gebhart/patrepeval huggingface dataset:
S-Acyl and N-Acyl Derivatives of Benzothiazole-2-thiol: An Example of Acyl Group Rearrangement (2007)

Amides, thioamides and carbamates are versatile intermediates in the synthesis of natural products. Among the most well-known procedures to make amides and thioamides are the reactions between amines and acyl halides, or between amines and thioacyl halides. Acyl halides and thioacyl halides are, however, not easy to handle in general or available in stock most of the time. For instance, thiobenzoyl chloride, a purple liquid collection and purification via vaccum distillation, undergoes decomposition very easily in the presence of atmospheric oxygen at 78 C or above. Thus, effective acylating reagents or acylating intermediates such as acylimidazole, a reaction product of trisdialkylaminoborane and carboxylic acid, acyloxyborane, 1,1'-[carbonyldioxy]dibenzotriazole convertible into 1-acyloxybenzotriazole, and benzotriazole-1-yl diethyl phosphate have been carefully developed for the syntheses of amides. Moreover, the utility of thioacylimide explored by Geordeler, the usage of N-thiobenzoylbenztriazole, the reaction between diimidazole sulfide and dithiobenzoic acid reported by Walter, and Lawesson’s reagent played a key role for syntheses of thioamides. As for using leaving groups containing sulfur for the preparation of amides, 3-acylthiazolidine-2-thione by Y. Nagao, and utility of 2-mercaptobenzoxazole (MBO) by Ueda have been previously explored. In a previous paper, we have reported the syntheses for a variety of phenylamides, thiobenzamides and various carbamates by adopting S-benzoyl derivative of benzothiazole-2thiol, so called 2-mercaptobenzothiazole (MBT) as a good leaving group moiety. Here, we wish to report the phenomenon of the acyl group rearrangement between derivatives of MBT, the quantitative isolation of each derivative of MBT, and their chemical properties. Both acyl derivatives of MBT have demonstrated that they can be used in the facile syntheses of other alkylamides (alkyl = methyl, benzyl, cinnamyl) and benzylthioamide. Although Ueda observed the formation of S-acyl derivative and N-acyl derivative of MBO as result of the acyl group rearragement during the reaction, there was no mention of the ratio distribution of derivatives or mechanistic details. For a comparison to S-acyl/N-acyl rearrangement of MBO, Ueda also reported that the acylating reagent, derived from 1,2-benzisothiazol-3-ol and benzoyl chloride, also gives the benzoyl group rearrangement between the O-
Direct Method for Surface Silyl Functionalization of Mesoporous Silica (2004)

A direct method of surface silyl modification and simultaneous surfactant removal of mesoporous silica is investigated in its physicochemical details. Twelve different silanes of various functionalities are studied. The method employs an alcohol solution of silanes to allow the simultaneous surfactant/silyl exchange process, which results in a more uniform monolayer coverage of the surface and a higher amount of surface attachments of silane. We vary the solution concentration of silanes to study the effect on loadings. It is found that the variation of the surface loading of the silyl group follows a Langmuir adsorption model closely. The method gives one a well-controlled monolayer coverage of the surface. The loadings are determined by the exchange equilibrium. Fittings of the loading data to Langmuir adsorption isotherms give one the adsorption equilibrium constants and maximum surface loadings. We categorize the silanes into three different groups according to the values of the equilibrium constants and discuss them with respect to molecular structures. We also report on the extensive characterizations of the surface-functionalized mesoporous materials, such as nitrogen adsorptions, X-ray diffraction, 29Si magic-angle spinning NMR, 13C magic-angle spinning NMR, and IR spectroscopy. The method provides one with a convenient and highly controllable approach to the surface functionalization of mesoporous silica.
Two Models for Multiple Sclerosis: Experimental Allergic Encephalomyelitis and Theilerʼs Murine Encephalomyelitis Virus (1996)

In this review, we compare and contrast two popular models for multiple sclerosis (MS), Theiler's murine encephalomyelitis virus (TMEV) disease and experimental allergic encephalomyelitis (EAE). These models are used to investigate the viral and autoimmune etiology of MS, respectively. Infection with live TMEV is an essential component of TMEV demyelinating disease. TMEV-specific cellular and humoral immunity and apoptosis of infected cells eliminate virus from the gray matter of the central nervous system (CNS) during the acute phase of TMEV disease. In contrast, during the chronic phase, TMEV persistently infects glial cells and/or macrophages in the white matter. During the chronic phase, recruitment of macrophages, TMEV-specific T cells and antibody, with the induction of apoptosis are harmful to the host, leading to inflammation and demyelination. In EAE, induction of encephalitogenic CD4+ T cells is an important component for disease. After stimulation and activation, these T cells upregulate adhesion molecules and are able to enter the CNS. Th1 cytokines augment the recruitment of mononuclear cells in the CNS. Macrophages and/or glial cells secrete cytotoxic factors leading to demyelination in conjunction with B cells secreting anti-myelin antibody. Although immunopathological pathways during the course of the demyelination in TMEV infection and EAE are not always the same, oligodendroglial apoptosis is observed in both models, suggesting that their demyelinating processes share a common terminal pathway and finally lead to quite a similar clinical and pathological picture.
Effect of the damper coils on the rotational motion of the superconducting magnetically levitated bogie (2000)

Numerical simulation of a superconducting magnetically levitated bogie (JR Maglev) has been studied. A damper coil system was introduced to increase the damping of the levitation system. This damper coil system is designed for reducing the lateral and vertical vibration of the bogie. In this levitation system, the rotational motion is also caused by the lateral and vertical displacement of the bogie. Using the numerical simulation, its effect on the rotational motion of the bogie is assessed. The damper coil system is shown to improve damping for the rotational motion.
Gene Expression Profiling in Human Acute Ischemic Stroke (2009)

Background: Gene expression profiling of human acute ischemic stroke (AIS) has the potential to identify a diagnostic panel for differential diagnosis of AIS early in the treatment phase. Purpose: The objective of this dissertation was to identify peripheral blood biomarkers that could be further explored for use in differential diagnosis of AIS and the design of stroke therapeutics.Methods: A prospective gene expression profiling study of 39 patients and 25 healthy controls was conducted. Peripheral blood samples were collected in Paxgene Blood RNA tubes from patients who were ≥18 years of age with MRI diagnosed AIS after differential diagnosis and controls who were Non-stroke neurologically healthy. In stroke patients, blood was redrawn 24 hours following onset of symptoms to determine changes in gene expression profiles over time. RNA was hybridized to Illumina humanRef-8v2 bead chips. Validation was performed using Taqman Gene expression polymerase chain reaction on significant targets. Results: A nine gene profile has been identified for AIS. Five of these nine genes were identified in the previously published whole blood gene expression profiling study of stroke and therefore play a likely role in the response to AIS in humans. One of these nine genes (s100A12) was significantly associated with increasing age and therefore may be non-specific for stroke. Three genes were identified as the whole blood expression profile change over time (LY96, IL8, and SDPR). Pathway analysis revealed a robust innate immune response, with toll like receptor (TLR) signaling as a highly significant pathway present in the peripheral whole blood of AIS patients.Conclusion: The findings of this study support the claim that gene expression profiling of peripheral whole blood can be used to identify diagnostic markers of AIS. A plausible case for innate immunity through the activation of TLR4 as a mediator of response to AIS has been made from the results of this study. This study and those conducted by Moore et al (2005) and Tang et al (2006) provide the foundation of data that support the use of peripheral whole blood for future blood profiling studies of neurological disease; which significantly opens the door of opportunity.
Body conformable 915 MHz microstrip array applicators for large surface area hyperthermia (1992)

The optimal treatment with hyperthermia of superficially located tumors which involve large surface areas requires applicators which can physically conform to body contours, and locally alter their power deposition patterns to adjust for nonuniform temperature caused by tissue inhomogeneities and blood flow variations. A series of 915-MHz microstrip array applicators satisfying these criteria have been developed and clinically tested. Clinical and engineering design tradeoff's for practical devices are discussed. Measurements taken in tissue equivalent phantoms and a summary of clinical experiences with these microstrip arrays are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Automatic generation and verification of railway interlocking control tables using FSM and NuSMV (2009)

Due to their important role in providing safe conditions for train movements, railway interlocking systems are considered as safety critical systems. The reliability, safety and integrity of these systems, relies on reliability and integrity of all stages in their lifecycle including the design, verification, manufacture, test, operation and maintenance.In this paper, the Automatic generation and verification of interlocking control tables, as one of the most important stages in the interlocking design process has been focused on, by the safety critical research group in the School of Railway Engineering, SRE. Three different subsystems including a graphical signalling layout planner, a Control table generator and a Control table verifier, have been introduced. Using NuSMV model checker, the control table verifier analyses the contents of control table besides the safe train movement conditions and checks for any conflicting settings in the table. This includes settings for conflicting routes, signals, points and also settings for route isolation and single and multiple overlap situations. The latest two settings, as route isolation and multiple overlap situations are from new outcomes of the work comparing to works represented on the subject recently.
Color Graphs for Automated Cancer Diagnosis and Grading (2009)

This paper reports a new structural method to mathematically represent and quantify a tissue for the purpose of automated and objective cancer diagnosis and grading. Unlike the previous structural methods, which quantify a tissue considering the spatial distributions of its cell nuclei, the proposed method relies on the use of distributions of multiple tissue components for the representation. To this end, it constructs a graph on multiple tissue components and colors its edges depending on the component types of their endpoints. Subsequently, it extracts a new set of structural features from these color graphs and uses these features in the classification of tissues. Working with the images of colon tissues, our experiments demonstrate that the color-graph approach leads to 82.65% test accuracy and that it significantly improves the performance of its counterparts.
Heterogeneous Hydrogenation of Organic Halogen Compounds by Carrier‐Supported Organotin Hydrides (1981)

Organotin hydrides supported on inorganic carriers such as Al2O3 or SiO2 exhibit high stability and regenerability. Such reagents, which are effective reducing agents, have now been prepared for the first time. With the Al2O3-supported tin hydride reagent (1), it is possible to reduce 1,1-dichloro-2,2-di-phenylcyclopropane quantitatively to 1,1-diphenylcyclopropane.
Isolation and characterization of alkaline protease-deficient mutants of Pseudomonas aeruginosa in vitro and in a mouse eye model (1984)

Mutants of Pseudomonas aeruginosa are described which are markedly deficient in alkaline protease production. Characterization of these mutants in vitro suggests that the mutations in two of these strains are specific for alkaline protease production. Examination of these mutants in a mouse eye model demonstrates that alkaline protease is required for the establishment of corneal infections with P. aeruginosa PA103. Mutants deficient in alkaline protease production could not colonize traumatized cornea and did not produce the corneal damage characteristic of infection by the parental strain. Addition of subdamaging amounts of alkaline protease to eyes infected with the protease-deficient mutants resulted in infections which were indistinguishable from infections caused by the parental strain.
Prednisolone inhibits endotoxin-induced disseminated intravascular coagulation and improves mortality in rats (1999)

In order to determine whether prednisolone has a protective effect against the development of disseminated intravascular coagulation (DIC), we measured the effect of prednisolone on changes in hemostatic parameters and plasma levels of inflammatory cytokines in endotoxin-treated rats. Decreases in platelet count and fibrinogen levels, prolongation of prothrombin time, and increases in the plasma fibrin degradation products and levels of thrombin-antithrombin III (TAT) complex following the administration of endotoxin, all of which are associated with DIC, were significantly suppressed by the administration of prednisolone. Heparin administration significantly suppressed changes in all these parameters except for the decrease in platelet count. The combination of prednisolone and heparin was more effective than either treatment alone. In order to determine whether these effects of prednisolone are correlated with the suppression of inflammatory cytokine production, we examined the relationship between changes in plasma levels of cytokine, the hemostatic parameters listed above, and mortality using a number of intervention regimens designed to alter events of the experimentally induced DIC. Changes in hemostatic parameters associated with DIC following 30 mg/kg per 4 h of endotoxin infusion were significantly suppressed by treatment with 1 mg/kg prednisolone 30 min before beginning endotoxin infusion, followed by administration of 250 U/kg heparin 2 h after the start of endotoxin infusion (prednisolone-endotoxin-heparin regimen). The heparin and prednisolone were administrated subcutaneously. The administration of prednisolone and heparin in the reverse order (i.e. heparin first and prednisolone second: heparin-endotoxin-prednisolone regimen) also suppressed changes in hemostatic parameters, albeit to a smaller degree. Cytokine production was also significantly suppressed by the first treatment, but was not affected by the regimen in which heparin was administered first. Administration of prednisolone alone or heparin alone 30 min before endotoxin significantly reduced the number of renal glomeruli with fibrin thrombi. Plasma levels of creatinine and alanine transferase were reduced only by prednisolone. Increased plasma levels of interleukin-1beta, tissue necrosis factor-alpha and interleukin-6 were suppressed by prednisolone but not by heparin, and there were significant correlations between plasma levels of TAT and cytokines. Prednisolone was more effective than heparin in reducing mortality at 24 h after 100 mg/kg over 4 h of endotoxin infusion (four of 20 versus 15 of 20 deaths for prednisolone and heparin, respectively). These findings suggest that prednisolone inhibits the development of endotoxin-induced DIC and reduces mortality by a different mechanism than heparin, possibly through suppressing the production of inflammatory cytokines. Prednisolone may be efficacious in preventing DIC and multiple organ dysfunction caused by endotoxin.
Computational inference of the molecular logic for synaptic connectivity in <i>C. elegans</i> (2006)

Here we present computational techniques linking these two types of information. A systems-based approach (EMBP: Entropy Minimization and Boolean Parsimony) identifies sets of synergistically interacting genes whose joint expression predicts neural connectivity. We introduce an information theoretic measure of the multivariate synergy, a fundamental concept in systems biology, connecting the members of these gene sets. We present and validate our preliminary results based on publicly available information, and demonstrate that their synergy is exceptionally high indicating joint involvement in pathways. Our strategy provides a robust methodology that will yield increasingly more accurate results as more neuron-specific gene expression data emerge. Ultimately, we expect our approach to provide important clues for universal mechanisms of neural interconnectivity.
Zyxin, a Regulator of Actin Filament Assembly, Targets the Mitotic Apparatus by Interacting with H-Warts/Lats1 Tumor Suppressor (2000)

The mitotic apparatus plays a pivotal role in dividing cells to ensure each daughter cell receives a full set of chromosomes and complement of cytoplasm during mitosis. A human homologue of the Drosophila warts tumor suppressor, h-warts/LATS1, is an evolutionarily conserved serine/threonine kinase and a dynamic component of the mitotic apparatus. We have identified an interaction of h-warts/LATS1 with zyxin, a regulator of actin filament assembly. Zyxin is a component of focal adhesion, however, during mitosis a fraction of cytoplasmic-dispersed zyxin becomes associated with h-warts/LATS1 on the mitotic apparatus. We found that zyxin is phosphorylated specifically during mitosis, most likely by Cdc2 kinase, and that the phosphorylation regulates association with h-warts/LATS1. Furthermore, microinjection of truncated h-warts/LATS1 protein, including the zyxin-binding portion, interfered with localization of zyxin to mitotic apparatus, and the duration of mitosis of these injected cells was significantly longer than that of control cells. These findings suggest that h-warts/LATS1 and zyxin play a crucial role in controlling mitosis progression by forming a regulatory complex on mitotic apparatus.
Microtubule-Associated Protein 2 Levels Decrease in Hippocampus Following Traumatic Brain Injury (1992)

We examined microtubule-associated protein 2 (MAP2) levels in hippocampal and cortical tissue 3 h following moderate traumatic brain injury (TBI) in the rat. MAP2 levels were assayed by quantitative immunoreactivity in tissue fractions obtained from naive, sham-injured, or fluid percussion-injured animals. Tissues were homogenized in the presence of protease inhibitors (0.3 mM phenylmethylsulfonyl fluoride, PMSF), a specific calpain inhibitors (0.1 mM leupeptin), and chelators (2 mM ethylene glycol-bis-tetraacetic acid, EGTA; 1 mM ethylenedinitrilo-tetraacetic acid, EDTA) to eliminate in vitro MAP2 proteolysis during tissue processing. Compared to naive rats, sham injury had no effect on soluble MAP2 levels in either cortex (105.0 +/- 4.4% of naive value) or hippocampus (106.6 +/- 5.2% of naive value). However, TBI caused a significant (p < 0.005) decrease in hippocampal MAP2 levels (55.7 +/- 5.9% of sham-injured controls). The effect appeared to be regionally selective, since the MAP2 decrease did not occur in cortex (89.1 +/- 1.4%). The degree of MAP2 decrease in hippocampus was similar in both membrane (57.8%) and cytosolic (55.7%) fractions, ruling out the possibility of partitioning artifacts. The data suggest that sublethal alterations of neuronal structure and function caused by MAP2 degradation may play an important role in the development of TBI-induced functional deficits. Since MAP2 is exclusively associated with the cytoskeleton in somal and dendritic compartments of neurons, the pathophysiology of sublethal magnitudes of TBI may also involve dendritic and somal dysfunction.
Optical lithography: 40 years and holding (2007)

Optical lithography has been the dominant patterning process for semiconductor fabrication for over 40 years. The patterning process evolved initially from methods used in the printing industry, but as integrated circuits became more complex, and as device geometries shrank, sophisticated new imaging methods evolved. Today’s optical lithography systems represent the highest resolution, most accurate optical imaging systems ever produced. This remarkable evolutionary process continues to this day, paced by "Moore's Law". The evolutionary development of lithography systems over the last 40 years is reviewed along with a brief discussion of options for the future.
A new route to nitriles. Dehydration of aldoximes using 2,4,6-trichloro-s-triazine (cyanuric chloride) (1972)

J. K. Chakrabarti and T. M. Hotten, J. Chem. Soc., Chem. Commun., 1972, 1226 DOI: 10.1039/C39720001226
Synthesis and characterization of aromatic polymers containing pendant silyl groups. I. Polyarylates (1992)

Abstract Polyarylates containing pendant silyl group were prepared by the phase‐transfer catalyzed, two‐phase polycondensations of 2,2‐bis (4‐hydroxyphenyl) propane with corresponding dicarbonyl chlorides such as 2‐trimethylsilylterephthaloyl chloride, 5‐trimethylsilylisophthaloyl chloride, 5‐dimethylphenylsilylisophthaloyl chloride, and 5‐triphenylsilylisophthaloyl chloride. The resulting amorphous polyarylates with glass transition temperatures of 163–214°C had inherent viscosities in the range of 0.41–0.95 dL/g. These polyarylates were readily soluble in common chlorinated hydrocarbons and it was possible to obtain transparent, flexible, and tough films from the polymer solutions. The prepared polyarylates showed fairly good thermal stabilities as well as tensile strengths, i.e., the tensile strengths of the cast films from chloroform solution were 6.0–6.7 kg/mm 2 . And TGA data revealed 10% weight losses and residual weights at 800°C were 437–495°C and 27–40% under nitrogen atmosphere, respectively. © 1992 John Wiley & Sons, Inc.
Incidence of Adenocarcinoma of the Esophagus Among White Americans by Sex, Stage, and Age (2008)

Rapid increases in the incidence of adenocarcinoma of the esophagus have been reported among white men. We further explored the temporal patterns of this disease among white individuals by sex, stage, and age by use of data from the Surveillance, Epidemiology, and End Results program. We identified 22,759 patients from January 1, 1975, through December 31, 2004, with esophageal cancer, of whom 9526 were diagnosed with adenocarcinoma of the esophagus. Among white men, increases in the incidence of esophageal cancer were largely attributed to a 463% increase in the incidence of adenocarcinoma over this time period, from 1.01 per 100,000 person-years (95% confidence interval [CI] = 0.90 to 1.13) in 1975-1979 to 5.69 per 100,000 person-years (95% CI = 5.47 to 5.91) in 2000-2004. A similar rapid increase was also apparent among white women, among whom the adenocarcinoma rate increased 335%, from 0.17 (95% CI = 0.13 to 0.21) to 0.74 per 100,000 person-years (95% CI = 0.67 to 0.81), over the same time period. Adenocarcinoma rates rose among white men and women in all stage and age groups, indicating that these increases are real and not an artifact of surveillance.