases non-invasively using maternal blood samples. Other and smaller aberrations can be detected with this kind of blood samples using high coverage NGS, but this makes these methods more expensive. Our goal was to find a method to detect small aberrations using only shallow sequencing (low coverage NGS), keeping the costs per sample to a minimum. Methods: We developed an approach (called WISECONDOR) that determines whether a small region is aberrated by looking whether the read count within that region differs abnormally compared to the read counts of other similarly behaving regions within the same test sample. The other similarly behaving regions are considered to have similar NGS biases, such as GC-richness, and are found by comparing read count correlations over a set of healthy samples. Results: The developed script was able to correctly identify all tested T13, T18 and T21 cases. Aberrations such as del(13)(q12.3q14.3), i(12p10) and i(18q10) were also correctly called. The amount of false positives was minimal and even zero when the size of the aberrations was at least 20Mb, while the test samples varied from only 0.15 to 1.66 fold coverage. This shows that most fetal fetal copy number aberrations can be detected by shallow sequencing of maternal blood samples.
Gingival Crevicular Fluid Levels of Thymosin Beta4 in Periodontal Health and Disease

Objective: To determine if Thymosin β4 (Tβ4) levels in gingival crevicular fl uid (GCF) vary in healthy patients and in patients with periodontal disease. Materials and Methods: Adult patients of the University of Detroit Mercy School of Dentistry clinic were used in this study. One hundred and twenty GCF samples were obtained from 25 patients from regions of the gingiva that showed no clinical signs of disease and from regions with periodontal disease determined by probing depths ranging from 5 to 10 mm. Samples were analyzed by EIA to determine Tβ4 concentration. Results: Tβ4 concentration demonstrated wide variability within and between patient samples. Compared to healthy controls as defi ned in this study of probing depths 3-4 mm, Tβ4 concentration was highest in GCF taken from sulci with probing depths of 5 mm. As probing depths increased beyond 5 mm, the concentration of Tβ4 in GCF decreased. At a probing depth of 10 mm, Tβ4 levels were nearly equivalent to those found in probing depths of 3-4 mm. Conclusions: Periodontal disease results in Tβ4 protein concentrations in GCF that differ from periodontal health. Tβ4 concentration appears to be inversely correlated to the severity of periodontal disease as defi ned by probing depth.