gebhart/patrepeval huggingface dataset:
Artificial Intelligence and Large Scale Scientific Experiments (1992)

As ever larger scientific endeavors are made, it becomes even more crucial that they be designed, performed, and analyzed very carefully. Artificial intelligence (AI) techniques are seen as a methodology for automating some of the tasks involved in large scale scientific ex-perimentation. Scientific experimentation, in turn, is seen as a methodology for improving the capabilities of AI through the special demands it makes. This paper discusses how large scale scientific experimentation can be helped by AI and vice-versa. Large Scale Scientific Experiments Scientific experimentation has challenges that no other domain has to offer. It differs in large part by its ex-ploratory nature which means that the theories and
Reaction of Arylphosphines with Singlet Oxygen:  Intra- vs Intermolecular Oxidation (2001)

[reaction--see text] The chemistry of singlet oxygen with all three isomers of tris(methoxyphenyl)phosphine has been studied. For the severely hindered ortho isomer, intramolecular rearrangement to form phenyl diphenyl phosphinate is preferred to formation of phosphine oxide at low concentration in aprotic solvents. In protic solvents, no intramolecular reactivity is observed. A detailed kinetic analyses has been undertaken. There is no physical quenching, regardless of solvent. Mechanistic implications of these findings are discussed.
Dépôt de silicium polycristallin contenant du carbone pour des applications radiofréquence (2019)

Pour les futures applications en telecommunications 5G, des substrats a base de silicium presentant une faible perte de signal et une excellente linearite sont necessaires. Parmi les solutions envisagees, la technologie RF-SOI est la plus avancee. Son empilement contient une couche de Haute Resistivite (HR), riche en pieges pour les porteurs de charges, composee de silicium polycristallin (poly-Si) de haute purete deposee sur l’oxyde natif d'un substrat HR (HR-Si). Ce systeme presente certaines limitations provenant essentiellement de l'interface HR-Si/SiO2 et de sa stabilite thermique, mais egalement de la resistivite insuffisante de la couche riche en pieges. L'objectif principal de cette these etait d'explorer des approches innovantes pour resoudre ces difficultes tout en restant compatible avec la technologie silicium. Afin d’atteindre ces objectifs, du carbone a ete ajoute dans le systeme au cours des differentes etapes d'elaboration: i) remplacement de la couche interfaciale de SiO2 par une couche mince de 3C-SiC et ii) ajout de carbone pendant le depot de poly-Si.En utilisant la technique de depot chimique en phase vapeur a pression atmospherique, des couches HR de poly-Si a l'etat de l'art ont ete deposee sur oxyde natif avec une epaisseur pouvant aller jusqu'a quelques dizaines de µm. Les resultats ont montre que la resistivite de la couche de poly-Si n'etait pas directement dependante de la taille moyenne des grains. Le remplacement de l'oxyde interfacial par une couche mince de mono- ou de poly-SiC, ainsi que l'adaptation des conditions de croissance ont permis d'atteindre des proprietes equivalentes a l'etat de l'art des couches HR de poly-Si. Cet empilement a l'avantage d'etre plus stable thermiquement en evitant la dissolution de la couche interfaciale. Cependant, ces ameliorations sont accompagnees d’une chute de la resistivite a l’interface attribuee a la conductivite importante du materiau SiC. Par ailleurs, les proprietes de la couche HR et sa stabilite thermique peuvent etre ameliorees en dopant le poly-Si avec du Carbone, si une concentration adequate de cette impurete est utilisee. L'insertion periodique de couches minces de SiC dans le poly-Si conduit a la stabilite thermique la plus elevee et a une augmentation de la resistivite moyenne de la couche. Neanmoins, des diminutions periodiques de la resistivite sont observees a chaque insertion de SiC
Coupled Formation of an Amidotransferase Interdomain Ammonia Channel and a Phosphoribosyltransferase Active Site, (1997)

Activation of gluatmine phosphoribosylpyrophosphate (RPPP) amidotransferase (GPATase) by binding of a PRPP substrate analog results in the formation of a 20 A channel connecting the active site for glutamine hydrolysis in one domain with the PRPP site in a second domain. This solvent-inaccessible channel permits transfer of the NH3 intermediate between the two active sites. Tunneling of NH3 may be a common mechanism for glutamine amidotransferase-catalyzed nitrogen transfer and for coordination of catalysis at two distinct active sites in complex enzymes. The 2.4 A crystal structure of the active conformer of GPATase also provides the first description of an intact active site for the phosphoribosyltransferase (PRTase) family of nucleotide synthesis and salvage enzymes. Chemical assistance to catalysis is provided primarily by the substrate and secondarily by the enzyme in the proposed structure-based mechanism. Different catalytic and inhibitory modes of divalent cation binding to the PRTase active site are revealed in the active conformer of the enzyme and in a feedback-inhibited GMP complex.
ChemInform Abstract: Synthesis of 3′‐(Ureido)adenosine Derivatives and Their High Binding Affinity at the Mutant A3 Adenosine Receptor (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Knee Angle Analysis Using a Wearable Motion Analysis System for Detection and Rehabilitation of Mild Traumatic Brain Injury (2013)

Mild traumatic brain injuries (mTBI) are common in soldiers and athletes, and can affect many areas of a person’s daily life including gait [1]. Current methods of measuring gait parameters involve expensive optical motion capture systems, time intensive setup, wires, complicated filtering techniques, and a laboratory setting. A wearable and wireless motion analysis system would allow gait analysis to be performed outside of a laboratory setting during activities of daily living, in a clinical setting or on a football field. The purpose of this study was to develop and verify an algorithm to calculate knee flexion during slow gait, particularly during terminal stance and pre-swing phases, using wireless wearable sensors.
Monitoring SARS-CoV-2 Infection Using a Double Reporter-Expressing Virus (2022)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the highly contagious agent responsible for the coronavirus disease 2019 (COVID-19) pandemic. An essential requirement for understanding SARS-CoV-2 biology and the impact of antiviral therapeutics is a robust method to detect the presence of the virus in infected cells or animal models. Despite the development and successful generation of recombinant (r)SARS-CoV-2-expressing fluorescent or luciferase reporter genes, knowledge acquired from their use in <i>in vitro</i> assays and/or in live animals is limited to the properties of the fluorescent or luciferase reporter genes. Herein, for the first time, we engineered a replication-competent rSARS-CoV-2 that expresses both fluorescent (mCherry) and luciferase (Nluc) reporter genes (rSARS-CoV-2/mCherry-Nluc) to overcome limitations associated with the use of a single reporter gene. In cultured cells, rSARS-CoV-2/mCherry-Nluc displayed similar viral fitness as rSARS-CoV-2 expressing single reporter fluorescent and luciferase genes (rSARS-CoV-2/mCherry and rSARS-CoV-2/Nluc, respectively) or wild-type (WT) rSARS-CoV-2, while maintaining comparable expression levels of both reporter genes. <i>In vivo</i>, rSARS-CoV-2/mCherry-Nluc has similar pathogenicity in K18 human angiotensin-converting enzyme 2 (hACE2) transgenic mice than rSARS-CoV-2 expressing individual reporter genes or WT rSARS-CoV-2. Importantly, rSARS-CoV-2/mCherry-Nluc facilitates the assessment of viral infection and transmission in golden Syrian hamsters using <i>in vivo</i> imaging systems (IVIS). Altogether, this study demonstrates the feasibility of using this novel bioreporter-expressing rSARS-CoV-2 for the study of SARS-CoV-2 <i>in vitro</i> and <i>in vivo</i>. <b>IMPORTANCE</b> Despite the availability of vaccines and antivirals, the coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to ravage health care institutions worldwide. Previously, we generated replication-competent recombinant (r)SARS-CoV-2 expressing fluorescent or luciferase reporter proteins to track viral infection <i>in vitro</i> and/or <i>in vivo</i>. However, these rSARS-CoV-2 are restricted to express only a single fluorescent or a luciferase reporter gene, limiting or preventing their use in specific <i>in vitro</i> assays and/or <i>in vivo</i> studies. To overcome this limitation, we have engineered a rSARS-CoV-2 expressing both fluorescent (mCherry) and luciferase (Nluc) genes and demonstrated its feasibility to study the biology of SARS-CoV-2 <i>in vitro</i> and/or <i>in vivo</i>, including the identification and characterization of neutralizing antibodies and/or antivirals. Using rodent models, we visualized SARS-CoV-2 infection and transmission through <i>in vivo</i> imaging systems (IVIS).
The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat (2016)

Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (<i>Varanus komodoensis</i>) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals' environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. <b>IMPORTANCE</b> Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.
Cytotoxic murine monoclonal antibody recognizing an ovine lymphocyte subpopulation similar to the human OKT4-positive set. (1986)

A cytotoxic murine immunoglobulin G2b monoclonal antibody was produced from immunization with ovine thymocytes. It reacts with a monomorphic determinant on ovine lymphocytes. This antibody 11.2 G11 does not react with B cells, lyses 50 to 60% of peripheral blood T cells, and precipitates a single chain protein with an apparent m.w. of 57,000. Its effect on mitogen- and antigen-driven lymphocyte proliferation supports its similarity in the sheep to the OKT4 antibody in humans.
Phosphoinositides and cell proliferation (1985)

Certain growth factors act by stimulating the hydrolysis of inositol lipids to yield putative second messengers such as diacylglycerol (DG) and inositol trisphosphate (IP3). One function of the former is to stimulate C-kinase, which may act by switching on a sodium/hydrogen exchanger to induce the increase in pH that appears to have a permissive effect on DNA synthesis. Studies on Swiss 3T3 cells have revealed that growth factors stimulate an increase in two separate isomers of IP3. In addition to inositol 1,4,5-trisphosphate there was a large increase in inositol 1,3,4-trisphosphate. While the former functions to elevate intracellular calcium, which has been implicated in the control of growth of many different cell types, the function of the latter is unknown. Since the 1,3,4 isomer turns over very slowly, it may control long-term events and thus could play a role in cell growth. There are other growth factors such as insulin and epidermal growth factor (EGF), which apparently do not work through the inositol lipids but they may initiate ionic events similar to those just described for calcium-mobilizing receptors. The bifurcating signal pathway based on IP3/Ca2+ and DG/C-kinase provides an interesting framework within which to consider the mode of action of oncogenes.
A Congratulatory Note (2003)

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Synthesis and characterization of nanogranular Fe3O4/biomimetic hydroxyapatite (2015)

A major concern about the biomedical application of magnetic nanoparticles is their biocompatibility. A possible solution is coating them with hydroxyapatite (HA) [Ca5(PO4)3OH], which is the inorganic component of biological hard tissues, e.g. bone and teeth. This approach appears especially appealing for uses in the field of bone tissue engineering. &#13;\nWe have synthetized a novel nanogranular system, consisting of magnetite nanoparticles embedded in biomimetic carbonate HA, through an original two-step method: i) magnetite nanoparticles are prepared by refluxing an aqueous solution of Fe(SO4) and Fe2(SO4)3 in an excess of Tetrabutilammonium hydroxide acting as surfactant; ii) the nanoparticles are coated with a Ca(OH)2 layer, to induce the growth of HA directly on their surface, by reaction of Ca(OH)2 with HPO42-. &#13;\nTwo samples have been collected with magnetite content ~ 0.8 wt. % and ~ 4 wt.%. The magnetite nanoparticles and the nanogranular material have been investigated by X-ray Diffraction, Fourier Transform Infrared Spectroscopy and Transmission Electron Microscopy. These analyses have provided structural information on the as-prepared nanoparticles (mean size ~ 6 nm) and revealed the presence of surface hydroxyl groups, which promote the growth of the HA phase featuring a nanocrystalline lamellar structure. &#13;\nHysteresis loops (temperature range 5-300 K), thermal and time dependence of the magnetization under different magnetic fields and field dependence of the remanence have been measured by SQUID magnetometer. Moreover, a Mössbauer spectroscopy investigation on the as-prepared nanoparticles has been carried out between T = 4 K and room temperature; to better distinguish the contribution coming from Fe different lattice sites, low temperature measurements were performed with and without an applied magnetic field of 8 T; the field was applied parallel to the direction of the incoming 14.4 keV -radiation direction. Room temperature Mössbauer spectra show just the presence of a doublet contribution; below 200 K, a sextet contribution appears and it gets narrower as T is decreased. If the sextet is described in terms of a hyperfine fields distribution, that shows three main contributions that shift to higher hyperfine fields values as T approaches 4 K. At 4 K, with the external magnetic field, two sextets can be clearly observed corresponding to Fe in tetrahedral and octahedral sites, showing a slight canting with respect to the field direction. Both the as-prepared and the HA-coated magnetite nanoparticles show a superparamagnetic behaviour at T=300 K. However, the magnetization relaxation process is affected by dipolar magnetic interactions of comparable strength in the three samples, also inducing the onset of a collective frozen magnetic regime below T~20 K. The results indicate that the magnetite nanoparticles tend to form agglomerates in the as-prepared state, which are not substantially altered by the HA growth, coherently with the creation of electrostatic hydrogen bonds among the surface hydroxyl groups.
Crystallization and preliminary X-ray analysis of the chemokine-binding protein from orf virus (Poxviridae) (2010)

The parapoxvirus orf virus (ORFV) encodes a chemokine-binding protein (CBP) that functions to downregulate the host's immune response at the site of infection by blocking the chemokine-induced recruitment of immune cells. In order to shed light on the structural determinants of CBP-chemokine binding, ORFV CBP was crystallized as part of an ongoing structure-function study on this protein. ORFV CBP crystals were obtained by the sitting-drop vapour-diffusion technique using ammonium citrate as a precipitant. The crystal quality was greatly improved through the addition of small-molecule additives to the crystallization mother liquor. ORFV CBP crystals diffracted X-rays to 2.50 A resolution and belonged to the hexagonal space group P6(1)22 or its enantiomorph P6(5)22, with unit-cell parameters a = b = 75.62, c = 282.49 A, alpha = 90, beta = 90, gamma = 120 degrees.
International standardization of criteria for histologic diagnosis of chronic rejection in renal allografts (1994)

An accurate diagnosis of acute rejection in renal allografts can be made histologically by quantitating specific morphologic changes observed on biopsy. The Banff Schema, an internationally standardized system of renal allograft biopsy assessment published in the August 1993 issue of Kidney International (1) has been shown to be highly reproducible and clinically valid for acute rejection. The schema also includes quantitation of the lesions of chronic rejection: fibrous intimal thickening, chronic transplant glomerulopathy, interstitial fibrosis, tubular atrophy. Biopsies that demonstrate these lesions are assigned the noncommittal term "chronic transplant nephropathy," as other conditions such as cyclosporine toxicity, hypertension, infection, and reflux can generate these lesions as well. In certain clinical settings, some lesions probably are specific for chronic rejection, such as fibrous intimal thickening with fragmentation of the elastic lamina, but because of their extreme focality they are infrequently seen on biopsy. It is possible that chronic rejection involves a specific pattern of scarring and peritubular capillary injury, but these changes have yet to be fully characterized. Late allograft biopsies in ongoing clinical trials of new immunosuppressive agents will help to further define the specific pathologic changes of chronic rejection.
New Enzymatic Assay with Urea Amidolyase for Determining Potassium in Serum (1997)

We developed a new simple assay for potassium ion in serum using urea amidolyase (UAL) from yeast sp. The method is based on activation of the enzyme by potassium ion. We eliminated endogenous ammonium ion by use of glutamate dehydrogenase (GLDH), and then monitored the production of ammonium ion by UAL, urea, ATP, bicarbonate and magnesium ions. Ammonium ion was produced proportional to the potassium ion concentration and was determined by adding GLDH to produce NADP+ in the presence of 2-oxoglutarate and NADPH. We monitored the change of absorbance at 340 nm. The inhibitory effect of calcium ion to this assay was eliminated by adding glycoletherdiamine-N, N, N', N'-tetraacetic acid to the reaction. The within-assay coefficients of variation (CV) of this method were 0.9-1.55% (n = 10) at 3.32-6.18 mmol/L. Day-to-day CVs ranged from 1.49% to 2.46%. The analytical recovery was 96-108%. The correlation coefficient between the values obtained by our method (y) and those by the ion-selective electrode (ISE) method (x) was 0.994 (y = 1.032x-0.166 mmol/L, Syx = 0.110, n = 100). The presence of bilirubin, haemoglobin or other ions did not affect this assay, confirming the usefulness of this assay for clinical purposes.
Automating the detection of snapshot isolation anomalies (2007)

Snapshot isolation (SI) provides significantly improved concurrency over 2PL, allowing reads to be non-blocking. Unfortunately, it can also lead to non-serializable executions in general. Despite this, it is widely used, supported in many commercial databases, and is in fact the highest available level of consistency in Oracle and Post-greSQL. Sufficient conditions for detecting whether SI anomalies could occur in a given set of transactions were presented recently, and extended to necessary conditions for transactions without predicate reads.

In this paper we address several issues in extending the earlier theory to practical detection/correction of anomalies. We first show how to mechanically find a set of programs which is large enough so that we ensure that all executions will be free of SI anomalies, by modifying these programs appropriately. We then address the problem of false positives, i.e., transaction programs wrongly identified as possibly leading to anomalies, and present techniques that can significantly reduce such false positives. Unlike earlier work, our techniques are designed to be automated, rather than manually carried out. We describe a tool which we are developing to carry out this task. The tool operates on descriptions of the programs either taken from the application code itself, or taken from SQL query traces. It can be used with any database system. We have used our tool on two real world applications in production use at IIT Bombay, and detected several anomalies, some of which have caused real world problems. We believe such a tool will be invaluable for ensuring safe execution of the large number of applications which are already running under SI.
Algorithms for quad-double precision floating point arithmetic (2000)

A quad-double number is an unevaluated sum of four IEEE double precision numbers, ca-pable of representing at least 212 bits of signicand. We present the algorithms for various arithmetic operations (including the four basic operations and various algebraic and transcen-dental operations) on quad-double numbers. The performance of the algorithms, implemented in C++, is also presented. 1