gebhart/patrepeval huggingface dataset:
Improved troponin T ELISA specific for cardiac troponin T isoform: assay development and analytical and clinical validation (1997)

The first generation of troponin T ELISA (TnT 1) can yield false-positive results in patients with severe skeletal muscle injury. Therefore, a cardiac-specific second-generation troponin T ELISA (TnT 2) was developed, in which the cross-reactive antibody 1B10 has been replaced by a high-affinity cardiac-specific antibody M11.7. No cross-reactivity of TnT 2 was observed with purified skeletal muscle troponin T (1000 micrograms/L) or in test samples from 43 marathon runners and 24 patients with rhabdomyolysis and highly increased creatine kinase. TnT 2 was increased > 0.2 microgram/L in 5 of 40 patients with renal failure and in 4 of 20 muscular dystrophy patients. The detection limit is 0.012 microgram/L. Day-to-day imprecision (CV) within the range 0.19-14.89 micrograms/L was < 5.8%. In 4955 patients without myocardial damage, 99.6% had TnT < 0.10 microgram/L. Assay comparison (TnT 1 vs TnT 2) over the whole concentration range (i.e., in 323 samples from AMI-suspected patients) showed a slope, intercept, and standard error of estimate (Sey) of 1.18, 0.01 micrograms/L, and 0.81 microgram/L, respectively.
The Impact of General Medical Conditions in Obsessive-Compulsive Disorder (2018)

Patients with OCD have high rates of comorbid GMCs. A longer DUI is associated with having at least one GMCs; this might be due to the long-lasting adoption of unhealthy lifestyles, not counterbalanced by appropriate treatment and psychoeducation.
Serum phospholipases A2 in inflammatory diseases (1993)

Abstract Phospholipase A2 (EC 3.1.1.4; PLA2) is detected in serum by determination of either the catalytic activity of the enzyme or the concentration of the enzyme protein by immunoassays. The most sensitive methods for determining PLA2 catalytic activity are radiometric assays, with a substrate of synthetic phospholipid (e.g., phosphatidylcholine or phosphatidylethanolamine) containing a 14C- or 3H-labeled fatty acid at the sn-2-position. Membranes of autoclaved Escherichia coli grown in the presence of radioactive oleic acid may also be used as a substrate. The released fatty acids are separated from the unreacted substrate and quantified by liquid scintillation counting. PLA2 catalytic activities are increased in serum in sepsis, acute pancreatitis, peritonitis, multiple injuries, rheumatoid arthritis, and other arthropathies. Immunoassays--radioimmunoassay, enzyme-linked immunosorbent assay, or time-resolved fluoroimmunoassay--are based on the use of either polyclonal or monoclonal antibodies to purified PLA2s. Specific assays have been developed for both pancreatic group I PLA2 (PLA2-I) and nonpancreatic group II PLA2 (PLA2-II). The cellular source of PLA2-I in serum is the pancreatic acinar cell. Increased serum PLA2-I values have been reported in acute pancreatitis, pancreatic cancer, and abdominal trauma. Increased PLA2-II values are found in conditions involving inflammation, e.g., sepsis, infections, acute pancreatitis, various forms of arthritis, cancer, complications of pregnancy, and postoperative states. Good correlations have been found in serum samples between the catalytic activity of PLA2 and the concentration of PLA2-II but not PLA2-I. PLA2-II may represent an acute-phase protein. The cellular source of the PLA2-II in serum is unknown; it is present in large amounts in cartilage and Paneth cells, prostatic gland cells, seminal fluid, lacrimal gland cells, and tears, but cannot be demonstrated by immunohistochemical or immunochemical methods in inflammatory cells.
Pathophysiology, Transmission, Diagnosis, and Treatment of Coronavirus Disease 2019 (COVID-19) (2020)

As of July 1, 2020, more than 10 million people worldwide had been infected with SARS-CoV-2. Many aspects of transmission, infection, and treatment remain unclear. Advances in prevention and effective management of COVID-19 will require basic and clinical investigation and public health and clinical interventions.
Determining the Cost of Producing Ethanol from Corn Starch and Lignocellulosic Feedstocks (2000)

The mature corn-to-ethanol industry has many similarities to the emerging lignocellulose-to-ethanol industry. It is certainly possible that some of the early practitioners of this new technology will be the current corn ethanol producers. In order to begin to explore synergies between the two industries, a joint project between two agencies responsible for aiding these technologies in the Federal government was established. This joint project of the USDA-ARS and DOE/NREL looked at the two processes on a similar process design and engineering basis, and will eventually explore ways to combine them. This report describes the comparison of the processes, each producing 25 million annual gallons of fuel ethanol. This paper attempts to compare the two processes as mature technologies, which requires assuming that the technology improvements needed to make the lignocellulosic process commercializable are achieved, and enough plants have been built to make the design well-understood. Ass umptions about yield and design improvements possible from continued research were made for the emerging lignocellulose process. In order to compare the lignocellulose-to-ethanol process costs with the commercial corn-to-ethanol costs, it was assumed that the lignocellulose plant was an Nth generation plant, built after the industry had been sufficiently established to eliminate first-of-a-kind costs. This places the lignocellulose plant costs on a similar level with the current, established corn ethanol industry, whose costs are well known. The resulting costs of producing 25 million annual gallons of fuel ethanol from each process were determined. The figure below shows the production cost breakdown for each process. The largest cost contributor in the corn starch process is the feedstock; for the lignocellulosic process it is the capital cost, which is represented by depreciation cost on an annual basis.
Molecular Weights of Bovine and Porcine Heparin Samples: Comparison of Chromatographic Methods and Results of a Collaborative Survey (2017)

In a collaborative study involving six laboratories in the USA, Europe, and India the molecular weight distributions of a panel of heparin sodium samples were determined, in order to compare heparin sodium of bovine intestinal origin with that of bovine lung and porcine intestinal origin. Porcine samples met the current criteria as laid out in the USP Heparin Sodium monograph. Bovine lung heparin samples had consistently lower average molecular weights. Bovine intestinal heparin was variable in molecular weight; some samples fell below the USP limits, some fell within these limits and others fell above the upper limits. These data will inform the establishment of pharmacopeial acceptance criteria for heparin sodium derived from bovine intestinal mucosa. The method for MW determination as described in the USP monograph uses a single, broad standard calibrant to characterize the chromatographic profile of heparin sodium on high-resolution silica-based GPC columns. These columns may be short-lived in some laboratories. Using the panel of samples described above, methods based on the use of robust polymer-based columns have been developed. In addition to the use of the USP's broad standard calibrant for heparin sodium with these columns, a set of conditions have been devised that allow light-scattering detected molecular weight characterization of heparin sodium, giving results that agree well with the monograph method. These findings may facilitate the validation of variant chromatographic methods with some practical advantages over the USP monograph method.
Heteromeric intermolecular interactions as synthetic tools for the formation of binary co-crystals (2004)

The crystal structure of 4-nitrobenzamide pyrazinecarboxamide (1 ∶ 1) contains two homomeric amide⋯amide dimers, which is in sharp contrast with the structural motifs displayed by the vast majority of binary co-crystals (illustrated here with five new examples), where the driving force for the supramolecular assembly is one or more strong heteromeric intermolecular interactions.
Biochemical Indication for Myristoylation-Dependent Conformational Changes in HIV-1 Nef (2006)

The accessory HIV-1 Nef protein is essential for viral replication, high virus load, and progression to AIDS. These functions are mediated by the alteration of signaling and trafficking pathways and require the membrane association of Nef by its N-terminal myristoylation. However, a large portion of Nef is also found in the cytosol, in line with the observation that myristoylation is only a weak lipidation anchor for membrane attachment. We performed biochemical studies to analyze the implications of myristoylation on the conformation of Nef in aqueous solution. To establish an in vivo myristoylation assay, we first optimized the codon usage of Nef for Escherichia coli expression, which resulted in a 15-fold higher protein yield. Myristoylation was achieved by coexpression with the N-myristoyltransferase and confirmed by mass spectrometry. The myristoylated protein was soluble, and proton NMR spectra confirmed proper folding. Size exclusion chromatography revealed that myristoylated Nef appeared of smaller size than the unmodified form but not as small as an N-terminally truncated from of Nef that omits the anchor domain. Western blot stainings and limited proteolysis of both forms showed different recognition profiles and degradation pattern. Analytical ultracentrifugation revealed that myristoylated Nef prevails in a monomeric state while the unmodified form exists in an oligomeric equilibrium of monomer, dimer, and trimer associations. Finally, fluorescence correlation spectroscopy using multiphoton excitation revealed a shorter diffusion time for the lipidated protein compared to the unmodified form. Taken together, our data indicated myristoylation-dependent conformational changes in Nef, suggesting a rather compact and monomeric form for the lipidated protein in solution.
On the Acceleration of Test Generation Algorithms (1983)

In order to accelerate an algorithm for test generation, it is necessary to reduce the number of backtracks in the algorithm and to shorten the process time between backtracks. In this paper, we consider several techniques to accelerate test generation and present a new test generation algorithm called FAN (fan-out-oriented test generation algorithm). It is shown that the FAN algorithm is faster and more efficient than the PODEM algorithm reported by Goel. We also present an automatic test generation system composed of the FAN algorithm and the concurrent fault simulation. Experimental results on large combinational circuits of up to 3000 gates demonstrate that the system performs test generation very fast and effectively.
Extreme ultraviolet lithography and three dimensional integrated circuit—A review (2014)

Extreme ultraviolet lithography (EUVL) and three dimensional integrated circuit (3D IC) were thoroughly reviewed. Since proposed in 1988, EUVL obtained intensive studies globally and, after 2000, became the most promising next generation lithography method even though challenges were present in almost all aspects of EUVL technology. Commercial step-and-scan tools for preproduction are installed now with full field capability; however, EUV source power at intermediate focus (IF) has not yet met volume manufacturing requirements. Compared with the target of 200 W in-band power at IF, current tools can supply only approximately 40-55 W. EUVL resist has improved significantly in the last few years, with 13 nm line/space half-pitch resolution being produced with approximately 3-4 nm line width roughness (LWR), but LWR needs 2 improvement. Creating a defect-free EUVL mask is currently an obstacle. Actual adoption of EUVL for 22 nm and beyond technology nodes will depend on the extension of current optical lithography (193 nm immersion lithography, combined with multiple patterning techniques), as well as other methods such as 3D IC. Lithography has been the enabler for IC performance improvement by increasing device density, clock rate, and transistor rate. However, after the turn of the century, IC scaling resulted in short-channel effect, which decreases power efficiency dramatically, so clock frequency almost stopped increasing. Although further IC scaling by lithography reduces gate delay, interconnect delay and memory wall are dominant in determining the IC performance. 3D IC technology is a critical technology today because it offers a reasonable route to further improve IC performance. It increases device density, reduces the interconnect delay, and breaks memory wall with the application of 3D stacking using through silicon via. 3D IC also makes one chip package have more functional diversification than those enhanced only by shrinking the size of the features. The main advantages of 3D IC are the smaller form factor, low energy consumption, high speed, and functional diversification. EUVL, if adopted, will continue to enable IC performance improvement at a slower rate, but 3D IC provides an alternative way to improve the system performance. The best scenario is the adoption of both EUVL and 3D IC. However, the possible further delay of EUVL could enhance the realization of 3D IC for IC system improvement.
Pyrazolo[4,3-e]1,2,4-triazolo[1,5-c]pyrimidine Derivatives as Highly Potent and Selective Human A3Adenosine Receptor Antagonists:  Influence of the Chain at the N8Pyrazole Nitrogen (2000)

An enlarged series of pyrazolotriazolopyrimidines previously reported, in preliminary form (Baraldi et al. J. Med. Chem. 1999, 42, 4473-4478), as highly potent and selective human A(3) adenosine receptor antagonists is described. The synthesized compounds showed A(3) adenosine receptor affinity in the sub-nanomolar range and high levels of selectivity evaluated in radioligand binding assays at human A(1), A(2A), A(2B), and A(3) adenosine receptors. In particular, the effect of the chain at the N(8) pyrazole nitrogen was analyzed. This study allowed us to identify the derivative with the methyl group at the N(8) pyrazole combined with the 4-methoxyphenylcarbamoyl moiety at the N(5) position as the compound with the best binding profile in terms of both affinity and selectivity (hA(3) = 0.2 nM, hA(1)/hA(3) = 5485, hA(2A)/hA(3) = 6950, hA(2B)/hA(3) = 1305). All the compounds proved to be full antagonists in a specific functional model where the inhibition of cAMP generation by IB-MECA was measured in membranes of CHO cells stably transfected with the human A(3) receptor. The new compounds are among the most potent and selective A(3) antagonists so far described. The derivatives with higher affinity at human A(3) adenosine receptors proved to be antagonists, in the cAMP assay, capable of inhibiting the effect of IB-MECA with IC(50) values in the nanomolar range, with a trend strictly similar to that observed in the binding assay. Also a molecular modeling study was carried out, with the aim to identify possible pharmacophore maps. In fact, a sterically controlled structure-activity relationship was found for the N(8) pyrazole substituted derivatives, showing a correlation between the calculated molecular volume of pyrazolo[4,3-e]1,2, 4-triazolo[1,5-c]pyrimidine derivatives and their experimental K(i) values.
Identification of Common Blood Gene Signatures for the Diagnosis of Renal and Cardiac Acute Allograft Rejection (2013)

To test, whether 10 genes, diagnostic of renal allograft rejection in blood, are able to diagnose and predict cardiac allograft rejection, we analyzed 250 blood samples from heart transplant recipients with and without acute rejection (AR) and with cytomegalovirus (CMV) infection by QPCR. A QPCR-based logistic regression model was built on 5 of these 10 genes (AR threshold composite score >37% = AR) and tested for AR prediction in an independent set of 109 samples, where it correctly diagnosed AR with 89% accuracy, with no misclassifications for AR ISHLT grade 1b. CMV infection did not confound the AR score. The genes correctly diagnosed AR in a blood sample within 6 months prior to biopsy diagnosis with 80% sensitivity and untreated grade 1b AR episodes had persistently elevated scores until 6 months after biopsy diagnosis. The gene score was also correlated with presence or absence of cardiac allograft vasculopathy (CAV) irrespective of rejection grade. In conclusion, there is a common transcriptional axis of immunological trafficking in peripheral blood in both renal and cardiac organ transplant rejection, across a diverse recipient age range. A common gene signature, initially identified in the setting of renal transplant rejection, can be utilized serially after cardiac transplantation, to diagnose and predict biopsy confirmed acute heart transplant rejection.
Modulation of the Startle Response and Startle Laterality in Relatives of Schizophrenic Patients and in Subjects With Schizotypal Personality Disorder: Evidence of Inhibitory Deficits (2000)

These data suggest a genetically transmitted deficit in prepulse inhibition (sensorimotor gating) in patients with schizophrenia spectrum disorders, including subjects with schizotypal personality disorder and relatives of patients with schizophrenia.
Improved cell survival by the reduction of immediate-early gene expression in replication-defective mutants of herpes simplex virus type 1 but not by mutation of the virion host shutoff function (1994)

Derivatives of herpes simplex virus type 1 (HSV-1) have elicited considerable interest as gene transfer vectors because of their ability to infect a wide range of cell types efficiently, including fully differentiated neurons. However, it has been found that infection of many types of cell with vectors derived from replication-defective mutants of HSV-1 is associated with cytopathic effects (CPE). We have previously shown that viral gene expression played an important role in the induction of CPE caused by an HSV-1 mutant deleted for the essential immediate-early gene 3 (IE 3) (P.A. Johnson, A. Miyanohara, F. Levine, T. Cahill, and T. Friedmann, J. Virol. 66:2952-2965, 1992). We have investigated which viral genes might be responsible for CPE by comparing the ability of each of the individual genes expressed by an IE 3 deletion mutant during a nonproductive infection to inhibit biochemical transformation after cotransfection of BHK or CV-1 cells with a selectable marker gene. Transfection of IE genes 1,2, and 4 individually all caused a marked inhibition of colony formation, while transfection of IE 5 and the large subunit of ribonucleotide reductase had little effect. These results suggested that it would be necessary to mutate or reduce the expression of nearly all HSV-1 IE genes to reduce virus-induced CPE. Therefore, we have used VP16 mutants, which are unable to transinduce IE gene expression (C. I. Ace, T. A. McKee, J. M. Ryan, J. M. Cameron, and C. M. Preston, J. Virol. 63:2260-2269, 1989), to derive two replication-defective strains: 14H delta 3, which is deleted for both copies of IE 3, and in 1850 delta 42, which has a deletion in the essential early gene UL42. The IE 3-VP16 double mutant, 14H delta 3, is significantly less toxic than a single IE 3 deletion mutant over a range of multiplicities of infection, as measured in a cell-killing assay, and has an enhanced ability to persist in infected cells in a biologically retrievable form. In contrast, the UL42-VP16 double mutant, in 1850 delta 42, showed reduced toxicity only at low multiplicities of infection. To test the role of the virion host shutoff function as an additional candidate to influence virus-induced CPE, we have introduced a large insertion mutation into the virion host shutoff gene of an IE 3 deletion mutant and the double mutant 14H delta 3.(ABSTRACT TRUNCATED AT 400 WORDS)
Purification of Single-Wall Carbon Nanotubes by Microfiltration (1997)

A purification procedure for single-wall carbon nanotubes (SWNTs) prepared by pulsed laser ablation is discussed, which separates coexisting carbon nanospheres (CNS), metal nanoparticles, polyaromatic carbons, and fullerenes from the SWNT fraction. The process involves the suspension of CNS, metal nanoparticles, and SWNTs in an aqueous solution using a cationic surfactant and the subsequent trapping of SWNTs on a membrane filter. No oxidative treatment is required. Scanning/transmission electron microscopy and Raman scattering were used to evaluate the purification process and the vibrational features of SWNTs. Purity of SWNTs at the final stage sample is in excess of 90% by weight, and no evidence of impurity carbon phases was revealed in the Raman spectrum of the SWNT fraction.
A Novel Genetically Engineered Pathway for Synthesis of Poly(Hydroxyalkanoic Acids) in Escherichia coli (2000)

A new pathway to synthesize poly(hydroxyalkanoic acids) (PHA) was constructed by simultaneously expressing butyrate kinase (Buk) and phosphotransbutyrylase (Ptb) genes of Clostridium acetobutylicum and the two PHA synthase genes (phaE and phaC) of Thiocapsa pfennigii in Escherichia coli. The four genes were cloned into the BamHI and EcoRI sites of pBR322, and the resulting hybrid plasmid, pBPP1, conferred activities of all three enzymes to E. coli JM109. Cells of this recombinant strain accumulated PHAs when hydroxyfatty acids were provided as carbon sources. Homopolyesters of 3-hydroxybutyrate (3HB), 4-hydroxybutyrate (4HB), or 4-hydroxyvalerate (4HV) were obtained from each of the corresponding hydroxyfatty acids. Various copolyesters of those hydroxyfatty acids were also obtained when two of these hydroxyfatty acids were fed at equal amounts: cells fed with 3HB and 4HB accumulated a copolyester consisting of 88 mol% 3HB and 12 mol% 4HB and contributing to 68.7% of the cell dry weight. Cells fed with 3HB and 4HV accumulated a copolyester consisting of 94 mol% 3HB and 6 mol% 4HV and contributing to 64.0% of the cell dry weight. Cells fed with 3HB, 4HB, and 4HV accumulated a terpolyester consisting of 85 mol% 3HB, 13 mol% 4HB, and 2 mol% 4HV and contributing to 68.4% of the cell dry weight.
Image restoration of arbitrarily warped documents (2004)

We present a framework for acquiring and restoring images of warped documents. The purpose of our restoration is to create a planar representation of a once planar document that has undergone an arbitrary and unknown rigid deformation. To accomplish this restoration, our framework acquires and flattens the 3D shape of a warped document to determine a nonlinear image transform that can correct for image distortion caused by the document's shape. Our framework is designed for use in library and museum digitization efforts where very old and badly damaged manuscripts are imaged.
Heparanase inhibition reduces proteinuria in a model of accelerated anti‐glomerular basement membrane antibody disease (2005)

These data suggest that heparanase contributes to the pathogenesis of proteinuria in a model of anti-GBM disease.