Miracle-dz/UniFAR-FTUs huggingface dataset:
MMP family protein expression as prognostic biomarkers in human soft tissue sarcoma of extremities

AbstractSoft tissue sarcomas (STS) are rare human malignant neoplasms, arising mostly from stem cells within non-skeletal connective tissues. They account for approximately 1% of all human malignancies. Matrix metalloproteinases (MMPs) are enzymes involved in degradation of the extracellular matrix and their expression by cancer cells allows the cells to penetrate basement membranes and tissue matrix, thereby invading and metastasising. The most studied malignant tumours from the perspective of MMP expression and its relationship to malignant behaviour are epithelial-derived carcinomas. MMPs role in invasion and metastasis of sarcomas has been very little investigated. This is in part because of the difficulty in accumulating sufficient tumour tissue to enable statistically relevant analysis of sufficient tumours. The purpose of this thesis was to examine the expression of key MMPs - MMP-2, MMP-7, MMP-9, and MMP-14 and their inhibitors (TIMP-1 and TIMP-2) at the invasive/subcapsular edge of human malignant and benign connective tissue tumours using immunohistochemistry, a technique that allows a very high level of reaction product localisation within tumours. In three different STS types and appropriate benign equivalents, the expression of MMPs -2, -7, -9, and -14 and their inhibitors (TIMPs -1 and -2) were measured using intensity of staining and the percentage area of staining by image analysis. The results were compared between tumour types and against histological grading that is widely used as a prognostic factor. The findings from this research indicated that metalloproteinases were commonly expressed in STS and benign equivalents. There were differences in expression of some benign versus malignant neoplasms of the same group. No uniform pattern of expression of any of MMPs was observed across the tumours, but some of the data, most notably that for expression of MMP-2 and -9 indicate, a role for MMPs in malignant behaviour and some showed (e.g. MMPs -7 and -14) change in expression with the grade of malignant tumours in the same broad category. There is some evidence of an inverse relationship between MMP and appropriate TIMP expression suggesting that a failure of inhibition, as much as increased expression, is a feature of malignancy.
Epigenetics of Nasopharyngeal Carcinoma

Cancer has been previously viewed as a disease exclusively driven by genetic changes, including mutations in tumor suppressor genes and oncogenes, and chromosomal abnormalities. However, recent data have demonstrated that the complexity of human carcinogenesis cannot be accounted for by only genetic machineries, but also involves extensive epigenetic abnormalities. The term “epigenetics” refers to the study of heritable changes in gene regulation that do not involve a change in the DNA sequence or the sequence of the proteins associated with DNA (Egger et al. 2004). Epigenetic machineries plays a fundamental role in several biological processes, such as embryogenesis, imprinting, and X chromosome inactivation, and in disease states such as cancer. Several mechanisms were included in the epigenetic machinery, the most studied of which are DNA methylation; histone modifications; and small, noncoding RNAs (Kargul and Laurent 2009; Jeltsch and Fischle 2011). The molecular mechanisms underlie the epigenetic changes in cancer cells are complicate and only began to be elucidated. The best understood component among which is the transcriptional repression of a growing list of tumor suppressor and candidate tumor suppressor genes (Jones and Laird 1999; Esteller 2007). This suppression is associated with abnormal methylation of DNA at certain CpG islands that often lie in the promoter regions of these genes (Esteller 2006, 2007).
Community Structure and Soil Properties of the Pinus densiflora Forests in Limestone Areas

Floristic composition and soil properties were analyzed in red pine() communities in the limestone areas. Tanyang, Ch ungbuk Province in Korea. The tree layer was composed of and others as well as , all of which also appeared in soils of grinite origin The shrub layer was dominated by and for $suberosa$. Among these and for belonged to calcicole plant. The herb layer dominated by . Soil pH ranged 7.9-8.3. Total nitrogen and available phosphorus content of the soil were lower than those of noncalcareous soils. However, exchangeable calcium and magnesium content were 10 times and 2~3 times greater than those of noncalcreous soils, respectively. The difference of soil texture between top soil(loam soil) and subsoil(sand soil), and higher soil organic matter content than noncalcareous red pine forest soils seemed related to the casts forming activities of earthworms.
Investigating genetic damage in workers occupationally exposed to methotrexate

目的 用3个遗传终点来研究接触甲氨喋呤(MTX)工人的遗传损伤. 方法外周血分别来自21名生产MTX工人和21名对照组工人. 用微核试验、彗星试验、hprt基因突变试验和TCR基因突变试验对两组人群进行检测. 结果工人组平均微核率(MNR)、平均微核细胞率(MCR)分别为10. 10‰±0.95‰和8. 05‰±0.75‰,明显高于对照组(5.48‰±0.82‰和4.38‰±0.58‰),差异有统计学意义(P 0.05). 工人组的hprt和TCR平均突变率分别为1. 00‰±0.02‰和(6.87±0.52)×10-4,明显高于对照组[0.86‰±0.01‰和(1.67±0.14)×10-4],差异有统计学意义(P<0.01). 结论生产MTX工人某种程度上存在遗传损伤。
Effect of body condition score on biochemical milk parameters having economic importance in dairy goat during the first month of postpartum period.

The data were collected from 20 Turkish Saanen goats raised in Ismailli village of Tunceli Province during first four weeks of postpartum period. In the research, 10 goats having BCS 1 and 10 goats having BCS 2 were used. The dams in BCS 1 group had showed lower milk fat content as compared to dams in BCS 2 group until third week. The total solids and protein levels of goats did not differ between BCS 1 and BCS 2 groups during all weeks of research. We found positive high correlations between total solids and protein (r=0.997; p<0.01) in BCS 1 group and BCS2 group (r=0.9998; p<0.01). Similar correlations were found for both BCS group in study. From our results, the lower BCS has negative significant influence on the milk fat synthesis for dams having low fat depots. © 2013 Friends Science Publishers
PTPRT/D MUTATION OR PROMOTER METHYLATION: IMPLICATIONS FOR STAT3 INHIBITION

Head and neck squamous cell carcinoma (HNSCC) is a morbid and frequently fatal malignancy arising from the squamous epithelium of the upper aerodigestive tract. Survival rates have remained low and stagnant in recent decades even as our understanding of this disease has led to new treatment approaches, most notably the approval in 2006 of cetuximab, a monoclonal antibody targeting the epidermal growth factor receptor. The paucity of broadly effective targeted therapies for HNSCC patients illustrates the need for new targets for pharmacologic inhibition and biomarkers for predicting exquisite response to such agents. STAT3 is a potent oncogene that is hyperactivated by constitutive tyrosine phosphorylation in nearly all HNSCCs, where STAT3 represents a rational target for inhibition. As it is increasingly clear that most targeted therapies are unlikely to be broadly effective in unselected groups of patients, we have sought to identify genetic/epigenetic alterations of phosphatases that normally downregulate STAT3 in order to assess the potential utility of these alterations as predictive biomarkers for STAT3-targeted therapeutics. Our findings reveal that somatic mutation or promoter hypermethylation of PTPRT or PTPRD leads to loss of function of these phosphatases in HNSCC, concomitant with increased activation of STAT3 in preclinical models and tumor specimens. Importantly, these events are also associated with increased sensitivity to inhibitors of the STAT3 pathway in preclinical models. Together, these studies indicate that genetic or epigenetic alterations leading to loss of function of phosphatases that target STAT3 may ultimately serve as biomarkers for the selection of patients who will be most likely to respond to STAT3 inhibitors that are currently in preclinical and clinical development.
Electroreception and Communication in Fishes

This concise review focuses on recent advances in the function and mechanism of electroreceptive systems in lower aquatic vertebrates and elucidates the sophisticated principles of communication, prey detection and orientation in these organisms. An introduction into electroreceptors, electric organs and sensory functions is followed by a review of electrocommunication and its behavioral physiology. Throughout each section, one finds a wide range of examples, from sharks, rays and skates to catfishes and stargazers, including also strongly and weakly electric fishes from tropical freshwater bodies.
Disruption of circadian rhythm impairs pancreatic islet function and increases susceptibility to beta-cell failure, while pathological complications of Type 2 Diabetes Mellitus have scant effects on the circadian system

The circadian system plays an essential role in regulation of glucose homeostasis, and the disruption of this system leads to deleterious health consequences, such as Type 2 Diabetes Mellitus (T2DM). Disruption of circadian organization in humans is strongly associated with development of metabolic dysfunction and increases the propensity for development of T2DM. Importantly, the correlation between circadian disruption and T2DM is partly attributed to loss of beta-cell function and mass, called beta-cell failure. To address this association, we first hypothesized that exposure to environmental conditions associated with disruption of circadian rhythms and susceptibility to T2DM in humans disrupts islet clock and beta-cell function. We reported that prolonged exposure to LL disrupts islet circadian clock function through impairment in the amplitude, phase, and interislet synchrony of clock transcriptional oscillations. We also reported that exposure to LL leads to diminished glucose-stimulated insulin secretion due to a decrease in insulin secretory pulse mass. Second, obesity-mediated insulin resistance is an important contributory factor to induction and progression of T2DM. We, therefore, hypothesized that disruption of circadian rhythms compromises pancreatic beta cell functional and morphological adaption to diet-induced obesity leading to development of T2DM. We found that concomitant exposure to LL and HFD resulted in development of hyperglycemia characterized by loss of circadian rhythms in insulin secretion, compromised beta cell function, and induction of beta cell apoptosis, suggesting that circadian disruption and diet-induced obesity synergize to promote development of beta cell failure, likely mediated as a consequence of impaired beta cell clock function. Third, as accumulating evidence pointed out that metabolic signals can feed back into the circadian system, we tested whether the impaired glucose homeostasis disturbs the circadian system in return. We examined the expression of circadian rhythms in the human islet amyloid polypeptide transgenic (HIP) rats: a validated non-obese, beta-cell dysfuntion model of T2DM. Diurnal and circadian rhythms of locomotor activity, circadian entrainment, and clock gene oscillation in SCN, pancreatic islets and aorta all remains intact in the HIP rats. In summary, these studies examined mechanisms by which circadian disruption predisposes to beta-cell failure in the development of T2DM. We also showed that glucose intolerance caused by beta-cell dysfunction might not be sufficient to cause circadian deficits, which emphasized the causal role of circadian disruption in the development of T2DM.
Its Greatest Benefit of Inclusion Is Its Challenge”: EFL Teachers' Attitudes towards Inclusion of Learners with Disabilities

Inclusion has long been a hotbed for debate in many educational fields but TEFL (Teaching English as a Foreign Language). To the best knowledge of the research, no study has been conducted on the issue of inclusion in Iran, especially considering EFL learners with special needs. Considering teachers as the central pillar of the inclusive education, the present study sought to investigate EFL (English as a Foreign Language) teachers' attitudes towards the inclusion of physically-impaired EFL learners in English language classes. To this end, a comprehensive survey was conducted using the 25-item Opinions Relative to Mainstreaming (ORM) scale (Antonak & Larrivee, 1995) to collect data from 254 Iranian EFL teachers, of whom 30 teachers were subsequently interviewed to guarantee the triangulation of the findings. The data were analyzed quantitatively and qualitatively, with the SPSS Software version 20 being used for the quantitative analysis. Findings indicating the Iranian EFL teachers’ neutral-to-positive attitudes are thoroughly discussed in this paper. The paper also contains some information about the perceived benefits/challenges of inclusion, its pedagogical implications and recommendations for further research.
Oriented Attachment of Cytochrome P450 2C9 to a Self-Assembled Monolayer on a Gold Electrode as a Biosensor Design

Cytochrome P450s (CYPs) are a family of enzymes implicated in the metabolism of drugs in the body. Consequently, P450 reactions are of high interest to the pharmaceutical industry, where lead compounds in drug development are screened as potential substrates of CYPs. The P450 reaction involves electron transfer to an iron heme via NADPH and the electron transfer partner enzyme P450 reductase (CPR). By immobilizing CYPs on an electrode however, NADPH and CPR are potentially no longer needed and the immobilized CYP can act as a biosensor by accepting electrons directly from the electrode. Such a biosensor could be used as an initial screening tool for CYP reactivity of pharmaceuticals in development. In this study, the drug-metabolizing enzyme CYP 2C9 was immobilized to a self-assembled monolayer (SAM) on a gold electrode in three different orientations to investigate the effect that orientation has on the direct electrochemistry of CYP and to evaluate oriented attachment of CYP to an electrode as a biosensor design. Three attachment methods were investigated: random attachment via amine coupling to a carboxy-terminated SAM, oriented attachment via C-terminal His-tag coupling to a Ni-NTA-functionalized SAM, and oriented attachment via maleimide/thiol coupling to a maleimide-functionalized SAM. Three 2C9 mutants (R125C, R132C, and K432C) were developed with a single cysteine mutation at the binding site for CPR on the side of the enzyme closest to the heme; attachment of these mutants to a gold electrode via maleimide/thiol coupling would orient the enzyme such that electron transfer occurs on the electrode in the same orientation that it does in vivo with CPR. Therefore, we expected oriented attachment via maleimide/thiol coupling to produce the most electroactive CYP biosensor. Electrochemical analysis and surface characterization of the SAMs on gold electrodes confirmed that electron transfer occurs through the SAMs, and activity assays of the 2C9 electrodes confirmed that wild-type 2C9 and the single Cys mutants R125C, R132C, and K432C were immobilized to the gold electrode via all three attachment methods. Cyclic voltammetry of the 2C9 electrodes revealed however, that direct electron transfer to 2C9 was not possible for all three attachment methods. Similar redox processes were observed for both the 2C9 electrodes and no-enzyme electrodes modified only with SAMs, suggesting that the redox process observed on the 2C9 electrodes is related to the underlying SAM. Thus, we were unable to make any conclusions regarding the effectiveness of oriented attachment in creating a 2C9 biosensor. However, to our knowledge, there are no examples in the literature of the oriented attachment of 2C9 to an electrode via coupling of an engineered cysteine to a maleimide-functionalized SAM on gold and therefore this study represents the first attempt towards such an electrode system.
The Development of Circadian Rhythms in Human Infants

Introduction The first four postnatal months, for a newborn infant, is a period of rapid adaptation and change. Infants undergo a series of integrated physiological changes that culminate in mature physiological diurnal rhythms by which they establish equilibrium with the new environment, all of which are under the genetic control of the biological clock. This is a longitudinal study of 35 infants in which the age related changes in physiology, are assessed during night time sleep and related to circadian genes, melatonin and cortisol. Aim The aim of the study is to monitor the physiological development of normal full-term human infants concomitantly assessing the expression of circadian genes. Method Full term healthy infants were selected. Infants were recruited into the study from 6 weeks until 18 weeks of age. Fortnightly home visits were conducted in which the overnight deep body temperature of infants was monitored. On each night of study, actigraphy was used to study infant and maternal sleep. Longitudinal measurements of melatonin and cortisol secretion by paired day-night urine collection and peripheral gene expression using buccal swabs were taken by mothers. Results There is evidence of a sequential and ordered development of circadian rhythms in human infant physiology. There was a temporal relationship demonstrated in the maturation of the infant circadian rhythms. Core body temperature demonstrated a robust rhythm, characterised by an abrupt change, the timing of which varied from infant to infant. Night time melatonin secretion increased with age. Cortisol played a key role. Infant sleep improved with physiological maturation. A number of complex relationships between aspects of the physiology and circadian gene expression were elucidated. Conclusion There is a demonstrable integration of genetic and physiological changes, during the immediate postnatal period when infants are most vulnerable to illnesses and particularly to sudden and unexpected death.
Isolation by distance, based on microsatellite data, tested with spatial autocorrelation (spaida) and assignment test (spassign)

spassign and spaida are two small programs useful to detect isolate by distance of microsatellite loci. The programs are written in C and are available for Linux and Windows system at http://www.hi. is/~snaebj/programs.html. spaida calculates two estimates of spatial autocorrelation, Moran's I and Geary's c, first by assuming the infinite allele model, and second by assuming a stepwise mutational model. spassign calculates the assignment probabilities of an individuals genotype to the location where it was sampled and compares probabilities of assignment to other locations. Genetic distances among regions based on the overall differences in likelihoods are calculated.
Food Borne Pathogens: A Threat to Dairy Industry

Food borne diseases is the major concern along with malnutrition in developing countries and developed countries as well. Milk is rich source of nutrition with large number of pathogenic bacteria which are more susceptible to cause illness or death. Millions of people stuck with food borne outbreaks throughout the globe because of presence of pathogenic bacteria – disease causing microbiota like E. coli O157:H7, Salmonella, Shigella, Listeria, Campylobacter, S.aureus and Clostrida and their heat stable and heat labile toxins. The presence of food borne pathogens in milk and milk products is due to direct contact with contaminated sources in dairy farm environment and to excretion from infected udder of animal suffering from disease. Generally very few percentage (app. 1–2%) people of the globe consume raw milk and milk products while others use pasteurized one. But sometimes inadequate or faulty heat treatment and post processing contamination through infected supply chain may lead to major consequences related to outbreaks. Keywords: Food borne disease, milk and milk products, pathogens, contamination Cite this Article Vaghela Nileshkumar R, Subrota Hati, Gawai K et al. Food Borne Pathogens: A Threat To Dairy Industry ; Research & Reviews: Journal of Dairy Science and Technology . 2015; 4(1): 28–36p.
The Regulatory Role of Dendritic Cells in the Innate Immune Response

Cells of the dendritic cells (DC) lineage are continuously produced; they arise from bone marrow hematopoietic stem cells as myeloid progenitors and seed all organism tissues. Although rare, they are ubiquitously distributed in lymphoid and nonlymphoid tissues; together with macrophages, they recognize pathogens and regulate the inflammatory processes. The responsiveness of mucosal DC populations to inflammatory stimuli, in particular their rapid kinetics of recruitment that surprisingly is equivalent to that of neutrophils, underscores their relevance as antigen sentinels and regulators at the mucosal sites. Indeed, in pathological conditions, such as in Crohn’s disease, a good deal of recent evidence suggests that the failure of a physiological innate immune response could degenerate into an autoimmune response. In the absence of inflammation, innocuous antigens that are continuously encountered in the lungs by DCs induce antigen-specific unresponsiveness. In the lymphoid organs, DCs have the unique opportunity to encounter and present antigens to the rare unprimed antigen-specific T cells. Mannose receptors are believed to be expressed by DCs because internalization and presentation of mannosylated proteins are very efficient in DCs. The movement of the pseudopodia in activated DCs involves actin binding proteins, and it can be blocked by the drug cytochalasin D, which stops the polymerization of actin and inhibits phagocytosis. Natural killer (NK) cells activity is primed during the early phases of an immune response, a few hours after infection. As a matter of fact, physiological immune responses originate from a well-controlled inflammatory process.
Developing Methods to Study Dynamic Biological Processes in Single Cells With Microscopy

Many aspects of intracellular dynamics are difficult to infer from bulk experiments: cell-cycle specific responses are hidden by averaging over an asynchronous population, spatial aspects are invisible, and many of the perturbations that cells respond to vary greatly between cells due to spontaneous, stochastic events. Some of these challenges can be addressed by using quantitative time-lapse microscopy. Great strides have been made in terms of imaging modalities with higher resolution, and fluorescent probes with improved properties. However, the methods for handling cells have lagged behind. Many assays are low-throughput, keep cells under poorly controlled conditions, are confounded by artefacts (e.g. due to the point-spread function of light when cells are close to each other), struggle to quantify components present in low numbers, and are often limited in terms of imaging individual cells in changing populations. In this thesis, we developed several methods to deal with these technological challenges, and applied these new tools to various biological processes. First we present a detailed and reproducible protocol for a platform termed MACS–microfluidics assisted cell screening. MACS provides a single device that can be used with a wide-range of cell types from E. coli to human red blood cells. With MACS, cells are subject to mechanical pressing from a PDMS valve that can exert controlled pressure on cells. By employing high pressure, MACS