Miracle-dz/UniFAR-FTUs huggingface dataset:
Krüppel-Like Factor 5 Protects against Murine Colitis and Activates JAK-STAT Signaling In Vivo

Inflammatory bowel disease (IBD), which is characterized by chronic or recurring inflammation of the gastrointestinal tract, affects 1.4 million persons in the United States alone. KLF5, a Krüppel-like factor (KLF) family member, is expressed within the epithelia of the gastrointestinal tract and has been implicated in rapid cell proliferation, migration, and remodeling in a number of tissues. Given these functions, we hypothesized that constitutive Klf5 expression would protect against the development of colitis in vivo. To examine the role of KLF5 in vivo, we used the Villin promoter to target Klf5 to the entire horizontal axis of the small intestine and colon. Villin-Klf5 transgenic mice were born at normal Mendelian ratios and appeared grossly normal to at least 1 year of age. Surprisingly, there were no significant changes in cell proliferation or in the differentiation of any of the intestinal lineages within the duodenum, jejunum, ileum, and colon of Villin-Klf5 mice, compared to littermate controls. However, when Villin-Klf5 mice were treated with dextran sodium sulfate (DSS) to induce colitis, they developed less colonic injury and significantly reduced disease activity scores than littermate controls. The mechanism for this decreased injury may come via JAK-STAT signaling, the activation of which was increased in colonic mucosa of DSS treated Villin-Klf5 mice compared to controls. Thus, KLF5 and its downstream mediators may provide therapeutic targets and disease markers for IBD or other diseases characterized by injury and disruption of intestinal epithelia.
Comparison of field inversion gel electrophoresis with contour-clamped homogeneous electric field electrophoresis as a typing method for Enterococcus faecium

Direct comparisons between contour-clamped homogeneous electric field (CHEF) electrophoresis and field inversion gel electrophoresis (FIGE) to determine the epidemiology of antibiotic-resistant enterococci have not been previously published. Fifty non-beta-lactamase-producing, ampicillin-resistant Enterococcus faecium isolates and 10 vancomycin-resistant E. faecium strains collected from multiple centers were analyzed in a blinded fashion by CHEF electrophoresis and FIGE after digestion with SmaI. Isolates were considered clonally related if there was a difference of three of fewer bands between electrophoretic patterns. Agreement between CHEF electrophoresis and FIGE was seen for 12 of 13 identified groups of ampicillin-resistant E. faecium and 7 of 7 groups of vancomycin-resistant E. faecium. The lone discordance was accounted for by a fourth band difference between two strains recognized near 350 kb by CHEF electrophoresis but not by FIGE, placing them into different clonal groups. Better band separation was noted in the 50- to 200-kb range for FIGE, while CHEF electrophoresis revealed better resolution over 250 kb more reliably, including detection of some bands not seen on FIGE. Molecular epidemiologic investigations of E. faecium by either technique should provide comparable results.
Low cost network planning tool development using Google maps, SRTM data and MATLAB

Network planning is an essential part of any wireless network deployment. The prices of commercial network planning tools are expensive, making them inaccessible to many researchers and organizations with small networks. However, in house development of network planning tools are not as hard as it was used to be. The freely available web maps and rapid development capability of MATLAB Graphical User Interfaces (GUIs) and recently integrated Object Oriented Programming to MATLAB make it much easier. Shuttle Radar Topography Mission (SRTM) data is a public database which gives access to elevation data for the whole world. In this paper we give the architecture details of our owned Network Planning Cell Tool (NPCET), a network planning tool that was designed for planning rural WiMAX networks in Malaysia. Developing a network planning tool is multi-disciplinary in nature, the scope of the project involves wireless propagation, geographical information systems and maps, network planning and programming. The paper can be used as a guide for researchers on how to integrate necessary data sources and propagation models for building a comprehensive planning tool for almost any type of communication system.
A 14.5 µW generic Carrier Width demodulator for telemetry-based Medical Devices

This paper investigates a Carrier Width Modulation (CWM) demodulator designed mainly for batteryless Implantable Medical Devices. The proposed circuit architecture is a generic demodulator; designed to operate at 27.12 MHz while supporting a wide range of data rates. It allows low power consumption, small silicon area and high immunity against noise and amplitude disturbance. A simplified CWM demodulator architecture and a corresponding fully integrated implementation elaborated using the 130 nm IBM CMOS technology are reported. Post-layout simulation results confirm the effectiveness of the CWM demodulator for wireless power transfer and downlink communication. The proposed CWM demodulator can reach data rates up to 1/3 of the carrier frequency, i.e., 9.04 Mbit/s in this case. The circuit occupies an 1826 µm2 silicon area and dissipates 14.5 µW, in worst conditions, when operating from a 1.2 V power supply. For lower data rates, it consumes less power and allows higher power transfer during communication through an inductive link.
An Automatic Gastrointestinal Polyp Detection System in Video Endoscopy Using Fusion of Color Wavelet and Convolutional Neural Network Features

Gastrointestinal polyps are considered to be the precursors of cancer development in most of the cases. Therefore, early detection and removal of polyps can reduce the possibility of cancer. Video endoscopy is the most used diagnostic modality for gastrointestinal polyps. But, because it is an operator dependent procedure, several human factors can lead to misdetection of polyps. Computer aided polyp detection can reduce polyp miss detection rate and assists doctors in finding the most important regions to pay attention to. In this paper, an automatic system has been proposed as a support to gastrointestinal polyp detection. This system captures the video streams from endoscopic video and, in the output, it shows the identified polyps. Color wavelet (CW) features and convolutional neural network (CNN) features of video frames are extracted and combined together which are used to train a linear support vector machine (SVM). Evaluations on standard public databases show that the proposed system outperforms the state-of-the-art methods, gaining accuracy of 98.65%, sensitivity of 98.79%, and specificity of 98.52%.
Draft Genome Sequence of Staphylococcus hominis BHG17 Isolated from Wild Bar-Headed Goose (Anser indicus) Feces

ABSTRACT Staphylococcus hominis belongs to a group of coagulase-negative staphylococci and is an opportunistic pathogen, usually found on the skin and mucous membranes. Studies involving S. hominis isolated from wild birds are scarce. Here, we report a 2.365-Mb draft genome sequence of S. hominis BHG17, isolated from the feces of a bar-headed goose.
A Race Model of Perceptual Forced Choice Reaction Time

We present a race model for forced-choice data that provides a unified account of both latency and accuracy. The model is applied in the domain of short-term priming, but could characterize many other response tasks. A series of perceptual identification experiments found systematic bias changes as a function of prime duration. Notably, reaction times (RTs) were observed to change along with response bias. Furthermore, correct RTs changed in an opposite manner to error RTs. These results are explained by assuming a race between choice alternatives. The theory provides an alternative to signal detection theory, with faster finish times, rather than greater signal strength, determining both accuracy and RT.
Laterality of basic auditory perception

Laterality (left–right ear differences) of auditory processing was assessed using basic auditory skills: (1) gap detection, (2) frequency discrimination, and (3) intensity discrimination. Stimuli included tones (500, 1000, and 4000 Hz) and wide-band noise presented monaurally to each ear of typical adult listeners. The hypothesis tested was that processing of tonal stimuli would be enhanced by left ear (LE) stimulation and noise by right ear (RE) presentations. To investigate the limits of laterality by (1) spectral width, a narrow-band noise (NBN) of 450-Hz bandwidth was evaluated using intensity discrimination, and (2) stimulus duration, 200, 500, and 1000 ms duration tones were evaluated using frequency discrimination. A left ear advantage (LEA) was demonstrated with tonal stimuli in all experiments, but an expected REA for noise stimuli was not found. The NBN stimulus demonstrated no LEA and was characterised as a noise. No change in laterality was found with changes in stimulus durations. The LEA for tonal stimuli is felt to be due to more direct connections between the left ear and the right auditory cortex, which has been shown to be primary for spectral analysis and tonal processing. The lack of a REA for noise stimuli is unexplained. Sex differences in laterality for noise stimuli were noted but were not statistically significant. This study did establish a subtle but clear pattern of LEA for processing of tonal stimuli.
MoSense: An RF-Based Motion Detection System via Off-the-Shelf WiFi Devices

Motion is a critical indicator of human presence and activities. Recent developments in the field of indoor motion detection have revealed their potentials in enhancing our living experiences through applications like intrusion detection and sleep monitoring. However, existing solutions still face several critical downsides such as the availability (specialized hardware), reliability (illumination and line-of-sight constraints), and privacy issues (being watched). To overcome such shortages, a radio frequency (RF) based device-free motion detection system (MoSense) is designed via leveraging the attenuation of ubiquitous WiFi signals induced by motions to deliver a reliable and transparent detection service in realtime. The design and implementation of MoSense face two challenges: 1) characterizing stationary states and 2) the noisy subcarriers. For the first challenge, a silence analysis model is proposed to characterize stationary states for distinguishing motions. For the second challenge, we design a distance-based mechanism to select certain subcarriers that better capture the impact of motions from the noisy channel through measuring the similarity between subcarriers. A prototype of MoSense is realized and evaluated in real environments. By comparing MoSense with other two state-of-the-art systems, i.e., FIMD and FRID, we have shown that MoSense is superior in terms of precision, false negative rate and computational complexity. Considering that MoSense is compatible with existing WiFi infrastructure, it constitutes a low-cost yet promising solution for motion detection.
Hybrid Versus Norwood Strategies for Single-Ventricle Palliation

Background— Hybrid and Norwood strategies differ substantially in terms of stage II palliative procedures. We sought to compare these strategies with an emphasis on survival and reintervention after stage II and subsequent Fontan completion. Methods and Results— Of 110 neonates with functionally single-ventricle physiology who underwent stage I palliation between 2004 and 2010, 75 (69%) infants (Norwood, n=43; hybrid, n=32) who subsequently underwent stage II palliation were studied. Survival and reintervention rates after stage II palliation, anatomic and physiologic variables at pre-Fontan assessment, and Fontan outcomes were compared between the groups. Predictors for reintervention were analyzed. Freedom from death/transplant after stage II palliation was equivalent between the groups (Norwood, 80.4% versus hybrid, 85.6% at 3 years, P=0.66). Hybrid patients had a higher pulmonary artery (PA) reintervention rate (P=0.003) and lower Nakata index at pre-Fontan evaluation (P=0.015). Aortic arch and atrioventricular valve reinterventions were not different between the groups. Ventricular end-diastolic pressure, mean PA pressure, and ventricular function were equivalent at pre-Fontan assessment. There were no deaths after Fontan completion in either group (Norwood, n=25, hybrid, n=14). Conclusions— Survival after stage II palliation and subsequent Fontan completion is equivalent between the groups. The hybrid group had a higher PA reintervention rate and smaller PA size. Both strategies achieved adequate physiology for Fontan completion. Evolution of the hybrid strategy requires refinement to provide optimal PA growth.
Explaining the size distribution of cities: x-treme economies

We criticize the theories used to explain the size distribution of cities. They take an empirical fact and work backward to obtain assumptions on primitives. The induced theoretical assumptions on consumer behavior, particularly about their inability to insure against the city-level productivity shocks in the model, are untenable. With either self insurance or insurance markets, and either an arbitrarily small cost of moving or the assumption that consumers do not perfectly observe the shocks to firms' technologies, the agents will never move. Even without these frictions, our analysis yields another equilibrium with insurance where consumers never move. Thus, insurance is a substitute for movement. We propose an alternative class of models, involving extreme risk against which consumers will not insure. Instead, they will move, generating a Frechet distribution of city sizes that is empirically competitive with other models.
An Extended Class of Instrumental Variables for the Estimation of Causal Effects

This paper examines the ways in which structural systems can yield observed variables, other than the cause or treatment of interest, that can play an instrumental role in identifying and estimating causal effects. We focus speciOcally on the ways in which structures determine exclusion restrictions and conditional exogeneity relations that act to ensure identification. We show that by carefully specifying the structural equations and by extending the standard notion of instrumental variables, one can identify and estimate causal effects in the endogenous regressor case for a broad range of economically relevant structures. Some of these have not previously been recognized. Our results there create new opportunities for identifying and estimating causal effects in non-experimental situations. Our results for more familiar structures provide new insights. For example, we extend results of Angrist, Imbens, and Rubin (1996) by taking into account an important distinction between cases where Z is an observed exogenous instrument and those where it is a proxy for an unobserved exogenous instrument. A main message emerging from our analysis is the central importance of sufficiently specifying the causal relations governing the unobservables, as these play a crucial role in creating obstacles or opportunities for identification. Because our results exhaust the possibilities for identification, we ensure that there are no other opportunities for identification based on exclusion restrictions and conditional independence relations still to be discovered. To accomplish this characterization, we introduce notions of conditioning and conditional extended instrumental variables (EIVs). These are not proper instruments, as they are endogenous. They nevertheless permit identification and estimation of causal effects. We analyze methods using these EIVs either singly or jointly.
Draft Genome Sequences of Two Clinical Isolates of Lactobacillus rhamnosus from Initial Stages of Dental Pulp Infection

ABSTRACT Here we report the draft genomic sequences of two clinical isolates of Lactobacillus rhamnosus from infected dental pulps representing the initial stages of infection of pulp tissue. Based on 454 FLX+ pyrosequencing, the two clinical isolates infecting vital pulp had a genome length of 2.9 Mbp with distinct genomic signatures.
Comparison of fibulin-3 and mesothelin as markers in malignant mesothelioma

Background Pleural malignant mesothelioma (MM) is a deadly tumour predominantly associated with asbestos exposure. A reliable diagnostic and prognostic marker for MM will significantly enhance clinical care and is an area of intense research. Soluble mesothelin is the most studied and an FDA-approved biomarker for MM. A recent report showed promising results using fibulin-3 as a new diagnostic marker. The aim of this study was to compare the utility of fibulin-3 versus mesothelin, singly or in combination. Methods Fibulin-3 and soluble mesothelin were determined by ELISA in the plasma and pleural fluid of 153 patients presenting with a pleural effusion including 82 with MM, 36 with non-MM malignant effusions and 35 with benign effusions. Biomarker concentrations were determined in the plasma of an additional 49 cases with benign asbestos-related disease. Results Mesothelin provides better diagnostic accuracy than fibulin-3 for MM whether measured in plasma or pleural effusion: area under the curve (AUC) for plasma was 0.822 (95% CI 0.76 to 0.87) compared with 0.671 (0.61 to 0.73), respectively, and for pleural fluid AUC was 0.815 (0.74 to 0.87) compared with 0.588 (0.51 to 0.67), respectively. Effusion fibulin-3 was an independent significant prognostic factor for survival in MM patients; HR 2.08 (1.14 to 3.82), p=0.017. MM patients with effusion fibulin-3 levels below the median survived significantly longer than those with levels above the median (14.1 vs 7.9 months, p=0.012). Mesothelin and neutrophil to lymphocyte ratio were not significant prognostic markers. Conclusions Soluble mesothelin is a superior diagnostic biomarker for MM compared with fibulin-3, whereas fibulin-3 provides superior prognostic information compared with mesothelin.
Striatum gray matter reduction in males with an overactive behavioral activation system

Using optimized voxel‐based morphometry, we studied the relationship between gray matter volume in brain areas associated with reward and scores on a behavioral activation system measure (the Sensitivity to Reward scale) in a sample of 50 male undergraduates. Voxel‐based morphometry analysis revealed a negative correlation between Sensitivity to Reward scores and gray matter volume in the dorsal striatum and prefrontal cortex. Results indicate that a reduced volume in the striatum might be associated with enhanced reward sensitivity and deficits in inhibitory control.
Effects of Low Sulfur Fuel and a Catalyzed Particle Trap on the Composition and Toxicity of Diesel Emissions

In this study we compared a “baseline” condition of uncontrolled diesel engine exhaust (DEE) emissions generated with current (circa 2003) certification fuel to an emissions-reduction (ER) case with low sulfur fuel and a catalyzed particle trap. Lung toxicity assessments (resistance to respiratory viral infection, lung inflammation, and oxidative stress) were performed on mice (C57Bl/6) exposed by inhalation (6 hr/day for 7 days). The engine was operated identically (same engine load) in both cases, and the inhalation exposures were conducted at the same exhaust dilution rate. For baseline DEE, this dilution resulted in a particle mass (PM) concentration of approximately 200 μg/m3 PM, whereas the ER reduced the PM and almost every other measured constituent [except nitrogen oxides (NOx)] to near background levels in the exposure atmospheres. These measurements included PM, PM size distribution, PM composition (carbon, ions, elements), NOx, carbon monoxide, speciated/total volatile hydrocarbons, and several classes of semi-volatile organic compounds. After exposure concluded, one group of mice was immediately sacrificed and assessed for inflammation and oxidative stress in lung homogenate. Another group of mice were intratracheally instilled with respiratory syncytial virus (RSV), and RSV lung clearance and inflammation was assessed 4 days later. Baseline DEE produced statistically significant biological effects for all measured parameters. The use of low sulfur fuel and a catalyzed trap either completely or nearly eliminated the effects.
Phosphorylation of GENOMES UNCOUPLED 4 Alters Stimulation of Mg Chelatase Activity in Angiosperms1[OPEN]

GENOMES UNCOUPLED 4, a positive regulator of tetrapyrrole biosynthesis, is phosphorylated at serine 264 within a conserved C-terminal motif leading to altered stimulation of Mg chelatase in angiosperms. GENOMES UNCOUPLED 4 (GUN4) is a positive regulator of light-dependent chlorophyll biosynthesis. GUN4 activates Mg chelatase (MgCh) that catalyzes the insertion of an Mg2+ ion into protoporphyrin IX. We show that Arabidopsis (Arabidopsis thaliana) GUN4 is phosphorylated at Ser 264 (S264), the penultimate amino acid residue at the C terminus. While GUN4 is preferentially phosphorylated in darkness, phosphorylation is reduced upon accumulation of Mg porphyrins. Expression of a phosphomimicking GUN4(S264D) results in an incomplete complementation of the white gun4-2 null mutant and a chlorotic phenotype comparable to gun4 knockdown mutants. Phosphorylated GUN4 has a reduced stimulatory effect on MgCh in vitro and in vivo but retains its protein stability and tetrapyrrole binding capacity. Analysis of GUN4 found in oxygenic photosynthetic organisms reveals the evolution of a C-terminal extension, which harbors the phosphorylation site of GUN4 expressed in angiosperms. Homologs of GUN4 from Synechocystis and Chlamydomonas lack the conserved phosphorylation site found in a C-terminal extension of angiosperm GUN4. Biochemical studies proved the importance of the C-terminal extension for MgCh stimulation and inactivation of GUN4 by phosphorylation in angiosperms. An additional mechanism regulating MgCh activity is proposed. In conjunction with the dark repression of 5-aminolevulinic acid synthesis, GUN4 phosphorylation minimizes the flow of intermediates into the Mg branch of the tetrapyrrole metabolic pathway for chlorophyll biosynthesis.
The Impact of Kt/V Urea-Based Dialysis Adequacy on Quality of Life and Adherence in Haemodialysis Patients: A Cross-Sectional Study in Greece

There is clear evidence of a link between dialysis adequacy (as measured by urea kinetic modeling or urea reduction ratio) and such important clinical outcomes as morbidity and mortality. Evidence regarding the relationship between dialysis adequacy and quality of life (QOL) outcomes as well as adherence is less clear. The present paper is a study protocol which is planning to answer the following research question: what is the impact of dialysis adequacy on QOL and adherence in a sample of hemodialysis patients? The final sample size will be around 100 patients undergoing hemodialysis. Each subject’s QOL and adherence will be measured using the following instruments: i) the Missoula-VITAS quality of life index 25; ii) the multidimensional scale of perceived social support and iii) the simplified medication adherence questionnaire. Dialysis adequacy is expected to be related to QOL and adherence scores.