Miracle-dz/UniFAR-FTUs huggingface dataset:
Genes involved in human sialic acid biology do not harbor signatures of recent positive selection

Sialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes; the overall diversity of sialic acids is often referred to as the host “sialome”. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activation to recycling and degradation, are involved in sialic acid biology. Several sialome genes have experienced higher rates of non-synonymous substitutions in the human lineage than their counterparts in other great apes, which may be indicative of ancient positive selection in response to pathogens. To test whether sialome genes have also experienced more recent positive selection in human populations, reflecting adaptation to contemporary cosmopolitan or geographically-restricted pathogens, we calculated several metrics that quantify changes in allele frequency spectra caused by recent selection on the protein-coding and putative enhancer regions of 55 sialome genes using whole genome sequencing data of 2,504 humans from five ethnic groups. To disentangle the effects of demography, we compared the observed patterns in sialome putative enhancer regions and genes to those of 189 housekeeping genes and their putative enhancer regions, which are known to be evolving under strong negative selection due to functional constraints. We found that the patterns of genetic variation of sialome genes and putative enhancers do not differ significantly from those of their housekeeping counterparts. Furthermore, the observed patterns of genetic variation were not significantly different among the four functional categories of sialome genes. These results suggest that the genic and putative enhancer regions of sialome genes have experienced strong purifying selection but not recent positive selection. We propose that the absence of signatures of recent positive selection is consistent with the view that human sialome genes regulate immune responses against ancient rather than contemporary cosmopolitan or geographically-restricted pathogens.
Evaluating a theory of stress and adjustment when predicting long-term psychosocial outcome after brain injury

Kendall and Terry (1996) include many psychosocial predictors in their theoretical model that explains individual differences in psychosocial adjustment (Lazarus & Folkman, 1984). The model depicts appraisal and coping variables as mediating relationships between situation factors, environmental and personal resources, and multidimensional outcome. The aim of this study was to explore these theoretical relationships at very late stages of recovery from traumatic brain injury. A total of 131 participants who were more than 10 years post-injury (mean = 15.31 years) completed several psychosocial measures relating to outcome dimensions comprising employment, community integration, life satisfaction, quality of life (QoL), and emotion. There was no evidence that appraisal and coping variables mediated relationships between psychosocial and any of the outcome variables. However, when appraisal and coping variables were combined with psychosocial variables as direct predictors of outcome, every outcome except employment status was reliably predicted, accounting for between 31 and 46% of the variance. Personality significantly influenced all predicted outcomes. Self-efficacy contributed to the prediction of all outcomes except QoL. Data did not support for the theory of stress and adjustment as a framework for explaining the nature of predictive relationships between psychosocial variables and very long-term, multidimensional outcome after brain injury. (JINS, 2006, 12, 359–367.)
The Clever Fetus: Responding to Inflammation to Minimize Lung Injury

Clinical and experimental information indicate that fetal exposure to inflammation can induce lung maturation. This inflammation may be chronic and indolent. We present clinical and experimental information that challenge assumptions about chorioamnionitis associated infection/inflammatory exposures to the fetus. We question the assumption that the fetal compartment is sterile, and that delivery is inevitable if chronic infection/inflammation is present. We demonstrate that the preterm fetus can develop a brisk and adequate inflammatory response, and the fetus also can quickly modulate and downregulate inflammation to prevent injury. The fetus at risk of early preterm delivery may be exposed to both chorioamnionitis and glucocorticoids. Both exposures can either increase or decrease fetal inflammatory responses depending on the timing of the exposures. The immunomodulatory ability of the fetus to fetal exposures remains an unexplored research field.
Hybrid PGS–PCL microfibrous scaffolds with improved mechanical and biological properties

Poly(glycerol sebacate) (PGS) is a biodegradable elastomer that has generated great interest as a scaffold material due to its desirable mechanical properties. However, the use of PGS in tissue engineering is limited by difficulties in casting micro‐ and nanofibrous structures, due to high temperatures and vacuum required for its curing and limited solubility of the cured polymer. In this paper, we developed microfibrous scaffolds made from blends of PGS and poly(ε‐caprolactone) (PCL) using a standard electrospinning set‐up. At a given PGS:PCL ratio, higher voltage resulted in significantly smaller fibre diameters (reduced from ∼4 µm to 2.8 µm; p < 0.05). Further increase in voltage resulted in the fusion of fibres. Similarly, higher PGS concentrations in the polymer blend resulted in significantly increased fibre diameter (p < 0.01). We further compared the mechanical properties of electrospun PGS:PCL scaffolds with those made from PCL. Scaffolds with higher PGS concentrations showed higher elastic modulus (EM), ultimate tensile strength (UTS) and ultimate elongation (UE) (p < 0.01) without the need for thermal curing or photocrosslinking. Biological evaluation of these scaffolds showed significantly improved HUVEC attachment and proliferation compared to PCL‐only scaffolds (p < 0.05). Thus, we have demonstrated that simple blends of PGS prepolymer with PCL can be used to fabricate microfibrous scaffolds with mechanical properties in the range of a human aortic valve leaflet. Copyright © 2010 John Wiley & Sons, Ltd.
Online network intrusion detection system using temporal logic and stream data processing

These days, the world are becoming more interconnected, and the Internet has dominated the ways to communicate or to do business. Network security measures must be taken to protect the organization environment. Among these security measures are the intrusion detection systems. These systems aim to detect the actions that attempt to compromise the confidentiality, availability, and integrity of a resource by monitoring the events occurring in computer systems and/or networks. The increasing amounts of data that are transmitted at higher and higher speed networks created a challenging problem for the current intrusion detection systems. Once the traffic exceeds the operational boundaries of these systems, packets are dropped. This means that some attacks will not be detected. In this thesis, we propose developing an online network based intrusion detection system by the combined use of temporal logic and stream data processing. Temporal Logic formalisms allow us to represent attack patterns or normal behaviour. Stream data processing is a recent database technology applied to flows of data. It is designed with high performance features for data intensive applications processing. In this work we develop a system where temporal logic specifications are automatically translated into stream queries that run on the stream database server and are continuously evaluated against the traffic to detect intrusions. The experimental results show that this combination was efficient in using the resources of the running machines and was able to detect all the attacks in the test data. Additionally, the proposed solution provides a concise and unambiguous way to formally represent attack signatures and it is extensible allowing attacks to be added. Also, it is scalable as the system can benefit from using more CPUs and additional memory on the same machine, or using distributed servers.
Different treatment of rice seed dormancy breaking , germination of both wild species and cultivated varieties ( Oryza sativa L . )

The present study was conducted at Genetics Departm ent, Hazara University Garden Campus and during 2008-09 as a part of PhD study. Seed dormancy break ing, germination tests of 2 wild speciesi.e. , O. longistaminata and O. rufipogon and 3 local cultivated rice varieties/ germplasm i . e. , Swat-1, F. Malakand and JP-5 were conducted under different treatments. Hulled s eds were exposed to: constant temperatures of 28 degree celsius to 38 degree celsius & room temp erature (25#1 degree celsius); and alternating temp eratures of 40/30 degree celsius to 45/35 degree celsius ( 12 hours/12 hours) and at a room temperature(25# d egree celsius). Third treatment ,intact seeds were expose d to dry heat at 50 degree celsius for 7 and 14 day s before germination of hulled and intact seeds under the ma xi um temperature for each wild species determined from treatments 1 2 species that showed minimum % of germination , various chemical treatment, for germination of intact seeds in 0.001M potassium nit rate, presoaking the seeds for 24 or 48 hours in ( 0.1 or 0.2 M Nitric acid , I M Hydrogen peroxide , 1000 ppm Gi bberellic acid (GA3) and in-combination of 0.1 M HNO, and 1 M H , 0.2 MHNO2O2 , 0.2 M HNO3 and 1 M3H2O2 were conducted . It was observed that: removal of the seed hull is extremely effective for breaking seed dormancy while species respond differently to vario us constant / alternating temperatures and heat genera lly p omotes germination of the species that respon d to certain constant and alternating temperature but no consistent differences observed in seed germinatio of most species between heat treatments at 50 degree c elsius for 7 or 14 days. O rufipogon and Swat-1 both respond to certain chemical treatments effectively under the optimum temperature regimes. An appropria te combination of seed hull removal, dry heat or chemi cal treatments, and germination under the optimum temperature regimes individual species provides the best results for braking seed dormancy of rice spe cies.
Recurrent aspiration in children: Lipid‐laden alveolar macrophage quantitation

We prospectively evaluated bronchial washings from 45 patients aged 1 month to 25 years (mean 3.3 years) for the presence of lipid‐laden macrophages. By grading the amount of intracellular oil‐red‐O‐positive material, we determined a semiquantitative lipid‐laden macrophage index for each patient. All patients observed to be definite aspirators (n = 22) had indexes ≥86 (mean ± SD, 139 ± 46). All patients with no clinical suspicion of aspiration (n = 23) had indexes ⩽72 (mean ± SD, 21 ± 20). Our results suggest that simply sighting lipid‐laden macrophages is a nonspecific finding, but quantitation of these cells may be a very good test for recurrent aspiration of food substances in children. This test appears to be more sensitive than radiographic studies. Pediatr Pulmonol 1987; 3:89–89.
State of the Art of Low‐density Lipoprotein Apheresis in the Year 2003

Abstract: Low‐density lipoprotein (LDL) apheresis is a last‐resort treatment for hypercholesterolemic patients resistant to conservative lipid‐lowering therapy. In the extracorporeal circuit, LDL, Lp(a) and coagulation factors are selectively eliminated, while the beneficial proteins like high‐density lipoprotein, albumin and immunoglobulins are returned to the patient. Clinical effects of LDL apheresis comprise improvement of symptoms like angina and exercise tolerance, reduction of clinical coronary events like unstable angina, need for angioplasty or bypass operation, myocardial infarction and ultimately coronary mortality. The reduction of atherogenic lipoproteins and of coagulation factors by LDL apheresis (LA) positively influences hemorheology, endothelial function and coronary reserve. In the controlled LAARS, LA significantly improved the electrocardiographic signs of myocardial ischemia in the treadmill test. In angiographically controlled trials such as LARS and L‐CAPS, a reduction of progression of coronary lesions was observed; in favorable cases, regression of the stenoses could be documented. In addition, in the LDL apheresis coronary morphology trial, LA decreased the coronary plaque area. The Hokuriku trial documented a 72% decrease of coronary events (MACE) in the LA group vs. controls treated only by statins. In longitudinal studies, the incidence of MACE after regular LA decreased compared with the preapheresis period in the same patients. Apart from coronary heart disease, recent studies indicate a positive effect of LA also on carotid artery stenoses and peripheral vascular disease. Prospective randomized studies showed the beneficial effects of cascade filtration on age‐related macular degeneration and of heparin‐induced LDL precipitation apheresis on acute inner ear deafness.
Use of aripiprazole in tardive dyskinesia: An open label study of six cases

Aripiprazole, a partial dopamine agonist has been reported to help reduce symptoms of tardive dyskinesia (TD). In a prospective, open label study of a series of cases, we examined the effectiveness of aripiprazole in reducing TD symptoms. Six clinically stable patients with schizophrenia or Schizoaffective disorder and a moderate to severe TD participated in this study. They were systematically cross-titrated from their current medication to aripiprazole and maintained for 16 weeks. The mean extra pyramidal symptom score measured by Abnormal Involuntary Movement Scale (AIMS) improved from a baseline score of 15.8 to final score of 5 (paired t-test; P=0.0009). The severity of psychiatric symptoms remained unchanged. This study supports our hypothesis that clinically stable patients with moderate tardive dyskinesia who are under treatment with other first- or second-generation antipsychotics may benefit from switching to aripiprazole with a reduction of TD symptoms but with out any significant benefit in psychiatric symptoms. The results need to be viewed with caution and not considered as indicative of a viable treatment option for TD as this is an open label study, and a small sample size.
The inhibitory effects of rosiglitazone on cardiac hypertrophy through modulating the renin‐angiotensin system in diet‐induced hypercholesterolemic rats

Cardiac hypertrophy is not only an adaptational state before heart failure but also is an independent risk factor for ischemia, arrhythmia, and sudden death. However, the direct effects of hypercholesterolemia on the myocardium and mechanisms are not completely understood. It has been demonstrated that peroxisome proliferator‐activated receptor‐γ (PPARγ) ligand agonists attenuate cardiac hypertrophy through anti‐inflammatory effects. The present study investigated the effects of PPARγ agonists on hypercholesterolemia‐dependent, renin‐angiotensin‐system‐related cardiac hypertrophy. The findings showed that left ventricular hypertrophy, eminent cardiomyocyte hypertrophy, and lipid deposits in myocardium were observed in the rats fed a cholesterol‐rich diet for 6 months, while these characteristic pathological alterations and the increase in angiotensin II (ANG II) level and over‐expression of angiotensin II type 1 receptor (AT1R) in the left ventricular tissues induced by the cholesterol‐rich diet were significantly suppressed to equal extents by rosiglitazone and irbesartan. In contrast, expression of angiotensin II type 2 receptor (AT2R) was upregulated by these two drugs. In addition, lipid metabolism was markedly improved. The above findings suggest that the cardioprotection of the PPARγ agonist against cardiac hypertrophy evoked by hypercholesterolemia in rats is mediated partially by the improvement of lipid profile, the reduction of ANG II level in the local tissue along with the downregulation of AT1R expression, and upregulation of AT2R expression. Copyright © 2009 John Wiley & Sons, Ltd.
Thermophysical Properties Characterization of Microencapsulated Phase Change Material Slurry

Current chilled water systems require vast amount of water and pumping power to meet increasing cooling demands. Existing cooling and heating distribution systems have an inherent thermal capacity limitation (e.g., specific heat, mass flow rate, delta T), which is often neglected when adding new buildings to military, industrial or commercial facilities, resulting in higher equipment and infrastructure costs. Through the use of an advanced material concept, namely Microencapsulated Phase Change Materials (MPCM), performance enhancement of an improved heat transfer fluid is now being pursued. This paper discusses the status of experimental efforts using a linear alkane phase change material intended for a secondary coolant for space cooling applications. Initial quantitative characterization of MPCM material properties including latent heat of fusion, melting and freezing points, and temperature- and concentration-dependent viscosity data are presented. State-of-the-art equipment was used to characterize the MPCM slurry including the use of a differential scanning calorimeter and a temperature-controlled concentric viscometer. Results indicate that the freezing and melting points of microencapsulated n-Tetradecane differed by 5° C or more when no effective nucleating agent was used. Current efforts have yielded the identification of a very effective nucleating agent, which can suppress supercooling almost entirely. Other experimental results indicate that MPCM slurry viscosity significantly depends not only on volume fraction but also on temperature, which can have an impact on the heat transfer process. MPCM slurry has the potential to become a successful heat transfer fluid, which may result in significant energy and cost savings.
Volume regulation in leukocytes: Requirement for an intact cytoskeleton

Animal cells regulate their volume by controlling the flux of ions across their plasma membrane. Recent evidence suggests that ion channels and pumps are physically associated with, and may be regulated by components of the cytoskeleton. To elucidate the role of elements of the cytoskeleton in volume regulation, we studied the effects of cytoskeletal disrupting agents on regulatory volume decrease (RVD) in three different leukocyte types: Jurkat lymphoma cells, HL‐60 cells, and human peripheral blood neutrophils. Cell volume was measured in two ways: (i) electronically with a Coulter counter and (ii) by forward light scattering in a flow cytometer. Exposure of all leukocyte types to hypotonic medium (200 mOsm) resulted in an immediate increase in cell volume followed by a regulatory decrease to baseline by 20 min. In the presence of the microtubule disrupting agents, colchicine and nocodazole, RVD was totally inhibited which corresponded to loss of microtubules as determined by immunofluorescence. Similarly, RVD was inhibited in Jurkat cells incubated with the actin binding agents, cytochalasin B (CB) or D (CD). In contrast, in HL‐60 cells and human neutrophils, RVD was unaffected by treatment with either CB or CD. While cytochalasins are generally thought of as microfilament disrupting agents, their primary action is to prevent F‐actin polymerization. The extent of ensuing microfilament disruption depends in part on the rate of filament turnover. In an attempt to understand the differential effects of the cytochalasins on RVD, the F‐actin content of the different cells was determined by NBD‐phallacidin staining and flow cytometry. Pretreatment with CB or CD resulted in profound actin disassembly in Jurkat cells (relative fluorescence index RFI: 1.0 control vs. 0.21 ± 0.01 for CB and 0.48 ± 0.02 for CD). However, the cytochalasins did not induce net disassembly in either HL‐60 cells or human neutrophils. To study the effects of an increase in F‐actin on volume regulation, neutrophils were treated with the chemoattractant f‐Met‐Leu‐Phe or with an antibody (Ab) to β2 integrins followed by a cross‐linking secondary Ab. Despite an increase in F‐actin in both circumstances, RVD remained intact. Taken together, these results suggest that both microtubules and microfilaments are important in volume regulation. © 1995 Wiley‐Liss, Inc.
Association of COL1A1 and otosclerosis: evidence for a shared genetic etiology with mild osteogenesis imperfecta.

HYPOTHESIS Otosclerosis is related to mild osteogenesis imperfecta with genetic defects in type I collagen. BACKGROUND Otosclerosis is a common bone disease of the human otic capsule that has an underlying hereditary predisposition. The histopathology and clinical manifestations are strikingly similar to the milder forms of osteogenesis imperfecta in which mutations of type I collagen genes have been established as the underlying cause. METHODS The authors investigated the genetic basis of otosclerosis by conducting an association study using polymorphic DNA markers from patients with clinical otosclerosis and random control subjects. RESULTS This study showed a significant association between clinical otosclerosis and the type I collagen COL1A1 gene using three different polymorphic markers within the gene. CONCLUSIONS Some cases of clinical otosclerosis may be related to mutations within the COL1A1 gene that are similar to those found in mild forms of osteogenesis imperfecta and result in null expression of the mutant allele.
Gender and Ethnic Differences in Health Beliefs and Behaviors

This study explored the extent to which college men and women of various racial and ethnic groups differ in their health beliefs and behaviors. Exploratory factor analyses of survey responses from a diverse sample of 1816 undergraduate students identified 21 items in six cohesive domains: Diet; Anger and Stress; Preventive Care; Medical Compliance; Substance Use; and Beliefs about Masculinity. Analyses of variance explored group differences across these domains. Findings revealed consistent gender differences, with men engaging in riskier behaviors and holding riskier beliefs than women. Main effects for ethnicity were also observed, but only for the diet domain was a gender by ethnicity interaction found. Implications for establishing gender- and ethnicity-based health promotion and disease prevention interventions are discussed.
EXPERT: A System for Developing Consultation Models

EXPERT Is a system for designing and building models for consultation. An EXPERT model consists of hypotheses (which can be structured Into causal and taxonomic networks); findings or observations; and decision rules for logically relating these components. A relatively simple language for describing models is employed. Logical and probabilistic rules are restricted to particular types which implicitly order the tasks performed by the control strategies: classification, question selection, and explanation. Explicit representations of decision rules are emphasized, as opposed to suboptimal scoring functions. This results in more easily predictable and correctable performance for a model. The system is currently being used to develop consultation models in domains such as rheumatology, ophthalmology, and endocrinology.