Miracle-dz/UniFAR-FTUs huggingface dataset:
A note on the empirical likelihood confidence band for hazards ratio with covariate adjustment

In medical studies comparing two treatments in the presence of censored data, the stratified Cox model is an important tool that has the ability to flexibly handle non‐proportional hazards while allowing parsimonious covariate adjustment. In order to capture the cumulative treatment effect, the ratio of the treatment specific cumulative baseline hazards is often used as a measure of the treatment effect. Pointwise and simultaneous confidence bands associated with the estimated ratio provide a global picture of how the treatment effect evolves over time. Recently, Dong and Matthews (2012, Biometrics 68, 408–418) proposed to construct a pointwise confidence interval for the ratio using a plug‐in type empirical likelihood approach. However, their result on the limiting distribution of the empirical likelihood ratio is generally incorrect and the resulting confidence interval is asymptotically undercovering. In this article, we derive the correct limiting distribution for the likelihood ratio statistic. We also present simulation studies to demonstrate the effectiveness of our approach.
Prevalence of Diabetes Mellitus and Prediabetes in Dalseong-gun, Daegu City, Korea

Background The aim of the present study was to determine the population-based prevalence of diabetes mellitus (DM) and prediabetes in a rural district of Daegu City, Korea. Methods Between August and November 2003, a community-based health survey of adults aged 20 years and older was performed in the rural district of Dalseong-gun in Daegu City. A total of 1,806 of all eligible individuals agreed to participate. Fasting plasma glucose was measured in all participants. Two hour oral glucose tolerance was measured in the 1,773 participants for whom there was neither an established diagnosis of DM nor evidence of DM according to fasting glucose levels. The prevalence of DM and prediabetes was determined according to the 2003 criteria of the American Diabetes Association. Subjects with prediabetes were classified into one of three categories of glucose intolerance: isolated impaired fasting glucose (IFG); isolated impaired glucose tolerance (IGT); or combined IFG and IGT. Results The prevalence of DM was 12.2%. The highest prevalence rates were observed in subjects in their seventies. A total of 34.7% of all subjects who were assigned a diagnosis of DM in the present study had not been diagnosed previously. The prevalence of prediabetes was 22.7%. The highest prevalence rates were observed in subjects in their fifties. Conclusion The present study identified prevalence rates of 12.2% for DM (age-standardized prevalence rate [ASR], 6.8%), and 22.7% for prediabetes (ASR 18.5%). These results emphasize the need for community health promotion strategies to prevent or delay the onset of DM in individuals with prediabetes.
Capturing Temporal Sequences for Text Representation Using Hierarchical SOMs

This paper explores a new representation for text document by using an unsupervised learning mechanism – a hierarchical structure of Self-Organizing Feature Maps. This architecture is based on a code-book model. Through this architecture, a document can be encoded to a sequence of neurons while the temporal sequences of words as well as their frequencies are kept. Our results show that this architecture can capture the characteristic temporal sequences of documents/categories which can be used for various text categorization and clustering tasks. Using this representation to sequentially analyze the data, we can automatically solve the high dimensionality and statistical sparseness problems with the conventional text representation .
Surveillance for HIV-1 incidence using tests for recent infection in resource-constrained countries

Over the past few years, several assays have been developed for the purpose of estimating HIV-1 incidence from cross-sectional population surveys. The tests detect features of the evolving virological or immunological response to HIV-1 infection that distinguish recent from established infection. Surveillance programmes that collect specimens from population surveys for HIV-1 prevalence can apply some of these tests to the same specimen sets to estimate incidence. We describe these tests and discuss the principle and strategy for implementation of a testing programme for recent infection in surveillance settings. Test-specific prerequisites, such as calibration, validation, and quality assurance, and other test-specific performance characteristics that may influence interpretation, epidemiological considerations that may guide application, and practical operational considerations for implementation in surveillance settings are considered. When properly and judiciously applied, the capacity to estimate incidence from existing programmes that conduct surveillance for prevalent HIV-1 infection will enhance the capacity for more precise and timely analysis of the dynamics of the epidemic and the effectiveness of public health interventions.
Patterns of Tracing Software Structures and Dependencies

Tracing the structures and dependencies in existing, formal source documents, such as code or design speciﬁcations, or in the running software system is required for many different software engineering areas. Typical uses include reengineeringtools, programming languages and language extensions, aspect composition frameworks, self documentation, and visualizations. There are many recurring techniques used to gather and manipulate the relevant trace information. This paper presents a pattern language covering common techniques in this area, as well as technology projections and known uses. The target audience of this paper are developers who want to develop new solution or modify an existing solution in one of the named software engineering areas, as well as developers who want to gain a deeper understanding of the internal workings of the software engineering tools and frameworks they use.
Modulation of murine pluripotential stem cell proliferation in vivo by lithium carbonate.

The effect of administering lithium in vivo on murine pluripotential stem cell proliferation was studied. Lithium was injected i.p. at various meq/liter concentrations (0.5-5.0 meq/liter). Data was obtained establishing that lithium increased the pluripotential stem cell population from normal mice as measured by the Till and McCulloch CFUs assay. Significant increases were demonstrated in: (1) bone marrow CFUs; (2) bone marrow organ cellularity, and (3) peripheral blood WBC. Marrow CFUs increase was maximum at 4 days post-lithium injection and greatest in the 1 meq/liter group (p < 0.001). Further increases in lithium concentration, i.e., 5 meq/liter, effectively reduced CFUs levels below normal, suggesting toxicity of the drug was apparent at this dose level. We conclude lithium may modulate granulopoiesis by increasing the CFUs stem cell compartment, thereby directly channeling differentiation into the granulopoietic pathway. This increases the committed progenitor stem cell (CFUc) population and ultimately peripheral blood end-stage cells.
Vasodilatory Effects of Carvedilol and Pindolol

Summary: The effects of three different nonselective &bgr;‐blockers on central and peripheral hemodynamics as well as on pulmonary function were compared in 13 healthy subjects (19–37 years). The subjects were given carvedilol 50 mg, pindolol 10 mg, propranolol 80 mg, and placebo orally twice daily for 1 week in a double‐blind, crossover, randomized manner. Heart rate, blood pressure, arterial calf blood flow (venous occlusion strain gauge plethysmography), and pulmonary function (flowvolume spirometry) were measured at the first and at the last trial day. Heart rate and blood pressure were lower on carvedilol and propranolol than on pindolol and placebo; the maximal bradycardiac effect was 13 and 17 beats/min and hypotensive effect 9/10 mm Hg and 10/7 mm Hg on carvedilol and propranolol, respectively. Both carvedilol and pindolol increased arterial flow by about 40% (p < 0.05 and p < 0.01, respectively) and reduced peripheral resistance by about 34% (p < 0.05 and p < 0.01, respectively), the effect persisting after 1 week of treatment. None of the medications had any noteworthy effects on pulmonary function. Two subjects complained of tremor on pindolol. We conclude that carvedilol and pindolol possess distinct vasodilatory properties. Carvedilol had a stronger hypotensive effect than pindolol and was well tolerated.
Dlx-Dependent and -Independent Regulation of Olfactory Bulb Interneuron Differentiation

Olfactory bulb interneuron development is a complex multistep process that involves cell specification in the ventral telencephalon, tangential migration into the olfactory bulb, and local neuronal maturation. Although several transcription factors have been implicated in this process, how or when they act remains to be elucidated. Here we explore the mechanisms that result in olfactory bulb interneuron defects in Dlx1&2−/− (distal-less homeobox 1 and 2) and Mash1−/− (mammalian achaete-schute homolog 1) mutants. We provide evidence that Dlx1&2 and Mash1 regulate parallel molecular pathways that are required for the generation of these cells, thereby providing new insights into the mechanisms underlying olfactory bulb development. The analysis also defined distinct anatomical zones related to olfactory bulb development. Finally we show that Dlx1&2 are required for promoting tangential migration to the olfactory bulb, potentially via regulating the expression of ErbB4 (v-erb-a erythroblastic leukemia viral oncogene homolog 4), Robo2 (roundabout homolog 2), Slit1 (slit homolog 1), and PK2 (prokineticin 2), which have all been shown to play essential roles in this migration.
On reconfiguration-based Fault Tolerance

Fault Tolerance (FT) aims at guaranteeing specified system properties, at least in a degraded sense, under system component faults. Fault Accommodation (FA) - which handles the faulty system - and System Reconfiguration (SR) - which handles the healthy part of the faulty system - are the two possible approaches to FT. This lecture focuses on System Reconfiguration. It presents and analyzes the key role played by the lattice of system configurations, a mathematical framework that also underlies the problem of architecture design. This framework provides useful concepts and tools that will be shown to cover many aspects of Fault Tolerance, both from the design (passive / active / reliable control or estimation laws), and from the evaluation (fault recoverability, fault tolerance effectiveness, components usefulness) points of view.
Super Resolution With Probabilistic Motion Estimation

Super-resolution reconstruction (SRR) has long been relying on very accurate motion estimation between the frames for a successful process. However, recent works propose SRR that bypasses the need for an explicit motion estimation [11], [15]. In this correspondence, we present a new framework that ultimately leads to the same algorithm as in our prior work [11]. The contribution of this paper is two-fold. First, the suggested approach is much simpler and more intuitive, relying on the classic SRR formulation, and using a probabilistic and crude motion estimation. Second, the new approach offers various extensions not covered in our previous work, such as more general re-sampling tasks (e.g., de-interlacing).
BILATERAL SAME-DAY INTRAVITREAL INJECTIONS USING A SINGLE VIAL AND MOLECULAR BACTERIAL SCREENING FOR SAFETY SURVEILLANCE

Purpose: To evaluate the safety of bilateral same-day intravitreal injections using a single vial and to introduce a molecular surveillance system to screen bacterial drug contamination using eubacterial polymerase chain reaction (PCR). Methods: Retrospective review of the medical records of 135 patients who received 574 bilateral same-day intravitreal injections for various retinal diseases in 2 tertiary referral hospitals between January 2008 and March 2010 was performed. Data were obtained regarding the diagnosis, kinds of drugs injected, postinjection complications, and the result of molecular bacterial screening of the injected drugs. Drugs for bilateral intravitreal injections were drawn from a single vial and injected using separate syringes or needles. Molecular bacterial screening was performed using the remaining drug in the syringe by 16S ribosomal DNA real-time PCR. Results: A total of 574 injections (384 bevacizumab, 154 ranibizumab, and 36 triamcinolone) were administered on bilateral eyes of 135 patients. There were no complications, including endophthalmitis, uveitis, retinal tear, or retinal detachment. Of the 278 injections screened for bacterial contamination using eubacterial PCR, no cases (0%) showed drug contamination by bacteria. The sensitivity of eubacterial PCR for molecular bacterial screening was 10 colony-forming units (CFUs)/mL or lower. Conclusion: Bilateral same-day intravitreal injections drawn from a single vial using separate syringes or needles are well tolerated by patients, and its safety profile may be equivalent to unilateral injections. The bacterial molecular surveillance system using eubacterial PCR demonstrated the safety of bilateral same-day intravitreal injections and may be used for safety surveillance and for timely intervention of possible drug-related endophthalmitis.
Comparing SVM and Naïve Bayes Classifier for Automatic Microaneurysm Detections

Diabetic retinopathy is characterized by the development of retinal microaneurysms. The damage can be prevented if disease is treated in its early stages. In this paper, we are comparing Support Vector Machine (SVM) and Naïve Bayes (NB) classifiers for automatic microaneurysm detection in images acquired through non-dilated pupils. The Nearest Neighbor classifier is used as a baseline for comparison. Detected microaneurysms are validated with expert ophthalmologists’ hand-drawn ground-truths. The sensitivity, specificity, precision and accuracy of each method are also compared. Keywords—Diabetic retinopathy, microaneurysm, Naïve Bayes classifier, SVM classifier.
Multilayer Mounting for Long-term Light Sheet Microscopy of Zebrafish

Light sheet microscopy is the ideal imaging technique to study zebrafish embryonic development. Due to minimal photo-toxicity and bleaching, it is particularly suited for long-term time-lapse imaging over many hours up to several days. However, an appropriate sample mounting strategy is needed that offers both confinement and normal development of the sample. Multilayer mounting, a new embedding technique using low-concentration agarose in optically clear tubes, now overcomes this limitation and unleashes the full potential of light sheet microscopy for real-time developmental biology.
Specialty Pharmaceuticals Care Management in an Integrated Health Care Delivery System with Electronic Health Records

The specialty pharmaceuticals market is expanding more rapidly than the traditional pharmaceuticals market. Specialty pharmacy operations have evolved to deliver selected medications and associated clinical services. The growing role of specialty drugs requires new approaches to managing the use of these drugs. The focus, expectations, and emphasis in specialty drug management in an integrated health care delivery system such as Kaiser Permanente (KP) can vary as compared with more conventional health care systems. The KP Specialty Pharmacy (KP-SP) serves KP members across the United States. This descriptive account addresses the impetus for specialty drug management within KP, the use of tools such as an electronic health record (EHR) system and process management software, the KP-SP approach for specialty pharmacy services, and the emphasis on quality measurement of services provided. Kaiser Permanente’s integrated system enables KP-SP pharmacists to coordinate the provision of specialty drugs while monitoring laboratory values, physician visits, and most other relevant elements of the patient’s therapy. Process management software facilitates the counseling of patients, promotion of adherence, and interventions to resolve clinical, logistic, or pharmacy benefit issues. The integrated EHR affords KP-SP pharmacists advantages for care management that should become available to more health care systems with broadened adoption of EHRs. The KP-SP experience may help to establish models for clinical pharmacy services as health care systems and information systems become more integrated.
Reconstructing Missing Areas in Facial Images

In this paper, we present a novel approach to reconstruct missing areas in facial images by using a series of Restricted Boltzman Machines (RBMs). RBMs created with a low number of hidden neurons generalize well and are able to reconstruct basic structures in the missing areas. On the other hand networks with many hidden neurons tend to emphasize details, when using the reconstruction of the previous, more generalized RBMs, as their input. Since trained RBMs are fast in encoding and decoding data by design, our method is also suitable for processing video streams.
Comparative Neuropathology of Kuru with the New Variant of Creutzfeldt‐Jakob Disease: Evidence for Strain of Agent Predominating Over Genotype of Host

The three major influences on the phenotype of the transmissible spongiform encephalopathies are believed to be strain of agent, route of infection and host genotype. We have compared the pathologic profiles and genotypes of the new variant of Creutzfeldt‐Jakob disease (vCJD) and kuru. The comparison reveals that there are distinct lesional differences particularly in the prion protein (PrP) load and distribution as seen by immunohistochemistry. The clinico‐pathologic phenotypes and the genotypes of these two diseases are sufficiently different to suggest that the strain of agent may play a greater role than any presumptive common route of peripherally acquired infection.
Monitoring Protein Kinase Activity in Cell Lysates Using a High-Density Peptide Microarray

Monitoring and targeting protein kinases is widely accepted as a promising approach for disease diagnosis and drug discovery. For this purpose, the authors have developed an original type of peptide array as a high-throughput screening assay for quantitatively evaluating kinase activity. A volume of 2 nL of peptide solution was spotted onto a formyl group-modified glass slide by using an arrayer, which was designed for use with protein chip technology. The phosphorylation was recognized by fluorescence-label antibody and detected with an automatic microarray scanner widely used in DNA chip technology. The system needs low sample volume, provides a high-density peptide array, and supplies high reproducibility. It provided enough sensitivity for inhibitor screening, even though a relatively low concentration of purified kinase was employed. The assay also proved useful for the detection of intracellular kinase activity as well as for the measurement of the fluctuations of intracellular protein kinase activity with drug stimulation. Thus, this peptide array would be applicable for kinase-targeted diagnosis, cell-based drug screening, and signal pathway investigation. (Journal of Biomolecular Screening 2009:256-262)
1 Joint Dependant Local Deformations ( JLD )

This report reviews the literature in the field of computer animation and robotics to illustrate the numerous approaches to simulating, controlling and displaying the realistic, real-time animation of virtual characters. Critical analyses of the various high-level approaches are conducted, with a view to identifying key areas of interest for future research in the area of “Real-Time Character Animation Techniques”
Characterization of complex renal cysts: A critical evaluation of the Bosniak classification

Abstract Objective. Complex renal cysts represent a major clinical problem, since it is often difficult to exclude malignancy. The Bosniak classification system, based on computed tomography (CT), is widely used to categorize cystic renal lesions. The aim of this study was to evaluate critically available data on the Bosniak classification. Material and methods. All publications from an Entrez Pubmed search were reviewed, focusing on clinical applicability and the use of imaging modalities other than CT to categorize complex renal cysts. Results. Fifteen retrospective studies were found. Most series were small, with only six studies comprising more than 30 patients. When the results of these six studies were pooled the percentage of malignancy was: category I, 0%; category II, 15.6%; category IIF, 0%; category III, 65.3%; and category IV, 91.7%. Category IIF was included in only three studies. Both magnetic resonance imaging and contrast-enhanced ultrasonography (US) seemed to have reasonable agreement with CT, although both modalities had a tendency to upgrade lesions. Conclusions. The main problem with the Bosniak classification is in separating category II and III lesions, which is of major importance, since decisions on intervention are based on this separation. The use of category IIF seems promising to detect those category II lesions that eventually will develop into malignancy and reduce overtreatment of lesions originally classified as category III. The scientific basis of this “new” classification strategy is, however, still missing. Data on other imaging modalities are too limited for conclusions to be drawn.
Security assessment of Eucalyptus' web management interface

Three approaches exist for a company to migrate its services in the cloud. The first is select the most appropriate commercial cloud provider, such as Microsoft, Amazon, Google or SalesForce, and to rent their resources and deploy its services. These cloud service providers The second approach is to build a private cloud with some of the open source cloud frameworks like Eucalyptus, OpenStack, OpenNebula or CloudStack. Finally, the third option is to build a hybrid cloud, i.e., to split the services and to migrate the confidential and private services in its own private cloud, which could be open source, while the public and non confidential services and data to migrate in some public commercial cloud. Commercial cloud providers encash for their resources as a service, but offer and guarantee secured resources and huge availability of minimum 99.9% through a SLAs (Service Level Agreements). On the other hand, building an open source private cloud is the lowest starting investment, which does not guarantee neither security nor availability. Therefore, it is important for a company to assess the security of the open source cloud frameworks, especially their web management interface since it is the front end application, through which a user can get an unauthorized access to the company's data or applications. Eucalyptus is one of the most common open source cloud frameworks for building IaaS (Infrastructure as a Service) private or hybrid clouds, which also has its own web management interface to manage the cloud resources. In this paper, we assess the security of the cloud framework web management interface of the newest version of the Eucalyptus cloud. The results of the security assessment analysis show that the cloud web management interface is vulnerable. We assess the security vulnerabilities and propose measures how to secure them.