Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the CaMAL2 promoter for regulated expression of genes in Candida albicans

An expression vector (CIp10–MAL2p) for use in Candida albicans has been constructed in which a gene of interest can be placed under the control of the CaMAL2 maltase promoter and stably integrated at the CaRP10 locus. Using this vector to express the Candida URA3 gene from the CaMAL2 promoter, we have demonstrated tight regulation of CaURA3 expression by carbon source. Thus under conditions when the CaMAL2 promoter is not induced, expression of Candida URA3 was unable either to complement a C. albicans ura3 mutation or to confer sensitivity to 5‐fluoroorotic acid, a compound which is highly toxic to URA3 strains. Since Candida albicans is an obligate diploid organism, analysis of gene function requires manipulation of both copies of any gene of interest. Our expression vector provides a strategy by which the remaining copy of a gene of interest can be placed under CaMAL2 promoter control in a strain where the first copy has been deleted, permitting analysis of gene function by manipulation of carbon source. CIp10–MAL2p should therefore provide a useful means for functional analysis of genes in C. albicans. We have used this strategy with C. albicans DPB2 to demonstrate that the gene is essential and that loss of function leads cells to adopt a hypha‐like morphology as they cease proliferation. Copyright © 2000 John Wiley & Sons, Ltd.
NEW RESULTS ON MODEL REDUCTION FOR DISCRETE-TIME SWITCHED SYSTEMS WITH TIME DELAY

This paper is concerned with the problem of delay-dependent exponential H∞ model reduction for discrete-time switched delay systems under switching signals with average dwell time (ADT). The objective is to construct a reduced-order model, which ensures that the resulting error system under switching signal with ADT is exponentially stable with an H∞ norm bound. A weighting factor α is introduced to construct a Lyapunov function for switched delay systems such that ADT approach is used with piecewise Lyapunov matrices instead of common Lyapunov function matrices. Furthermore, sufficient conditions for the solvability of this problem are obtained in terms of strict linear matrix inequalities (LMIs), which lessen the computation complexity. A numerical example is provided to show the effectiveness of the developed method.
A prospective evaluation of plasma prostate-specific antigen for detection of prostatic cancer.

OBJECTIVE To evaluate the validity of prostate-specific antigen (PSA) in identifying men who subsequently were or were not clinically diagnosed with prostate cancer, assess optimal test cutoff, measure lead time, and estimate relative risks (RRs) associated with discrete PSA levels. DESIGNS Nested case-control study of men providing plasma samples before a 10-year follow-up. SETTING The Physicians' Health Study, an ongoing randomized trial that enrolled 22,071 men aged 40 to 84 years in 1982. PARTICIPANTS A total of 366 men (cases) diagnosed with prostate cancer and 1098 men (three controls per case), matched by age, randomly selected from all cohort members at risk at the time of case diagnosis. MAIN OUTCOME MEASURES Sensitivity and specificity for each year of follow-up and for aggressive and nonaggressive cancers separately. RESULTS At a cutoff of 4.0 ng/mL, sensitivity for the entire 10-year follow-up was 46% for total cases. Sensitivities for detection of total, aggressive, and nonaggressive cancers occurring in the first 4 years were 73%, 87%, and 53%. Overall, specificity was 91% and changed little by year of follow-up. Optimal validity was achieved at a cutoff of 3.3 ng/mL. Estimated mean lead time for all cancers was 5.5 years. Only 40% of cancers detected more than 5 years from baseline were nonaggressive. Compared with men with PSA levels less than 1.0 ng/mL, those with PSA levels between 2.0 and 3.0 ng/mL had an RR of 5.5 (95% confidence interval, 3.7 to 9.2). CONCLUSIONS A single PSA measurement had a relatively high sensitivity and specificity for detection of prostate cancers that arose within 4 years. Prostate-specific antigen values less than the usual cutoff were associated with substantial increases in risk compared with the lowest levels. Final evaluation of PSA screening must also consider cost and the ability of current treatments to improve the prognosis of screen-detected cases.
An empirical study of surrogates' preferred level of control over value-laden life support decisions in intensive care units.

RATIONALE Despite ongoing ethical debate concerning who should control decisions to discontinue life support for incapacitated, critically ill patients, the perspectives of surrogate decision makers are poorly understood. OBJECTIVES To determine (1) what degree of decisional authority surrogates prefer for value-sensitive life support decisions compared with more technical biomedical decisions, and (2) what predicts surrogates' preferences for more control over life support decisions. METHODS This was a prospective study of 230 surrogate decision makers for incapacitated, mechanically ventilated patients at high risk of death. Surrogates reported their preferred degree of decisional authority using the Degner Control Preferences Scale for two types of decisions: a value-sensitive decision about whether to discontinue life support and a decision regarding which antibiotic to prescribe for an infection. MEASUREMENTS AND MAIN RESULTS The majority of surrogates (55%, 127/230; 95% confidence interval, 49-62%) preferred to have final control over the value-sensitive life support decision; 40% (91/230) wished to share control equally with the physician; 5% (12/230) of surrogates wanted the physician to make the decision. Surrogates preferred significantly more control over the value-sensitive life support decision compared with the technical decision about choice of antibiotics (P < 0.0001). Factors independently associated with surrogates' preference for more control over the life support decision were: less trust in the intensive care unit physician, male sex, and non-Catholic religious affiliation. CONCLUSIONS Surrogates vary in their desire for decisional authority for value-sensitive life support decisions, but prefer substantially more authority for this type of decision compared with technical, medical judgments. Low trust in physicians is associated with surrogates preferring more control of life support decisions.
Continuous ambulatory peritoneal dialysis.

We isolated an unusual gram-negative organism, rarely considered a human pathogen, which appeared to cause peritonitis in one of our continuous ambulatory peritoneal dialysis patients. A 54-year-old man with chronic glomerulonephritis developed end-stage renal disease in January 1981. His past medical history was also remarkable for adult-onset diabetes mellitus of approximately 15 years' duration. (Because his proteinuria predated the diabetes and was mild, and he did not have retinopathy, he was believed to have two separate diseases.) The patient was started on intermittent peritoneal dialysis with a Tenckhoff catheter in January 1981 and was trained and able to go home on intermittent peritoneal dialysis in March 1981. His course was uneventful, and he returned to work as a steamfitter. In August 1981, he developed peritonitis with Acinetobacter calcoaceticus var. anitratus. He was treated with tobramycin and peritoneal lavage and recovered without adverse sequelae. In October 1981, he again developed peritonitis. This time, an Escherichia coli isolate was identified. The organism was susceptible to cephalosporins, and the patient responded to treatment with cefazolin and peritoneal lavage. A retraining session revealed a problem with the patient's technique, which was considered the probable source of contamination and of the several episodes of peritonitis described. The errors were corrected, and the patient did well for some time thereafter. The patient subsequently decided to transfer to continuous ambulatory peritoneal dialysis, and his training course was begun in July 1982. On his first training day, his peritoneal fluid was cloudy. Cefazolin was added to his peritoneal dialysis bags. The patient was asymptomatic, his cultures were negative, and he made an uneventful recovery. On 10 September 1982, while participating in a study of a bacteriological filter for continuous ambulatory peritoneal dialysis (Peridex; Millipore Corp., Bedford, Mass.), the patient developed abdominal pain, nausea, vomiting, and cloudy peritoneal fluid. Gram stain of a centrifuged 10-ml sample of dialysate showed many polymorphonuclear cells but no organisms. Review of the patient's record revealed that 2 days previously, on 8 September, when the patient
A Threshold Voltage Model of Silicon-Nanotube-Based Ultrathin Double Gate-All-Around (DGAA) MOSFETs Incorporating Quantum Confinement Effects

In this paper, a quantum-mechanical threshold voltage model for ultrathin double gate-all-around DGAA MOSFETs has been developed by solving three-dimensional (3-D) Poisson's and 2-D Schrödinger's equations in the channel region. The parabolic potential approximation is considered for Poisson's equation solution, whereas a hollow cylindrical potential well in the channel region is assumed to solve Schrödinger's equation. Simple equations for the wave function and energy quantization in the channel of DGAA MOSFET have been formulated. Discretized energy levels have been used for channel charge calculation in subthreshold regime of device operation. The calculated channel charge is compared with a threshold charge to formulate the threshold voltage model. The effects of the device parameters such as the channel thickness, oxide thickness, doping, etc. on threshold voltage and DIBL have been extensively studied. The proposed model results have been verified by comparing with the numerical simulation results obtained from the 3-D device simulator Visual TCAD of Cogenda Int.
Quantitative ultrasonic characterization of layered polymer structures

Tubular layered polymer structures are used e.g. in the medical industry for controlling chemical release. An ultrasonic 50 MHz pulse-echo immersion method was employed to characterize layered polymer structures for quality control purposes. The method can non-invasively determine layer thickness, interface delaminations, and sound velocity in the samples. Assuming constant layer density allows determining the sound velocity from the first surface reflection. The layer thickness is then calculated from the time of flight inside the layer. The determined sound velocity value is linked to the cross-linkage degree of the polymer. Delaminated areas between the layers as well as embedded defects are detected in the ultrasonic images. The method could be used to study the quality of polymer structures in laboratory conditions and holds potential for on-line application.
Translating Health IT Policy into Practice in the UK National Health Service

The challenge to provide a nation-wide integrated health service is central to UK government policy. The National Program for Information Technology was launched in 2002 to transform healthcare using information and communications technology. As the largest, non-military, non-scientific government funded IT program worldwide, it was planned over a decade with an estimated total cost expected to exceed £20bn. This paper is a longitudinal study of the National Care Record Service, which was the largest part of the program, aimed to provide 50 million UK (English) citizens with an electronic health record. Using episodic interviewing techniques over ten years and secondary source material, the findings reveal a series of IT policy changes to the original Program. Delays to roll out electronic health records are linked to issues about procurement strategies with IT suppliers, benefits realisation, risk assessment and clinical engagement. This study extends academic work on the deployment of large scale, long-term publicly funded IT projects, which go beyond the technical imperative to transform healthcare. Findings suggest government agencies need to embed cultural, social and economic criteria into health IT policy-making. Tracking this Program for a decade, we observe how a centralised, top-down approach was replaced by localised IT procurement and implementation, giving NHS organisations more decision-making powers. However, the Program was beset by continuous policy changes affecting the structure, organisation and IT of the NHS, where attempts to achieve benefits finally resulted in the break-up of the Program.
DNS Security Introduction and Requirements

The Domain Name System Security Extensions (DNSSEC) add data origin authentication and data integrity to the Domain Name System. This document introduces these extensions and describes their capabilities and limitations. This document also discusses the services that the DNS security extensions do and do not provide. Last, this document describes the interrelationships between the documents that collectively describe DNSSEC. [STANDARDS-TRACK]
Analysis of contrast enhancement forensics in compressed and uncompressed images

The use of digital images for sharing information is spreading very fast. It has become more common in society, resulting in an increase in methodologies and incentives for creating digitally morphed images. Hence, we need a set of tools to detect digital image alterations. Passive-blind image forensics is an area of research which focuses on evolving techniques for verifying the originality of images by recovering its past. This paper is based on forgery detection using contrast enhancement detection in images. Digital image forgeries embed its fingerprints in images in the form of change in statistical characteristics. Globally applied enhancement fingerprints left by pixel value mappings used to detect the use of contrast enhancement in images. Performance of uncompressed, lossless and lossy image formats is compared. Performance on uncompressed and lossless formats found equally good but lossy format loses in comparison of uncompressed and lossless ones.
Chromosomal anomalies in human gametes and pre‐implantation embryos, and their potential effect on reproduction

Summary. This paper reviews the latest data on chromosomal abnormalities in human gametes and embryos. A close relationship between such anomalies and reproduction failure in humans has been postulated, thereby underscoring the importance of ongoing studies into the mechanisms leading to anomalies. Until recently, knowledge of chromosomal anomalies in human gametes and embryos has been limited. Newly developed strategies (in vitro fertilization combined with micromanipulation techniques followed by multicolour fluorescence in situ hybridization, and PCR analyses) allow precise investigation of this problem. This review of the available information on the etiology of chromosomal anomalies indicates that some of the genetic anomalies in human gametes and early embryos result in reproductive failure.
Improving Automatic Alignment for Translation Memory Creation

: Currently available TM systems usually include an alignment tool to create memories from existing parallel texts. However, the alignments proposed are rarely reliable enough to allow the newly created TM to be exploited without being checked by a human user. This paper will describe a series of experiments using the popular TRADOS WinAlign program with a collection of German-English parallel texts totalling roughly 80 000 words and will look at:
Combined strategies for enhancing the transdermal absorption of midazolam through human skin

Objectives Midazolam administration by intravenous or intramuscular injection produces pain and stress. For this reason, alternative methods of administration have been proposed. The transdermal administration of midazolam could improve patient comfort, which is especially important for children in the pre‐operative period. We aimed to assess the effect of iontophoresis and chemical percutaneous enhancers applied individually and together, to determine if a synergistic effect is achieved when both enhancement techniques are simultaneously employed.
Evolution of structure and function in Phenylalanine Hydroxylase. With the regulatory properties in sight

In the post-genomic era, an idea of how similar the genomes of different species actually are is on the horizon. Less than 10 years ago, the human genome was estimated to encode 100000 genes. That was an overestimation, as the real number of human genes is 20000-25000. Most genes are expressed as proteins. The 3D structure of a protein is more conserved than its sequence, and therefore the structural context of protein and gene evolution must not be forgotten. By its structure, the protein can propagate its function. In the early 90’s the estimated number of different protein structure classes, so called folds, was predicted to be about 10000. Today there are slightly above 1000 folds and the discovery of new folds has leveled off, despite an increase in the number of protein structures that have been solved over the last few years. Indeed, some folds are used for more than one function, and found in various functional contexts. Then, if the many components are so similar, how is the biological species divergence from same component genomes achieved? One way to study biological diversity is by dividing it into its smaller components, e.g. by studying protein or gene family evolution. Here the evolution and regulation of the aromatic amino acid hydroxylase (AAAHs) have been under examination. This gene family encodes the proteins phenylalanine hydroxylase (PAH), tyrosine hydroxylase (TH), and tryptophan hydroxylase (TPH). These enzymes are highly physiologically important. PAH, expressed in liver, regulates the homeostasis of L-Phe by hydroxylating it into L-Tyr. TH, expressed in the central nervous system, hydroxylates L-Tyr into L-Dopa. L-Dopa is part of two important pathways i)
Numerical estimation of HIFU focal error for breast cancer treatment

A numerical estimation of focal error after the propagation though breast tissue to realize precise focal control of HIFU (High Intensity Focused Ultrasound) targeting breast cancer was described. Breast model was constructed from a 3D MRI clinical breast data. All pixel intensity was assigned to 4 kinds of typical material; water, connective tissue, fat and glandula mammaria. HIFU simulator based on a finite-time-domain-method was employed. A 56-chnannel HIFU transducer with both aperture width and focal length were 100 mm and with a center frequency of 2 MHz was used. Three separated peaks were observed after propagation of breast tissue. The focal shift amount was a few millimeter in both lateral and propagation directions. To confirm the relation between the acoustical inhomogeneous and the focal error, time reversal method was employed. The results showed that focal error was successfully suppressed by time reversal method.
[Application of spontaneous acrosome reaction of sperm in prediction of outcome of in-vitro fertilization and embryo transfer].

OBJECTIVE To investigate the clinical application of spontaneous acrosome reaction (AR) rate of sperm in predicting the outcome of in-vitro fertilization and embryo transfer (IVF-ET). METHODS The spontaneous AR rate of the sperm of patients who underwent IVF-ET treatment in our center during the period from November to December 2014 were studied. The cut-off value from 6% to 12% were set and analyzed its association between the IVF-ET outcomes (including fertility rates, normal fertilization rates and high-quality embryo rates). For those who underwent fresh embryo transplantation, the rates of chemical pregnancy and clinical pregnancy were calculated, and compared the spontaneous AR rates and quantity of acrosomal enzyme according to the pregnancy outcome. RESULTS There were 202 patients in this study and the mean spontaneous AR rate was 5.99%±5.18%. For patients with the spontaneous AR rate ≥9% versus <9%, the fertility rate, normal fertilization rate and high-quality embryo rate were 81.33% vs 83.85%, 60.53% vs 60.99%, and 51.10% vs 59.67%, respectively, with statistically significant difference in the high-quality embryo rate (P=0.02). For patients who underwent fresh embryo transplantation, when comparison was made between those with spontaneous AR rate ≥8% and those <8%, the rate of chemical pregnancy and clinical pregnancy were 48.57% (17/35) vs 69.64% (78/112) and 37.14% (13/35) vs 63.39% (71/112), respectively, both with statistically significant difference (P=0.02 and P<0.01). The patients with clinical pregnancy had lower spontaneous AR rate than those without clinical pregnancy (5.41%±3.87% vs 7.40%±6.79%, P=0.04), while the quantity of acrosomal enzyme showed no significant difference [(131.79±68.50) vs (153.62±59.59) μU/10(6,) P=0.06]. Logistic regression analysis demonstrated association between spontaneous AR rates and clinical pregnancy (OR=0.93, 95%CI: 0.87-0.99, P=0.03). CONCLUSIONS The spontaneous AR rate of sperm may have clinical significance in predicting the outcome of IVF-ET, as it is reversely correlated with IVF high-quality embryo rate and pregnancy rate. The quantity of acrosomal enzyme may not have significant predictive value for the outcome of IVF.
Regulation of promoter-CAT stress genes in HepG2 cells by suspensions of particles from ambient air.

A panel of HepG2-derived cell lines (CAT-Tox [L] assay, Xenometrix), harboring stress genes consisting of a sequence for chloramphenicol acetyltransferase (CAT) under the transcriptional regulation from mammalian promoters and response elements, was exposed for 18-24 hr to aqueous suspensions of urban dusts (SRM-1648, SRM-1649, EHC-93) or PM2.5 particles (particulate matter < 2.5 micron). Expression of CAT protein was measured by enzyme-linked immunosorbent assay. Induction of the CAT genes was verified with benzo[a]pyrene (CYP1A1, cytochrome P450 1A1 promoter; GSTYa, glutathione transferase subunit Ya promoter; XRE, xenobiotic response element), cadmium sulfate, and copper sulfate (HMTIIa, metallothionein IIa promoter; HSP70, heat shock protein 70 promoter). The urban dust suspensions were active on CYP1A1, GSTYa, and XRE cell lines. SRM-1648 and SRM-1649 were twice as potent as EHC-93 per unit mass in inducing the xenobiotic-dependent responses, which correlated with contents in polycyclic aromatic hydrocarbons. These three reference particles, as well as six PM2.5 preparations collected on hi-vol filters in the Great Lakes basin, were also found to induce HMTIIa and HSP70, the magnitude of the responses correlating closely with the amount of soluble copper in the particulate preparations. The results indicate that bioavailable chemical species in the unfractionated particles can directly and quantitatively induce xenobiotic, metal, and stress-dependent responses in a target cell model, resulting in patterns of gene induction consistent with the chemical compositions of the environmental materials. We propose that cell culture models could be helpful for toxicodynamic inferences in adjunct to environmental monitoring and exposure assessments.
Reweighted message passing revisited

We propose a new family of message passing techniques for MAP estimation in graphical models which we call {\em Sequential Reweighted Message Passing} (SRMP). Special cases include well-known techniques such as {\em Min-Sum Diffusion} (MSD) and a faster {\em Sequential Tree-Reweighted Message Passing} (TRW-S). Importantly, our derivation is simpler than the original derivation of TRW-S, and does not involve a decomposition into trees. This allows easy generalizations. We present such a generalization for the case of higher-order graphical models, and test it on several real-world problems with promising results.