Miracle-dz/UniFAR-FTUs huggingface dataset:
Congenital abnormalities in newborn lambs after infection of pregnant sheep with Akabane virus

Akabane virus (a Bunyavirus) has been associated with epizootics of congenital deformities in cattle, sheep, and goats. Experimental studies using mouse-adapted virus inoculated intravenously into pregnant sheep gave an inapparent infection. Neutralizing antibodies were detected on day 5, and peaks in the titer were seen at days 10 and 48. Ewes infected at day 30 to 36 of pregnancy produced five (31% incidence) deformed lambs. Sera from four of these possessed neutralizing antibodies to Akabane virus before ingesting colostrum. Two lambs had arthrogryposis, hydranencephaly, kyphosis, scoliosis, and brachygnathia; one had micrencephaly; and the other two had porencephaly. The two lambs with arthrogryposis and hydranencephaly also had extensive lesions in other tissues. In the spinal cord there was a marked decrease in the number of ventral horn neurones and a depletion of myelin. Skeletal muscles showed marked atrophy. The medulla of the thymus possessed large Hassall's corpuscles and a reduced number of thymocytes in the cortex. It would appear that the pathogenic effects of Akabane virus are related to the gestational age (30 to 36 days) at which the fetus is infected. Akabane virus can now be included in the growing list of teratogenic viruses and provides an interesting system for studying such congenital diseases.
A Peer-to-Peer Media Streaming System Based on the iVCE Platform

With the advancement of peer-to-peer technology, media streaming applications become more and more popular in the Internet. However, the traditional development methods for this kind of applications need developers not only to consider the application logic but also to manage the dynamics of Internet resources, thus increasing the difculty of development and limiting the deployment of personal video distribution applications. In this paper, we design and implement a peer-to- peer streaming system in a much easier way. In this way we can concentrate on the application itself without distraction from the dynamics of Internet resources. Such simplication owes to the Internet-based Virtual Computing Environment (iVCE), which provides programming abstractions and runtime utilities that can encapsulate the complexity of managing transient resources into the platform, thus facilitating the construction of Internet applications. When we build our streaming application based on the iVCE, we only need to dene the interaction protocols among distributed nodes with the Owlet programming language. Also, we implement a JavaBean, which can be used by the Owlet program, to assist the transfering and rendering of the content. Our implementation shows that peer-to-peer applications such as media streaming, can be elegantly built using the iVCE platform, and it can serve as a reference implementation for developing similar applications.
Phase II study of interim PET-CT-guided response-adapted therapy in advanced Hodgkin's lymphoma.

BACKGROUND Combination chemotherapy ABVD (doxorubicin, bleomycin, vinblastine and dacarabazine) cures ∼70% of patients with advanced Hodgkin's lymphoma (aHL, stages IIB, III and IV) while more toxic escalated BEACOPP (EB, combination of bleomycin, etoposide, doxorubicin, cyclophosphamide, vincristine, procarbazine and prednisolone) increases cure rates to 85%. Patients with a positive interim positron emission tomography-computerized tomography (PET-CT) scan after two cycles (PET-2) of ABVD have very poor outcomes with continued ABVD. Intensifying therapy with EB in PET-2-positive patients ('response-adapted therapy') may improve cure rates, whereas the negative patients can continue ABVD alone. PATIENTS AND METHODS Eligible patients with newly diagnosed aHL received two cycles of ABVD and underwent PET-2 (scored with semi-quantitative 5-point visual criteria, 'Deauville score'). PET-2-negative patients continued four additional cycles of ABVD, whereas PET-2-positive patients received four cycles of EB. A phase II sample size of 50 was estimated keeping the lower and higher proportion of rejection of the event-free survival (EFS) as 70% and 85%, respectively. RESULTS Fifty patients [median age 28 (12-60) years; male : female: 39 : 11; stages: IIB-3 (6%), III-29 (58%) and IV-18 (36%); International Prognostic Score (IPS): 0-3: 34 (68%); 4-7: 16 (32%)] were enrolled; 49 underwent PET-2. Eight (16%) were PET-2-positive, whereas 41 (84%) were negative. Forty-seven were evaluable for EFS and all 50 for overall survival (OS). The 2-year EFS was 76% (95% CI: 68-83) and OS was 88% (95% CI: 82-94). PET-2 was strongly prognostic-2-year EFS, negative versus positive: 82% versus 50%; P = 0.013. CONCLUSION PET-2 response-adapted strategy could not achieve EFS of 85% in aHL. However, escalated therapy improved outcomes in PET-2-positive patients compared with historical data. TRIAL REGISTRATION CTRI/2012/06/002741 (http://www.ctri.nic.in) and NCT01304849 (http://www.clinicaltrials.gov).
Including Design in e-Manufacturing

This paper reviews major issues in the implementation of e-manufacturing, particularly the design aspects. It will examine recent progress, drawing out particular issues that are being addressed. Use will be made of the work by the author and colleagues to devise rule-based design and Internet-based control of machines to illustrate how these developments affect the integrated e-manufacturing environment. A dynamic Simulink™ model of the way emanufacture is affected by overall design delays is used to evaluate general solutions for partial and complete e-based companies. These models show how changing to improved designs reduces WIP.
Testing Consistency of Two Histograms

Several approaches to testing the hypothesis that two histograms are drawn from the same distribution are investigated. We note that single-sample continuous distribution tests may be adapted to this two-sample grouped data situation. The difficulty of not having a fully-specified null hypothesis is an important consideration in the general case, and care is required in estimating probabilities with “toy” Monte Carlo simulations. The performance of several common tests is compared; no single test performs best in all situations.
Inactivation of BRCA1 and BRCA2 in ovarian cancer.

BACKGROUND Although BRCA1 and BRCA2 play important roles in hereditary ovarian cancers, the extent of their role in sporadic ovarian cancers and their mechanisms of inactivation are not yet well understood. Our goal was to characterize BRCA2 mutations and mRNA expression in a group of ovarian tumors previously evaluated for BRCA1 mutations and mRNA expression. METHODS The tumors of 92 unrelated women with "ovarian" cancer (i.e., ovarian, peritoneal, or fallopian tube cancer) were screened for BRCA2 null mutations using a protein truncation test. Methylation-specific polymerase chain reaction (PCR) was used to examine the BRCA2 promoter for hypermethylation in tumors that did not express BRCA2 mRNA. All statistical tests were two-sided. RESULTS Nine tumors had a germline (n = 5) or somatic (n = 4) BRCA2 mutation; each was associated with loss of heterozygosity. All of the somatic (1445delC, E880X, 4286del8, and 5783delT) and one of the germline (5984ins4) mutations were unique to this study. One tumor had somatic mutations in both BRCA1 and BRCA2. Two tumors are, to our knowledge, the first cases of germline BRCA2-associated peritoneal cancer. Twelve additional tumors lacked detectable BRCA2 mRNA, but the BRCA2 promoter was hypermethylated in only one of them, suggesting that other mechanisms effect transcriptional silencing of BRCA2. Tumors lacking BRCA1 mRNA were more likely to lack BRCA2 mRNA than tumors expressing BRCA1 mRNA (P<.001). Overall, 82% (95% confidence interval [CI] = 74% to 90%) of the tumors contained alterations in BRCA1, BRCA2, or both genes. Of 41 informative tumors with some alteration in BRCA2, 36 also had an alteration in BRCA1. The frequency, but not the mechanism, of BRCA1 or BRCA2 dysfunction in ovarian cancer was independent of family history. CONCLUSIONS Multiple mechanisms cause nearly universal dysfunction of BRCA1 and/or BRCA2 in hereditary and sporadic ovarian carcinoma. Ovarian cancers with BRCA2 dysfunction often have simultaneous BRCA1 dysfunction.
Mitochondrial Topoisomerase I (Top1mt) Is a Novel Limiting Factor of Doxorubicin Cardiotoxicity

Purpose: Doxorubicin is one of the most effective chemotherapeutic agents. However, up to 30% of the patients treated with doxorubicin suffer from congestive heart failure. The mechanism of doxorubicin cardiotoxicity is likely multifactorial and most importantly, the genetic factors predisposing to doxorubicin cardiotoxicity are unknown. On the basis of the fact that mtDNA lesions and mitochondrial dysfunctions have been found in human hearts exposed to doxorubicin and that mitochondrial topoisomerase 1 (Top1mt) specifically controls mtDNA homeostasis, we hypothesized that Top1mt knockout (KO) mice might exhibit hypersensitivity to doxorubicin. Experimental Design: Wild-type (WT) and KO Top1mt mice were treated once a week with 4 mg/kg doxorubicin for 8 weeks. Heart tissues were analyzed one week after the last treatment. Results: Genetic inactivation of Top1mt in mice accentuates mtDNA copy number loss and mtDNA damage in heart tissue following doxorubicin treatment. Top1mt KO mice also fail to maintain respiratory chain protein production and mitochondrial cristae ultrastructure organization. These mitochondrial defects result in decreased O2 consumption, increased reactive oxygen species production, and enhanced heart muscle damage in animals treated with doxorubicin. Accordingly, Top1mt KO mice die within 45 days after the last doxorubicin injection, whereas the WT mice survive. Conclusions: Our results provide evidence that Top1mt, which is conserved across vertebrates, is critical for cardiac tolerance to doxorubicin and adaptive response to doxorubicin cardiotoxicity. They also suggest the potential of Top1mt single-nucleotide polymorphisms testing to investigate patient susceptibility to doxorubicin-induced cardiotoxicity. Clin Cancer Res; 20(18); 4873–81. ©2014 AACR.
Reliability Models for Almost-Series and Almost-Parallel Systems

When assessing system reliability using system, subsystem, and component-level data, assumptions are required about the form of the system structure in order to utilize the lower-level data. We consider model forms which allow for the assessment and modeling of possible discrepancies between reliability estimates based on different levels of data. By understanding these potential conflicts between data, we can more realistically represent the true uncertainty of the estimates and gain understanding about inconsistencies which might guide further improvements to the system model. The new methodology is illustrated with several examples.
Short-pulsed diode lasers as an excitation source for time-resolved fluorescence applications and confocal laser scanning microscopy in PDT

This article describes a setup for subcellular time-resolved fluorescence spectroscopy and fluorescence lifetime measurements using a confocal laser scanning microscope in combination with a short pulsed diode laser for fluorescence excitation and specimen illumination. The diode laser emits pulses at 398 nm wavelength with 70 ps full width at half maximum (FWHM) duration. The diode laser can be run at a pulse repetition rate of 40 MHz down to single shot mode. For time resolved spectroscopy a spectrometer setup consisting of an Czerny Turner spectrometer and a MCP-gated and -intensified CCD camera was used. Subcellular fluorescence lifetime measurements were achieved using a time-correlated single photon counting (TCSPC) module instead of the spectrometer setup. The capability of the short pulsed diode laser for fluorescence imaging, fluorescence lifetime measurements and time-resolved spectroscopy in combination with laser scanning microscopy is demonstrated by fluorescence analysis of several photosensitizers on a single cell level.
Preparation and Performance Evaluation of the Analgesic and Anti-Inflammatory Effects of Chitosan Composite Materials

The author had used salivation method to prepareQuercetin-ornidazole-chitosan composite material (QOCCM) and then used this film to the treatment for the rat model of oral ulcer. and finally found that it can promote the healing of ulcers. In order to investigate the mechanism of action in the treatment of oral ulcers, we prepare Quercetin-ornidazole-chitosan complex solution, and then used the application of carrageenan induced paw edema and croton oil-induced mouse ear swelling to observe its anti-inflammatory role, application of hot plate method to observe the analgesic effect of inflammatory and evaluate the effects of chitosan composite materials.
A theory for the atmospheric energy spectrum: Depth-limited temperature anomalies at the tropopause

The horizontal spectra of atmospheric wind and temperature at the tropopause have a steep −3 slope at synoptic scales, but transition to −5/3 at wavelengths of the order of 500–1,000 km [Nastrom, G. D. & Gage, K. S. (1985) J. Atmos. Sci. 42, 950–960]. Here we demonstrate that a model that assumes zero potential vorticity and constant stratification N over a finite-depth H in the troposphere exhibits the same type of spectra. In this model, temperature perturbations generated at the planetary scale excite a direct cascade of energy with a slope of −3 at large scales, −5/3 at small scales, and a transition near horizontal wavenumber kt = f/NH, where f is the Coriolis parameter. Ballpark atmospheric estimates for N, f, and H give a transition wavenumber near that observed, and numerical simulations of the previously undescribed model verify the expected behavior. Despite its simplicity, the model is consistent with a number of perplexing features in the observations and demonstrates that a complete theory for mesoscale dynamics must take temperature advection at boundaries into account.
Field-aware Factorization Machines for CTR Prediction

Click-through rate (CTR) prediction plays an important role in computational advertising. Models based on degree-2 polynomial mappings and factorization machines (FMs) are widely used for this task. Recently, a variant of FMs, field-aware factorization machines (FFMs), outperforms existing models in some world-wide CTR-prediction competitions. Based on our experiences in winning two of them, in this paper we establish FFMs as an effective method for classifying large sparse data including those from CTR prediction. First, we propose efficient implementations for training FFMs. Then we comprehensively analyze FFMs and compare this approach with competing models. Experiments show that FFMs are very useful for certain classification problems. Finally, we have released a package of FFMs for public use.
Predicting Unplanned Transfers to the Intensive Care Unit: A Machine Learning Approach Leveraging Diverse Clinical Elements

Background Early warning scores aid in the detection of pediatric clinical deteriorations but include limited data inputs, rarely include data trends over time, and have limited validation. Objective Machine learning methods that make use of large numbers of predictor variables are now commonplace. This work examines how different types of predictor variables derived from the electronic health record affect the performance of predicting unplanned transfers to the intensive care unit (ICU) at three large children’s hospitals. Methods We trained separate models with data from three different institutions from 2011 through 2013 and evaluated models with 2014 data. Cases consisted of patients who transferred from the floor to the ICU and met one or more of 5 different priori defined criteria for suspected unplanned transfers. Controls were patients who were never transferred to the ICU. Predictor variables for the models were derived from vitals, labs, acuity scores, and nursing assessments. Classification models consisted of L1 and L2 regularized logistic regression and neural network models. We evaluated model performance over prediction horizons ranging from 1 to 16 hours. Results Across the three institutions, the c-statistic values for our best models were 0.892 (95% CI 0.875-0.904), 0.902 (95% CI 0.880-0.923), and 0.899 (95% CI 0.879-0.919) for the task of identifying unplanned ICU transfer 6 hours before its occurrence and achieved 0.871 (95% CI 0.855-0.888), 0.872 (95% CI 0.850-0.895), and 0.850 (95% CI 0.825-0.875) for a prediction horizon of 16 hours. For our first model at 80% sensitivity, this resulted in a specificity of 80.5% (95% CI 77.4-83.7) and a positive predictive value of 5.2% (95% CI 4.5-6.2). Conclusions Feature-rich models with many predictor variables allow for patient deterioration to be predicted accurately, even up to 16 hours in advance.
Estimation of crop gross primary production ( GPP ) : fAPARchl versus MOD 15 A 2 FPAR

a Universities Space Research Association, Columbia, MD 21044, USA b Biospheric Sciences Laboratory, National Aeronautics and Space Administration/Goddard Space Flight Center, Greenbelt, MD 20771, USA c Sigma Space Corporation, Lanham, MD 20706, USA d Climate and Radiation Laboratory, Code 613, National Aeronautics and Space Administration Goddard Space Flight Center, Greenbelt, MD 20771, USA e Goddard Earth Sciences and Technology Center, University of Maryland Baltimore County, Baltimore, MD 21228, USA f Hydrology and Remote Sensing Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD 20705, USA g School of Natural Resources, University of Nebraska—Lincoln, Lincoln, NE 68588, USA
Genescene: An ontology-enhanced integration of linguistic and co-occurrence based relations in biomedical texts

The increasing amount of publicly available literature and experimental data in biomedicine makes it hard for biomedical researchers to stay up-to-date. Genescene is a toolkit that will help alleviate this problem by providing an overview of published literature content. We combined a linguistic parser with Concept Space, a co-occurrence based semantic net. Both techniques extract complementary biomedical relations between noun phrases from MEDLINE abstracts. The parser extracts precise and semantically rich relations from individual abstracts. Concept Space extracts relations that hold true for the collection of abstracts. The Gene Ontology, the Human Genome Nomenclature, and the Unified Medical Language System, are also integrated in Genescene. Currently, they are used to facilitate the integration of the two relation types, and to select the more interesting and high-quality relations for presentation. A user study focusing on p53 literature is discussed. All MEDLINE abstracts discussing p53 were processed in Genescene. Two researchers evaluated the terms and relations from several abstracts of interest to them. The results show that the terms were precise (precision 93%) and relevant, as were the parser relations (precision 95%). The Concept Space relations were more precise when selected with ontological knowledge (precision 78%) than without (60%).
3 D Mesh Streaming and Rendering – An approach based on Predictive Modeling

The complexity in 3D environment over the web is growing rapidly. This 3D environment comprises of set of structured scenes and each scene has multiple 3D objects/meshes. In such environment, it is required to give user interactions for every 3D object and at any point of time, it is enough if the system streams and brings in only the visible portion of the object from server to the client by utilizing the limited network bandwidth and the limited client memory space. Further to reduce the time and effectively utilize the bandwidth and memory space, in proposed work, an attempt is made to exploit the user interactions on 3D object and built a Predictive Agent(PA) which would minimize the latency in rendering of the 3D mesh that is being streamed.
The VACS Index Accurately Predicts Mortality and Treatment Response among Multi-Drug Resistant HIV Infected Patients Participating in the Options in Management with Antiretrovirals (OPTIMA) Study

Objectives The VACS Index is highly predictive of all-cause mortality among HIV infected individuals within the first few years of combination antiretroviral therapy (cART). However, its accuracy among highly treatment experienced individuals and its responsiveness to treatment interventions have yet to be evaluated. We compared the accuracy and responsiveness of the VACS Index with a Restricted Index of age and traditional HIV biomarkers among patients enrolled in the OPTIMA study. Methods Using data from 324/339 (96%) patients in OPTIMA, we evaluated associations between indices and mortality using Kaplan-Meier estimates, proportional hazards models, Harrel’s C-statistic and net reclassification improvement (NRI). We also determined the association between study interventions and risk scores over time, and change in score and mortality. Results Both the Restricted Index (c = 0.70) and VACS Index (c = 0.74) predicted mortality from baseline, but discrimination was improved with the VACS Index (NRI = 23%). Change in score from baseline to 48 weeks was more strongly associated with survival for the VACS Index than the Restricted Index with respective hazard ratios of 0.26 (95% CI 0.14–0.49) and 0.39(95% CI 0.22–0.70) among the 25% most improved scores, and 2.08 (95% CI 1.27–3.38) and 1.51 (95%CI 0.90–2.53) for the 25% least improved scores. Conclusions The VACS Index predicts all-cause mortality more accurately among multi-drug resistant, treatment experienced individuals and is more responsive to changes in risk associated with treatment intervention than an index restricted to age and HIV biomarkers. The VACS Index holds promise as an intermediate outcome for intervention research.
Behavior of some growth performance indexes for exploited Mediterranean hake

Exploited marine living resources are at present assessed in the Mediterranean by refer‐ ring to 26 geographical sub‐areas (GSA: GFCM, 2009), mainly delimited on the basis of politi‐ In this paper, some life‐history estimates concerning the females of the Mediterranean hake Merluccius merluccius (L., 1758), i.e. the parameters of the von Bertalanffy growth function (L∞, K, and t0), the maximum‐ever lengths (Lmx‐e), and the lengths at full maturity (Lmst) were gathered from the pertinent literature and used to derive 5 growth performance indexes (K, φ’, RL=Lmst/ L∞, t50% and ω). The original datasets (n= 70) and the corresponding growth performance indexes were organized and analyzed by various geographical units (GFCM’s geographical sub‐area, GSA; GFCM’s statistical division, GD; and biological province, BP). The parameter distribution resulted to be normal only for the growth performance indexes K and RL; a significant relationship correlation was detected between K and t50%, between φ’ and ω, and between K and ω. The examination of the available historical data showed a scattered and unbalanced geographical distribution by GSA (e.g. 13 of 20 GSAs had less than 5 datasets each), a variability which was higher intra‐GSA than inter‐GSAs (as evidenced by the box‐plots) and no clear geographical trend. GD and BP presented similar patterns, with significant geographical effects only in the RL. Present results suggest that, even if geographical effects are expected, they are obscured by the uncertainty of the original parameters, especially those related to the von Bertalanffy growth function (vBGF). Consequently, growth performance indexes should be used (and interpreted) with caution.