Miracle-dz/UniFAR-FTUs huggingface dataset:
The Impact of HIV Infection and CD4 Cell Count on the Performance of an Interferon Gamma Release Assay in Patients with Pulmonary Tuberculosis

Background The performance of the tuberculosis specific Interferon Gamma Release Assays (IGRAs) has not been sufficiently documented in tuberculosis- and HIV-endemic settings. This study evaluated the sensitivity of the QuantiFERON TB-Gold In-Tube (QFT-IT) in patients with culture confirmed pulmonary tuberculosis (PTB) in a TB- and HIV-endemic population and the effect of HIV-infection and CD4 cell count on test performance. Methodology/Principal Findings 161 patients with sputum culture confirmed PTB were subjected to HIV- and QFT-IT testing and measurement of CD4 cell count. The QFT-IT was positive in 74% (119/161; 95% CI: 67–81%). Sensitivity was higher in HIV-negative (75/93) than in HIV-positive (44/68) patients (81% vs. 65%, p = 0.02) and increased with CD4 cell count in HIV-positive patients (test for trend p = 0.03). 23 patients (14%) had an indeterminate result and this proportion decreased with increasing CD4 cell count in HIV-positive patients (test for trend p = 0.03). Low CD4 cell count (<300 cells/µl) did not account for all QFT-IT indeterminate nor all negative results. Sensitivity when excluding indeterminate results was 86% (95% CI: 81–92%) and did not differ between HIV-negative and HIV–positive patients (88 vs. 83%, p = 0.39). Conclusions/Significance Sensitivity of the QFT-IT for diagnosing active PTB infection was reasonable when excluding indeterminate results and in HIV-negative patients. However, since the test missed more than 10% of patients, its potential as a rule-out test for active TB disease is limited. Furthermore, test performance is impaired by low CD4 cell count in HIV-positive patients and possibly by other factors as well in both HIV-positive and HIV-negative patients. This might limit the potential of the test in populations where HIV-infection is prevalent.
Cell cycle progression dictates the requirement for BCL2 in natural killer cell survival

Natural killer (NK) cells are innate lymphoid cells with antitumor functions. Using an N-ethyl-N-nitrosourea (ENU)–induced mutagenesis screen in mice, we identified a strain with an NK cell deficiency caused by a hypomorphic mutation in the Bcl2 (B cell lymphoma 2) gene. Analysis of these mice and the conditional deletion of Bcl2 in NK cells revealed a nonredundant intrinsic requirement for BCL2 in NK cell survival. In these mice, NK cells in cycle were protected against apoptosis, and NK cell counts were restored in inflammatory conditions, suggesting a redundant role for BCL2 in proliferating NK cells. Consistent with this, cycling NK cells expressed higher MCL1 (myeloid cell leukemia 1) levels in both control and BCL2-null mice. Finally, we showed that deletion of BIM restored survival in BCL2-deficient but not MCL1-deficient NK cells. Overall, these data demonstrate an essential role for the binding of BCL2 to BIM in the survival of noncycling NK cells. They also favor a model in which MCL1 is the dominant survival protein in proliferating NK cells.
2‐D protein maps of rat gastrocnemius and soleus muscles: A tool for muscle plasticity assessment

Functional characterization of muscle fibers relies on ATPase activity and on differential measurements of metabolic proteins, including mitochondrial and glycolytic enzymes, glucose, lactate and lactic acid transporters, calcium cycling proteins and components of the contractile machinery. The recent introduction of microarray technology has enabled detailed gene expression studies under different physiological and pathological conditions, thus generating novel hypotheses on muscle function. However, microarray approaches are limited by the incomplete genome coverage of currently available chips, and by poor correlation between mRNA concentration and protein expression level. We have used 2‐DE and MS to build a reference map of proteins from rat mixed gastrocnemius and soleus muscle, and to assess qualitative and quantitative differences in protein distribution between these two functionally dissimilar muscles. More than 800 spots on each gel were detected by silver staining, of which 167 were excised, digested in‐gel with trypsin and analyzed by ESI‐MS/MS. One hundred and twenty eight distinct gene products were identified, including metabolic, transport and contractile proteins. Forty one spots displayed differences in relative expression level between mixed gastrocnemius and soleus samples. These data not only enable differentiation of functionally distinct slow‐twitch and fast‐twitch fiber types, but also provide tools for investigating muscle plasticity in response to physiological and environmental conditions such as aging or hypoxia.
Do Non-Financial Stakeholders Affect the Pricing of Risky Debt? Evidence from Unionized Workers

The authors study the impact of a powerful nonfinancial stakeholder--unionized workers--on the pricing of corporate debt. Firms in more unionized industries have lower bond yields. This relation is stronger in firms with weaker financial conditions and cannot be explained by the correlation of unionization with industry characteristics, governance mechanisms, or financial leverage. Firms in unionized industries implement less risky investment policies and are less likely targets of acquisitions. Unionization reduces yields by more when firms' takeover barriers are lower. Hence, unions are viewed favorably in the bond market because, through their influence on corporate affairs, they protect bondholders' wealth. Copyright 2011, Oxford University Press.
A Novel Wire-Density-Driven Full-Chip Routing System for CMP Variation Control

As nanometer technology advances, the post chemical-mechanical polishing (CMP) topography variation control becomes crucial for manufacturing closure. To improve the CMP quality, dummy-feature filling is typically performed by foundries after the routing stage. However, filling dummy features may greatly degrade the interconnect performance and significantly increase the input data in the following time-consuming reticle enhancement techniques. It is, thus, desirable to consider wire-density uniformity during routing to minimize the side effects from aggressive post-layout dummy filling. In this paper, we present a new full-chip grid-based routing system considering wire density for reticle planarization enhancement. To fully consider a wire distribution, the router applies a novel two-pass top-down planarity-driven routing framework, which employs new density critical area analysis based on Voronoi diagrams and incorporates an intermediate stage of a density-driven layer/track assignment based on incremental Delaunay triangulation. Experimental results show that our methods can achieve a more balanced wire distribution than state-of-the-art works.
Brain Injury

The brain serves as the control center for all of the body's functions including conscious activities (walking and talking) and unconscious ones (breathing, heart rate, etc.). The brain also controls thought, comprehension, speech and emotion. Injury to the brain, whether the result of severe head trauma or a closed head injury in which there is no fracture or penetration of the skull, can disrupt some or all of these functions.
Experimental Validation of a New Distributed Cooperative Control Algorithm for Multi-agent Systems with Switching Communication Topologies and Time-Delays

In this thesis, we present practical experimental results to demonstrate a control law for consensus of multiagent systems with switching topologies and time delays. The nonlinear control law utilizes discontinuous cooperative control gains and uses contraction mapping to achieve consensus of multiagent systems. The testing platform we used consists of a number of mobile robots and software simulations both in Matlab and Microsoft Studio C++. We present the effectiveness of the control law design by Aria mobile robots with applications in distributed cooperative formation control. Computer simulations and hardware experiments presented include point consensus control and formation control, both with changing topologies and time-delays. In addition to 2D simulations and experiments, we also developed the 3D model for more practical applications, such as Unmanned Aerial Vehicles (UAVs) and Autonomous Underwater vehicles (AUVs). The research presented was supported by Air Force Research Laboratory / Information Directorate (AFRL/RI)’s Machine Intelligence for Mission Focused Autonomy program. The research presented in this thesis was included in multiple presentations to AFRL program managers, who provided very favorable feedback to our research. Recently, some of our research results was published in the proceedings of 2014 IEEE International Conference on Electro/Information Technology [1], and the paper received Best Paper Award at the conference. In addition, a poster presentation describing our research was made to ERAU College of Engineering’s Industry Advisory Board. The process of implementing the research results in AUVs has also been progressing significantly. Upon invitation, some hardware tests were performed as part of NASA NEEMO 19 (Extreme Environment Mission Operations) experiments, and were subsequently reported twice in the headlines of the Science and Education section in the Daytona Beach News Journal. Technical papers describing proposed cooperative control in AUVs were submitted to 2015 ACM and IEEE conferences.
Research to Understand Milk Consumption Behaviors in a Food-Insecure Low-Income SNAP Population in the US

Milk, due to its affordability and nutritional value, can fortify the diets of families that experience food insecurity or find a high-quality diet cost-prohibitive. However, it can also be a leading source of excess calories and saturated fat. Yet, little is known about what influences consumer behavior of Supplemental Nutrition Assistance Program (SNAP) recipients toward the type of milk used or the prevalence of low-fat milk use among this population. This cross-sectional telephone survey of SNAP recipients (n = 520) documented that 7.5% of this population usually consumes low-fat milk, a prevalence that lags behind national figures (34.4%) for the same time-period. There was a weak association between sociodemographic characteristics of SNAP recipients and low-fat milk use. Instead, less low-fat milk consumption was associated with a knowledge gap and misperceptions of the nutritional properties of the different types of milk. Promoting low-fat milk use by correcting these misperceptions can improve the diet of America’s low-income population and reduce food insecurity by maximizing the nutritional value of the foods consumed.
Cannabinoid CB2 receptor expression in the rat brainstem cochlear and vestibular nuclei

Conclusion. This evidence suggests that both CB1 and CB2 receptors are important in the control of balance and hearing. Objective. Although the cannabinoid CB1 receptor has been identified in the brainstem vestibular and cochlear nuclei, the existence of the second cannabinoid receptor subtype, the CB2 receptor, has been more controversial. The aim of this study was to determine whether or not CB2 receptors are expressed in the vestibular and cochlear nuclei. Materials and methods. Data were obtained from four young male Wistar rats In analyzing the presence of CB2 receptors in the vestibular and cochlear nuclei, the immunohistochemical complex was visualized by exposure to diaminobenzidine for 20 min. Positive immunoreactivity to CB2 was expressed as brown staining in the cytoplasm, nucleus, nuclear membrane and cell membrane. Results. We confirmed the existence of the CB2 receptor in the vestibular and cochlear nuclei in the brainstem of Wistar rats.
Early parental death and remarriage of widowed parents as risk factors for Alzheimer disease: the Cache County study.

OBJECTIVES Early parental death is associated with lifelong tendencies toward depression and chronic stress. We tested the hypothesis that early parental death is associated with higher risk for Alzheimer disease (AD) in offspring. DESIGN A population-based epidemiological study of dementia with detailed clinical evaluations, linked to one of the world's richest sources of objective genealogical and vital statistics data. SETTING Home visits with residents of a rural county in northern Utah. PARTICIPANTS 4,108 subjects, aged 65-105. MEASUREMENTS Multistage dementia ascertainment protocol implemented in four triennial waves, yielding expert consensus diagnoses of 570 participants with AD and 3,538 without dementia. Parental death dates, socioeconomic status, and parental remarriage after widowhood were obtained from the Utah Population Database, a large genealogical database linked to statewide birth and death records. RESULTS Mother's death during subject's adolescence was significantly associated with higher rate of AD in regression models that included age, gender, education, APOE genotype, and socioeconomic status. Father's death before subject age 5 showed a weaker association. In stratified analyses, associations were significant only when the widowed parent did not remarry. Parental death associations were not moderated by gender or APOE genotype. Findings were specific to AD and not found for non-AD dementia. CONCLUSIONS Parental death during childhood is associated with higher prevalence of AD, with different critical periods for father's versus mother's death, with strength of these associations attenuated by remarriage of the widowed parent.
Posterior-approach Vertebral Replacement With Rectangular Parallelepiped Cages (PAVREC) for the Treatment of Osteoporotic Vertebral Collapse With Neurological Deficits

Study Design: A retrospective clinical study. Objective: To assess the efficacy of a new spinal reconstruction technique (posterior-approach vertebral replacement with rectangular parallelepiped cages: PAVREC) for the treatment of osteoporotic late vertebral collapse with neurological deficits. Summary of Background Data: Poor bone quality and medically complicated situations obfuscate precise treatment for paraplegia caused by osteoporotic vertebral collapse. Recently, posterior-approach corpectomy and replacement with a cylindrical cage have been proposed. However, postoperative cage subsidence and kyphosis progression frequently occurs. Methods: Surgical invasiveness, perioperative complications, and clinical and radiographic outcomes in a total of 19 consecutive patients with osteoporosis (7 men and 12 women; mean age, 75 y) who underwent PAVREC with a mean follow-up period of 45.6 months (range, 16–79 mo) were reviewed. The affected vertebral levels ranged from T12–L4. The mean bone mineral density of the femoral neck was 0.611±0.077 g/cm2 (mean±SD). Results: Mean operative time was 261 minutes (range, 155–326 min). Mean blood loss was 664 mL (range, 197–1595 mL). There were no reported surgical complications. Neurological deficits evaluated with the Frankel grading score improved >1 grade after surgery in all patients. Mean preoperative visual analog scale scores for back or leg pain (7.2; range, 6–9) significantly improved after surgery (1.4; range, 0–2) (P<0.05). Local kyphosis improved from a mean of 24.6 degrees before surgery to a mean of 1.5 degrees after surgery (P<0.05), and it was maintained at a mean of 2.5 degrees at the final follow-up. Although screw loosening, cage subsidence, and subsequent vertebral fracture were seen in several cases, no additional surgeries were needed. Solid bony fusion was confirmed in all cases. Conclusions: PAVREC provided a satisfactory clinical and radiologic outcome without severe complications. This procedure can be a treatment option for osteoporotic vertebral collapse and an alternative to an anterior-approach or single posterior-approach reconstruction with a cylindrical cage.
Using Bayes to get the most out of non-significant results

No scientific conclusion follows automatically from a statistically non-significant result, yet people routinely use non-significant results to guide conclusions about the status of theories (or the effectiveness of practices). To know whether a non-significant result counts against a theory, or if it just indicates data insensitivity, researchers must use one of: power, intervals (such as confidence or credibility intervals), or else an indicator of the relative evidence for one theory over another, such as a Bayes factor. I argue Bayes factors allow theory to be linked to data in a way that overcomes the weaknesses of the other approaches. Specifically, Bayes factors use the data themselves to determine their sensitivity in distinguishing theories (unlike power), and they make use of those aspects of a theory’s predictions that are often easiest to specify (unlike power and intervals, which require specifying the minimal interesting value in order to address theory). Bayes factors provide a coherent approach to determining whether non-significant results support a null hypothesis over a theory, or whether the data are just insensitive. They allow accepting and rejecting the null hypothesis to be put on an equal footing. Concrete examples are provided to indicate the range of application of a simple online Bayes calculator, which reveal both the strengths and weaknesses of Bayes factors.
A comparative gender based evaluation of e-commerce website: A hybrid MCDM approach

Past few years have seen an escalated addition in ecommerce websites along with the users, with significant additions from both male and female populations. With the proliferated competition knowing your customer base becomes important. The disquisition focuses on the parallel evaluation of these websites for both genders. The factors individuate itself for males and females, which has been considered in the comparative evaluation. This segregation has been done through calculation of weights using fuzzy AHP which is inputted to TOPSIS for the culminating evaluation. The differentiation of the factor behaviour for males and females provides the industry with the improvement area to enhance their customer base in both the bifurcations, with the findings concreting facts and needs of both the genders.
Radiometric Correction of Terrestrial LiDAR Point Cloud Data for Individual Maize Plant Detection

Detailed geoinformation on in-field variations of plant properties (e.g., density, height) is required in precision agriculture and serves as a valuable input for plant growth models and crop management strategies. This letter presents a novel workflow for object-based point cloud analysis for individual maize plant mapping, using radiometric and geometric features of terrestrial laser scanning. The performed radiometric correction achieves a reduction of amplitude variation of homogeneous areas to 1/3 of the original variation and offers a distinct separability of the target class maize plant from soil. The developed procedure, including 3-D point cloud filtering and segmentation, is able to reliably detect single plants with a completeness and correctness . Experiments on reduced point densities show stability of detection rates above 100 points per 0.01 m2. The results indicate that the developed workflow will lead to even higher detection accuracy with LiDAR point clouds captured by mobile platforms, with less occlusion effects and more homogeneous point density.
Treatment Outcome of Combination Therapy Including Clarithromycin for Mycobacterium avium Complex Pulmonary Disease

Background/Aims The frequency of nontuberculous mycobacteria pulmonary disease in HIV-negative patients is increasing; the most common pathogen in Korea is the Mycobacterium avium complex (MAC). However, few studies have evaluated the treatment outcome of MAC pulmonary disease in Korea. Methods The efficacy of a clarithromycin-containing regimen for MAC pulmonary disease was studied in 42 patients treated for more than 6 months between January 2005 and December 2008. All patients were treated with a regimen consisting of clarithromycin, rifampin, and ethambutol. Streptomycin was added in 10 patients. Results Among the 42 patients, a negative culture conversion was achieved in 33 (78.6%), and the median duration of treatment in these patients was 19 months (interquartile range [IQR], 16 to 22). Of the 33 patients with a negative culture conversion, 14 completed treatment. During the follow-up period (median, 10 months; IQR, 4 to 20) for the 14 patients, one relapsed at 24 months after treatment completion. The culture conversion rate was significantly higher in patients who were treated with more than 500 mg/day clarithromycin (87.1% vs. 54.5%, p = 0.038). Conclusions The combined regimen including clarithromycin was effective against MAC pulmonary disease. High-dose clarithromycin of more than 500 mg/day may improve the outcome of patients with MAC pulmonary disease.
Can the Elephants Handle the NoSQL Onslaught?

In this new era of "big data", traditional DBMSs are under attack from two sides. At one end of the spectrum, the use of document store NoSQL systems (e.g. MongoDB) threatens to move modern Web 2.0 applications away from traditional RDBMSs. At the other end of the spectrum, big data DSS analytics that used to be the domain of parallel RDBMSs is now under attack by another class of NoSQL data analytics systems, such as Hive on Hadoop. So, are the traditional RDBMSs, aka "big elephants", doomed as they are challenged from both ends of this "big data" spectrum? In this paper, we compare one representative NoSQL system from each end of this spectrum with SQL Server, and analyze the performance and scalability aspects of each of these approaches (NoSQL vs. SQL) on two workloads (decision support analysis and interactive data-serving) that represent the two ends of the application spectrum. We present insights from this evaluation and speculate on potential trends for the future.
Insights into the osteoblast precursor differentiation towards mature osteoblasts induced by continuous BMP-2 signaling

Summary Mature osteoblasts are the cells responsible for bone formation and are derived from precursor osteoblasts. However, the mechanisms that control this differentiation are poorly understood. In fact, unlike the majority of organs in the body, which are composed of “soft” tissue from which cells can easily be isolated and studied, the “hard” mineralized tissue of bone has made it difficult to study the function of bone cells. Here, we established an in vitro model that mimics this differentiation under physiological conditions. We obtained mature osteoblasts and characterized them on the basis of the following parameters: the strong expression of osteoblastic markers, such as Runx2 and Col-I; the achievement of specific dimensions (the cell volume increases 26-fold compared to the osteoblast precursors); and the production of an abundant extracellular matrix also called osteoid. We demonstrated that the differentiation of osteoblast precursors into mature osteoblasts requires the continuous activation of Bone Morphogenetic Protein (BMP) receptors, which we established with the immobilization of a BMP-2mimetic peptide on a synthetic matrix mimicking in vivo microenvironment. Importantly, we demonstrated that the organization of the F-actin network and acetylated microtubules of the cells were modified during the differentiation process. We showed that the perturbation of the F-actin cytoskeleton organization abolished the differentiation process. In addition, we demonstrated that expression of the Runx2 gene is required for this differentiation. These findings demonstrate the retro-regulation of cytoplasmic and genic components due to the continuous induction of BMP-2 and also provide more detailed insights into the correct signaling of BMPs for cell differentiation in bone tissue.