Miracle-dz/UniFAR-FTUs huggingface dataset:
p38γ regulates interaction of nuclear PSF and RNA with the tumour-suppressor hDlg in response to osmotic shock

Activation of p38γ modulates the integrity of the complex formed by the human discs large protein (hDlg) with cytoskeletal proteins, which is important for cell adaptation to changes in environmental osmolarity. Here we report that, in response to hyperosmotic stress, p38γ also regulates formation of complexes between hDlg and the nuclear protein polypyrimidine tract-binding protein-associated-splicing factor (PSF). Following osmotic shock, p38γ in the cell nucleus increases its association with nuclear hDlg, thereby causing dissociation of hDlg-PSF complexes. Moreover, hDlg and PSF bind different RNAs; in response to osmotic shock, p38γ causes hDlg-PSF and hDlg-RNA dissociation independently of its kinase activity. These findings identify a novel nuclear complex and suggest a previously unreported function of p38γ, which is independent of its catalytic activity and could affect mRNA processing and/or gene transcription to aid cell adaptation to osmolarity changes in the environment.
Laser speckle reduction based on angular diversity induced by Piezoelectric Benders

Speckle reduction techniques have been investigated in display systems with coherent light sources. We propose a simple but efficient method to reduce speckle via two fast vibrating piezoelectric benders. The concept is modulating laser beams to have angle diversity and reducing speckle by temporal averaging in the integration time of the detector. Experiments demonstrate that the speckle contrast is suppressed down to 0.06. Both free space and imaging geometry are considered. In order to fairly evaluate the speckle reduction, the optical configuration as well as the camera settings, which largely affect the speckle contrast, is discussed.
Multiresolution infrared optical properties for Gaussian sea surfaces: theoretical validation in the one-dimensional case

We improve the validation of the sea surface infrared optical properties multiresolution model implemented in MATISSE-v2.0, in the 1D case, by comparison with a reference model using a sub-millimeter discretization of the surface. A set of numerical tests is made for various wind speeds, resolutions and realizations of the sea surface. The tests show a good agreement between the results except for grazing angles, where the influence of inner and mutual multiple reflections and adjacent shadowing has still to be investigated.
Improving the SNR during color image processing while preserving the appearance of clipped pixels

An image processing path typically involves color correction or white balance resulting in higher than unity color gains. A gain higher than unity increases the noise in that respective channel, and therefore degrades the SNR performance of the input signal. If the input signal does not have enough SNR to accommodate the extra gain, the resultant color image has increased color noise. This is the usual case for color processing in cell phone cameras, which have sensors with limited SNR and high color crosstalk. This phenomenon degrades images more as illuminants differ from D65. In addition, the incomplete information for clipped pixels often results in unsightly artifacts during color processing. To correct this dual problem, we investigate the use of under unity color gains, which, by increasing the exposure of the sensor, would improve the resultant SNR of the color corrected image. The proposed method preserves the appearance of clipped pixels and the overall luminance of the image, while applying the appropriate color gains.
The neuropeptide Y monomer in solution is not folded in the pancreatic‐polypeptide fold

Fluorescence‐labelled analogs of NPY, a 36‐amino acid peptide amide, were synthesized by solid‐phase peptide synthesis and used for fluorescence‐resonance energy transfer studies to investigate the conformation. Energy‐transfer efficiency measurements in different media at the concentration of 10 μM are in agreement with a model of the NPY structure proposed by NMR studies (performed at millimolar concentration) in which the C‐terminal part of the molecule adopts an α‐helical conformation while the N‐terminal part is flexible. According to this model, the α‐helix is stabilized by intermolecular hydrophobic interactions because of the formation of dimers. The decrease of the peptide concentration causes a shift of the dimerization equilibrium toward the monomeric form. Energy‐transfer efficiency measurements performed at lower concentrations do not support the hypothesis of the folding back of the N‐terminal tail onto the C‐terminal α‐helix to yield the so‐called “PP‐fold” conformation. This structure is observed in the crystal structure of avian pancreatic polypeptide, a member of the NPY peptide hormone family, and it has been considered to be the bioactive one. Our results complete the structural characterization of NPY in solution at concentration ranges in which NMR experiments are not feasible. Furthermore, these results open the way to study the conformation of the receptor‐bound ligand.
JALA Special Issue

Since the idea was originally proposed in the 1960s by Clark and Lyons, biosensors have developed into a thriving field and have been extensively applied in fermentation processes, environmental monitoring, food engineering, clinical medicine, and military medicine. Thereafter, industry became actively involved in the development and commercialization of biosensor production, and the first-generation product for blood glucose testing launched into the market in 1979. The second generation of biosensors was defined by the use of an antibody or receptor protein as recognition components with a more diversified selection of transducers, such as a field effect semiconductor, pressure of the transistor, an optical fiber, or a surface acoustic wave filter. In 1985, the Pharmacia company successfully developed the surface plasma resonance technique, which pushed biosensor detection limits down to as low as 10 g/mL and made real-time detection of biological interactions possible. Recently, the third generation of biosensors has been positioned for more portable, automated, real-time measurement capabilities.
Functional assessment of patients with systemic sclerosis by the use of 'Six-minutes-walking-test'.

AIMS Systemic Sclerosis (SS) is a chronic inflammatory disease of the connective tissues, characterised by alterations in the functions and structures of the small blood vessels (capillaries and arterioles) and by modifications associated with the disposition of collagen in the tissues. One of the most frequent complication of the SS is the pulmonary arterial hypertension (PAH). Aim of this study was to assess the various pathophysiological relationships betweens SS and PAH in order to establish whether the presence of this systemic disease can represent a risk factor. MATERIALS AND METHODS Ten patients affected by SS (9 women and 1 man, with a mean age of 55.7 +/- 11.4 years) were enrolled in our study, as inpatients at Dept. of Internal Medicine and Rheumatology Unit of Perugia University School of Medicine in the "Santa Maria" General Hospital in Terni, Italy. A control group of 10 clinically healthy subjects (CHS, 9 women and 1 man, ranging in age from 35 to 55 years) was also recruited in order to obtain normal clinical data of reference In subjects recruited, we have conducted a functional evaluation, based on physical tests (6-minute-walking-test, 6MWT), equipment and laboratory, on subjects suffering from SS with suspected PAH, in order to calculate the degree of cardio-pulmonary compromission brought on by this disease, taking into consideration important variables such as age and gender. RESULTS The 6 MWT showed that the mean value at rest of the O2 saturation (%) was 97.1 +/- 1.20, heart rate (hr/min) 76 +/- 8.8, and respiratory rate (rr/min) 20.4 +/- 2.8. HS had 98.6 +/- 0.52, 75.7 +/- 6.86, and 16.8 +/- 1.61, respectively. After the the test, the results showed that the patients had O2 saturation 93.8 +/- 3.42, hr 113 +/- 20.27, and rr 31 +/- 2.86. HS had 97.6 +/- 0.69, 90.7 +/- 5.67, and 20.1 +/- 1.59, respectively. CONCLUSIONS Our study has confirmed the high involvement of PAH and other cardio-respiratory disturbances in patients with SS. In fact, we have verified PAP to be above the normal range in 3 out of 10 patients, while the other 3 patients presented borderline values. Because it is a simple method to conduct at low cost, in addition to being non-invasive, reproducible and well accepted, we must affirm that the 6MWT should be more utilized and exploited, especially during the fi rst phases of diagnosis. This in turn can help us to assess the patients and to determine a course of treatment which is more complex and onerous, as in therapeutic monitoring for verifying efficacy.
Visualization of sound field and sound source vibration using laser measurement method

Visualizations help us to understand the sound field behavior. A well-known method of sound field visualization is Kunt’s experiment which visualizes standing waves using light particles. Comprehending of both accurate and transient information on sound fields requires measurement of information at multiple points, and also their visualization. Microphones are commonly used to implement such measurements, which means that numerous microphones are needed. On the other hand, Laser Doppler Vibrometer (LDV) can be used to measure an average sound pressure over a laser path. We have conducted fundamental research on sound field measurement and visualization using LDV and Computed Tomography (CT) without ordinary microphones. The measured value contains integrated information on the laser path. If we have data on an area measured from all directions using LDV, we can estimate the sound field in the area without having to measure at many points using microphones. The new technology of observing sound field and vibration is proposed and being put to practical use in this way. The sound field is generated by sound source and it is important to know the relationship between sound field and sound source. It is very useful to observe both sound field and sound source vibration simultaneously. In this paper, we describe the integrated visualization of sound field and sound source vibration using 3D laser measurement method. We used Processing programming language in order to realize the interactive visualization of sound field and sound source vibration. In addition, we conducted an experimental measurement of impulse responses with laser CT and Time Stretched Pulse (TSP) signal.
Denoising Volumetric Data on GPU

Volumetric data is currently gradually being used more and more in everyday aspect of our lives. Processing such data is computationally expensive and until now more sophisticated algorithms could not be used. The possibilities of processing such data have considerably widened since the increase of parallel computational power in modern GPUs. We present a novel scheme for running a nonlocal means denoising algorithm on a commodity-grade GPU. The speedup is considerable, shortening the time needed for denoise one abdominal CT scan in minutes instead of hours without compromising the result quality. Such approach allows for example lowering the radiation doses for patients being examined with a CT scan.
Fast and efficient bandwidth-delay constrained routing algorithm for SDN networks

In this paper, we propose a new routing algorithm which calculates bandwidth-delay constrained routes in the fast and efficient manner. The algorithm is designed for the software-defined backbone networks, where the control plane is separated from the data plane and logically centralized. Besides providing the required quality of service (QoS), the algorithm aims to maximize utilization of network resources, as that is the major interest of the infrastructure providers. To reduce the computational complexity of this complex traffic engineering task, we consider the control framework which classifies traffic flows in a finite number of categories based on the level of delay sensitivity. The simulation results show that the proposed approach to QoS provisioning, although relatively simple, leads to smaller amount of rejected QoS requests under a wide range of system parameters than the competitive complex solutions.
Efficient evaluation of relevance feedback algorithms for XML content-based retrieval systems

Purpose – Information retrieval (IR) and feedback in Extensible Markup Language (XML) are rather new fields for researchers; natural questions arise, such as: how good are the feedback algorithms in XML IR? Can they be evaluated with standard evaluation tools? Even though some evaluation methods have been proposed in the literature it is still not clear yet which of them are applicable in the context of XML IR, and which metrics they can be combined with to assess the quality of XML retrieval algorithms that use feedback. This paper aims to elaborate on this.Design/methodology/approach – The efficient evaluation of relevance feedback (RF) algorithms for XML collection posed interesting challenges on the IR and database researchers. The system based on the keyword‐based queries whether on the main query or in the RF processing instead of the XPath and structure query languages which were more complex. For measuring the efficiency of the system, the paper used the extended RF algorithms (residual collection.
Cultivation and in vitro cloning or procyclic culture forms of Trypanosoma brucei in a semi-defined medium. Short communication.

Attempts to cultivate the vector forms of Trypanosoma brucei in defined media have made good progress in the last few years. Good growth of most T. brucei stocks which were tested could be achieved in semi-defined media (supplemented with 5-10% foetal bovine serum): RE I (Steiger and Steiger, and modifications of this medium (R. Steiger, personal communication); SDM-77 (Brun and Jenni, 1977); SM (Cunningham, 1977). Fully defined media (e.g. HX 25, Cross and Manning, 1973) are still unsuitable for most T. brucei stocks.
Effect of Pipe Sags on Wastewater Collection System Performance

Sagging of pipelines is a common problem in centralized wastewater collection systems. Wastewater flowing through sags experiences several changes of slope, and the flow through flat and negative slope sections is prone to a significant reduction in mean velocity. The objective of this study is to determine when pipe sags would result in significant velocities below design conditions, which also would increase the risk of a sewer backup. A sagged pipe configuration that could be encountered in sanitary sewer systems was depicted; thereby, analyses on uniform and gradually varied flows were conducted to determine velocity profiles through different segments of the sagged pipeline setup used for the study. The results indicate that there are significant occurrences when either the velocity in the pipe sags goes below minimum, as recommended in the Ten States Standards (Health Research, Inc., 2004) (0.61 m/s [2.0 ft/sec]), or flow depth rises to pipe diameter (full section flow). Additionally, velocities along a sagged pipe were calculated for temporal flow rates to account for daily and seasonal flow rate changes in a typical wastewater collection system. Results of the temporal flow rate analysis suggest that, for a 200‐mm (8‐in.) diameter sagged pipe segment with full‐section (wet weather) flow, 75% of the mean velocities would be below the minimum velocity recommended as a Ten States Standard.
The complete mitochondrial genomes of natural diploid and tetraploid loaches Misgurnus anguillicaudatus (Cypriniformes: Cobitidae)

Abstract Dojo loach Misgurnus anguillicaudatus, a small-sized freshwater fish species, is not only one of the most important cultured fish in East Asia, but also a promising model animal to study evolutionary biology for polyploidy. We sequenced the complete mitochondrial genomes from the natural diploid and tetraploid individuals of this species. The two different cytotypes loaches share the same length (16,646 bp) and structural organization of mitochondrial genome. The two genomes have 98.3% nucleotide sequence similarity, and the biggest nucleotide sequence divergence between homologous genes is observed in CYTB gene.
The Influence of the Ventilatory Pattern on Ventilation, Circulation and Oxygen Transport during Continuous Positive‐Pressure Ventilation An Experimental Study

In IPPV, the ventilatory pattern produced by the ventilator and the lung systems is known to influence pulmonary and cardiovascular functions. In this study on dogs the ventilatory pattern of a conventional respirator (Siemens‐Elema Servo Ventilator 900=SV‐900) constituted the norm for comparison with that produced by a system for volume‐controlled HFPPV. The experimental conditions were kept identical (pentobarbital anaesthesia and normoventilation, i.e. arterial PCO2=40 mm Hg, pH=7.4 and constant FIO2 of the inspired air).
A New Algorithm for Finger-Vein Image Enhancement and Segmentation

In order to achieve accurate extraction of human finger-vein (FV) network, this paper addresses the problems of FV image restoration, enhancement and segmentation. Due to strong scattering occurring in the biological tissue in imaging, FV images always are of contrast deterioration. Considering blur reduction and visibility improvement, a scattering removal scheme is firstly used for image restoration. Then, a new FV image enhancement method is proposed based on a bank of even Gabor filters. Finally, a matting-based method is used to segment FV networks by automatically estimating and scribbling the foreground and background in FV images. Experimental results show that the proposed method is capable of enhancing and segmenting FV networks in images reliably and effectively.
The use of tissue plasminogen activator infusion to re-establish function of tunneled hemodialysis catheters.

PURPOSE To evaluate the safety and efficacy of the recombinant tissue plasminogen activator alteplase in the clearance of poorly functioning tunneled hemodialysis catheters. METHODS We retrospectively reviewed the outcomes of 25 patients who presented with poorly functioning hemodialysis catheters and were treated with alteplase. After confirming fluoroscopically the need for thrombolytic therapy, alteplase was administered over 2 hours as a 2.5-mg/hour/catheter lumen infusion (total 10 mg). Treatment was considered a clinical success if a flow rate of 250 mL or more per minute was established. RESULTS Clinical success was achieved in each of 25 patients (100%). There were no thrombolytic-related complications. Catheter survival was extended 30 days in 54% of patients and 45 days in 33% of patients. CONCLUSION Alteplase is a safe and effective means of producing clearance of blocked tunneled catheters.
Genetic Diversity and Bottleneck Analysis of Indigenous Grey Cattle Breeds of India Based on Microsatellite Data

Bovine microsatellite data of 21 loci was used for the assessment of genetic diversity and bottleneck analysis of 10 indigenous grey cattle breeds from different agroclimatic regions of India. A total of 448 alleles were observed across 21 loci and the observed number of alleles varied from 11 (INRA 05) to 35 (ILSTS-05). The overall observed and expected heterozygosity was 0.722 and 0.802, the PIC and Shannon index values were 0.779 and 2.065 indicating high genetic diversity. The mean number of alleles was 12.33 across 10 grey cattle breeds. The maximum observed heterozygosity was observed in Hariana and minimum in Hill Cattle breed. The FST estimates revealed 92.5% of the total genetic variation within breed, while 7.5% of the total genetic variation was among breeds. Three different tests, viz., Sign rank, Standardized differences and Wilcoxon tests using 3 models of microsatellite evolution (IAM, SMM and TPM) were employed to investigate whether any of the ten Indian grey cattle populations have undergone recent bottleneck or were in mutation drift equilibrium. The tests revealed no genetic bottleneck in recent past and this was confirmed by mode shift test which gave L-shaped distribution for proportion of alleles.
Uniform spectral partition method for the propagation of Gaussian pulses on lossy transmission lines using the Monte Carlo method

In this article we present a probabilistic spectral partition theory for a previously derived Monte Carlo method and show how to use it for the numerical simulation of Gaussian pulse propagation in a lossy transmission line with resistive boundary conditions. The spectral partition method consists in the random generation of frequencies, inside the source that feeds the line, and establishes the connection between the Monte Carlo line method and the tools of circuit analysis in the frequency domain. The main aspects regarding the implementation of this Monte Carlo algorithm are also addressed.
Evaluation of the clinical usefulness of COBAS AMPLICOR HCV MONITOR assay (ver2.0): Comparison with AMPLICOR HCV MONITOR assay (ver1.0) and HCV core protein level

The quantitation of serum levels of hepatitis C virus (HCV) RNA in chronic hepatitis C has been regarded as one of the most important indicators for the outcome of interferon (IFN) therapy. The AMPLICOR HCV MONITOR version 1.0 (AMPLICOR v1.0) assay is widely used for the evaluation of the HCV level. A new generation assay called the COBAS AMPLICOR HCV MONITOR version 2.0 (COBAS v2.0) assay, which is semiautomated and modified to amplify all genotypes equally, has been developed. The aim of this study was to evaluate the clinical relevance of the COBAS v2.0 assay in comparison with the AMPLICOR v1.0 assay and HCV core protein assay in patients with chronic hepatitis C before IFN therapy. HCV RNA was detectable in 230 cases (97.5%) and undetectable in 6 cases (2.5%) by the COBAS v2.0 assay. The RNA levels measured by the AMPLICOR v1.0 assay correlated significantly with those measured by the COBAS v2.0 assay, and the sensitivity of the new version 2.0 assay was better than that of version 1.0, especially in serotype 2. In relation to the outcome of IFN therapy, HCV RNA levels from virologically sustained responders by the AMPLICOR v1.0 assay were 82.3 ± 22.9 kcopies/ml in serotype 1 and 36.9 ± 13.4 kcopies/ml in serotype 2, and those from virologically nonsustained responders were 525.2 ± 48.6 kcopies/ml in serotype 1 and 76.7 ± 19.5 kcopies/ml in serotype 2.The rates of sustained response to <100 kcopies/ml were 34/63 (54.0%) in serotype 1 and 24/48 (50.0%) in serotype 2. A statistically significant virological response was seen in serotype 1 (P < 0.0001), but not in serotype 2. In contrast, the levels in virologically sustained responders by the COBAS v2.0 assay were 88.2 ± 20.5 KIU/ml in serotype 1 and 136.8 ± 40.1 KIU/ml in serotype 2, and those in virologically nonsustained responders were 608.8 ± 48.4 KIU/ml in serotype 1 and 328.3 ± 62.8 KIU/ml in serotype 2. The rates of sustained response to <100 KIU/ml were 33/60 (55.0%) in serotype 1 and 21/35 (60.0%) in serotype 2. Statistical significance in virological response was seen in both serotype 1 (P < 0.0001) and serotype 2 (P < 0.05). Although the sensitivity of the HCV core protein assay was lower than that with the COBAS v2.0 assay, the HCV core protein levels also correlated well with the results of the COBAS v2.0 assay. The HCV core protein levels of virologically sustained responders were 37.6 ± 12.0 pg/ml in serotype 1, 81.3 ± 37.0 pg/ml in serotype 2, and those of virologically nonsustained responders were 289.9 ± 23.5 pg/ml in serotype 1, 191.4 ± 32.1 pg/ml in serotype 2. This assay could predict the outcome of IFN therapy in both serotype 1 (P < 0.0001) and serotype 2 (P < 0.05). Thus, both the COBAS v2.0 assay and the HCV core protein assay showed that the viral load was an indicator of virologically sustained response in serotype 2 and in serotype 1. J. Med. Virol. 68:343–351, 2002. © 2002 Wiley‐Liss, Inc.