Miracle-dz/UniFAR-FTUs huggingface dataset:
'Anaerobic protists': some misconceptions and confusions.

An interesting and important cohort of protists, now widely referred to as ‘anaerobic protists’, has become a focus of interdisciplinary research. Although there are many free-living species (e.g. Metopus contortus in marine sediments), those best studied are parasites that cause some of the most widespread diseases of humans and animals. Giardia intestinalis is the most prevalent water-borne protist, parasitic in humans and cattle worldwide; its cysts survive in water supplies for months. Trichomonas vaginalis, a sexually transmitted flagellate, is the most common of all human parasitic protists; Tritrichomonas foetus, causing abortion in cattle, leads to enormous economic losses in large herds in Australia and the USA. The fact that these organisms have poorly developed mitochondria (Fenchel & Finlay, 1995; Lloyd et al., 2002) has encouraged the view that they may be unusual, as being representative of present-day counterparts of organisms that evolved soon after an endosymbiotic a-proteobacterium became the energy-yielding organelle of the earliest eukaryotic lineage. Accumulating evidence, obtained by biochemical investigations, improved ultrastructural studies and work on molecular phylogeny (Lloyd & Harris, 2002), invalidates this hypothesis. We still know little of the events that occurred to make possible the development and emergence of lower eukaryotes, plants and animals. As yet, we know nothing about the long line of ancestral forms of present day lower eukaryotes, so that we cannot identify a missing link (Fenchel, 2002).
Serious bodily harm related to Obsessions from Sri Lanka.

An obsession is a thought that persists and dominates an individual’s thinking despite the individual’s awareness that the thought is either entirely without purpose or else has persisted and dominated their thinking beyond the point of relevance or usefulness (Fish & Hamilton 1985). Obsessions occur in many psychiatric disorders such as Obsessive Compulsive disorder (OCD), Major Depressive disorder and Schizophrenia (APA 2013, Bahceci et al. 2014, Doyle et al. 2014). In certain patients medication such as clozapine may induce obsessions (Doyle et al. 2014). In the 5th edition of the Diagnostic and Statistical Manual of mental disorders (DSM 5), OCD has been categorized together with few other related disorders (APA 2013). Among these disorders there are several disorders with direct physical self-harm. They include Trichotillomania and Excoriation disorder which are presumably related to OCD in terms of a range of diagnostic validators (APA 2013). There have been case reports on patients with OCD who presented with self-injurious behaviour. A description of an older male presenting with late onset OCD and genital self-mutilation has been published from India, the closest neighbour to Sri Lanka (Pandit & Vardhan 2013). There are cases of Tourette’s disorder with comorbid OCD presenting with severe self-injurious behaviour (Krüger & Müller-Vahl 2015). In a series of patients with self-injurious skin picking, 52% of them was found to be suffering from comorbid OCD (Wilhelm et al. 1999). We could not find any larger studies on OCD and bodily harm. Sri Lanka is an island in the Indian Ocean with a multi-ethnic population of about 21 million (World Bank 2015). The psychiatrist to patient ratio is low and in 2012 there was approximately one consultant psychiatrist per 500,000 persons (Jenkins et al. 2012). Only 1.6% of the total health budget is spent on mental health (Jenkins et al. 2012). We describe two Sri Lankan patients presenting with significant bodily harm related to their obsessions. There is very few published data regarding bodily harm in relation to obsessions. Therefore we hope this description of two patients would be valuable to other clinicians treating patients with similar presentations.
Colocalization and Membrane Association of Murine Hepatitis Virus Gene 1 Products and De Novo-Synthesized Viral RNA in Infected Cells

ABSTRACT Murine hepatitis virus (MHV) gene 1, the 22-kb polymerase (pol) gene, is first translated into a polyprotein and subsequently processed into multiple proteins by viral autoproteases. Genetic complementation analyses suggest that the majority of the gene 1 products are required for viral RNA synthesis. However, there is no physical evidence supporting the association of any of these products with viral RNA synthesis. We have now performed immunofluorescent-staining studies with four polyclonal antisera to localize various MHV-A59 gene 1 products in virus-infected cells. Immunoprecipitation experiments showed that these antisera detected proteins representing the two papain-like proteases and the 3C-like protease encoded by open reading frame (ORF) 1a, the putative polymerase (p100) and a p35 encoded by ORF 1b, and their precursors. De novo-synthesized viral RNA was labeled with bromouridine triphosphate in lysolecithin-permeabilized MHV-infected cells. Confocal microscopy revealed that all of the viral proteins detected by these antisera colocalized with newly synthesized viral RNA in the cytoplasm, particularly in the perinuclear region of infected cells. Several cysteine and serine protease inhibitors, i.e., E64d, leupeptin, and zinc chloride, inhibited viral RNA synthesis without affecting the localization of viral proteins, suggesting that the processing of the MHV gene 1 polyprotein is tightly associated with viral RNA synthesis. Dual labeling with antibodies specific for cytoplasmic membrane structures showed that MHV gene 1 products and RNA colocalized with the Golgi apparatus in HeLa cells. However, in murine 17CL-1 cells, the viral proteins and viral RNA did not colocalize with the Golgi apparatus but, instead, partially colocalized with the endoplasmic reticulum. Our results provide clear physical evidence that several MHV gene 1 products, including the proteases and the polymerase, are associated with the viral RNA replication-transcription machinery, which may localize to different membrane structures in different cell lines.
Serum levels, tissue expression and cellular secretion of macrophage migration inhibitory factor in limited and diffuse systemic sclerosis.

OBJECTIVES To investigate serum levels, tissue/cellular expression of macrophage migration inhibitory factor (MIF) in patients with limited (lSSc) and diffuse (dSSc) systemic sclerosis. METHODS 10 lSSc-patients, 10 dSSc-patients and 10 controls were enrolled. MIF serum levels were assayed by ELISA. MIF and its receptors CD74/CD44 were evaluated by immunohistochemistry on skin biopsies from patients with dSSc, lSSc (affected and not-affected skin) and controls. MIF levels were assessed (ELISA) in supernatants of healthy dermal microvascular endothelial cells (MVECs) and in control (CTR), non-affected SSc (NA) and affected (SSc) fibroblasts treated for 48 h with 10% control serum and 10% SSc-serum. MIF supernatant (ELISA) and mRNA (quantitative real-time PCR) levels were determined in SSc dermal fibroblasts and in control dermal fibroblasts untreated or stimulated at 6 h-24 h-48 h with bleomycin (50 mU/ml). RESULTS Serum MIF was significantly higher in dSSc (18.7±4.1 ng/ml, p<0.001) and in lSSc (10.4±4.4 ng/ml, p<0.001) patients respect to controls (2.6±1.4 ng/ml). Enhanced MIF immunoreactivity was found in keratinocytes, fibroblasts, endothelium, sebaceous/sweat glands from lSSc/dSSc affected skin. Faint MIF immunoreactivity was found in control skin and not-affected skin of lSSc patients. No differences were found in CD74/CD44 receptors' analysis among control and dSSc/lSSc affected and non-affected skin. MVECs and fibroblasts (CTR, NA and SSc) produced significantly more MIF, when stimulated with SSc serum respect to control-serum (p<0.001). Finally, MIF mRNA levels significantly increased at 6h (p<0.001) and decreased at 48 h (p<0.001) in control fibroblasts treated with bleomycin compared to control untreated. Simultaneously, MIF supernatant protein levels increased after 48 h (p<0.01) in bleomycin-treated fibroblasts respect to untreated ones. CONCLUSIONS These results suggest that MIF could be implicated in the pathogenesis of SSc, probably acting as protective factor against the SSc stressful conditions.
Associations between polymorphisms in five inflammation‐related genes and cognitive ability in older persons

Several studies have found associations between inflammatory biomarker levels and cognitive ability. This study tested the relationship between polymorphisms in genes that are associated with or encode the biomarkers and cognitive ability and estimated lifetime cognitive change. Data came from the aspirin for asymptomatic atherosclerosis trial (n = 2091, mean age = 67.2 years ). Twelve single nucleotide polymorphisms (SNPs) were genotyped from five genes (IL‐1α, IL‐1β, IL‐6, HNF‐1A and F13A1). Cognition was assessed via administration of a five‐test battery of psychometric tests, which were used to derive a general intelligence factor, g. A vocabulary‐based cognitive test was also administered and adjusted for in the analysis to enable an estimation of lifetime cognitive change. Age‐ and sex‐adjusted analyses yielded one weakly significant association between the IL‐1α rs2856838 SNP and a measure of mental flexibility/processing speed (P = 0.044). Adjustment for the vocabulary‐based scores resulted in a single, significant association between the IL‐1α rs3783546 SNP and a measure of processing speed (P = 0.048). There is little evidence to suggest an association between SNPs in the inflammation‐related genes IL‐1α, IL‐1β, IL‐6, TCF‐1 and F13A1 and cognition in an elderly population of community‐dwelling Scottish citizens.
Value-based software engineering: reinventing

The Value-Based Software Engineering (VBSE) agenda described in the preceding article has the objectives of integrating value considerations into current and emerging software engineering principles and practices, and of developing an overall framework in which they compatibly reinforce each other. In this paper, we provide a case study illustrating some of the key VBSE practices, and focusing on a particular anomaly in the monitoring and control area: the "Earned Value Management System. " This is a most useful technique for monitoring and controlling the cost, schedule, and progress of a complex project. But it has absolutely nothing to say about the stakeholder value of the system being developed. The paper introduces an example order-processing software project, and shows how the use of Benefits Realization Analysis, stake-holder value proposition elicitation and reconciliation, and business case analysis provides a framework for stakeholder-earned-value monitoring and control.
Reticular erythrokeratoderma: A new disorder of cornification

Heritable disorders of cornification form a large, clinically and genetically heterogeneous group. Recent advances in molecular genetics provide for the first time the opportunity to reliably classify some of these disorders based on their underlying etiology. Many rare phenotypes, however, still remain unclassified and do not fit into established classification schemes. We report here a 12‐year‐old girl who developed an ichthyosis vulgaris‐like skin disorder 6 months after birth. Several years later, the clinical features had changed considerably. The patient had developed streaks of hyperkeratotic, slightly scaling skin with underlying erythema distributed in a reticulate, occasionally annular pattern on the trunk and extremities. The lesions were stable and had not changed significantly in size or distribution over the ensuing years. Histopathologic and ultrastructural findings were nonspecific and there was no evidence for metabolic disorders. The partial clinical overlap with erythrokeratodermia variabilis prompted us to screen several connexin genes but no pathogenic mutations were identified. We believe that this disorder belongs to the group of erythrokeratodermas and represents a novel, previously unrecognized entity. © 2003 Wiley‐Liss, Inc.
State estimation for nonlinear dynamic systems using Gaussian processes and pre-computed local linear models

State estimation of nonlinear dynamic systems is an important problem in practice. This paper proposes a recursive state estimation method for nonlinear dynamic systems using Gaussian processes (GP) and pre-computed local linear models. Gaussian processes exhibit remarkable learning, or nonlinear regression capabilities from measurement data. The incorporation of pre-computed local linear models reduces the amount of data required and improves the regression performance of the GP. Based on such an improved GP model for nonlinear dynamic systems, a recursive Bayesian filtering method is implemented for the estimation of the unknown states of the system. Simulations on an aircraft benchmark model demonstrate that the proposed method is capable of estimating the unknown angle of attack of the aircraft, and the existence of the local linear models significantly improves the estimation performance of the filter. This method is especially useful in a control systems design context in which local linearisations of nonlinear dynamic systems are usually readily available.
Rough assessment of GPU capabilities for parallel PCC-based biclustering method applied to microarray data sets

Abstract Parallel computing architectures are proven to significantly shorten computation time for different clustering algorithms. Nonetheless, some characteristics of the architecture limit the application of graphics processing units (GPUs) for biclustering task, whose function is to find focal similarities within the data. This might be one of the reasons why there have not been many biclustering algorithms proposed so far. In this article, we verify if there is any potential for application of complex biclustering calculations (CPU+GPU). We introduce minimax with Pearson correlation – a complex biclustering method. The algorithm utilizes Pearson’s correlation to determine similarity between rows of input matrix. We present two implementations of the algorithm, sequential and parallel, which are dedicated for heterogeneous environments. We verify the weak scaling efficiency to assess if a heterogeneous architecture may successfully shorten heavy biclustering computation time.
Acute and sustained isoflurane neuroprotection: The effect of culture age and duration of oxygen and glucose deprivation

Objectives: Organotypic hippocampal slice (OHS) cultures provide the opportunity to dissect factors influencing volatile anaesthetic neuroprotective efficacy. It was hypothesized that three conditions—OHS culture age, oxygen glucose deprivation (OGD) duration and day of evaluation for cell death after OGD—influence isoflurane's ability to provide acute and sustained protection against OGD-induced cell death. Methods: OHS were prepared from PND 9–11 rat pups and maintained in vitro for 0.5, 1, 2 or 3 weeks. The slices were exposed to OGD for 0, 10, 30, 60 or 90 minutes with or without 1.5% isoflurane. Sytox staining was used to determine the amount of cell death on post-OGD days 1, 3 and 7 and was compared to the amount of cell death in culture–age matched controls (no OGD). Results: The duration of OGD necessary to produce cell death was inversely related to culture age. All culture ages showed evidence of both acute and sustained neuroprotection, but the magnitude of protection depended on OHS culture age, duration of OGD and post-OGD day of evaluation. In 1 and 2-week old slices early isoflurane neuroprotection was best observed with 90 minutes OGD and late isoflurane protection was best observed with 10 minutes OGD. Conclusions: In OHS, acute and sustained isoflurane neuroprotection in OGD-induced cell death is dependent on the conditions being studied.
Total Quality Management in Information Systems Development: Key Constructs and Relationships

The availability of high-quality software is critical for the effective use of information technology in organizations. Research in software quality has focused largely on the technical aspects of quality improvement, while limited attention has been paid to the organizational and sociobehavioral aspects of quality management. This study represents one effort at addressing this void in the information systems literature. The quality and systems development literatures are synthesized to develop eleven quality management constructs and two quality performance constructs. Scales for these constructs are empirically validated using data collected from a national survey of IS organizations. A LISREL framework is used to test the reliability and validity of the thirteen constructs. The results provide support for the reliability and validity of the constructs. A cluster analysis of the data was conducted to examine patterns of association between quality management practices and quality performance. The results suggest that higher levels of institutionalization of all quality management practices are associated with higher levels of quality performance. Our results also suggest that key factors that differentiated high- and low-quality performing IS units include senior management leadership, mechanisms to promote learning and the management infrastructure of the IS unit. Future research efforts directed at causally interrelating the quality management practices should lead to the development of a theory of quality management in systems development.
Surface Lightness Influences Perceived Room Height

Surprisingly little scientific research has been conducted on the effects of colour and lightness on the perception of spaciousness. Practitioners and architects typically suggest that a room's ceiling appears higher when it is painted lighter than the walls, while darker ceilings appear lower. Employing a virtual reality setting, we studied the effects of the lightness of different room surfaces on perceived height in two psychophysical experiments. Observers judged the height of rooms varying in physical height as well as in the lightness of ceiling, floor, and walls. Experiment 1 showed the expected increase of perceived height with increases in ceiling lightness. Unexpectedly, the perceived height additionally increased with wall lightness, and the effects of wall lightness and ceiling lightness were roughly additive, incompatible with a simple effect of the lightness contrast between the ceiling and the walls. Experiment 2 demonstrated that the floor lightness has no significant effect on perceived height, and that the total brightness of the room is not the critical factor influencing the perceived height. Neither can the results be explained by previously reported effects of brightness on apparent depth or perceived distance.
Association of the Phe206Leu Allele of the L-Selectin Gene with Coronary Artery Disease

Background and Aims: The aim of this study was to assess the association between the L-selectin Phe206Leu polymorphism and coronary artery disease. Methods: A total of 322 patients (221 men and 101 women) with coronary artery disease in one or more vessels documented by angiography were studied; 157 subjects (85 men and 72 women) without atherosclerosis were included as controls. All subjects were genotyped for the L-selectin Phe206Leu gene polymorphism using polymerase chain reaction with sequence-specific primer (PCR-SSP). To assess disease severity, all patients were classified by numbers of coronary arteries with 50% stenosis. Results: A significantly increased frequency of the 206Leu mutant allele was observed in patients with coronary artery disease compared to the controls. The 206Leu allele frequency occurred in 42% of the patients with coronary artery disease compared to 30% of the controls (p < 0.009). No association was found between the severity of coronary artery disease and the L-selectin Phe206Leu polymorphism. Conclusion: Our findings suggest that carriage of L-selectin 206Leu mutant allele could contribute to susceptibility of Iranian individuals to contracting coronary artery disease.
Venomous bites and stings in the tropical world*

Snakes of the families Viperidae and Elapidae are responsible for the high incidence of morbidity and mortality after snake bites in countries of West Africa, the Indian subcontinent, South‐East Asia, New Guinea and Latin America. Envenoming can cause local effects, notably tissue necrosis; and systemic effects, including paralysis, haemostatic disturbances, shock, increased capillary permeability, myocardial damage, rhabdomyolysis and acute renal failure. Specific hyperimmune serum (antivenom) is the mainstay of medical treatment for severe envenoming. Ancillary treatments such as assisted ventilation, repletion of circulating volume, renal dialysis and surgical debridement of necrotic tissues are needed in some cases. Scorpion stings are a common medical problem in middle and southern America, North Africa and the Middle East. Vasodilator drugs are important to counter the effects of massive catecholamine release. Bites by spiders and stings by hymenoptera and marine animals are responsible for deaths and morbidity in some tropical countries. (Med J Aust 1993; 159: 773‐779)
TGF-β 1509 C / T polymorphism and the risk of ESCC in a Chinese Han population

Background: The studies investigating whether transforming growth factor (TGF)-β1-509C/T polymorphism is associated with the risk of ESCC is inconsistent. Methods: The TGF-β1-509C/T genotypes were determined by using a polymerase chain reaction (PCR)-restriction fragment length polymorphism assay and DNA sequencing analysis. The differences in demographic variables and genotype distributions of TGF-β1-509C/T polymorphism between ESCC patients and controls were calculated by Pearson’s Chi square test. Associations between TGF-β1-509C/T polymorphism genotypes and ESCC risk were estimated by OR and their 95% CIs computed using unconditional logistic regression model. Results: There was a significant difference of TGF-β1-509C/T polymorphism genotype distribution between ESCC group and control group (P<0.001). With the CC genotype as reference, the adjusted OR for CT genotype reached to 0.78 (95% CI: 0.65-0.89; P=0.041), and the adjusted OR for TT homozygous carriers was 0.52 (95% CI: 0.33-0.78; P=0.017). The T allele carriage also presented a lower risk for ESCC (adjusted OR=0.43; 95% CI, 0.29-0.71; P=0.009). Conclusion: TGF-β1-509C/T polymorphism may contributes to ESCC susceptibility in Chinese population.
FEM On Nonlinear Free-surface Flow

Recently there has been a growing need for the treatment of the nonlinear water wave problems. In this paper we will present an overview on the finite element method applied to the nonlinear water wave problems, i.e., in ship motions, wave resistance, lifting problems, and initial value problems. The present numerical scheme can be used for the validation of the existing approximate theories, i.e., the KdV and the Boussinesq equations or Green-Naghdi equation as well as for a better prediction for more realistic physical models. In the paper we discuss the following applications: The finite element method applied to a two dimensional hydrofoil problem. An initial-value problem for a physical model of an axi-symmetric container filled with water freely falling into a flat solid surface. The generation of solitons in shallow water towing-tank near the critical speed as well as a numerical towing tank simulation for arbitrary tank conditions. A sloshing and a diffraction problems. Finally, a brief concluding remark is given. A full account of this paper can be found in [1]