Miracle-dz/UniFAR-FTUs huggingface dataset:
Neurological Level in Spinal Cord Injury: Comparison Between ASIA Standards and Transcranial Magnetic Stimulation

Amaç: Travmatik komplet omurilik yaralanmalı (OY) hastaların, American Spinal Injury Association (ASIA) standartlarına uygun olarak yapılan nörolojik muayene bulguları ile Transkraniyal Manyetik Uyarım (TMU) ile paravertebral kaslardan saptanan Motor Uyandırılmış Potansiyelleri (MUP) değerlerinin karşılaştırılması. Gereç ve Yöntem: Komplet travmatik OY’li (C8-T12) olduğu aynı fiziyatrist tarafından ASIA standartlarına göre yapılan muayene sonucunda belirlenen 20 hasta çalışmaya alındı. Ekstremite ve paravertebral kaslardan, TMU ile saptanan MUP değerleri ayrıntılı nörolojik muayene sonuçlarını bilmeyen aynı nöroloji uzmanı tarafından gerçekleştirildi ve kaydedildi. Bulgular: Çalışmamızda TMU ile saptanan en kaudal paravertebral MUP düzeyleri ile ASIA muayenesi ile bulunan nörolojik seviyeler arasında ileri derecede anlamlı fark bulunmuştur (p<0,001). Çalışmamızdaki 20 hastanın 19’unda nörolojik seviyeler T2-L1 segmentleri arasında olmasından dolayı neredeyse tüm hastalarımızın, duyu seviyeleri motor seviye olarak kabul edilmiştir. Sonuç: Daha önceki çalışmalar göz önüne alındığında, bu sonuçların olası nedenlerinden birinin paravertebral kasların multisegmental innervasyonu ve uzun kas lifi iletimi olduğunu düşünüyoruz. Bu çalışmada elde edilen bulgular sonucunda, OY’li hastalarda elektrofizyolojik çalışma yapacak klinisyenlerin, muayenelerde bulunan nörolojik seviyeler ile paravertebral kaslardan TMU ile saptanan MUP seviyeleri arasında önemli farklılık olabileceğini akılda tutmaları gerektiği bizce önemlidir. Elde edilen bu sonuçlarda ASIA standartları ile ilgili bazı kuralların da etkili olabileceğine inanmaktayız. Türk Fiz T›p Re hab Derg 2012;58 Özel Sayı 1:49-55. Anah tar Ke li me ler: Omurilik yaralanması; transkraniyal manyetik uyarım; motor uyandırılmış potansiyel; paravertebral kaslar Sum mary
Presynaptic depression maintains stable synaptic strength in developmentally arrested Drosophila larvae

Positive and negative modes of regulation typically constrain synaptic growth and function within narrow physiological ranges. However, it is unclear how synaptic strength is maintained when both pre- and post-synaptic compartments continue to grow beyond stages imposed by typical developmental programs. To address whether and how synapses can adjust to a novel life stage for which they were never molded by evolution, we have characterized synaptic growth, structure and function at the Drosophila neuromuscular junction (NMJ) under conditions where larvae are terminally arrested at the third instar stage. While wild type larvae transition to pupae after 5 days, arrested third instar (ATI) larvae persist for up to 35 days, during which NMJs exhibit extensive overgrowth in muscle size, presynaptic release sites, and postsynaptic glutamate receptors. Remarkably, despite this exuberant growth of both pre- and post-synaptic structures, stable neurotransmission is maintained throughout the ATI lifespan through a potent homeostatic reduction in presynaptic neurotransmitter release. Arrest of the larval stage in stathmin mutants reveals a degree of progressive instability and neurodegeneration that was not apparent during the typical larval period. Hence, during a period of unconstrained synaptic growth through an extended developmental period, a robust and adaptive form of presynaptic homeostatic depression can stabilize neurotransmission. More generally, the ATI manipulation provides an attractive system for studying neurodegeneration and plasticity across longer time scales. SIGNIFICANCE STATEMENT It is unclear whether and how synapses adjust to a novel life stage for which they were never molded by evolution. We have characterized synaptic plasticity at the Drosophila neuromuscular junction in third instar larvae arrested in development for over 35 days. This approach has revealed that homeostatic depression stabilizes synaptic strength throughout the life of arrested third instars to compensate for excessive pre- and post-synaptic growth. This system also now opens the way for the study of synapses and degeneration over long time scales in this powerful model synapse.
The tissue angiotensin system in the lung: roles in human pulmonary fibrosis

THE TISSUE ANGIOTENSIN SYSTEM IN THE LUNG ROLES IN HUMAN PULMONARY FIBROSIS By My-Trang Thi Dang Idiopathic Pulmonary Fibrosis (IPF) is the most common form of interstitial lung disease with a 3-year median survival upon diagnosis. The lack of effective therapies in treating this disease highlights our incomplete understanding in the pathogenesis of IPF. The prevailing hypothesis is that IPF is a result of abnormal wound healing which consists of persistent injury and apoptosis to alveolar epithelial cells (AECs), aberrant fibroblast proliferation, and the accumulation of extracellular matrix proteins. Our laboratory has implicated a role of the angiotensin (ANG) system in these events. In IPF, both angiotensinogen (AGT), the only known precursor to angiotensin II (ANGII), and Transforming Growth Factor-Beta (TGF-β1) mRNA and protein are up-regulated, as well as the profibrotic peptide, ANGII. In human pulmonary fibroblasts, TGF-β1-inducible AGT transcription is mediated by the core promoter spanning from -46 to +22. At the -20, -18, and -6 positions lies single nucleotide polymorphisms (SNPs) that have been shown to influence its transcription rate in hepatocytes. Our results in human pulmonary fibroblasts parallel those observed in hepatocytes where the CA haplotype at -20 and -6 respectively, had about a 1.5fold increase in AGT transcription compared to the AG haplotype (p = 0.011). The increase in AGT transcription would result in an increase in ANGII, which we predict to be associated with greater severity of IPF as measured by pulmonary function tests. Studies in IPF cohorts from the United States and Spain demonstrated that the CC genotype at -20 (p = 0.0028 for U.S. and p = 0.017 for Spain), the AA genotype at -6 (p = 0.021 for U.S.), and the CA haplotype (p = 0.0048 for U.S. and p = 0.014 for Spain) predicted lower diffusing capacity. Additionally, the Proline/Proline variant at codon 10 in TGF-β1 was also associated with lower diffusing capacity (p = 0.0014). Surprisingly, the results of both studies were only significant in males, reflecting the male bias of this disease. Preliminary data indicates that in addition to inducing AGT transcription, TGF-β1 also upregulates cathepsin D and down-regulates ACE-2. Cathepsin D and AGT are both part of the rate-limiting step in the generation of ANGII whereas ACE-2 functions in its removal. This suggests that TGF-β1 may cause an imbalance in the ANG system by favoring the ANGII producing axis. The mechanism by which ACE-2 is down-regulated has not been well studied. However, results from our lab suggests that this down-regulation may be related to ACE-2 ectodomain shedding or through a JNK-mediated mechanism as seen with inducers of ER-stress and cell-cycling in AECs.
Proposed mechanism of kinesin backstepping

Kinesins are molecular motors that walk along microtubules, hauling cargo through the crowded cytoplasm of eukaryotic cells. At low load, kinesins almost always step towards microtubule plus ends, but at high load, forward stepping slows down and backsteps appear. Current models envisage that backsteps occur by directional reversal of the forwards walking mechanism. Here we report to the contrary, that at substall forces, kinesin steps back using a rescued detachment mechanism. We show (1) that dwell times for forward steps are shorter, on average, than dwell times for backsteps or detachments; (2) that dwell times for backsteps and detachments are indistinguishable and (3) that the balance of backsteps and detachments can be tilted dramatically, without affecting forward steps. All three points hold not only for kinesin stepping on brain GDP-taxol MTs, but also for brain GDP MTs, brain GMPCPP-epothilone MTs, S. pombe GMPCPP-epothilone MTs and subtilisin-treated GDP-taxol MTs. Our data establish that forward steps originate from a different and earlier state in the kinesin mechanism than the state that generates backsteps and detachments. Accordingly, we propose a model in which ATP binding to the waiting state of kinesin opens a time window exclusively for forward stepping, whilst Pi release closes this window and generates a semi-detached state which then either slips back and re-engages, completing an effective backstep, or, less usually, detaches altogether. Backstepping via this rescued detachment pathway greatly enhances kinesin’s processive forwards progress under load. Significance statement Kinesin-1 molecular motors typically walk towards microtubule plus ends. Under load however, backsteps also occur. Backsteps have previously been thought to occur by directional reversal of forwards walking. We report that kinesin waits before forward steps for less time than before backsteps and detachments, that it waits for the same amount of time before backsteps and detachments, and that the relative numbers of backsteps and detachments can be shifted experimentally without affecting forward stepping. As we discuss, this argues for a mechanism in which motors that fail to step forward within a time window can slip back, re-engage, and retry forward stepping. Our findings speak to the mechanisms of directional bias and mechanochemical coupling in kinesins, and potentially other motors.
Mechanisms of Particulate Toxicology: Systemic Effects in Sensitive Animal Models and Susceptible Humans

Particle-induced lung injury and heart responses were measured in young adult and geriatric (senescent) rats exposed to laboratory generated particles composed of elemental carbon and ammonium nitrate. The particle compositions and concentrations used were consistent with ambient aerosols collected and characterized in California. This study was part of a coordinated multicampus program. The biological responses studied focused on cardiophysiologic factors (changes in blood pressure, variability in heart rate and abnormal heart rhythms) in the animal studies and macrophage superoxide production in the human studies. Acute (4 hour) single day exposures to particles alone were compared with the effects of a mixture of particles and ozone at approximately the same particle concentrations. Both exposures produced decreases in blood pressure and heart rate. Blood pressure changes (differences between pre-exposure and post-exposure levels) were significantly different from controls. Heart rate was decreased by pollutant exposure but the response was not statistically significant. The changes induced by single day exposure to particles alone were not significantly different from those induced by the single day ozone + particle mixture. Thus, the effects observed may be those of the particles and not due to the presence of ozone in the mixture. Repeated 3-day (4 hour per day) exposures to particles caused changes in heart rate and blood pressure that were statistically significant immediately post-exposure, but there were no changes in baseline levels measured 20 hours after exposure. Heart rate variability was not significantly changed after a single exposure to particles, but showed progressive reduction after 2 and three days of consecutive exposure, compared to clean air exposures.
Antibacterial and Antifungal Activity of Litsea monopetala Leaves on Selected Pathogenic Strains

Aims: To evaluate the antibacterial and antifungal activity of some solvent extracts of Litsea monopetala (LM) leaves. Study Design: Examination of antibacterial and antifungal activity of petroleum ether fraction (PEF), chloroform fraction (CLF), ethyl acetate fraction (EAF) and crude methanol extract (CME) of Litsea monopetala (LM) leaves. Place and Duration of Study: Department of Pharmacy, Southeast University, Dhaka-1213, Bangladesh, from September to November 2014. Methodology: Fresh LM leaves were extracted with methanol followed by fractionation. Antibacterial and antifungal activities of the crude extract were determined by using the Agar disk Short Research Article Hasan et al.; EJMP, 12(4): 1-8, 2016; Article no.EJMP. 23658 2 diffusion method against gram positive, gram negative bacterial and fungal strains. Results: All tested plant extracts, showed varying zones of inhibition against bacteria and fungi tested. The zone of inhibition for bacteria was found to be in the range from 5 to 15 mm and 5 to 13 mm for fungi. The CME and EAF of the methanolic extract of LM has greater antibacterial activity against all tested gram positive and gram negative bacteria compare to other fraction. CME and EAF has also strong antifungal activity against tested fungi except Candida albicans in which CLF showed maximum antifungal activity. Conclusion: The present study shows that LM leaves possess an excellent source of natural antibacterial and antifungal agents which could be developed in the treatment of bacterial and fungal diseases.
Effect of arbuscular mycorrhizal fungi (AMF) and plant growth promoting rhizobacteria (PGPR) on microbial community structure of phenanthrene and pyrene contaminated soils using Illumina HiSeq sequencing

In order to determine the influence of arbuscular mycorrhizal fungi (AMF, Glomus versiforme) and plant growth promoting rhizobacteria (PGPR, Pseudomonas fluorescens, PS2-6) on degradation of phenanthrene (PHE) and pyrene (PYR) and the change of microbial community structure in soils planted with tall fescue (Festuca elata), four treatments were set up in phenanthrene (PHE) and pyrene (PYR) contamined soil: i.e., tall fescue (CK), AMF + tall fescue (GV), PGPR + tall fescue (PS) and AMF + PGPR + tall fescue (GVPS), PHE and PYR dissipation in the soil and accumulated in the tall fescue were investigated. Our results showed that highest removal percentage of PHE and PYR in contaminated soil as well as biomass of tall fescue were observed in GVPS. PHE and PYR accumulation by tall fescue roots were higher than shoots, the mycorrhizal status was best manifested in the roots of tall fescue inoculated with GVPS, and GVPS significantly increased the number of PGPR colonization in tall fescue rhizosphere soil. And paired-end Illumina HiSeq analysis of 16S rRNA and Internal Transcribed Spacer (ITS) gene amplicons were also employed to study change of bacterial and fungal communities structure in four treatments. GVPS positively affected the speices and abundance of bacteria and fungi in PHE and PYR contaminated soil, an average of 71,144 high quality bacterial 16S rDNA tags and 102,455 ITS tags were obtained in GVPS, and all of them were assigned to 6,327 and 825 operational taxonomic units (OTUs) at a 97% similarity, respectively. Sequence analysis revealed that Proteobacteria was the dominant bacterial phylum, Ascomycota was the dominant fungal phylum in all treatments, whereas Proteobacteria and Glomeromycota were the most prevalent bacterial and fungal phyla in GVPS, respectively. And in the generic level, Planctomyces is the richest bacterial genus, and Meyerozyma is the richest fungal genus in all treatments, whereas Sphingomona was the dominant bacterial genus, while the dominant fungi was Fusarium in GVPS. Overall, our findings revealed that application of AMF and PGPR had an effective role in improving the growth characteristics, root colonization of F. elata and soil microbial community structure in PHE and PYR contaminated soils, but no obvious in degradation efficiencies of PAHs as compared to the control.
A deep learning-based model of normal histology

Deep learning models have been applied on various tissues in order to recognize malignancies. However, these models focus on relatively narrow tissue context or well-defined pathologies. Here, instead of focusing on pathologies, we introduce models characterizing the diversity of normal tissues. We obtained 1,690 slides with rat tissue samples from the control groups of six preclinical toxicology studies, on which tissue regions were outlined and annotated by pathologists into 46 different tissue classes. From these annotated regions, we sampled small patches of 224 × 224 pixels at six different levels of magnification. Using four studies as training set and two studies as test set, we trained VGG-16, ResNet-50, and Inception-v3 networks separately at each of these magnification levels. Among these models, Inception-v3 consistently outperformed the other networks and attained accuracies up to 83.4% (top-3 accuracy: 96.3%). Further analysis showed that most tissue confusions occurred within clusters of histologically similar tissues. Investigation of the embedding layer using the UMAP method revealed not only pronounced clusters corresponding to the individual tissues, but also subclusters corresponding to histologically meaningful structures that had neither been annotated nor trained for. This suggests that the histological representation learned by the normal histology network could also be used to flag abnormal tissue as outliers in the embedding space without a need to explicitly train for specific types of abnormalities. Finally, we found that models trained on rat tissues can be used on non-human primate and minipig tissues with minimal retraining. Significance statement Like many other scientific disciplines, histopathology has been profoundly impacted by recent advances in machine learning with deep neural networks. In this field, most deep learning models reported in the literature are trained on pathologies in specific tissues/contexts. Here, we aim to establish a model of normal tissues as a foundation for future models of histopathology. We build models that are specific to histopathology images and we show that their embeddings are better feature vectors for describing the underlying images than those of off-the shelf CNN models. Therefore, our models could be useful for transfer learning to improve the accuracy of other histopathology models.
Gene Expression Analysis in Dunaliella salina Under Salt Stress

Different salt concentrations are found in the large portion of water resources and agriculture lands in which most of the plant species cannot be grown. Some microalgae species can be grown either in seawater or in brackish water which is not usable for normal agriculture. The present study analyzed the gene expressions associated with salt stress in Dunaliella Salina. The expression of three coding genes namely acetyl-CoA carboxylase (ACC), channelrhodopsin-1 DChR1 protein (DC), and sodium-coupled phosphate transporter protein (DSSPT) were evaluated at three salinity levels: 3 gl-1 (low), 32 gl-1 (control), 100 gl-1 (high) . The analysis were performed on the 5th, 10th and 17th day of culture. The results revealed that for low and high salt treatments, the lowest gene expressions were observed on 5th day of growth, however, the gene 10th day. It should be noted that, under low salinity conditions (3 gl-1), gene expressions were lower than high salinity concentration during the growth phase.
White adipose tissue inflammation is not attenuated by short-term calorie restriction in obese humans

Obesity is a growing global health problem due to its association with chronic low-grade inflammation contributing to metabolic complications. Multiple studies indicate that white adipose tissue (WAT) inflammation can promote type 2 diabetes. However, the function and regulation of both innate and adaptive immune cells in human WAT under conditions of obesity and calorie restriction (CR) is not fully understood yet. Using a randomized interventional design, we investigated postmenopausal obese women who either underwent CR for three months followed by a 4 weeks phase of weight maintenance or had to maintain a stable weight over the whole study period. A comprehensive immune phenotyping protocol was conducted using validated multiparameter flow cytometry analysis in blood and subcutaneous WAT (SAT) (n=21). The T cell receptor repertoire was analyzed by next generation sequencing (n=20) and cytokine levels were determined in SAT (n=22). Metabolic parameters were determined by hyperinsulinemic-euglycemic clamp and then correlated to immune cell subsets. We found that insulin resistance (IR) correlates significantly with a shift towards the memory T cell compartment in SAT. Among various T cell subsets, predominantly CD8+ effector memory T cells were associated with obesity-related IR. Interestingly, T cell receptor analysis revealed a diverse repertoire in SAT arguing against an antigen-driven intra-SAT expansion of effector memory T cells. Surprisingly, neither inflammatory cytokine levels nor leucocyte subpopulations were significantly altered upon CR. Our findings demonstrate the accumulation of effector memory T cells in obese SAT contributing to chronic inflammation. The long-standing effect of obesity-induced changes in SAT was demonstrated by preserved immune cell composition after short-term CR induced weight loss.
Prognostic factors in liver transplantation, with a focus on the role of CD4 and CD8

Aim The aim of this studywas to assess liver tissues from both donors and their recipients of liver transplantation in order to analyze the prognostic factors that influence the prognosis of liver transplantation, especially T-cell subpopulations, to determine their relationship with the degree of severity of ACR according to the Banff schema (1997) and recurrent hepatitis C according to the modified Knodell and Ishak score (1995). Materials and methods This was a retrospective study of 38 needle liver biopsy specimens, 19 specimens collected before transplantation from donors and 19 specimens collected after transplantation from recipients. Nine cases were studied for rejection and 10 cases for recurrent hepatitis C. All cases were formalin-fixed and paraffin-embedded, examined routinely by hematoxylin and eosin, and submitted for immunohistochemical staining for CD4 and CD8. Immunohistological findings were correlated to the Rejection Activity Index score according to the Banff schema (1997), and the grade of recurrent hepatitis C according to the modified Knodell and Ishak score (1995) was compared. In cases of acute cellular rejection (ACR), an increased number of CD8+ cells than CD4+ cells in the donor increased the risk of ACR after transplantation. In recipients, the number of CD8+ cells increased according to the ACR grade, whereas CD4+ cells tended to decrease. In recurrent hepatitis C, the number of CD4+ cells increased with an increase in the grade of recurrent hepatitis, whereas CD8+ cells tended to decrease. Results The results indicate that CD8+ cells play important roles in the ACR severity of living-related liver transplantation, whereas CD4+ cells play a major role in recurrent hepatitis C. Thus, the ratio of CD4 and CD8 in both the donor and the recipient can be helpful in the prediction of the outcome of liver transplantation.
Displacement interference between wild ungulate species: does it occur?

Among mammals, interspecific interference is common in carnivores, primates and rodents, but it seems to be a rare occurrence in ungulate communities. We summarised the knowledge on interspecific displacements through behavioural interactions between ungulate species in temperate areas to evaluate the conditions under which ungulate behavioural competitive interactions may occur. We found 18 studies reporting interspecific behavioural dominance between wild ungulates, for a total of 37 reports of interspecific displacement, involving 15 species. Only eight reports showed over more than 10 displacements. Over 60% reports involved at least one alien species. The larger one displaced the smaller one in 69% reports involving only native species and in 58% reports involving at least one alien species. Among ungulates, resource exploitation rather than behavioural interference seems to be the main mechanism for interspecific competition. Behavioural interference may increase when non-coevolved species come into contact (e.g. alien taxa, or species expanding their distribution range following environmental changes), in turn generating the potential for interspecific competition.