Miracle-dz/UniFAR-FTUs huggingface dataset:
Accuracy of diagnostic tests for Legionnaires’ disease: a systematic review

Purpose. Rapid and effective diagnosis of Legionnaires’ disease (LD) cases is extremely important so that timely and appropriate therapy can be provided, thereby lowering the morbidity and mortality rates and reducing the health and economic costs associated with this disease. Methodology. Diagnosis is established solely by microbiological tests. There are several methods available, each with different performance, sensitivity and specificity characteristics, and further understanding is required. Our objective was to assess the accuracy of urinary antigen detection, direct fluorescent antibody (DFA) staining, serological testing and the polymerase chain reaction (PCR) method versus culture analysis (the reference standard) in patients suspected of being infected with Legionella or patients with laboratory‐confirmed LD. We performed a MEDLINE search in November 2014. Two authors independently assessed the trials and extracted data. Pooled analysis was performed through Meta‐DiSc version 1.4. Result. The inclusion criteria were met by 11 studies. All the studies evaluated PCR and DFA tests to detect Legionella in clinical specimens, comparing them to culture techniques, and were included in the meta‐analysis. The pooled sensitivity and specificity for PCR were 83% [95% confidence interval (CI): 79‐87%] and 90% (95% CI: 88‐92%), respectively. DFA was evaluated in one study and the sensitivity and specificity of this test were 67% (95% CI: 30‐93%) and 100% (95% CI: 91‐100%), respectively. PCR had high sensitivity and specificity for early diagnosis of LD. Conclusion. Culture analysis is deemed necessary for epidemiological studies, molecular strain typing and antibiotic sensibility evaluations; however, the performance of PCR in recent studies calls for additional, well‐designed studies in order to achieve the best standard test, which will enable optimization of the Legionella infection diagnostic.
Absence of histological lesions in primate models of ECT and magnetic seizure therapy.

OBJECTIVE The authors present preliminary findings from the first nonhuman primate neuropathological study of ECT to use perfusion fixation and adequate controls and the first to compare ECT with magnetic seizure therapy, to their knowledge. METHOD Twelve Macaca mullata received 6 weeks of daily ECT, magnetic seizure therapy, or anesthesia alone. After perfusion fixation, their brains were examined while masked to intervention. RESULTS No identified lesions were attributable to the interventions. Cortical and hippocampal immunoreactivity for glial fibrillary acidic protein (an astrocytic marker) was most intense in the group that received ECT. CONCLUSIONS This small but rigorous primate study supports the view that ECT does not produce histological lesions in the brain and provides the first comparable safety data on magnetic seizure therapy.
Fgf signaling induces posterior neuroectoderm independently of Bmp signaling inhibition

Whereas according to the neural default model, neural specification is induced by extracellular inhibitors of bone morphogenetic proteins (Bmps), the role of fibroblast growth factors (Fgfs) during neural induction is heavily debated. Here, we show that, in zebrafish embryos, Bmps and Fgfs play differential roles during the induction and patterning of the anterior vs. the posterior neuroectoderm. Induction of anterior neuroectoderm, giving rise to fore‐ and midbrain, is accomplished by Bmp inhibition, with Fgfs playing a moderate posteriorizing/patterning role, possibly by blocking Bmp signaling at the level of Smad proteins. In contrast, in the posterior‐most neuroectoderm, which is located in marginal regions of the early gastrula embryo to give rise to spinal cord and hindbrain, Fgfs play a neural‐inducing rather than a neural‐patterning role. This Fgf‐dependent posterior neural induction takes place during late blastula and early gastrula stages, after mesoderm has been induced and cannot be blocked by Bmps or the Bmp target gene and downstream effector ΔNp63α, indicating that here, Fgfs act independently of Bmp signaling inhibition. Developmental Dynamics 231:750–757, 2004. © 2004 Wiley‐Liss, Inc.
Optimum Tension for Partial Ossicular Replacement Prosthesis Reconstruction in the Human Middle Ear

Objective: Hearing results from ossiculoplasty are unpredictable. There are many potentially modifiable parameters. One parameter that has not been adequately investigated in the past is the effect of tension on the mechanical functioning of the prosthesis. Our goal was to investigate this parameter further, with the hypothesis that the mechanical functioning of partial ossicular replacement prostheses (PORP) from the stapes head to the eardrum will be affected by the tension that they are placed under.
Cell Cycle Regulation of the Human Polo-like Kinase (PLK) Promoter*

Plk (polo-like kinase) is a serine-threonine kinase that appears to function in mitotic control in mammalian cells. We demonstrated previously that PLK mRNA expression is low at the G1-S transition, increases during S phase, and is maximally expressed during G2-M. In the present study, we have cloned the human PLK gene and analyzed the structure and function of 2 kilobases of its 5′-flanking region. Using synchronized cultures of HeLa cells transfected with PLK promoter/luciferase constructs, we show that the promoter of PLK is activated at S phase and is maximal at G2-M phase. Using various PLK promoter/luciferase constructs, we show that three activating regions are located between 35 and 93 base pairs upstream of the transcription initiation site. We identified a repressor element (CDE/CHR) in the region of the transcription start site, and mutations within this element diminished cell cycle regulation of transcription.
Factorized geometrical autofocus: On the geometry search

This paper deals with local geometry optimization within the scope of Factorized Geometrical Autofocus (FGA). The FGA algorithm is a Fast Factorized Back-Projection (FFBP) formulation with six free geometry parameters. These are tuned until a sharp image is obtained, i.e. with respect to an object function. To optimize the geometry (from a focus perspective) for a small image area, we propose an efficient routine based on correlation, sensitivity analysis and Broyden-Fletcher-Goldfarb-Shanno (BFGS) minimization. The new routine is evaluated using simulated Ultra-WideBand (UWB) data. By applying the FGA algorithm step-by-step, an erroneous geometry is compensated. This gives a focused image. In regard to run time, the new routine is approximately 100 times faster than a brute-force approach, i.e. for this FGA problem. For a general problem, the run time reduction will be far greater. To be more specific: with x parameters and N values to assess for each parameter; it is anticipated that the computational effort will decrease exponentially by a factor close to Nx.
new antiviral screening method that simultaneously detects viral eplication , cell viability , and cell toxicity igal

Viruses cause a variety of illnesses in humans, yet only a few antiviral drugs have been developed; thus, new antiviral drugs are urgently needed. Plants could be a good source of antiviral drugs, they do not have mobility and can only defend themselves by producing compounds against pathogens such as viruses in their own fix environment. These compounds may have the potential to inhibit animal and human viruses as well. In this study, a fast and reliable method for screening plant extracts for specific antiviral activity against Herpes simplex virus type-1 (HSV-1) was developed. This method distinguishes between host cell death lant antiviral activity
A New Approach of Fault Localization Using Value Replacement

We present a new method that bases on value replacement which considers both the control dependence and the data dependence. The key idea of value replacement is to see which program statements exercised during a failing run use values that can be altered so that the execution instead produces correct output. This approach is effective in locating statements that either faulty statements or directly effecting the faulty statements. Our approach also analyze the possibility of the statements that are faulty, this can be applied to more areas.
Research on 3D measuring based binocular vision

Auto-Measuring via vision is meaningful to the reconstruction of 3D model. There are many problems to be solved in this area. This article presents a complete flow of 3d measuring system with two CCD cameras, which includes camera calibration, rectification of stereo pair, stereo match and disparity optimization. Introduced the parameters in camera pinhole model, the principle of re-projection in rectification, steps of stereo match and difficulty.
Bio-Inspired Photonic Structures: Prototypes, Fabrications and Devices

Like the ability of electron regulation of electronic semiconductors, the photonic analogs usually considered as photonic structure materials are regarded as essential for light manipulation [1, 2]. With particular designs of photonic structures, they are expected to achieve different far-field and near-field optical features and thus lead to a perspective in all-optical circuit [3]. Though humankind has entered the nano-scale realm several decades ago, it is still a hard task for engineers to explore novel optical functional devices due to the limited experiences and originalities on artificial photonic structures design and the desired optical features. Additionally, it is also great challenges to fabricate photonic structures, owing to their sub-optical-wavelength to sub-micron featured sizes, especially in a high dimensional way by nano-fabrication technologies today.
An Output Oriented Super-Efficiency Model for Considering Time Lag Effect

Abstract—There exists some time lag between the consumption of inputs and the production of outputs. This time lag effect should be considered in calculating efficiency of decision making units (DMU). Recently, a couple of DEA models were developed for considering time lag effect in efficiency evaluation of research activities. However, these models can’t discriminate efficient DMUs because of the nature of basic DEA model in which efficiency scores are limited to ‘1’. This problem can be resolved a super-efficiency model. However, a super efficiency model sometimes causes infeasibility problem. This paper suggests an output oriented super-efficiency model for efficiency evaluation under the consideration of time lag effect. A case example using a long term research project is given to compare the suggested model with the MpO model.
Modelling the impact of aquaculture on early diagenetic processes in sea loch sediments

We present a novel approach for the simulation of the impacts of finfish aquaculture on sedimentary redox dynamics, based on the coupling of a fish farm waste deposition model (DEPOMOD) and a knowledge-based reactive transport model (RTM) of early diagenesis. The integrated model was applied to a salmon fish farm located in a Scottish fjordic sealoch. The major diagenetic processes of the reaction network were first identified on the basis of literature information and historic data. Next, the organic carbon (OC) flux at a pristine site near the farm was estimated by fitting the vertical profiles of pore water and solid-state chemical species measured in the field. DEPOMOD was then used to predict the fluxes of OC due to the release of uneaten feed and faeces at various distances away from the farm. These fluxes were added to the background 'natural' fluxes and used as forcing functions for the RTM. Comparison of the simulated transient profiles with data collected at an impacted site revealed that the RTM model satisfactorily predicted the transient dynamics of the system. We discuss the use of the model for cost-effective environmental impact assessments, site selection and the optimization of husbandry practices. © Inter-Research 2009.
Uterus transplantation - substantial progress in research but not yet ready for the clinic

The very rapid advancements in assisted reproductive techniques (ART) during the last decades have been driven by a general progress in medical research but also by a great desire of the society to be able to fulfill the basic human need to reproduce. Since the birth of the first IVF-baby in 1978, new techniques such as intra-cytoplasmic sperm injection (ICSI), pregestational diagnosis (PGS) and ovarian cryopreservation have been introduced. The vast majority of infertile couples can now become parents with the aid of new sophisticated treatment modalities. The last hurdle to overcome in the effort to treat infertility is absolute uterine infertility. The women with absolute uterine infertility are those that either are born with no uterus, women that have lost the uterus through hysterectomy, or women that have a deficient uterus in regards to implantation or pregnancy.
Moving Forward by Looking Backward: Using Backward Design to Develop an Innovative MSIS Program

Program design is a challenging task that involves significant effort and resources. The challenge is compounded if the program is being designed for an interdisciplinary discipline. Multiple approaches are available for program designers, and varying approaches may work well in different contexts and settings. The fundamental core of Backward design is that the selected approach may be successfully applied in different contexts if it begins with the end in mind. This research describes how a Midwestern public university used backward design to construct a curriculum process that gives voice to the expertise, proclivities, and preferences of individual faculty members in curriculum development while aligning course objectives with the program’s mission and vision. As a major contribution, the paper shares lessons learned from a collaborative program design effort using the principles of Backward design. This effort was undertaken to design the Masters of Science in Information Systems (MSIS) program at a Midwestern public research university.
One‐Dimensional SDS Gel Electrophoresis of Proteins

Electrophoresis is used to separate complex mixtures of proteins (e.g., from cells, subcellular fractions, column fractions, or immunoprecipitates), to investigate subunit compositions, and to verify homogeneity of protein samples. It can also serve to purify proteins for use in further applications. In polyacrylamide gel electrophoresis, proteins migrate in response to an electrical field through pores in a polyacrylamide gel matrix; pore size decreases with increasing acrylamide concentration. The combination of pore size and protein charge, size, and shape determines the migration rate of the protein. In this unit, the standard Laemmli method is described for discontinuous gel electrophoresis under denaturing conditions, that is, in the presence of sodium dodecyl sulfate (SDS). Both full‐size and minigel formats are detailed. Several modifications are provided for specific applications. For separation of peptides and small proteins, the standard buffers are replaced with either a Tris‐tricine buffer system or a modified Tris buffer in the absence of urea. Continuous SDS‐PAGE is a simplified method in which the same buffer is used for both the gel and the electrode solutions and the stacking gel is omitted. Other protocols cover the preparation and use of ultrathin gels and gradient gels, and the simultaneous preparation of multiple gels. Curr. Protoc. Cell Biol. 37:6.1. 1‐6.1. 38. © 2007 by John Wiley & Sons, Inc.
A 3D-Space Vector Modulation Algorithm for Three Phase Four Wire Neutral Point Clamped Inverter Systems as Power Quality Compensator

A Unified Power Quality Conditioner (UPQC) is designed using a Neutral Point Clamped (NPC) multilevel inverter to improve the power quality. When designed for high/medium voltage and power applications, the voltage stress across the switches and harmonic content in the output voltage are increased. A 3-phase 4-wire NPC inverter system is developed as Power Quality Conditioner using an effectual three dimensional Space Vector Modulation (3D-SVM) technique. The proposed system behaves like a UPQC with shunt and series active filter under balanced and unbalanced loading conditions. In addition to the improvement of the power quality issues, it also balances the neutral point voltage and voltage balancing across the capacitors under unbalanced condition. The hardware and simulation results of proposed system are compared with 2D-SVM and 3D-SVM. The proposed system is stimulated using MATLAB and the hardware is designed using FPGA. From the results it is evident that effectual 3D-SVM technique gives better performance compared to other control methods.
Access Control Management for SCADA Systems

The information technology revolution has transformed all aspects of our society including critical infrastructures and led a significant shift from their old and disparate business models based on proprietary and legacy environments to more open and consolidated ones. Supervisory Control and Data Acquisition (SCADA) systems have been widely used not only for industrial processes but also for some experimental facilities. Due to the nature of open environments, managing SCADA systems should meet various security requirements since system administrators need to deal with a large number of entities and functions involved in critical infrastructures. In this paper, we identify necessary access control requirements in SCADA systems and articulate access control policies for the simulated SCADA systems. We also attempt to analyze and realize those requirements and policies in the context of role-based access control that is suitable for simplifying administrative tasks in large scale enterprises.
Longitudinal Predictors of Human Papillomavirus Vaccine Initiation Among Adolescent Girls in a High-Risk Geographic Area

Background: Human papillomavirus (HPV) vaccine uptake is low among adolescent girls in the United States. We sought to identify longitudinal predictors of HPV vaccine initiation in populations at elevated risk for cervical cancer. Methods: We interviewed a population-based sample of parents of 10- to 18-year-old girls in areas of North Carolina with elevated cervical cancer rates. Baseline interviews occurred in summer 2007 and follow-up interviews in fall 2008. Measures included health belief model constructs. Results: Parents reported that 27% (149/567) of their daughters had initiated HPV vaccine between baseline and follow-up. Of parents who at baseline intended to get their daughters the vaccine in the next year, only 38% (126/348) had done so by follow-up. Of parents of daughters who remained unvaccinated at follow-up but had seen a doctor since baseline, only 37% (122/388) received an HPV vaccine recommendation. Rates of HPV vaccine initiation were higher among parents who at baseline perceived lower barriers to getting HPV vaccine, anticipated greater regret if their daughters got HPV because they were unvaccinated, did not report “needing more information” as the main reason they had not already vaccinated, intended to get their daughters the vaccine, or were not born-again Christians. Conclusions: Missed opportunities to increase HPV vaccine uptake included unrealized parent intentions and absent doctor recommendations. While several health belief model constructs identified in early acceptability studies (e.g., perceived risk, perceived vaccine effectiveness) were not longitudinally associated with HPV vaccine initiation, our findings suggest correlates of uptake (e.g., anticipated regret) that offer novel opportunities for intervention.
A nanoporous optofluidic microsystem for highly sensitive and repeatable surface enhanced Raman spectroscopy detection.

We report the demonstration of an optofluidic surface enhanced Raman spectroscopy (SERS) device that leverages a nanoporous microfluidic matrix to improve the SERS detection performance by more than two orders of magnitude as compared to a typical open microfluidic channel. Although it is a growing trend to integrate optical biosensors into microfluidic channels, this basic combination has been detrimental to the sensing performance when applied to SERS. Recently, however, synergistic combinations between microfluidic functions and photonics (i.e., optofluidics) have been implemented that improve the detection performance of SERS. Conceptually, the simplest optofluidic SERS techniques reported to date utilize a single nanofluidic channel to trap nanoparticle-analyte conjugates as a method of preconcentration before detection. In this work, we leverage this paradigm while improving upon the simplicity by forming a 3D nanofluidic network with packed nanoporous silica microspheres in a microfluidic channel; this creates a concentration matrix that traps silver nanoclusters and adsorbed analytes into the SERS detection volume. With this approach, we are able to achieve a detection limit of 400 attomoles of Rhodamine 6G after only 2 min of sample loading with high chip-to-chip repeatability. Due to the high number of fluidic paths in the nanoporous channel, this approach is less prone to clogging than single nanofluidic inlets, and the loading time is decreased compared to previous reports. In addition, fabrication of this microsystem is quite simple, as nanoscale fabrication is not necessary. Finally, integrated multimode fiber optic cables eliminate the need for optical alignment, and thus the device is relevant for portable and automated applications in the field, including point-of-sample and point-of-care detection. To illustrate a relevant field-based application, we demonstrate the detection of 12 ppb of the organophosphate malathion in water using the nanofluidic SERS microsystem.
Global Time-Delay Estimation in Ultrasound Elastography

A critical step in quasi-static ultrasound elastography is the estimation of time delay between two frames of radio-frequency (RF) data that are obtained while the tissue is undergoing deformation. This paper presents a novel technique for time-delay estimation (TDE) of all samples of RF data simultaneously, thereby exploiting all the information in RF data for TDE. A nonlinear cost function that incorporates similarity of RF data intensity and prior information of displacement continuity is formulated. Optimization of this function involves searching for TDE of all samples of the RF data, rendering the optimization intractable with conventional techniques given that the number of variables can be approximately one million. Therefore, the optimization problem is converted to a sparse linear system of equations, and is solved in real time using a computationally efficient optimization technique. We call our method GLobal Ultrasound Elastography (GLUE), and compare it to dynamic programming analytic minimization (DPAM) and normalized cross correlation (NCC) techniques. Our simulation results show that the contrast-to-noise ratio (CNR) values of the axial strain maps are 4.94 for NCC, 14.62 for DPAM, and 26.31 for GLUE. Our results on experimental data from tissue mimicking phantoms show that the CNR values of the axial strain maps are 1.07 for NCC, 16.01 for DPAM, and 18.21 for GLUE. Finally, our results on in vivo data show that the CNR values of the axial strain maps are 3.56 for DPAM and 13.20 for GLUE.
The Neglected Half of Alzheimer Disease: Cognitive and Functional Concomitants of Severe Dementia

OBJECTIVE: Traditional mental status and psychometric assessments bottom out in the late stages of Alzheimer disease (AD). A method adapted from cognitive testing in infants, the Ordinal Scales of Psychological Development was modified (M‐OSPD) and applied to a severely demented population. The concurrent validity of this method was tested in comparison with Functional Assessment Staging (FAST). Internal consistency as a measure for reliability was also determined.