Miracle-dz/UniFAR-FTUs huggingface dataset:
Gateway compatible vectors for analysis of gene function in the zebrafish

The recent establishment of recombination‐based cloning systems has greatly facilitated the analysis of gene function by allowing rapid and high‐efficiency generation of plasmid constructs. However, the use of such an approach in zebrafish requires the availability of recombination‐compatible plasmids that are appropriate for functional studies in zebrafish embryos. In this work, we describe the construction and validation of Gateway compatible vectors based on commonly used zebrafish plasmids. We have generated pCS‐based plasmids that allow rapid generation of both N‐terminal and C‐terminal fusion proteins, and we demonstrate that mRNA synthesized from these plasmids encodes functional native or fusion proteins in injected zebrafish embryos. In parallel, we have established similar Gateway plasmids containing Tol2 cis elements that promote efficient integration into the zebrafish genome and allow expression of native or fusion proteins in a tissue‐specific manner in the zebrafish embryo. Finally, we demonstrate the use of this system to rapidly identify tissue‐specific cis elements to aid the establishment of blood vessel‐specific transgenic constructs. Taken together, this work provides an important platform for the rapid functional analyses of open reading frames in zebrafish embryos. Developmental Dynamics 236:3077–3087, 2007. © 2007 Wiley‐Liss, Inc.
The loss of signal detectability in band-pass limiters

A loss of signal detectability results from ideal symmetric limiting of a very narrow-band signal in narrow-band Gaussian noise. At small input snr this loss can be expressed in terms of the degradation of the effective signal energy-to-noise power per cycle ratio. Proceeding from results derived previously by Davenport and Price, an expression is derived for this degradation in terms of the autocorrelation function of the input noise. The degradation is evaluated for three typical input noise autocorrelation functions and is found to be quite small in all these cases. It is seen that the degradation can be made to vanish by appropriately shaping the spectrum of the input noise. Regulation of the input noise spectrum to obtain conditions of limiter operation assumed in this paper may often prove to be a convenient method for reducing loss of signal detectability in band-pass limiters.
ASSESSMENT OF ZERO DRIFT IN THE CODMAN INTRACRANIAL PRESSURE MONITOR: A STUDY FROM 2 NEUROINTENSIVE CARE UNITS

OBJECTIVEIntraparenchymal monitoring devices play an important role in the daily management of head injury and other critically ill neurosurgical patients. Although zero drift data exist for the Camino system (Camino Laboratories, San Diego, CA), only in vitro data exist for the Codman system (Codman and Shurtleff, Inc., Raynham, MA). The aim of this study was to assess the extent of zero drift for the Codman intracranial pressure (ICP) monitor in patients being monitored in 2 neurointensive care units. METHODSThis was a prospective study conducted at 2 neurointensive care units. Eighty-eight patients who required ICP monitoring and who presented to the 2 neurosurgical departments, Center 1 (n = 48) and Center 2 (n = 40), were recruited for participation. The duration of ICP monitoring was noted, as was the resultant pressure reading in normal saline on removing the ICP monitor (zero drift). RESULTSThe median absolute zero drift for the group was 2.0 mm Hg (interquartile range, 1–3 mm Hg). The median time in situ was 108 hours (interquartile range, 69–201 hours). There was a positive correlation between the drift and time of the probe spent in situ (Spearman's correlation coefficient = 0.342; P = 0.001). Of the readings, 20 and 2% showed a drift greater than 5 and 10 mm Hg in magnitude, respectively. CONCLUSIONThese data demonstrate that a small amount of zero drift exists in ICP monitors and that this drift increases with time. The wide range in the data demonstrates that some drift readings are quite excessive. This reinforces the school of thought that, although ICP readings contribute significantly to the management of neurosurgical patients, they should be interpreted carefully and in conjunction with clinical and radiological assessment of patients.
SecDF as Part of the Sec-Translocase Facilitates Efficient Secretion of Bacillus cereus Toxins and Cell Wall-Associated Proteins

The aim of this study was to explore the role of SecDF in protein secretion in Bacillus cereus ATCC 14579 by in-depth characterization of a markerless secDF knock out mutant. Deletion of secDF resulted in pleiotropic effects characterized by a moderately slower growth rate, aberrant cell morphology, enhanced susceptibility to xenobiotics, reduced virulence and motility. Most toxins, including food poisoning-associated enterotoxins Nhe, Hbl, and cytotoxin K, as well as phospholipase C were less abundant in the secretome of the ΔsecDF mutant as determined by label-free mass spectrometry. Global transcriptome studies revealed profound transcriptional changes upon deletion of secDF indicating cell envelope stress. Interestingly, the addition of glucose enhanced the described phenotypes. This study shows that SecDF is an important part of the Sec-translocase mediating efficient secretion of virulence factors in the Gram-positive opportunistic pathogen B. cereus, and further supports the notion that B. cereus enterotoxins are secreted by the Sec-system.
Circulating levels of soluble CD30 are increased in patients with localized scleroderma and correlated with serological and clinical features of the disease.

OBJECTIVE To determine serum soluble CD30 (sCD30) levels in patients with localized scleroderma. METHODS Serum soluble CD30 levels were assayed by a sensitive ELISA in 55 patients with localized scleroderma, in 15 with systemic sclerosis (SSc), and in 20 healthy controls. RESULTS Serum levels of sCD30 were significantly higher in patients with localized scleroderma than in healthy controls. Serum levels of sCD30 were correlated with the number of sclerotic lesions, the number of involved areas, levels of anti-histone antibody IgM, and levels of interleukin 6. sCD30 levels in sera from patients with SSc were also significantly higher than in healthy controls. CONCLUSION These results suggest possible involvement of Th2 cells in the immunopathogenesis in localized scleroderma, and serum sCD30 levels may be helpful in following the outcome of the disease.
Interaction of Ribonucleoside Triphosphates with the Gene 4 Primase of Bacteriophage T7*

The primase fragment of bacteriophage T7 gene 4 protein catalyzes the synthesis of oligoribonucleotides in the presence of ATP, CTP, Mg2+ (or Mn2+), and DNA containing a primase recognition site. During chain initiation, ATP binds with a K m of 0.32 mm, and CTP binds with a K m of 0.85 mm. Synthesis of the dinucleotides proceeds at a rate of 3.8/s. The dinucleotide either dissociates or is extended to a tetranucleotide. The primase preferentially inserts ribonucleotides forming Watson-Crick base pairs with the DNA template >200-fold more rapidly than other ribo- or deoxynucleotides. 3′-dCTP binds the primase with a similar affinity as CTP and is incorporated as a chain terminator at a rate 1 100 that of CTP. ATP analogues α,β-methylene ATP, β,γ-methylene ATP, and β,γ-imido ATP are incorporated by the primase fragment at the 5′-ends of the oligoribonucleotides but not at the 3′-ends. A model is presented in which the primase fragment utilizes two nucleotide-binding sites, one for the initiating ATP and one for the nucleoside triphosphate which elongates the primer on the 3′-end. The initiation site binds ATP or oligoribonucleotides, whereas the elongation site binds ATP or CTP as directed by the template.
Evaluation of dermal pericapillary fibrin cuffs in venous ulceration using confocal microscopy

Dermal pericapillary fibrin is a hallmark of venous disease and is thought to play a pathogenic role in the development of ulceration. However, the actual spatial configuration of pericapillary fibrin is unknown, and it remains unclear whether it truly represents a barrier that can impair physiological exchanges between the blood and dermis. Using confocal microscopy on tissue specimens taken from the edges of venous ulcers in six patients, we report a detailed analysis of dermal pericapillary fibrin deposits. Sections were evaluated with an antibody to human fibrinogen/fibrin and viewed, vertically and horizontally, with confocal microscopy. The distribution of fibrin deposition was highly variable and patchy, with areas of great intensity next to others of marginal intensity. Vertical cut sections showed the highest concentration of fluorescent material next to the lumen of dermal capillaries. Horizontal sections showed that maximal fluorescence was distributed at random. Our findings indicate that fibrin deposits in venous ulcers are patchy and discontinuous around dermal vessels. As such, these deposits are unlikely to act as a true and stable anatomic barrier as originally proposed. However, pericapillary fibrin may still act as a physiological barrier under conditions of poor blood flow where even marginal or patchy fibrin deposition might have a greater effect on the exchange of oxygen and other nutrients between blood and dermis.
Outcomes of non-acute coronary syndrome patients discharged from the emergency department with troponin positivity.

BACKGROUND Cardiac troponin elevation portends a worse prognosis in diverse patient populations. The significance of troponin elevation in patients discharged from emergency departments (EDs) without inpatient admission is not well known. METHODS Patients without a diagnosis of acute coronary syndrome discharged from two EDs between April 1, 2006, and December 31, 2007, with an abnormal cardiac troponin (troponin positive [TP]) were compared to a troponin-negative (TN) cohort matched for age, sex, and primary discharge diagnosis. Outcomes were obtained by linking with a regional ED and a provincial vital statistics database and adjusted for the following: estimated glomerular filtration rate, do-not-resuscitate status, history of coronary artery disease, Canadian Triage and Acuity Scale, and left ventricular hypertrophy on electrocardiography. The primary outcome was a composite of death or admission to hospital within 1 year. RESULTS Our total cohort (n = 344) consisted of 172 TP and 172 TN patients. In the univariate analysis, TP patients had a higher rate of the primary outcome (OR 3.2, 95% CI 2.1-5.0, p < 0.001) and both of its components (p < 0.001). After adjusting for covariates, positive troponin remained an independent predictor of the primary outcome (OR 2.1, 95% CI 1.3-3.4, p = 0.005) and inpatient admission (OR 2.0, 95% CI 1.2-3.4, p = 0.006). There was no significant difference in death (OR 1.3, 95% CI 0.6-2.9, p = 0.5) after adjustment. CONCLUSIONS A positive troponin assay during ED stay in discharged patients is an independent marker for risk of subsequent admission. Our findings suggest that the prognostic power of an abnormal troponin extends to patients discharged from the ED.
Alterations of serum brain type natriuretic peptide (BNP) in patients with Crimean-Congo hemorrhagic fever.

BACKGROUND Crimean-Congo hemorrhagic fever (CCHF) is known to be associated with cardiac damage. Brain type natriuretic peptide (BNP) is secreted from stressed myocardium. OBJECTIVES This study investigated that BNP levels in CCHF and its association with clinical course of disease. METHODS Consecutive CCHF diagnosis confirmed patients were enrolled to the study. Results of patients were compared with age-sex-matched healthy volunteers. Blood samples for BNP levels were collected from the patients during emergency room applications. Mortality, hospitalization duration and other disease severity predictors (thrombocyte count, hemoglobin, white blood cell count, alanine aminotransferase, aspartate aminotransferase, prothrombin time, lactate dehydrogenase, international normalized ratio, activated partial thromboplastin time) were recorded. These parameters' correlations with BNP levels were analyzed. RESULT Forty-three CCHF patients and 28 control subjects recruited to the study. Groups were similar for age and gender. There was no mortality. Levels of BNP were found to be significantly higher in patients than control subjects (100.4±45.4 vs. 78.0±40.4, P=0.033). But BNP levels were not correlated with duration of hospitalization and disease severity predictors (P > 0.05). CONCLUSIONS This study showed that BNP levels are modestly increased in CCHF but this increase does not correlated with disease severity predictors.
TUNEL Apoptotic Cell Detection in Tissue Sections: Critical Evaluation and Improvement

TUNEL, i.e., terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling, has become a widely used staining method to assist in detection of apoptotic cells in tissue sections. However, despite its apparent simplicity, this technique has led to considerable disappointment because of its serious limitations in sensitivity and, even more, in specificity. We reviewed the limitations and artifacts of TUNEL and designed a comprehensive protocol to reassess the various procedures in use for five crosslinking and/or precipitating fixatives. By introducing microwave heating in extreme pH-value solutions (pH 3 for formalin and pH 10.6 for Bouin's fixative) coupled with proteolysis, we obtained an intense staining of 70–80% of apoptotic cells and bodies on archival tissue blocks, with little or no background. Owing to the enhanced sensitivity, early stages of apoptosis could be visualized and may enlarge our vision of the apoptotic cell beyond the mere image of shrinkage necrosis. We conclude that TUNEL remains a technique as useful as it is delicate, requiring critical interpretation of the staining. This study points out that, on archival tissues, despite the technical improvements we propose no protocol can be the final answer to all problems. Technique must be readjusted for any variation in tissue processing. However, step-by-step progress has rendered this method not only applicable but also performable within the constraints of archival surgical pathology specimens.
Tax structure, growth, and welfare in the UK

This paper studies the quantitative implications of changes in the composition of taxes for long-run growth and welfare in the UK economy. Our results suggest that if the goal of tax policy is to promote long-run growth by altering relative tax rates in a budget neutral fashion, then it should reduce labour taxes and increase capital and-or consumption taxes. In contrast, if the aim is to promote welfare, substantial gains can be obtained from tax reforms that decrease the capital tax rate relative to the labour and consumption tax rates or that reduce labour relative to consumption taxes. These findings highlight the importance of the choice of tax structure in policy design. Copyright 2012 Oxford University Press 2011 All rights reserved, Oxford University Press.
Pioglitazone attenuates prostatic enlargement in diet‐induced insulin‐resistant rats by altering lipid distribution and hyperinsulinaemia

BACKGROUND AND PURPOSE Increased incidence of benign prostatic hyperplasia among insulin‐resistant individuals suggests a role for hyperinsulinaemia in prostatic enlargement. We have already reported increased cell proliferation and enlargement of prostate gland in insulin‐resistant rats. The present study aimed to elucidate the molecular mechanisms underlying the reversal of prostatic enlargement in insulin‐resistant rats by the peroxisome proliferator‐activated receptor γ agonist pioglitazone.
Advances in the development of hormonal modulators for the treatment of benign prostatic hyperplasia

Benign prostatic hyperplasia (BPH) is a leading disorder of the ageing male population and is characterized by a progressive enlargement of the prostate, resulting in the obstruction of the proximal urethra and hence the disturbance in normal urinary flow and further quality of life of the patients. Therefore, there is an imperative need to develop a therapeutic modality to combat the overgrowth of the prostate with improvements in both the urinary flow rate and the quality of life of the patients. At present, α-blockers, which act on the dynamic component of the disease to regulate the increased adrenergic tone of the lower urinary tract smooth muscles, and 5-α-reductase inhibitors, which control the overgrowth of the prostate and hence static component by regulating the levels of androgens, are the mainstay of therapies for the treatment of BPH and associated lower urinary tract symptoms. However, each target class has its own limitations in terms of compromised efficacy or tolerability. Therefore, it is pertinent to have an effective and safe therapeutic modality for the further improvement of life of the geriatric male population. Hormone modulators, which regulate the overgrowth of the prostate, represent one of the important categories that have been explored and that is still undergoing certain investigations towards the development of a therapeutic entity for the treatment of BPH. The key lies in achieving the differentiation in terms of improved tolerability with comparable or better efficacy over the existing class of drugs. Gonadotropin receptor modulators and vitamin D receptor agonists may represent promising druggable targets in this therapeutic area, due to the availability of proof of principles and concepts in preclinical animal models and human subjects.
Model of Inception and Growth of Damage from Microvoids in Polyethylene-based Materials for HVDC Cables. 2. Parametric Investigation and Data Fitting

A new, physical, aging and life model for damage inception and growth in polymeric insulation starting at the level of microscopic cavities has been presented in Part 1, by illustrating extensively its theoretical background and derivation. In the present paper a parametric analysis, relevant to a polyethylene-based compound, is carried out that illustrates the sensitivity of the model to technological and material parameters, first of all applied electric field, temperature, conductivity and cavity size. In addition, fitting to experimental times-to-failure relevant to HVDC cable insulation is discussed in order to confirm soundness and validity of the proposed approach.
Interpolation Routines Assessment in ALS-Derived Digital Elevation Models for Forestry Applications

Airborne Laser Scanning (ALS) is capable of estimating a variety of forest parameters using different metrics extracted from the normalized heights of the point cloud using a Digital Elevation Model (DEM). In this study, six interpolation routines were tested over a range of land cover and terrain roughness in order to generate a collection of DEMs with spatial resolution of 1 and 2 m. The accuracy of the DEMs was assessed twice, first using a test sample extracted from the ALS point cloud, second using a set of 55 ground control points collected with a high precision Global Positioning System (GPS). The effects of terrain slope, land cover, ground point density and pulse penetration on the interpolation error were examined stratifying the study area with these variables. In addition, a Classification and Regression Tree (CART) analysis allowed the development of a prediction uncertainty map to identify in which areas DEMs and Airborne Light Detection and Ranging (LiDAR) derived products may be of low quality. The Triangulated Irregular Network (TIN) to raster interpolation method produced the best result in the validation process with the training data set while the Inverse Distance Weighted (IDW) routine was the best in the validation with GPS (RMSE of 2.68 cm and RMSE of 37.10 cm, respectively).
Production performance of lactating Nili-Ravi buffaloes under the influence of bovine somatotropic hormone with varying levels of dietary energy.

each group in a completely randomized design. All the experimental animals were injected bST at fortnightly interval after 60 ± 3 days postpartum for a period of 90 days. The nutritional requirements of these animals were met through total mixed ration with different densities of energy (high energy density, 115 %; medium energy density, 100 %; and low energy density, 80 % of NRC, 2001 standards). The increase in milk yield on high energy density (HED) ration was significantly higher (P<0.05) than medium e nergy density (MED) and low energy density (LED) diets. However, the difference was non significant between MED and LED rations. The values for feed efficiency were 0.61, 0.66 and 0.74 on LED, MED and HED diets and difference was significant (P<0.05) with best efficiency on ration HED. Difference in nutrient intake on LED ration was significantly higher (P<0.05) (except for ether extract) than other two other rations. However, the milk composition and body weight gain were similar on all rations. Results indicated that 15% higher energy than recommended by NRC, favored milk production in Nili -Ravi buffaloes when they were given bST hormone.
Due Diligence and Investee Performance

We estimate the economic value of due diligence (DD) in the context of private equity by investigating the relationship between DD and investee performance, while controlling for endogeneity. With the adoption of a novel dataset, we find evidence highly consistent with the view that a thorough DD is associated with improved investee performance. We also distinguish the role of different types of DD and show that the DD performed by fund managers has a more pronounced impact on performance. Instead, the DD mainly performed by external agents, i.e., consultants, lawyers and accountants, gives rise to puzzling results and imperfect matching.
Internet Banking and Customers' Acceptance in Jordan: The Unified Model's Perspective

Internet banking in Jordan has developed rapidly since the year 2001 as most of the Jordanian banks have adopted some form of Internet usage and launched websites to serve their customers. Such efforts will not be successful without customers accepting Internet banking. The study added to the body of knowledge in the technology acceptance domain by testing and validating the Unified Theory of Acceptance and Use of Technology. This study extends the model by adding personality dimensions and validates two relationships that were suggested in previous literature (the influence of performance expectancy in mediating the relationship between effort expectancy and social influence and behavioral intention). This study explores the individuals' Internet banking acceptance using multiple regression. The population of the study was "counter bank customers" sampled in three Jordanian banks and in three major cities in the country. The model proposed is a comprehensive model with ten independent variables and one dependent variable. The study involved translating the instrument to Arabic and using it to explore the hypothesized relationships. The results of the study indicated a support of the UTAUT with respect to the predictors' effect on behavioral intentions, and a partial support in the moderation effect. Also, the hypothesized mediation effect was supported for both relationships (effort expectancy and social influence and their relationship to behavioral intention). The proposed model of this study supported the influence of performance expectancy, social influence, self-efficacy, perceived trust and locus of control on Jordanian's intentions to use Internet banking. Part of these relationships was moderated by gender, age, education and experience. Effort expectancy (part of the UTAUT), perceived facilitating conditions, anxiety, personal innovativeness and perceived risk were not significant in predicting behavioral intention. Finally, this study developed an Arabic instrument that can be used in future research in the area of technology acceptance and with acceptable level of reliability. Implications for research and practice, limitations, future research, and conclusions are discussed at the end of the study.