Miracle-dz/UniFAR-FTUs huggingface dataset:
Intercohort Gene Expression Co-Analysis Reveals Chemokine Receptors as Prognostic Indicators in Ewing's Sarcoma

Purpose: We report a novel analytic method, named intercohort co-analysis or Ican, which aids in the discovery of genes with predictive value for the progression or outcome of diseases from small-size cohorts. We tested this premise in Ewing's sarcoma (ES), a highly metastatic cancer of bone and soft tissues that lacks validated molecular metastasis and prognostic indicators. Experimental Design: To uncover genes significantly expressed in ES patient subsets, we first determined a nonarbitrary gene expression significance cutoff based on expression levels in validated expressing and nonexpressing tissues. We next searched for genes that were consistently significantly expressed in several ES cohort and cell line datasets. Significantly expressed genes were independently validated by quantitative reverse transcription-PCR in an additional ES cohort. Results: Analysis of ES cohorts revealed marked intercohort gene expression variability. After filtering out the intercohort variability, CXCR4 and CXCR7 were found to be consistently associated with specific ES subsets. Pairwise analyses showed CXCR4 to correlate with ES metastases, and CXCR4 and CXCR7 to patient survival, but not with several other clinicopathological variables. Conclusion: Ican is a powerful novel method to identifying genes consistently associated with particular disease states in cancers for which large cohorts are not available, currently the case of most cancers. We report for the first time that high CXCR4 expression preferentially associates with metastatic ES, and that of CXCR7 with poor patient survival. Clin Cancer Res; 16(14); 3769–78. ©2010 AACR.
Nasal Carriage of Methicillin-Resistant Staphylococcus aureus Among Patients With End-Stage Renal Disease

Infections due to methicillin-resistant Staphylococcus aureus (MRSA) are associated with high morbidity and mortality among patients with end-stage renal disease. MRSA often colonizes the anterior nares and disseminates to infect other parts of the body; among end-stage renal disease patients undergoing long-term dialysis, these sites include vascular access sites. Recognition and isolation of persons either colonized or infected with MRSA is recommended, to minimize the spread of MRSA within hospitals. Recent guidelines published by the Society for Healthcare Epidemiology of America recommend that surveillance culture be performed at the time of hospital admission for patients at high risk of MRSA carriage. However, there is limited data on MRSA colonization in end-stage renal disease patients. Community-associated MRSA strains usually carry the staphylococcal cassette chromosome mec type IV or V (SCCmec IV or V) complex and often have the genes for the Panton-Valentine leukocidin (PVL) toxin. Healthcare-associated MRSA strains typically carry SCCmec types I, II, or III and lack the genes for PVL. Previous MRSA infections among dialysis patients are considered to be healthcare associated, which means that infecting strains in this population will more closely resemble the healthcare-associated MRSA strains. Nevertheless, recently some papers pointed out that community-associated MRSA strains have been found more frequently than healthcare-associated MRSA strains among end-stage renal disease patients. ' Therefore, the objective of this study was to determine the prevalence of MRSA colonization among end-stage renal disease patients and the molecular characteristics of colonizing isolates recovered from these patients.
Digital Commons @ University of South Florida Digital Commons @ University of South Florida

Countries that rely on natural resource rents (that is, the revenue generated from the sale of natural resources) may suffer from a variety of social problems. This exploratory study reviews the natural resource extraction literature to derive a ‘natural resource rents–homicide’ hypothesis. Data for 173 countries for the years 2000 to 2012 are examined to determine if there is a correlation between natural resource rents and homicide rates. Multilevel growth models suggest that natural resource rents are positively correlated with homicide rates within countries (level 1) but not between them (level 2). Importantly, the correlation between natural resource rents and homicide is strongest when natural resource rents are lagged. We conclude by suggesting that increasing natural resource rents may be counterproductive over the long run and sow the seeds for a future increase in homicide.
The induction of HIF‐1 reduces astrocyte activation by amyloid beta peptide

Reduced glucose metabolism and astrocyte activation in selective areas of the brain are pathological features of Alzheimer’s disease (AD). The underlying mechanisms of low energy metabolism and a molecular basis for preventing astrocyte activation are not, however, known. Here we show that amyloid beta peptide (Aβ)‐dependent astrocyte activation leads to a long‐term decrease in hypoxia‐inducible factor (HIF)‐1α expression and a reduction in the rate of glycolysis. Glial activation and the glycolytic changes are reversed by the maintenance of HIF‐1α levels with conditions that prevent the proteolysis of HIF‐1α. Aβ increases the long‐term production of reactive oxygen species (ROS) through the activation of nicotinamide adenine dinucleotide phosphate oxidase and reduces the amount of HIF‐1α via the activation of the proteasome. ROS are not required for glial activation, but are required for the reduction in glycolysis. These data suggest a significant role for HIF‐1α‐mediated transcription in maintaining the metabolic integrity of the AD brain and identify the probable cause of the observed lower energy metabolism in afflicted areas. They may also explain the therapeutic success of metal chelators in animal models of AD.
VerSE: towards hypertext versioning styles

Much of the previous work on version support for hypertext has focused primarily on the development of functionality for specific hypertext systems and/or a specific hypertext ap plication domain. Although these models address crucial version support problems in specific hypertext application domains, they cannot be easily adapted and then integrated into other hypertext applications. Hypertext version support environments have been introduced to help alleviate these problems. They are de signed to meet the version support needs of a wide range of hypertext applications. However , so far few high level versioning facilities have been constructed in these environ ments, creating a gap between the facilities provided direct ly within the environment and the versioning needs of some applications. The intent of this research is to bridge this gap. It turned out that task-based versioning styles are easy to use by both hy pertext application developers and hypertext application us ers. As shown in previous work, task-based versioning helps to alleviate cognitive overhead and disorientation problems for users. In addition, it requires little investment from the point of view of application development, since task-based versioning does not necessarily require an application to in corporate an extra notion for individual versions. This paper presents a set of task-based hypertext versioning styles that are offered in the VerSE flexible version support environ ment and shows the direction towards the design of addition al versioning styles.
EARLY SONOGRAPHIC DIAGNOSIS OF FETAL SMALL LEFT HEART VENTRICLE WITH A NORMAL PROXIMAL OUTLET TRACT: A MEDICAL DILEMMA

A small left heart ventricle with a normal outflow tract was detected by transvaginal ultrasound in 16 fetuses at 14–16 weeks' gestation. A high incidence of associated anomalies was found in these fetuses, namely coarctation of the aorta (5), abnormal karyotype (4), cystic hygroma (4), and ventricular septal defect (3). The incidence of extracardiac anomalies was probably even higher, since post‐mortem and karyotpye examinations were not performed in all cases of termination of pregnancy. In patients who decided to continue the pregnancy (7), a normal left ventricle was observed in four cases on follow‐up scans. Three of these neonates were normal after delivery and one had several cardiovascular anomalies. Out of three fetuses with asymmetric ventricles on follow‐up scan, one infant had a normal outcome. The high incidence of associated fetal anomalies in cases of a small left ventricle raises a medical dilemma in counselling the parents. © 1997 by John Wiley & Sons, Ltd.
Long-term surgical results in microvascular decompression for hemifacial spasm: efficacy, morbidity and quality of life

SUMMARY Hemifacial spasm is a condition that may severely reduce patients' quality of life. Microvascular decompression is the neurosurgical treatment of choice. The objective of this work was to describe the efficacy and morbidity of microvascular decompression for hemifacial spasm, evaluate the long-term efficacy on the quality of life and investigate prognostic factors for failure of the procedure. A retrospective study of 446 cases of hemifacial spasm treated by 511 retrosigmoid microvascular decompression over 22 years was conducted. Epidemiological, clinical and imaging findings, treatment modalities and outcomes of patients with pre- and postoperative HSF-8 quality of life questionnaire were studied. Success rate was 82% after first surgery and 91.6% after revision surgery. A low rate of perioperative morbidity was found. Facial palsy was mostly transient (5.5% transient and 0.2% permanent) and cochleovestibular deficit was seen in 4.8% of patients. Revision surgery increased nervous lesions (10.6% to 20.7%). Mean quality of life scores were significantly improved from 18 to 2 over 32, evaluated 7.3 years after surgery. Predictive factors of surgical failure were single conflicts (p = 0.041), atypical vasculo-nervous conflicts involving other vessel than postero-inferior cerebellar artery (p = 0.036), such as vein (p = 0.045), and other compression sites than root exit zone (p = 0.027). Retrosigmoid microvascular decompression is a safe and effective treatment of hemifacial spasm. Revision surgery is not to be excluded in case of failure, but does place patients at risk for more complications. Quality of life is improved in the long-term, indicating objective and subjective satisfaction.
A new accurate and precise 3-D segmentation method for skeletal structures in volumetric CT data

We developed a highly automated three-dimensionally based method for the segmentation of bone in volumetric computed tomography (CT) datasets. The multistep approach starts with three-dimensional (3-D) region-growing using local adaptive thresholds followed by procedures to correct for remaining boundary discontinuities and a subsequent anatomically oriented boundary adjustment using local values of cortical bone density. We describe the details of our approach and show applications in the proximal femur, the knee, and the skull. The accuracy of the determination of geometrical parameters was analyzed using CT scans of the semi-anthropomorphic European spine phantom. Depending on the settings of the segmentation parameters cortical thickness could be determined with an accuracy corresponding to the side length of 1 to 2.5 voxels. The impact of noise on the segmentation was investigated by artificially adding noise to the CT data. An increase in noise by factors of two and five changed cortical thickness corresponding to the side length of one voxel. Intraoperator and interoperator precision was analyzed by repeated analysis of nine pelvic CT scans. Precision errors were smaller than 1% for trabecular and total volumes and smaller than 2% for cortical thickness. Intraoperator and interoperator precision errors were not significantly different. Our segmentation approach shows: 1) high accuracy and precision and is 2) robust to noise, 3) insensitive to user-defined thresholds, 4) highly automated and fast, and 5) easy to initialize.
Transvascular Low-Density Lipoprotein Transport in Patients With Diabetes Mellitus (Type 2): A Noninvasive In Vivo Isotope Technique

Objective—The increased risk of atherosclerosis associated with diabetes cannot be explained by conventional cardiovascular risk factors alone. We hypothesized that transvascular lipoprotein transport may be increased in patients with diabetes, possibly explaining increased intimal lipoprotein accumulation and, thus, atherosclerosis. Methods and Results—We developed an in vivo method for measurement of transvascular transport of low density lipoprotein (LDL) and applied it in 16 patients with maturity-onset diabetes (type 2) and 29 healthy control subjects. Autologous 131I-labeled LDL was reinjected intravenously in addition to 125I-labeled albumin, and the 1-hour fractional escape rates were taken as indices of transvascular transport. Both parameters were normally distributed, and they were tightly correlated (R2=0.69, P <0.0001). Transvascular LDL transport was 5.4±2.9%/h and 4.1±1.5%/h in patients with diabetes and control subjects, respectively (P <0.05); equivalent values for albumin were 6.5±2.5%/h and 5.3±1.6%/h (P <0.05). This difference most likely was not caused by altered hepatic LDL receptor expression, glycosylation of LDL, small LDL size, nephropathy, statin use, or different plasma insulin levels in diabetic patients. Conclusions—Transvascular LDL transport may be increased in patients with type 2 diabetes. This suggests that lipoprotein flux into the arterial wall is increased in people with diabetes, possibly explaining the accelerated development of atherosclerosis.
Temperature dependence of magnetic properties of AF-biased CoFe films with high FMR

We investigate the temperature dependence of static and dynamic magnetic properties of AF/F/AF multilayers consisting in NiMn as AF-layer and Co/sub 90/Fe/sub 10/, Co/sub 50/Fe/sub 50/ and Co/sub 35/Fe/sub 65/ as F-layer, respectively. The T-dependences of the hysteresis loops have been analyzed in relation with the corresponding microwave permeability spectra. The results indicate a lowering of both the exchange bias (Hex) and the anisotropy field (Hk dc) above 150/spl deg/C, in agreement with blocking temperature considerations from literature. However, microwave characterizations show better high temperature stability, with a shift of ferromagnetic resonance frequency less than 20% up to 300/spl deg/C. This reveals a strong discrepancy between the anisotropy field from the static and dynamic measurements including the T-dependence. Finally, this work points out unexpected excellent temperature stability up to 300/spl deg/C proving that such multilayers are available for future use in RF devices at very high frequencies.
Implementing elements of a context-adapted chronic care model to improve first-line diabetes care: effects on assessment of chronic illness care and glycaemic control among people with diabetes enrolled to the First-Line Diabetes Care (FiLDCare) Project in the Northern Philippines

Aim The purpose of this study was to investigate the effects of implementing elements of a context-adapted chronic disease-care model (CACCM) in two local government primary healthcare units of a non-highly urbanized city and a rural municipality in the Philippines on Patients’ Assessment of Chronic Illness Care (PACIC) and glycaemic control (HbA1c) of people with diabetes. Background Low-to-middle income countries like the Philippines are beset with rising prevalence of chronic conditions but their healthcare systems are still acute disease oriented. Attention towards improving care for chronic conditions particularly in primary healthcare is imperative and ways by which this can be done amidst resource constraints need to be explored. Methods A chronic care model was adapted based on the context of the Philippines. Selected elements (community sensitization, decision support, minor re-organization of health services, health service delivery-system re-design, and self-management education and support) were implemented. PACIC and HbA1c were measured before and one year after the start of implementation. Findings The improvements in the PACIC (median, from 3.2 to 3.5) as well as in four of the five subsets of the PACIC were statistically significant (P-values: PACIC=0.009; ‘patient activation’=0.026; ‘goal setting’=0.017; ‘problem solving’<0.001; ‘follow-up’<0.001). The decrease in HbA1c (median, from 7.7% to 6.9%) and the level of diabetes control of the project participants (increase of optimally controlled diabetes from 37.2% to 50.6%) were likewise significant (P<0.000 and P=0.014). A significantly higher rating of the post-implementation PACIC subsets ‘problem solving’ (P=0.027) and ‘follow-up’ (P=0.025) was noted among those participants whose HbA1c improved. The quality of chronic care in general and primary diabetes care in particular may be improved, as measured through the PACIC and glycaemic control, in resource-constrained settings applying selected elements of a CACCM and without causing much strain on an already-burdened healthcare system.
Population dynamics of Cytophaga-Flavobacteria during marine phytoplankton blooms analyzed by real-time quantitative PCR

We analyzed the dynamics of the Cytophaga-Flavobacterium (CF) cluster during a Thalassiosira sp. -dominated diatom bloom in a mesocosm and a coastal bloom of the dinoflagellate Lingulodinium polyedrum using quantitative (TaqMan) PCR. Particle colonization was tracked by quantifying CF small subunit (SSU) rDNA copies as a percentage of total bacterial SSU rDNA copies in operationally defined free-living ( ca. 1.0 µm) size fractions. During both blooms, the percentage of CF rDNA in the free-living fraction was greater than in the particle-associated fraction, yet ranged widely from almost undetectable to 10-40% of total SSU rDNA. The percentage of CF rDNA copies in the attached fraction was low overall (≤3.2% of total), except at the chl a peak of the dinoflagellate bloom when CF rDNA copies comprised >50% of the total bacterial SSU rDNAs in that fraction. In addition, the timing of peaks in attached CF differed between blooms, occurring at the peak in chlorophyll a for the dinoflagellate bloom, but during the detrital phase of the diatom bloom. Our data suggests that different bloom types may encourage different attachment responses by CF and indicate that high abundance of CF during a phytoplank- ton bloom is transient in nature, with shifts in abundance and group composition occurring on the order of 1 d to a few days.
Production of 10-Ketostearic Acid from Oleic Acid by Flavobacterium sp. Strain DS5 (NRRL B-14859)

A microbial isolate, Flavobacterium sp. strain DS5, produces 10-ketostearic acid (10-KSA) from oleic acid in 85% yield. This is the first report on this type of reaction catalyzed by a Flavobacterium strain. The product was purified to give white, plate-like crystals melting at 79.2°C. The optimum time, pH, and temperature for the production of 10-KSA are 36 h, 7.5, and 30°C, respectively. A small amount of 10-hydroxystearic acid (10-HSA) (about 10% of the amount of the main product, 10-KSA) is also produced during the bioconversion. 10-KSA is not further metabolized by strain DS5 and accumulates in the medium. In contrast to growing cells, a resting-cell suspension of strain DS5 produces 10-HSA and 10-KSA in a ratio of 1:3. The crude cell extract obtained from ultrasonic disruption of the cells converts oleic acid mainly to 10-HSA (10-HSA/10-KSA ratio, 97:3). This result strongly suggested that oleic acid is converted to 10-KSA via 10-HSA. Enzymes catalyzing the hydration and secondary alcohol dehydrogenation are cell associated. Product 10-HSA from strain DS5 is 66% enantiomeric excess in the 10(R) form. The oleic acid conversion enzyme(s) reacts with unsaturated fatty acids in the order oleic acid > palmitoleic acid > linoleic acid > linolenic acid > γ-linolenic acid > myristoleic acid.
The Neural Correlate of Speech Rhythm as Evidenced by Metrical Speech Processing

The present study investigates the neural correlates of rhythm processing in speech perception. German pseudosentences spoken with an exaggerated (isochronous) or a conversational (nonisochronous) rhythm were compared in an auditory functional magnetic resonance imaging experiment. The subjects had to perform either a rhythm task (explicit rhythm processing) or a prosody task (implicit rhythm processing). The study revealed bilateral activation in the supplementary motor area (SMA), extending into the cingulate gyrus, and in the insulae, extending into the right basal ganglia (neostriatum), as well as activity in the right inferior frontal gyrus (IFG) related to the performance of the rhythm task. A direct contrast between isochronous and nonisochronous sentences revealed differences in lateralization of activation for isochronous processing as a function of the explicit and implicit tasks. Explicit processing revealed activation in the right posterior superior temporal gyrus (pSTG), the right supramarginal gyrus, and the right parietal operculum. Implicit processing showed activation in the left supramarginal gyrus, the left pSTG, and the left parietal operculum. The present results indicate a function of the SMA and the insula beyond motor timing and speak for a role of these brain areas in the perception of acoustically temporal intervals. Secondly, the data speak for a specific task-related function of the right IFG in the processing of accent patterns. Finally, the data sustain the assumption that the right secondary auditory cortex is involved in the explicit perception of auditory suprasegmental cues and, moreover, that activity in the right secondary auditory cortex can be modulated by top-down processing mechanisms.
Haptoglobin Phenotypes distribution among Sickle Cell anemia patients with different genotypes

Introduction; Sickle cell anemia (SCA) is a haemoglobinopathy due to single point mutation in the β chain of human haemoglobin. Sickle cell anemia is a form of haemolytic anemia, and it provides the most well documented example of acute and chronic haemolysis, which leads to acute crisis and may develop frequently of infections, and acute chest syndrome. Haptoglobin (Hp) is a unique acute phase protein that primarily scavenges haemoglobin released into circulation by haemolysis. Materials and Methods; Across sectional study was done to determine and compare the frequency of haptoglobin phenotypes among Sudanese patients with sickle cell anemia (SS), and sickle cell trait (AS). A 100 Sudanese patients were recruited in this study after informed consent; and diagnosed by SCA, based on their clinical evaluation, Sickling test, complete blood count (CBC), and Hb electrophoresis. Patient's age was range between 2 to 45 years. An EDTA venous blood was collected from each patient for haptoglobin phenotypes. Hp phenotypes have been performed by PAGE (Poly-acrylamide-gel-electrophoresis) protocol. Results and discussion; To our Knowledge, this study was the first among Sudanese with SCA patients. It appeared that Hp1-1 was taking the high percent (59%) in distribution between the patients. There was high frequency of haptoglobin phenotype 1-1 among