gebhart/patrepeval huggingface dataset:
Comparative Evaluation of Three Assays for Measurement of Dengue Virus Neutralizing Antibodies (2008)

Plaque reduction neutralization tests (PRNTs) are commonly used for measuring levels of dengue virus (DENV) neutralizing antibodies. However, these assays lack a standardized format, generally have a low sample throughput, and are labor-intensive. The objective of the present study was to evaluate two alternative DENV neutralizing antibody assays: an enzyme-linked immunosorbent assay-based microneutralization (MN) assay, and a fluorescent antibody cell sorter-based, DC-SIGN expresser dendritic cell (DC) assay. False-positive rates, serotype specificity, reproducibility, sensitivity, and agreement among the assay methods were assessed using well-characterized but limited numbers of coded test sera. Results showed that all three assays had false-positive rates of less than 10% with titers near the cut-off and generally below the estimated limits of detection. All three methods demonstrated a high degree of specificity and good agreement when used to assay sera and serum mixtures from monovalent vaccinees and sera from patients after primary natural infection, with the only notable exception being moderate-to-high neutralizing antibody titers against DENV 2 measured by PRNT in a mixture containing only DENV 3 and DENV 4 sera. The MN and DC assays demonstrated good reproducibility. All three assays were comparable in their sensitivity, except that the PRNT was less sensitive for measuring DENV 4 antibody, and the MN and DC assays were less sensitive for measuring DENV 2 antibody. However, when used to test sera from persons after tetravalent DENV vaccination or secondary DENV infection, there was poor specificity and poor agreement among the different assays.
Potential use of aldose reductase inhibitors to prevent diabetic complications. (1990)

Reviewed are (1) the biochemical basis and pathophysiology of diabetic complications and (2) the structure-activity relationships, pharmacology, pharmacokinetics, clinical trials, and adverse effects of aldose reductase inhibitors (ARIs). ARIs are a new class of drugs potentially useful in preventing diabetic complications, the most widely studied of which have been cataracts and neuropathy. ARIs inhibit aldose reductase, the first, rate-limiting enzyme in the polyol metabolic pathway. In nonphysiological hyperglycemia the activity of hexokinase becomes saturated while that of aldose reductase is enhanced, resulting in intracellular accumulation of sorbitol. Because sorbitol does not readily penetrate the cell membrane it can persist within cells, which may lead to diabetic complications. ARIs are a class of structurally dissimilar compounds that include carboxylic acid derivatives, flavonoids, and spirohydantoins. The major pharmacologic action of an ARI involves competitive binding to aldose reductase and consequent blocking of sorbitol production. ARIs delay cataract formation in animals, but the role of aldose reductase in cataract formation in human diabetics has not been established. The adverse effects of ARIs include hypersensitivity reactions. Although the polyol pathway may not be solely responsible for diabetic complications, studies suggest that therapy with ARIs could be beneficial. Further research is needed to determine the long-term impact and adverse effects of ARIs in the treatment of diabetic complications.
The biochemical basis of hereditary fructose intolerance (2010)

Hereditary fructose intolerance is a rare, but potentially lethal, inherited disorder of fructose metabolism, caused by mutation of the aldolase B gene. Treatment currently relies solely on dietary restriction of problematic sugars. Biochemical study of defective aldolase B enzymes is key to revealing the molecular basis of the disease and providing a stronger basis for improved treatment and diagnosis. Such studies have revealed changes in enzyme activity, stability and oligomerisation. However, linking these changes to disease phenotypes has not always been straightforward. This review gives a general overview of the features of hereditary fructose intolerance, then concentrates on the biochemistry of the AP variant (Ala149Pro variant of aldolase B) and molecular pathological consequences of mutation of the aldolase B gene.
Reliable and sensitive detection of premature termination mutations using a protein truncation test designed to overcome problems of nonsense-mediated mRNA instability (1999)

The protein truncation test (PTT) is a mutation-detection method used to scan for premature termination (nonsense) mutations. PCR amplification of the DNA or mRNA source material is performed using forward primers containing a T7-promoter sequence and translation initiation signals such that the resultant products can be transcribed and translated in vitro to identify the smaller truncated protein products. mRNA is commonly used as the source material, but success of the PTT and other RNA-based mutation detection methods can be severely compromised by nonsense mutation-induced mRNA decay, a well-documented process that is often overlooked in mutation detection strategies. In this study, we develop an RNA-based PTT that overcomes the problem of mRNA decay by preincubating cells with cycloheximide to stabilise the mutant mRNA. The effectiveness of this method for mutation detection in abundant mRNAs was demonstrated in osteogenesis imperfecta fibroblasts by the protection of type I collagen (COL1A1) mRNA containing nonsense mutations that normally resulted in mutant mRNA degradation. Stabilisation of mutant mismatch repair gene (MLH1) mRNA was also observed in transformed lymphocytes from patients with hereditary nonpolyposis colorectal cancer (HNPCC). Importantly, our strategy also stabilised very low-level (or illegitimate) nonsense-containing transcripts in lymphoblasts from patients with Bethlem myopathy (COL6A1), familial adenomatous polyposis (APC), and breast cancer (BRCA1). The greatly increased sensitivity and reliability of this RT-PCR/PTT protocol has broad applicability to the many genetic diseases in which only blood-derived cells may be readily available for analysis. Hum Mutat 13:311–317, 1999. © 1999 Wiley-Liss, Inc.
Spatial relationship patterns: elements of reusable tracking and calibration systems (2006)

With tracking setups becoming increasingly complex, it gets more difficult to find suitable algorithms for tracking, calibration and sensor fusion. A large number of solutions exists in the literature for various combinations of sensors, however, no development methodology is available for systematic analysis of tracking setups. When modeling a system as a spatial relationship graph (SRG), which describes coordinate systems and known transformations, all algorithms used for tracking and calibration correspond to certain patterns in the graph. This paper introduces a formal model for representing such spatial relationship patterns and presents a small catalog of patterns frequently used in augmented reality systems. We also describe an algorithm to identify patterns in SRGs at runtime for automatic construction of data flows networks for tracking and calibration.
On the propagation of long-range dependence in the Internet (2000)

This paper analyzes how TCP congestion control can propagate self-similarity between distant areas of the Internet. This property of TCP is due to its congestion control algorithm, which adapts to self-similar fluctuations on several timescales. The mechanisms and limitations of this propagation are investigated, and it is demonstrated that if a TCP connection shares a bottleneck link with a self-similar background traffic flow, it propagates the correlation structure of the background traffic flow above a characteristic timescale. The cut-off timescale depends on the end-to-end path properties, e.g., round-trip time and average window size. It is also demonstrated that even short TCP connections can propagate long-range correlations effectively. Our analysis reveals that if congestion periods in a connection's hops are long-range dependent, then the end-user perceived end-to-end traffic is also long-range dependent and it is characterized by the largest Hurst exponent. Furthermore, it is shown that self-similarity of one TCP stream can be passed on to other TCP streams that it is multiplexed with. These mechanisms complement the widespread scaling phenomena reported in a number of recent papers. Our arguments are supported with a combination of analytic techniques, simulations and statistical analyses of real Internet traffic measurements.
Baroreflex Control of Sympathetic Nerve Activity in Essential and Secondary Hypertension (1998)

Studies performed in experimental animals and in humans have documented that high blood pressure markedly impairs baroreceptor control of heart rate. Whether a similar impairment also characterizes baroreceptor control of sympathetic activity modulating peripheral vasomotor tone is still unknown. In 28 untreated essential hypertensive subjects [14 of moderate and 14 of more severe degree, age 51.6+/-2.4 and 52.6+/-2.1 years (mean+/-SEM)] and in 13 untreated secondary hypertensives (renovascular or pheochromocytoma, age 50.1+/-4.6 years), we measured beat-to-beat arterial blood pressure (finger photoplethysmographic device), heart rate (electrocardiogram), and efferent postganglionic muscle sympathetic nerve activity (microneurography) at rest and during baroreceptor stimulation and deactivation induced by stepwise intravenous infusions of phenylephrine and nitroprusside, respectively. Data were compared with those obtained in 15 age-matched normotensive control subjects. Muscle sympathetic nerve activity (bursts per 100 heart beats) showed a progressive and significant (P<.01) increase from normotension (40.3+/-3.3) to moderate (55.6+/-4.1) and more severe essential hypertension (68.2+/-4.1), paralleling the progressive increase in blood pressure values. In contrast, muscle sympathetic nerve activity was not increased in secondary hypertensives (40.5+/-6.7) despite blood pressure values similar to or even greater than those of severe essential hypertensives. In both essential and secondary hypertensives, baroreceptor-heart rate control was displaced toward elevated blood pressure values and markedly impaired compared with normotensive subjects (average reduction, 38.5%). In contrast, the sympathoinhibitory and sympathoexcitatory responses to baroreceptor stimulation and deactivation were displaced toward elevated blood pressure values but similar in all groups. Thus, sympathetic activation characterizes essential but not secondary hypertension. Regardless of its nature, however, hypertension is not accompanied by an impairment of baroreceptor modulation of sympathetic activity.
Characterization of high affinity binding between laminin and Alzheimer's disease amyloid precursor proteins. (1992)

These avid interactions with extracellular matrix proteins likely reflect normal functions of the AAPs and may be involved in nucleation events in Alzheimer-type amyloid formation.
Sterically-Hindered Hydroxylamines as Bioactive Spin Labels (1990)

The use of sterically hindered hydroxylamines for the regulation of free radical reactions in biological systems and for the pharmacological correction of pathological conditions is described. They are shown to possess a number of advantages over nitroxyl radicals. They are more soluble in water, are less toxic and are easily oxidized to nitroxyl radicals in aqueous solutions. Hindered hydroxylamines can be also used for the study of pharmacokinetics of bioactive spin labels by the EPR technique. Pharmacokinetic parameters for spin-labeled analogues of tetronal are evaluated. Sulfur-containing hindered hydroxylamines are effective bioantioxidants, inhibiting efficiently the LPO of the microsomal fraction of liver and ADP- and thrombin induced plasma platelet aggregation. They increase also the survival of animals under ischemic shock. A cyclic mechanism for its antioxidative action is suggested. Recent data on the influence of the nitroxyl in equilibrium hydroxylamine moiety on bio-activity are summarized.
Extramammary Paget's disease: a report of three cases and review of the literature. (1995)

Extramammary Paget's disease (FMPD) is a rare skin disease with a tendency to recur even in the face of adequate excision. It was first suggested by Weiner in 1937 to be a carcinoma of the apocrine sweat gland with intraepithelial excision. Thus, most cases of EMPD occur in the perianal, perigenital and axilla regions where sweat glands abound, with scrotal EMPD being the commonest. EMPD can occur in both benign or malignant form and is often confused with chronic dermatitis. Diagnosis can only be confirmed by an excision biopsy. The long-term survival in patients without an underlying carcinoma is good. However, EMPD associated with an underlying adnexal carcinoma tends to be more aggressive and the prognosis is poor in such cases. EMPD is also associated with other malignancies such as prostatic, rectal, cervical, breast, bladder and skin carcinomas. Incidences of up to 40% have been reported. Thus, patients with EMPD should be thoroughly screened for associated primary growths. The treatment of EMPD is essentially by surgical excision with clear margins. The options available for a clear margin include intraoperative frozen section,Moh's surgery and paraffin section with delayed re-excision. In this report, we present three cases of EMPD with markedly different outcomes and a review of the literature.
Cancer gene therapy (2005)

Cancer gene therapy can be defined as transfer of nucleic acids into tumor or normal cells with aim to eradicate or reduce tumor mass by direct killing of cells, immunomodulation or correction of genetic errors, and reversion of malignant status. Initially started with lots of optimism and enthusiasm, cancer gene therapy has shown limited success in treatment of patients. This review highlights current limitations and almost endless possibilities of cancer gene therapy. The major difficulty in advancing gene therapy technology from the bench to the clinical practice is problem with gene delivery vehicles (so called vectors) needed to ferry genetic material into a cell. Despite few reports of therapeutic responses in some patients, there is still no proof of clinical efficacy of most cancer gene therapy approaches, primarily due to very low transduction and expression efficacy in vivo of available vectors. An "ideal" gene therapy vector should be administrated through a noninvasive route and should be targeted not only to primary tumor mass but also to disseminated tumor cells and micrometastases; it should also carry therapeutic gene with tumor-restricted, time-regulated, and sustained expression. Current strategies for combating the cancer with gene therapy can be divided into four basic concepts: (1) replacement of missing tumor suppressor gene and/or blocking of oncogenes or pro-inflammatory genes, (2) suicide gene strategies, (3) induction of immune-mediated destruction, and (4) inhibition of tumor angiogenesis. The advance in the clinical benefit of gene therapy will probably be first achieved with combining it with standard cancer treatment: chemotherapy, radiotherapy, and immunotherapy.
Reduction of fixed-pattern noise of BASIS due to low kinetic energy reactive ion and native-oxide-free processing (1991)

Reduction of fixed-pattern noise in the base-stored image sensor (BASIS) is achieved with newly developed processes based on ultraclean technology. One is low kinetic-energy reactive ion etching to keep the Si/SiO/sub 2/ interface free from plasma damage. The dark current decreases down to 0.4 nA/cm/sup 2/. The other of these processes is native-oxide-free processing to suppress the growth of native oxide on the Si surface. The uniformity of the current gain in a bipolar transistor has been improved with the introduction of these processing methods. These methods improve the Al to n/sup +/ region contact, exhibiting low and uniform contact resistance without any thermal annealing treatment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Novel Marker for Traumatic Brain Injury: CSF αII-Spectrin Breakdown Product Levels (2004)

Currently, there is no definitive diagnostic test for traumatic brain injury (TBI) to help physicians determine the seriousness of injury or the extent of cellular pathology. Calpain cleaves alphaII-spectrin into breakdown products (SBDP) after TBI and ischemia. Mean levels of both ipsilateral cortex (IC) and cerebral spinal fluid (CSF) SBDP at 2, 6, and 24 h after two levels of controlled cortical impact (1.0 mm and 1.6 mm of cortical deformation) in rats were significantly elevated by injury. CSF and IC SBDP levels were significantly higher after severe (1.6 mm) injury than mild (1.0 mm) injury over time. The correlation between CSF SBDP levels and lesion size from T2-weighted magnetic resonance images 24 hours after TBI as well as correlation of tau and S100beta was assessed. Mean levels of CSF SBDP (r = 0.833) and tau (r = 0.693) significantly correlated with lesion size while levels of CSF S100beta did not (r = 0.188). Although levels of CSF and IC SBDP and lesion size are all significantly higher after 1.6 mm than 1.0 mm injury, the correlation between CSF SBDP and lesion size was not significant following the removal of controls from the analysis. This indicates CSF SBDP is a reliable marker of the presence or absence of injury. Furthermore, larger lesion sizes 24 h after TBI were negatively correlated with motor performance on days 1-5 after TBI (r = -0.708). Based on these data, evaluation of CSF SBDP levels as a biomarker of TBI is warranted in clinical studies.
A high-performance microsystem for isolating circulating tumor cells (2011)

A unique flow field pattern in a bio-functional microchannel is utilized to significantly enhance the performance of a microsystem developed for selectively isolating circulating tumor cells from cell suspensions. For high performance of such systems, disposal of maximum non-target species is just as important as retention of maximum target species; unfortunately, most studies ignore or fail to report this aspect. Therefore, sensitivity and specificity are introduced as quantitative criteria to evaluate the system performance enabling a direct comparison among systems employing different techniques. The newly proposed fluidic scheme combines a slow flow field, for maximum target-cell attachment, followed by a faster flow field, for maximum detachment of non-target cells. Suspensions of homogeneous or binary mixtures of circulating breast tumor cells, with varying relative concentrations, were driven through antibody-functionalized microchannels. Either EpCAM or cadherin-11 transmembrane receptors were targeted to selectively capture target cells from the suspensions. Cadherin-11-expressing MDA-MB-231 cancer cells were used as target cells, while BT-20 cells were used as non-target cells as they do not express cadherin-11. The attachment and detachment of these two cell lines are characterized, and a two-step attachment/detachment flow field pattern is implemented to enhance the system performance in capturing target cells from binary mixtures. While the system sensitivity remains high, above 0.95, the specificity increases from about 0.85 to 0.95 solely due to the second detachment step even for a 1 : 1000 relative concentration of the target cells.
Computer assisted medical interventions (1995)

Many medical or surgical interventions can benefit from the use of computers. Through progress of technology and growing consciousness of the possibilities of real clinical improvements with computers, what was in the past the privilege of very few operations (mostly stereotactic neurosurgery) is now entering many surgical specialities. Although many technical issues remain to be solved, there is virtually no limit to the introduction of computers and robots in any surgical speciality. This tendency can take on the most varied forms. At the authors' institute, three golden rules have guided the computer assisted medical interventions (CAMI) project for about ten years: 1) conceive systems for which the clinical value is well defined; 2) develop generic tools that can be applied to many different clinical applications; and 3) provide efficient collaboration between the surgeon and the system through simple interfaces.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Energetics of AlN thin films on the Al2O3(0001) surface (1998)

We present an ab initio study of the energetics and atomic structure of films consisting of approximately 1 bilayer of AlN on the c-plane sapphire surface. We show that these films are unstable with respect to three-dimensional islands, and we attribute this instability to both strain and chemical mismatch between the oxide and the nitride. The relative stability of the AlN films depends on the chemical potentials of Al and N. Films having (0001) polarity are expected to form under Al-rich conditions. Films with (0001̄) polarity appear to form only for undersaturation conditions of bulk AlN in the initial stages of growth.
Dead Ends and Detours En Route to Total Syntheses of the 1990s (2000)

From the very beginning organic chemistry and total synthesis have been intimately joined. In fact, one of the first things that freshmen in organic chemistry learn is how to join two molecules together to obtain a more complex one. Of course they still have a long way to go to become fully mature synthetic chemists, but they must have the primary instinct to build molecules, as synthesis is the essence of organic chemistry. With the different points of view that actually coexist in the chemical community about the maturity of the science (art, or both) of organic synthesis, it is clear that nowadays we know how to make almost all of the most complex molecules ever isolated. The primary question is how easy is it to accomplish? For the readers of papers describing the total synthesis of either simple or complex molecules, it appears that the routes followed are, most of the time, smooth and free of troubles. The synthetic scheme written on paper is, apparently, done in the laboratory with few, if any, modifications and these, essentially, seem to be based on finding the optimal experimental conditions to effect the desired reaction. Failures in the planned synthetic scheme to achieve the goal, detours imposed by unexpected reactivity, or the absence of reactivity are almost never discussed, since they may diminish the value of the work reported. This review attempts to look at total synthesis from a different side; it will focus on troubles found during the synthetic work that cause detours from the original synthetic plan, or on the dead ends that eventually may force redesign. From there, the evolution from the original route to the final successful one that achieves the synthetic target will be presented. The syntheses discussed in this paper have been selected because they contain explicit information about the failures of the original synthetic plan, together with the evolution of the final route to the target molecule. Therefore, they contain a lot of useful negative information that may otherwise be lost.
Identification of Marker Genes from High‐Dimensional Microarray Data for Cancer Classification (2007)

This chapter contains sections titled: Feature Selection Gene Selection Comparative Study of Gene Selection Methods Conclusions and Discussion Acknowledgments References