Miracle-dz/UniFAR-FTUs huggingface dataset:
Myxococcus xanthus sasS encodes a sensor histidine kinase required for early developmental gene expression

Initiation of Myxococcus xanthus multicellular development requires integration of information concerning the cells' nutrient status and density. A gain-of-function mutation, sasB7, that bypasses both the starvation and high cell density requirements for developmental expression of the 4521 reporter gene, maps to the sasS gene. The wild-type sasS gene was cloned and sequenced. This gene is predicted to encode a sensor histidine protein kinase that appears to be a key element in the transduction of starvation and cell density inputs. The sasS null mutants express 4521 at a basal level, form defective fruiting bodies, and exhibit reduced sporulation efficiencies. These data indicate that the wild-type sasS gene product functions as a positive regulator of 4521 expression and participates in M. xanthus development. The N terminus of SasS is predicted to contain two transmembrane domains that would locate the protein to the cytoplasmic membrane. The sasB7 mutation, an E139K missense mutation, maps to the predicted N-terminal periplasmic region. The C terminus of SasS contains all of the conserved residues typical of the sensor histidine protein kinases. SasS is predicted to be the sensor protein in a two-component system that integrates information required for M. xanthus developmental gene expression.
Adenovirus vector-mediated in vivo gene transfer into adult murine retina.

PURPOSE To determine whether a reporter gene can be introduced into the adult mammalian retina in vivo through means of a recombinant replication-deficient adenovirus. METHODS A dilution series of purified Ad.CMVlacZ ranging from 10(5) to 10(11) pfu/ml was prepared and microinjected into the subretinal space of adult CD-1 mice. This virus contained the cytomegalovirus (CMV)-promoted Escherichia coli reporter gene, lacZ. LacZ expression was assessed in enucleated eyes from 0 to 95 days after injection by beta-galactosidase (beta-Gal) assay. RESULTS The efficiency of transfection increased as a function of concentration of recombinant virus injected. Eyes injected with greater than 10(7) pfu of Ad.CMVlacZ demonstrated beta-Gal activity lasting at least 95 days. LacZ expression was apparent only in those cells directly exposed to the adenovirus. LacZ expression was observed in the retinal pigment epithelium (RPE) at high efficiency at 48 hours after exposure. By 2 weeks after injection of > 10(7) pfu, lacZ was also expressed in photoreceptors, but at lower density. CONCLUSIONS These results demonstrate that high efficiency stable transfer of functional genes can be achieved in vivo in post-mitotic mammalian retina using recombinant adenoviral vectors. Adenovirus vectors appear to be a promising means for delivering therapeutic genes in vivo to the mammalian neural retina and particularly to the RPE.
Magnesium intake in relation to risk of colorectal cancer in women.

CONTEXT Animal studies have suggested that dietary magnesium may play a role in the prevention of colorectal cancer, but data in humans are lacking. OBJECTIVE To evaluate the hypothesis that a high magnesium intake reduces the risk of colorectal cancer in women. DESIGN, SETTING, AND PARTICIPANTS The Swedish Mammography Cohort, a population-based prospective cohort of 61,433 women aged 40 to 75 years without previous diagnosis of cancer at baseline from 1987 to 1990. MAIN OUTCOME MEASURE Incident invasive colorectal cancer. RESULTS During a mean of 14.8 years (911 042 person-years) of follow-up, 805 incident colorectal cancer cases were diagnosed. After adjustment for potential confounders, we observed an inverse association of magnesium intake with the risk of colorectal cancer (P for trend = .006). Compared with women in the lowest quintile of magnesium intake, the multivariate rate ratio (RR) was 0.59 (95% confidence interval [CI], 0.40-0.87) for those in the highest quintile. The inverse association was observed for both colon (RR, 0.66; 95% CI, 0.41-1.07) and rectal cancer (RR, 0.45; 95% CI, 0.22-0.89). CONCLUSION This population-based prospective study suggests that a high magnesium intake may reduce the occurrence of colorectal cancer in women.
Word recognition performance in continuous and interrupted broad-band noise by normal-hearing and simulated hearing-impaired listeners.

Word recognition performance was investigated in 12 normal-hearing young adults in continuous and interrupted broad-band noise as a function of signal-to-noise ratio (S:N) with and without a simulated high frequency hearing loss (i.e., low-pass filtered at 2000 Hz). Subjects exhibited conventional sigmoid performance-intensity functions in continuous noise, for both unfiltered and filtered conditions. In contrast, subjects demonstrated shallower performance-intensity functions in the interrupted noise conditions with overall superior performance under adverse signal-to-noise ratios relative to the continuous noise conditions. Separate two-way analyses of variances investigating mean word recognition performance differences as a function of normal listening (unfiltered) versus the simulated hearing loss (filtered). Signal-to-noise ratio for both continuous and interrupted noise conditions revealed a significant main effects for S:N with both noise conditions (p < .05) and a significant main effect for the simulated hearing loss only in the interrupted noise condition (p < .05). It was hypothesized that subjects' diminished performance in the interrupted noise condition with the stimulated high frequency hearing loss reflected a reduced ability to temporally resolve auditory information between the gaps of noise.
Oxidized Regenerated Cellulose/Collagen Dressings: Review of Evidence and Recommendations

OBJECTIVE: Healthcare systems are being challenged to manage increasing numbers of nonhealing wounds. Wound dressings are one of the first lines of defense in wound management, and numerous options exist. The oxidized regenerated cellulose (ORC)/collagen dressing may offer healthcare providers a robust and cost-effective tool for use in a variety of wounds. DESIGN: A multidisciplinary panel meeting was convened to discuss the use of ORC/collagen dressings in wound care and provide practice recommendations. A literature search was conducted to provide a brief review of the peer-reviewed studies published between January 2000 and March 2016 to inform the meeting. SETTING: A 2-day panel meeting convened in February 2017. PARTICIPANTS: Healthcare providers with experience using ORC/collagen dressings. This multidisciplinary panel of 15 experts in wound healing included podiatrists, wound care specialists (doctors, certified wound care nurses, and research scientists), and an orthopedist. RESULTS: The literature search identified 58 articles, a majority of which were low levels of evidence (69.3% were level 3 or lower). Panel members identified wound types, such as abrasions, burns, stalled wounds, diabetic foot ulcers, and pressure injuries, where ORC/collagen dressing use could be beneficial. Panel members then provided recommendations and technical pearls for the use of ORC/collagen dressings in practice. Barriers to ORC/collagen dressing use were discussed, and potential resolutions were offered. CONCLUSIONS: An ORC/collagen dressing can be a critical tool for clinicians to help manage a variety of wounds. Clinical and economic studies comparing standard-of-care dressings and plain collagen dressings to ORC/collagen dressings are needed.
A new method for ulcer detection in endoscopic images

The entire visualization of GastroIntestinal (GI) tract is not possible with conventional endoscopic exams. Wireless Capsule Endoscopy (WCE) is a low risk, painless, noninvasive procedure for diagnosing diseases such as bleeding, polyps, ulcers, and Crohns disease within the human digestive tract, especially the small intestine that was unreachable using the traditional endoscopic methods. However, analysis of massive images of WCE detection is tedious and time consuming to physicians. Hence, researchers have developed software methods to detect these diseases automatically. Thus, the effectiveness of WCE can be improved. In this paper, a novel textural feature extraction method is proposed based on Contourlet transform and Log Gabor filter to distinguish ulcer regions from normal regions. The results show that the proposed method performs well with a high accuracy rate of 94.16% using Support Vector Machine (SVM) classifier in HSV colour space.
Transcervical chorionic villus biopsy with a brush

A brush delivered to the biopsy site by a metal introducer and cannula set was tested as an alternative implement for transcervical collection of chorionic villi. This implement was easy to use and readily identified by ultrasound. With only one attempt at sampling, the overall collection rate for 83 patients was 65 per cent. With practice 84 per cent successful collection was achieved. Gestations between 8 and 11 weeks was the best time for collection of chorionic villi. A single sampling can produce adequate material (15 mg wet weight) suitable for diagnostic purposes. No gestation sac was perforated but some slight bleeding followed the procedure. Appreciable success following a single sampling attempt coupled with the low complication rate suggests that this technique may have clinical application and deserves further investigation.
Image denoising using directional filter banks

The use of wavelet thresholding has been investigated with much success in the areas of denoising, density estimation, image restoration, etc. Significant attention has been given to wavelet thresholding as a signal denoising technique. The algorithm is simple and provides good results. The 2-D discrete wavelet transform (DWT) and its relatives have been used to generalize the denoising methods to images. However the DWT is limited in its representation of directional information like edges and some types of texture. We propose the use of a directional filter bank for image denoising under the same premise as wavelet thresholding: small magnitude subband coefficients represent noise and can be replaced with zeros while large coefficients reflect, in our case, strong signal content in a given direction. We show that the directional filter bank is capable of preserving edge information better than DWT based techniques while effectively removing noise. The proposed technique provides sharp images with higher perceptual quality.
What We Know about Software Test Maturity and Test Process Improvement

In many companies, software testing practices and processes are far from mature and are usually conducted in an ad hoc fashion. Such immature practices lead to negative outcomes—for example, testing that doesn’t detect all the defects or that incurs cost and schedule overruns. To conduct test maturity assessment (TMA) and test process improvement (TPI) systematically, researchers and practitioners have proposed various approaches and frameworks. Motivated by a recent industrial project in TMA and TPI and wanting to identify the state of the art and practice in this area, researchers conducted a review of both the scientific literature and practitioners’ gray literature (for example, blog posts). The review identified 58 test maturity models and many sources with varying degrees of empirical evidence. The review’s results can serve as an evidence-based overview of and index to the vast body of knowledge in this important, fast-growing area. Using this knowledge, both researchers and practitioners should be able to assess and improve the maturity of test processes.
IPPB‐assisted coughing in neuromuscular disorders

In neuromuscular disorders, reduced peak cough flows (PCFs) are considered to increase the risk of respiratory complications such as pneumonia or chronic atelectasis. Different methods were described to improve PCF. However, these studies were primarily carried out in adults, and there is limited information regarding the use and efficacy of these methods in children with respiratory muscle weakness. The aim of this study was to investigate whether hyperinsufflation with an intermittent positive‐pressure breathing (IPPB) device is effective in cough augmentation in pediatric patients. Spirometry (forced inspiratory vital capacity, FIVC; forced expiratory volume in 1 sec, FEV1), respiratory muscle pressures (peak inspiratory pressure, PIP; peak expiratory pressure, PEP), and PCF were measured in 29 schoolchildren with various neuromuscular disorders. IPPB‐assisted hyperinsufflation was taught individually to increase lung volumes (maximum insufflation capacity, MIC) above FIVC. The impact of hyperinsufflation on peak cough flow was documented. In 28/29 patients, IPPB‐assisted hyperinsufflation enhanced FIVC from 0.68 ± 0.40 l to an MIC of 1.05 ± 0.47 l (P < 0.001). Unassisted PCF was 119.0 ± 57.7 l/min, and increased to 194.5 ± 74.9 l/min (P < 0.001) in 27/29 patients. This effect was similar in young patients (ages 6–10 years) and older patients (aged >10 years). Augmentation of lung volumes from FIVC to MIC correlated with an increase of PCF (R = 0.42, P < 0.05). IPPB‐assisted hyperinsufflation improves PCF in pediatric neuromuscular disorders. The results suggest that this technique can be used to improve clearance of airway secretions and therefore reduce respiratory morbidity in children with NMD. Pediatr Pulmonol. © 2006 Wiley‐Liss, Inc.
Advances in understanding and assessing malnutrition

Purpose of reviewTo describe the varying views on the pathophysiology of malnutrition in different populations and the definitions that result from these views. To propose an umbrella definition for different malnutrition syndromes and principles of assessment of nutritional state. Recent findingsAt present, tacitly or openly inflammatory activity is considered to contribute to the malnourished state. The malnourished state, therefore, arises from a combination of inflammation and a disturbed nutrient balance (undernutrition or overnutrition). The undernourished category of malnutrition leads to loss of body cell mass, which, together with inflammation diminish host response and quality of life. On the basis of these findings, malnutrition may be assessed by estimating nutrient balance but, subsequently, to measure body composition (muscle mass), inflammatory activity (plasma albumin and C-reactive protein) and muscle endurance and force. Changes in muscle function in patients with chronic obstructive pulmonary disease are associated with changes in fiber composition. Few data exist in other malnourished states. SummaryThere is an increasing acknowledgement of the fact that malnutrition is caused by disturbances in nutrient balance and inflammatory activity. This leads to changes in body composition and diminished function. An umbrella definition has been proposed including the pathogenetic factors, underlying the different malnutrition syndromes and dictating the methods to assess malnutrition.
Measuring cable sheath currents to detect defects in cable sheath connections

This paper presents a method for detecting different types of defects in the cable sheaths interconnected in a cross bonding configuration of a HV cable system installed in flat or trefoil layout using the sheath currents as input data. Three different defects have been analyzed: electric continuity loss of earth connection, short-circuit between sectionalized metal sheaths of a cable joint and link-box flooding. The sheath current has been calculated by two different approaches, one on the basis of theoretical equations, programed in MATLAB® and the other on the basis of ATP software simulating the cable system model. The results obtained using both methods have achieved a good agreement between them. A simple criterion by the means of a easy normalized code of four discrete levels 0, 1, 2 and 3 has been developed to distinguish the magnitude level of change of sheath currents in case of the indicated defect existence in order to trigger alarm.
Expression patterns of novel genes during mouse preimplantation embryogenesis

Little is known about the repertoire of genes expressed following zygotic gene activation, which occurs during the two‐cell stage in the mouse. As an initial attempt to isolate novel genes, we used previously prepared two‐cell and two‐cell subtraction cDNA libraries (Rothstein et al., Genes Dev 6:1190–1201, 1992) to isolate a panel of seven cDNA clones. Three cDNA had no match in the current DNA sequence data banks and three others revealed sequence homology to portions of sequences in the data banks. One cDNA was 90% homologous to the ras‐related gene Krev/rap 1A. The temporal patterns of expression of these genes during oocyte maturation and preimplantation development were analyzed by a reverse transcription‐polymerase chain reaction (RT‐PCR) assay developed to measure relative levels of mRNAs. Three distinct temporal patterns of expression, designated Classes 1–3, were found. The two Class 1 genes displayed an actin‐like pattern, with a gradual decline in expression during oocyte maturation and through the two‐cell stage, followed by increases at the eight‐cell and/or blastocyst stages. The four genes in Class 2 were expressed at relatively high levels during oocyte maturation and through the one‐cell stage and then declined abruptly between the one‐ and two‐cell stages; an increase then occurred at the eight‐cell and/or blastocyst stages. The expression of the gene in Class 3 declined during oocyte maturation, but then showed a transient increase at the one‐cell stage, with only a very slight increase in synthesis at either the eight‐cell or blastocyst stage. © 1994 Wiley‐Liss, Inc.
Private information retrieval from MDS coded data in distributed storage systems

We consider the problem of providing privacy, in the private information retrieval (PIR) sense, to users requesting data from a distributed storage system (DSS). The DSS uses an (n, k) Maximum Distance Separable (MDS) code to store the data reliably on unreliable storage nodes. Some of these nodes can be spies which report to a third party, such as an oppressive regime, which data is being requested by the user. An information theoretic PIR scheme ensures that a user can satisfy its request while revealing, to the spy nodes, no information on which data is being requested. A user can achieve PIR by downloading all the data in the DSS. However, this is not a feasible solution due to its high communication cost. We construct PIR schemes with low download communication cost. When there is b = 1 spy node in the DSS, we construct PIR schemes with download cost 1/1-R per unit of requested data (R = k/n is the code rate), achieving the information theoretic limit for linear schemes. The proposed schemes are universal since they depend on the code rate, but not on the generator matrix of the code. When there are 2 ≤ b ≤ n - k spy nodes, we devise linear PIR schemes that have download cost equal to b + k per unit of requested data.
Homologous Recombination in Human Embryonic Stem Cells: A Tool for Advancing Cell Therapy and Understanding and Treating Human Disease

Human embryonic stem cells (hESCs) hold great promise for ushering in an era of novel cell therapies to treat a wide range of rare and common diseases, yet they also provide an unprecedented opportunity for basic research to yield clinical benefit. HESCs can be used to better understand human development, to model human diseases, to understand the contribution of specific mutations to the pathogenesis of disease, and to develop human cell‐based screening systems to identify novel therapeutic agents and evaluate potential toxicity of therapeutic agents under development. Such basic research will benefit greatly from efficient methods to perform targeted gene modification, an area of hESC investigation that is currently in its infancy. Moreover, the reality of hESC‐based cellular therapies will require improved methods for generating the specific cells of interest, and reporter cell lines generated through targeted gene modifications are expected to play an important role in developing optimal cell‐specific differentiation protocols. Herein, we review the current status of homologous recombination in hESCs, a gene targeting technique that is sure to continue to improve, and to play an important role in realizing the maximal human benefit from hESCs. Clin Trans Sci 2011; Volume 4: 298–305
Maspin, p53, p63, and Ki-67 in epithelial lesions of the tongue: from hyperplasia through dysplasia to carcinoma.

BACKGROUND The pattern of changes in the expression of mammary serine protease inhibitor (maspin) tumor suppressor protein in tongue epithelial lesions [hyperplasia (HP), mild dysplasia (MD), moderate-to-severe dysplasia (MSD) and squamous cell carcinoma (SCC)] was investigated and correlated to the expression of maspin-regulating factors p53 and p63, and the proliferation marker Ki-67. METHODS Cases of HP (n = 16), MD (n = 12), MSD (n = 11), and SCC (n = 22) were immunostained for maspin, p53, p63, and Ki-67. Maspin expression was scored separately for the basal, middle, and upper thirds of the epithelial width, and as the total sum of all 'thirds' (maspin-total). p53, p63, and Ki-67 were immuno-morphometrically assessed for the entire epithelial width. RESULTS Maspin expression was differential and progressive extending to higher epithelial layers as dysplastic changes aggravated and culminated in carcinoma. Strong expression was related to MSD in the middle third and to carcinoma in the upper third. It was frequently lost at the invasion front, where the tumor was less differentiated. The changes in mean scores of maspin-total in the different study groups were positively correlated to the mean scores of p63 (r = 0.5, P < 0.001), p53 (r = 0.4, P = 0.004), and Ki-67 (r = 0.5, P < 0.001). CONCLUSIONS Strong expression of maspin in the middle third of the epithelium may be considered a diagnostic sign of mild-to-moderate dysplasia and an indication of carcinoma in the upper third. The correlations between maspin and controlling factors (e.g. p63 and p53) may be events with key roles in the development of tongue carcinoma.
Development and validation of a capillary electrophoresis method for the determination of phenothiazines in human urine in the low nanogram per milliliter concentration range using field‐amplified sample injection

A capillary zone electrophoresis (CZE) method with ultraviolet‐visible detection has been established and validated for the determination of five phenothiazines: thiazinamium methylsulfate, promazine hydrochloride, chlorpromazine hydrochloride, thioridazine hydrochloride, and promethazine hydrochloride in human urine. Optimum separation was obtained on a 64.5 cm × 75 µm bubble cell capillary using a buffer containing 150 mM tris(hydroxymethyl)aminomethane and 25% acetonitrile at pH 8.2, with temperature and voltage of 25°C and 20 kV, respectively. Naphazoline hydrochloride was used as an internal standard. Field‐amplified sample injection (FASI) has been applied to improve the sensitivity of the detection. Considering the influence of parameters affecting the on‐line preconcentration (nature of preinjection plug, sample solvent composition, injection times, and injection voltage) and due to the significant interactions among them, in this paper we propose for the first time the application of a multivariate approach to carry out the study. The optimized conditions were as follows: preinjection plug of water for 7 s at 50 mbar, electrokinetic injection for 40 s at 6.2 kV, and 32 µm of H3PO4 in the sample solvent. Also, a solid‐phase extraction (SPE) procedure is developed to obtain low detection limits and an adequate selectivity for urine samples. The combination of SPE and FASI‐CZE‐UV allows adequate linearities and recoveries, low detection limits (from 2 to 5 ng/mL), and satisfactory precisions (3.0–7.2% for an intermediate RSD %).