Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous Detection, Subgrouping, and Quantitation of Respiratory Syncytial Virus A and B by Real-Time PCR

ABSTRACT Timely diagnosis of respiratory syncytial virus (RSV) infection is critical for appropriate treatment of lower respiratory infection in young children. To facilitate diagnosis, we developed a rapid, specific, and sensitive TaqMan PCR method for detection of RSV A and RSV B. Two sets of primer-probe pairs were selected from the nucleotide sequences encoding the nucleocapsid protein—one targeting RSV A and the other targeting RSV B. The specificity of the TaqMan reverse transcription-PCR assay was evaluated by testing each primer-probe pair against various viruses derived from laboratory virus stocks, as well as clinical respiratory specimens. Fluorescent signals were observed only in the presence of RSV A and/or RSV B. The sensitivity of our quantitative PCR assay was determined on the basis of PFU and virus particle counts. The resulting assay sensitivity was found to be 0.023 PFU, or two copies of viral RNA, for RSV A and 0.018 PFU, or nine copies of viral RNA, for RSV B. This quantitative TaqMan PCR assay was utilized to diagnose 175 nasopharyngeal aspirates obtained from children in Hong Kong with respiratory symptoms during the winter of 2000 and 2001. Among these specimens, TaqMan PCR detected 36 RSV-positive samples, 10 of which were identified as RSV A and 26 of which were identified as RSV B, whereas culture confirmation identified 21 RSV-positive specimens and immunofluorescence identified 32 RSV-positive specimens, all of which were among those identified by PCR. The results confirmed the accuracy of our TaqMan PCR assay and demonstrated its improved sensitivity versus classical methods.
Research as Praxis: Perspectives on Interpreting Data from a Science and Indigenous Knowledge Systems Project

This article presents a reflection on an aspect of research methodology, particularly on the interpretation strategy of data from a Science and Indigenous Knowledge Systems Project (SIKSP) in a South African university. The data interpretation problem arose while we were analysing the effects of a series of SIKSP-based workshops on the views of a group of participating science teachers concerning the importance and place of their religious, cultural and philosophical beliefs relative to their professional practice. When interpreting the data we noticed what seemed to us to be an incongruity in the data. In one instance teachers seemed to favour subjectivity in science teaching, but in another instance the views of science from the same teachers were distinctly objective. For some time we tried to make sense of this incongruity. In the midst of the confusion an emergent perspective surfaced concerning our own subjectivities in interpreting the data. We postponed the initial intention in interpreting the data—to evaluate the impact of the workshops—and our problem became the contradiction found in the data. Our emergent research questions underlying this article thus focused on methodological issues in terms of: (1) which epistemological standpoint did we take in analysing the data? (2) what possible different standpoints were taken by the subjects? and (3) what are the implications if different standpoints are taken? The purpose of this article, therefore, is to present our developing engagement with the data, a meta-reflection about the lenses we used in interpreting the data.
Reduced Daily Recalibration of Myoelectric Prosthesis Classifiers Based on Domain Adaptation

Control scheme design based on surface electromyography (sEMG) pattern recognition has been the focus of much research on a myoelectric prosthesis (MP) technology. Due to inherent nonstationarity in sEMG signals, prosthesis systems may need to be recalibrated day after day in daily use applications; thereby, hindering MP usability. In order to reduce the recalibration time in the subsequent days following the initial training, we propose a domain adaptation (DA) framework, which automatically reuses the models trained in earlier days as input for two baseline classifiers: a polynomial classifier (PC) and a linear discriminant analysis (LDA). Two novel algorithms of DA are introduced, one for PC and the other one for LDA. Five intact-limbed subjects and two transradial-amputee subjects participated in an experiment lasting ten days, to simulate the application of a MP over multiple days. The experiment results of four methods were compared: PC-DA (PC with DA), PC-BL (baseline PC), LDA-DA (LDA with DA), and LDA-BL (baseline LDA). In a new day, the DA methods reuse nine pretrained models, which were calibrated by 40 s training data per class in nine previous days. We show that the proposed DA methods significantly outperform nonadaptive baseline methods. The improvement in classification accuracy ranges from 5.49% to 28.48%, when the recording time per class is 2 s. For example, the average classification rates of PC-BL and PC-DA are 83.70% and 92.99%, respectively, for intact-limbed subjects with a nine-motions classification task. These results indicate that DA has the potential to improve the usability of MPs based on pattern recognition, by reducing the calibration time.
KnoFusius: a New Knowledge Fusion System for Interpretation of Gene Expression Data

This paper introduces a new architecture that aims at combining molecular biology data with information automatically extracted from relevant scientific literature (using text mining techniques on PubMed abstracts and fulltext papers) to help biomedical experts to interpret experimental results in hand. The infrastructural level bears on semantic-web technologies and standards that facilitate the actual fusion of the multi-source knowledge.
A Study on Bootstrapping Bilingual Vector Spaces from Non-Parallel Data (and Nothing Else)

We present a new language pair agnostic approach to inducing bilingual vector spaces from non-parallel data without any other resource in a bootstrapping fashion. The paper systematically introduces and describes all key elements of the bootstrapping procedure: (1) starting point or seed lexicon, (2) the confidence estimation and selection of new dimensions of the space, and (3) convergence. We test the quality of the induced bilingual vector spaces, and analyze the influence of the different components of the bootstrapping approach in the task of bilingual lexicon extraction (BLE) for two language pairs. Results reveal that, contrary to conclusions from prior work, the seeding of the bootstrapping process has a heavy impact on the quality of the learned lexicons. We also show that our approach outperforms the best performing fully corpus-based BLE methods on these test sets.
The Factor Structure of the CIBS-II-Readiness Assessment

The Brigance Comprehensive Inventory of Basic Skills-II (CIBS-II)-Readiness form is a diagnostic battery intended for children aged 5 and 6 years. The CIBS-II-Readiness is a new version of the CIBS-Revised-Readiness and includes updated normative information on a larger representative sample in comparison to the CIBS-Revised-Readiness. Empirical support for the CIBS-Revised-Readiness was lacking, especially score validity evidence. Adequate score validity information needs to be provided. The purpose of this study was to investigate evidence of construct validity of the composite scores on the CIBS-II-Readiness by examining the internal structure of the instrument and correlations with external measures. Confirmatory factor analysis was employed to compare the model implied by the composite score structure of the assessment to other plausible models. A six-factor model was supported. CIBS-II-Readiness scores had significant correlations with the Dynamic Indicators of Basic Early Literacy Skills scores, another widely used measure assessing five major components of early literacy.
Bone marrow CD169+ macrophages promote the retention of hematopoietic stem and progenitor cells in the mesenchymal stem cell niche

Hematopoietic stem cells (HSCs) reside in specialized bone marrow (BM) niches regulated by the sympathetic nervous system (SNS). Here, we have examined whether mononuclear phagocytes modulate the HSC niche. We defined three populations of BM mononuclear phagocytes that include Gr-1hi monocytes (MOs), Gr-1lo MOs, and macrophages (MΦ) based on differential expression of Gr-1, CD115, F4/80, and CD169. Using MO and MΦ conditional depletion models, we found that reductions in BM mononuclear phagocytes led to reduced BM CXCL12 levels, the selective down-regulation of HSC retention genes in Nestin+ niche cells, and egress of HSCs/progenitors to the bloodstream. Furthermore, specific depletion of CD169+ MΦ, which spares BM MOs, was sufficient to induce HSC/progenitor egress. MΦ depletion also enhanced mobilization induced by a CXCR4 antagonist or granulocyte colony-stimulating factor. These results highlight two antagonistic, tightly balanced pathways that regulate maintenance of HSCs/progenitors in the niche during homeostasis, in which MΦ cross talk with the Nestin+ niche cell promotes retention, and in contrast, SNS signals enhance egress. Thus, strategies that target BM MΦ hold the potential to augment stem cell yields in patients that mobilize HSCs/progenitors poorly.
Suspected Nonalcoholic Fatty Liver Disease and Mortality Risk in a Population-Based Cohort Study

OBJECTIVE:Case series suggest that nonalcoholic fatty liver disease (NAFLD) is associated with increased all-cause and cardiovascular mortality. The current study compared the survival of subjects with and without suspected NAFLD in a population-based cohort, and placed the finding in the context of previously published case series.METHODS:Primary analysis assessed mortality for NHANES-III participants with and without suspected NAFLD using the National Death Index. Suspected NAFLD was based upon unexplained ALT elevation. The Olmsted County and Cleveland Clinic case series were also used for comparison. Survivals were compared using Proportional Hazards Model and direct age standardization.RESULTS:The NHANES cohort included 980 with and 6,594 subjects without suspected NAFLD. Over a mean of 8.7 yr, suspected NAFLD had a hazards ratio of 1.37 (95% CI 0.98–1.91) for all-cause mortality. In the 45–54 age group, suspected NAFLD had significantly higher all-cause (4.40 95% CI 1.27–13.23) and cardiovascular mortality (8.15, 95% CI 2.00–33.20) after adjusting for conventional cardiovascular risk factors. The age-standardized rate per 10,000 per year was 129 (95% CI 118–140) for the NHANES non-NAFLD cohort, 154 (95% CI 116–198) for the NHANES suspected NAFLD cohort, 214 (95% CI 157–279) for the Olmsted County series, and 426 (95% CI 298–573) for the Cleveland Clinic series.CONCLUSION:The magnitude of mortality risk in NAFLD depends on the setting and method of ascertainment. Suspected NAFLD in the 45–54 age group is a strong independent risk factor for cardiovascular death and warrants further cardiovascular risk management guidelines.
Private Outlier Detection and Content based Encrypted Search

Today, our daily lives are constantly driven and influenced b y services like social networking, personalized advertisements, cloud infrastructure etc. This makes any form of personal or professional data vulnerable to both security and privacy threats. User l ooses control over the data as soon as its published on the Internet. Recently, popular photo sharing serviceInstagramtried to change its privacy policy, giving itself the right to sell users’ information i cluding their photographs to advertisers without any notification or compensation. With incidents like AO L and Netflix debacle, organizations are refraining from releasing customer data even after anonymi zation. This hinders future research and developments in many ways due to unavailability of customer da ta, behavior and patterns. Techniques like k-anonymity and l-diversity help to preserve user privacy t o some extent but fails to provide any solid guarantees. Recently proposed, differential privacy prov ides promising results in this area with theoretical bounds on information leak and preservation of priv acy even against the auxiliary information. However, differential privacy considers individual’s rec ord independent of other data and can not be applied to linked data like social graph, time series etc. Fu rthermore, all these techniques compromise utility of the data while maintaining privacy. At present, two approaches are widely used to ensure securit y of the data. First one is based on Secure Multiparty Computations (SMC), where users communica te with each other using SMC protocol to securely evaluate any function on their data. SMC gives prov able security without compromising utility of the data. However, the solutions based on the general prot ocol of SMC requires enormous computational and communication overhead, thus limiting the pra ctic l deployment of the secure algorithms. The second approach is to encrypt the data at the user end and p erform any operations in the encrypted domain to preserve the confidentiality of the data. This lead s to difficulty in performing various operations like search, retrieval and computations. Homomorph ic encryption allows secure computations over encrypted data but its impractical due to high computat ion l cost. In this thesis, we focus on developing privacy preserving, c ommunication and computationally efficient algorithms in the domain of Data Mining and Informati on Retrieval. Specifically, we design efficient privacy preserving solutions for two widely used t asks outlier detection and content based similarity search over encrypted data. Private computatio n of outliers among data collected from different sources has many applications in the area of data mini ng. First, we propose a novel algorithm of distance based outlier detection using Locality Sensitive Hashing (LSH) in a distributed setting where data is horizontally partitioned among data owners. We show that the proposed algorithm is scalable
Analysis for Determining Factors That Place Elementary Students at Risk

Abstract A checklist survey was completed by all the elementary schoolteachers in an urban school district in Iowa for a total of 5,270 students in Grades 1 through 5. The purpose of the survey was to determine a profile of the most significant factors that caused elementary school students to be at risk. The instrument was developed by a panel of experts within the school district. A factor analysis of this survey revealed eight interpretable factors accounting for 52% of the variance. These factors included (a) Academically At Risk, (b) Behavior and Coping Skills, (c) Socially Withdrawn, (d) Family Income, (e) Parenting, (f) Language Development, (g) Retention, and (h) Attendance. Results indicated that Factor 1, Academically at Risk, and Factor 2, Behavior and Coping Skills, accounted for over half of the variance. The overall “hit rate” for both at-risk and not-at-risk students was 90.71%, using the 8-factor solution. The profile provides educators with a pattern of the significant at-risk factors tha.
Evaluating the Value of Lensing Wikipedia During the Information Seeking Process

While Wikipedia is an excellent source of information about entities, discovering relationships among them is not well-supported by its search features. Lensing Wikipedia was designed as an alternate search and summarization interface, providing a set of filtering, visualization, and exploration tools that enable searching among the connections between people, organizations, and locations. In this paper, we present the results of a user study on how these features are used in each of Vakkari's stages of information seeking (pre-focus, focus formulation, and post-focus), and the participants perceptions of the utility of these features to their overall information-seeking goals. Participants primarily used input and control features during the pre-focus stage, informational and personalization features during the focus formulation stage, and personalization features during the post-focus stage. Findings from this study contribute to understanding how people use advanced search, summarization, and visualization tools to aid their information seeking tasks.
Carotid intima-media thickness in young survivors of acute myocardial infarction.

BACKGROUND Carotid intima-media thickness (CIMT) is considered to be a useful surrogate marker of coronary atherosclerosis. However, it is unclear whether this applies to young patients with acute myocardial infarction (AMI), in whom most cases are attributable to the destabilization of focal atheroma. OBJECTIVE To assess CIMT in patients experiencing AMI at a young age. METHODS CIMT was investigated in young survivors of AMI (78 male and 20 female) occurring before 45 years of age in men and before 50 years of age in women. CIMT values were compared with those of a sex-, age- and smoking status-matched sample selected from participants of a large epidemiological survey (115 men and 144 women). CIMT was measured on the anterior and posterior walls of the distal common carotid artery. RESULTS In post-AMI male patients, the mean average CIMT, comprised of measurements of both the near and far walls on both sides, was significantly increased compared with controls (0.67±0.10 mm versus 0.60±0.09 mm; P<0.001), while it did not differ in post-AMI female patients (0.60±0.07 mm versus 0.60±0.10 mm). Mean maximum CIMT was greater in both male and female post-AMI patients (0.94±0.15 mm versus 0.81±0.13 mm; P<0.001 in men and 0.89±0.14 mm versus 0.80±0.11 mm; P=0.001 in women). CONCLUSIONS In young AMI survivors, CIMT appeared to be significantly increased to a greater extent in men than in women. Although most patients had single- or double-vessel coronary disease, the overall increase in CIMT suggests that their coronary events were not due to destabilization of a single focal atheroma but may have reflected a generalized atherosclerotic process.
EFFECTS OF RANAVIRUS INFECTION OF RED-EARED SLIDERS (TRACHEMYS SCRIPTA ELEGANS) ON PLASMA PROTEINS

Abstract: Ranavirus is an emerging disease that infects fish, amphibians, and reptiles. Ranavirus induces an inflammatory response leading to death in many susceptible species. Red-eared sliders (RES; Trachemys scripta elegans) are vulnerable to ranavirus infection and are economically significant chelonians kept in the pet trade and utilized in research. Early identification of RES with inflammatory diseases would allow for isolation of affected individuals and subsequent disease investigation, including molecular testing for ranavirus. Validation of an inexpensive, clinically relevant, and reproducible diagnostic test that detects inflammation in turtles is needed. Although commonly used, plasma protein electrophoresis to detect an inflammatory acute-phase protein response has not been evaluated in a controlled environment in turtles with experimentally induced inflammatory disease. The objective of this study was to measure plasma protein fractions by electrophoresis to determine if an acute-phase protein response occurs in RES during infection with a frog virus 3–like ranavirus (FV3-like virus) isolated from a chelonian. A Bradford assay and agarose gel electrophoresis (AGE) were performed using plasma collected during a study of the effect of temperature on the pathogenesis of ranavirus in RES. In RES at the time of viremia, total albumin (ALBmg/ml) and albumin to globulin ratio were significantly lower and β-globulin percentage was significantly higher in RES exposed to ranavirus (n = 4) as compared to matched, uninfected RES (n = 8). In the last sample collected prior to death, total protein (TPmg/ml), ALBmg/ml, α-globulin percentage, and total α-globulin (αmg/ml) were significantly lower in RES exposed to ranavirus (n = 4) than control individuals (n = 8). In summary, FV3-like virus induces a decrease in plasma albumin concentration at the onset of viremia and decreases in TPmg/ml, ALBmg/ml, and αmg/ml concentrations prior to death in RES as measured by AGE.
Development of the Hassles of Environmental Poverty Instrument

Abstract Contemporary research has shown that chronic hassles can be as debilitating as acute stress and may be more of a determinant in the development of mental and physical disorders. In fact, frequency and intensity of hassles can be better predictors of stress responses than major life events. Although daily hassles have been shown to be population specific, existing measures of hassles do not distinguish between the hassles that impact men and those that impact women, nor have they been normed on populations that are poor. The Hassles of Environmental Poverty (HOEP) Scale is a 74-item instrument designed to assess the stresses of daily mothering within the context of poverty. Items on the scale address mothering stressors with a level of detail not currently available in existing stress scales. In the paper, the authors report out the results of statistical analysis that were done on the field test respondents. The results indicated that the HOEP Scale can legitimately be used for practice and research purposes.
Genetic Dissection of a QTL Affecting Bone Geometry

Parameters of bone geometry such as width, length, and cross-sectional area are major determinants of bone strength. Although these traits are highly heritable, few genes influencing bone geometry have been identified. Here, we dissect a major quantitative trait locus (QTL) influencing femur size. This QTL was originally identified in an F2 cross between the C57BL/6J-hg/hg (HG) and CAST/EiJ strains and was referred to as femur length in high growth mice 2 (Feml2). Feml2 was located on chromosome (Chr.) 9 at ∼20 cM. Here, we show that the HG.CAST-(D9Mit249-D9Mit133)/Ucd congenic strain captures Feml2. In an F2 congenic cross, we fine-mapped the location of Feml2 to an ∼6 Mbp region extending from 57.3 to 63.3 Mbp on Chr. 9. We have identified candidates by mining the complete genome sequence of CAST/EiJ and through allele-specific expression (ASE) analysis of growth plates in C57BL/6J × CAST/EiJ F1 hybrids. Interestingly, we also find that the refined location of Feml2 overlaps a cluster of six independent genome-wide associations for human height. This work provides the foundation for the identification of novel genes affecting bone geometry.
Cortical surface registration for image-guided neurosurgery using laser-range scanning

In this paper, a method of acquiring intraoperative data using a laser range scanner (LRS) is presented within the context of model-updated image-guided surgery. Registering textured point clouds generated by the LRS to tomographic data is explored using established point-based and surface techniques as well as a novel method that incorporates geometry and intensity information via mutual information (SurfaceMI). Phantom registration studies were performed to examine accuracy and robustness for each framework. In addition, an in vivo registration is performed to demonstrate feasibility of the data acquisition system in the operating room. Results indicate that SurfaceMI performed better in many cases than point-based (PBR) and iterative closest point (ICP) methods for registration of textured point clouds. Mean target registration error (TRE) for simulated deep tissue targets in a phantom were 1.0 /spl plusmn/ 0.2,2.0 /spl plusmn/ 0.3, and 1.2 /spl plusmn/ 0.3 mm for PBR, ICP, and SurfaceMI, respectively. With regard to in vivo registration, the mean TRE of vessel contour points for each framework was 1.9 /spl plusmn/ 1.0, 0.9 /spl plusmn/ 0.6, and 1.3 /spl plusmn/ 0.5 for PBR, ICP, and SurfaceMI, respectively. The methods discussed in this paper in conjunction with the quantitative data provide impetus for using LRS technology within the model-updated image-guided surgery framework.