gebhart/patrepeval huggingface dataset:
Molecular cloning and analysis of autonomous replicating sequence of Candida maltosa (1992)

A Candida maltosa chromosomal DNA fragment which confers high frequency transformation of C. maltosa and autonomous replication of recombinant plasmids was cloned and sequenced. Analysis of the nucleotide sequence of the cloned DNA revealed a sequence homologous for C. maltosa autonomously replicating sequence (ARS) elements. Vector pRJ1 for C. maltosa was constructed, which contained a 1.3 kb ARS sequence, pICEM-19H and the ADE1 gene of C. maltosa. Southern blot analysis suggested that the copy number of pRJ1 in C. maltosa was approximately 20 per genome. The sequence analysis also revealed an open reading frame, encoding a polypeptide with high homology (70%) to the RS15 protein of Brugia pagangi. This open reading frame has an intron with canonical sites for correct splicing in Saccharomyces cerevisiae.
Aminimides. IV. Homo‐ and copolymerization studies on trimethylamine methacrylimide (1968)

Abstract Trimethylamine methacrylimide (TAMI) has been homo‐ and copolymerized with methyl methacrylate, vinyl acetate, vinyl chloride, hydroxypropyl methacrylate, and acrylonitrile by free‐radical initiators to soluble, low molecular weight polymers containing pendant aminimide groups along the backbone of the polymer chains. The reactivity ratios in the copolymerization of TAMI (M 1 ) with acrylonitrile (M 2 ) were determined: r 1 = 0.10 ± 0.01, r 2 = 0.37 ± 0.04. The Alfrey‐Price Q and e values for TAMI were also calculated: Q = 0.18, e = −0.60. This preliminary work indicates that TAMI has potential for the preparation of reactive polymers.
Production of L-forms of Streptococcus pyogenes and their antitumor effects. (1980)

Unstable L-forms of Streptococcus pyogenes were effectively isolated when protoplasts induced by muralysin were cultivated on a gradient plate containing penicillin-G. By this method, L-forms were obtained from the strains of serotype 3 and 4, from which they had been considered to be difficult to obtain. After 30 to 40 subcultures, two L-form strains (L-forms of Su and C-512) were successfully transferred into fluid medium without serum and penicillin. The antitumor effects of these stable L-forms were compared with these parent cocci. Treatment of the L-form of Su, which has antitumor effect, showed a considerable prolongation of life span in mice inoculated with Meth-A ascites tumor. On the other hand, the L-form of C-512, which has no antitumor effect, produced no effect on the tumor growth. Using two different transplantable tumors, the antitumor properties of th L-form of Su were investigated by comparing them with protoplast and cell wall fraction derived from the Su strain. In ascites tumors, the L-form treatment showed visible effects, while the cell wall produced no inhibitory effect. On the contrary, in solid tumors the antitumor effects obtained by the administration of the cell wall were never improved by the L-form. In both types of tumor, L-form showed antitumor activities similar to protoplast.
Novel Transthyretin Amyloid Fibril Formation Inhibitors: Synthesis, Biological Evaluation, and X-Ray Structural Analysis (2009)

Transthyretin (TTR) is one of thirty non-homologous proteins whose misfolding, dissociation, aggregation, and deposition is linked to human amyloid diseases. Previous studies have identified that TTR amyloidogenesis can be inhibited through stabilization of the native tetramer state by small molecule binding to the thyroid hormone sites of TTR. We have evaluated a new series of beta-aminoxypropionic acids (compounds 5-21), with a single aromatic moiety (aryl or fluorenyl) linked through a flexible oxime tether to a carboxylic acid. These compounds are structurally distinct from the native ligand thyroxine and typical halogenated biaryl NSAID-like inhibitors to avoid off-target hormonal or anti-inflammatory activity. Based on an in vitro fibril formation assay, five of these compounds showed significant inhibition of TTR amyloidogenesis, with two fluorenyl compounds displaying inhibitor efficacy comparable to the well-known TTR inhibitor diflunisal. Fluorenyl 15 is the most potent compound in this series and importantly does not show off-target anti-inflammatory activity. Crystal structures of the TTR:inhibitor complexes, in agreement with molecular docking studies, revealed that the aromatic moiety, linked to the sp(2)-hybridized oxime carbon, specifically directed the ligand in either a forward or reverse binding mode. Compared to the aryl family members, the bulkier fluorenyl analogs achieved more extensive interactions with the binding pockets of TTR and demonstrated better inhibitory activity in the fibril formation assay. Preliminary optimization efforts are described that focused on replacement of the C-terminal acid in both the aryl and fluorenyl series (compounds 22-32). The compounds presented here constitute a new class of TTR inhibitors that may hold promise in treating amyloid diseases associated with TTR misfolding.
Relation between breakdown mode and location in short-channel nMOSFETs and its impact on reliability specifications (2001)

A method to determine the breakdown position in short channel nMOSFETs is introduced. We find that soft breakdown occurs exclusively in the transistor channel, while the hardest circuit-killing breakdowns occur above the source and drain extension regions. Since these breakdowns make up only a small fraction of all breakdowns, a relaxation of the reliability specification is possible.
Drug Targeting Mycobacterium tuberculosis Cell Wall Synthesis: Development of a Microtiter Plate-Based Screen for UDP-Galactopyranose Mutase and Identification of an Inhibitor from a Uridine-Based Library (2002)

A microtiter plate assay for UDP-galactopyranose mutase, an essential cell wall biosynthetic enzyme of Mycobacterium tuberculosis, was developed. The assay is based on the release of tritiated formaldehyde from UDP-galactofuranose but not UDP-galactopyranose by periodate and was used to identify a uridine-based enzyme inhibitor from a chemical library.
Electrodeposition of CdTe Thin Films (1984)

Cadmium telluride thin films were fabricated on Ti and Nesatron® substrates by electrodeposition and characterized by x‐ray diffraction, scanning electron microscopy, energy dispersive x‐ray analyses (EDAX), optical transmission measurements, and photoelectrochemical (PEC) studies. The deposition‐bath preparation procedure was slightly modified from the literature method to permit initial speciation of and thereby increase the loading level of Te in the film. New data are presented on the electrochemistry of the deposition process and on the cyclic voltammetric behavior of containing electrolytes in the pH range from ∼0.7 to 11.0. The films after suitable annealing in an Ar atmosphere show x‐ray diffraction behavior consistent with a hexagonal structure. Data from EDAX show that the Cd/Te ratio in the film is sensitive to the annealing process. Concomitantly, the conductivity also changes from p‐type to n‐type, as shown by PEC measurements on the films containing a protective coating in contact with alkaline polysulfide electrolytes. Finally, some preliminary data are presented on PEC cells based on these thin films in a nonaqueous electrolyte system comprising the ferrocene/ferricenium ion redox couple.
Dramatically Enhanced Efficiency in Ultra-Fast Silicon MSM Photodiodes Via Light Trapping Structures (2019)

Due to relatively low responsivity at near infrared (NIR) wavelengths, surface-illuminated silicon (Si) photodiodes (PDs) are not attractive for ultra-fast data communication applications despite their CMOS-compatibility. Metal-semiconductor-metal (MSM) photodiodes are well-known for simplicity in fabrication compared to pin and pn junctions-based counterparts, but they usually work with lower efficiencies due to thin absorption layer that ensures high speed response. In this letter, we demonstrate a high efficiency and high-speed Si MSM PD with innovative photon-trapping surface structures. These wavelength-scale structures decrease the surface reflection and introduce laterally propagating waves parallel to the semiconductor surface. The responsivity of Si MSM PDs with the photon-trapping holes was measured to be ~0.59A/W, while the control devices without holes show ~0.08A/W. Such PDs with <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$50\mu \text{m}$ </tex-math></inline-formula> diameter and with 1 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{m}$ </tex-math></inline-formula> finger spacing provide a pulse response of 60ps and 38ps full-width at half-maximum (FWHM) at 3V and 10V applied bias, respectively. Surface-illuminated PDs with these dimensions can offer easy optical coupling options for fiber optic links while offering complete CMOS compatibility.
PC1D version 5: 32-bit solar cell modeling on personal computers (2002)

The computer program PC1D is widely used for modeling crystalline solar cells. This paper describes a new version of the program which takes advantage of the latest graphical environments of personal computers to offer improved visualization of cell design and operation, simpler comparison of experimental data with simulation results, greatly increased calculation speed, and improved models for generation and recombination effects. We demonstrate the use of some of these features to explore the importance of trap-assisted tunneling at heavily doped junctions in material with low carrier lifetime, as is often encountered in thin polycrystalline silicon cells.
CloneCloud: Boosting Mobile Device Applications Through Cloud Clone Execution (2010)

Mobile applications are becoming increasingly ubiquitous and provide ever richer functionality on mobile devices. At the same time, such devices often enjoy strong connectivity with more powerful machines ranging from laptops and desktops to commercial clouds. This paper presents the design and implementation of CloneCloud, a system that automatically transforms mobile applications to benefit from the cloud. The system is a flexible application partitioner and execution runtime that enables unmodified mobile applications running in an application-level virtual machine to seamlessly off-load part of their execution from mobile devices onto device clones operating in a computational cloud. CloneCloud uses a combination of static analysis and dynamic profiling to optimally and automatically partition an application so that it migrates, executes in the cloud, and re-integrates computation in a fine-grained manner that makes efficient use of resources. Our evaluation shows that CloneCloud can achieve up to 21.2x speedup of smartphone applications we tested and it allows different partitioning for different inputs and networks.
Molecular effects of lithium exposure during mouse and chick gastrulation and subsequent valve dysmorphogenesis (2008)

Cells existing already during gastrulation are associated with valve formation days later. The Wnt/beta-catenin signaling in PP cells is normally repressed by Wnt antagonists and Hex is up-regulated. The antagonism occurring at the receptor level is bypassed by Li exposure by its intracellular inactivation of GSK-3 directly to augment Wnt signaling.
Toward cord blood banking: density-separation and cryopreservation of cord blood progenitors. (1993)

It has been shown that cord blood collected at birth can be used to successfully engraft a human lymphocyte antigen (HLA)-matched sibling suffering from a malignant disease. It has been further suggested that this source of cells may be used in unrelated but HLA-compatible patients. These wide indications would imply the establishment of cord blood banks comprising 10(5) or more samples. In this report we show that it is possible to fractionate and freeze cord blood samples without major loss in granulomonocytic or erythroblastic progenitors (CFU-GM and BFU-E). Density separation should be carried out using Percoll of density 1.080. Separated samples should be frozen and thawed in the presence of DNase I. This procedure should allow the storage of approximately 10 mL samples in cryotubes containing a number of CFU-GM and BFU-E sufficient to engraft a patient weighing less than 30 kg. These data provide a rationale for establishing cord blood banks.
Butt welding of thin stainless steel sheets with the “rippled mode“ Nd-YAG laser (1991)

The “wide bead formation” method has been developed for butt-welding of thin steel sheets whose thickness are less than 300μm. This method eases the precise butting requirement in the practical production lines. The “rippled mode” Nd-YAG laser has been also developed in order to further improve the welding characteristic of thin steel sheets compared with that using CW YAG laser. By applying this laser for the wide bead formation method, less than 150μm thick steel sheets could be butt-welded without any defects.
The Clinical Implications of Mouse Models of Enhanced Anxiety (2011)

Mice are increasingly overtaking the rat model organism in important aspects of anxiety research, including drug development. However, translating the results obtained in mouse studies into information that can be applied in clinics remains challenging. One reason may be that most of the studies so far have used animals displaying 'normal' anxiety rather than 'psychopathological' animal models with abnormal (elevated) anxiety, which more closely reflect core features and sensitivities to therapeutic interventions of human anxiety disorders, and which would, thus, narrow the translational gap. Here, we discuss manipulations aimed at persistently enhancing anxiety-related behavior in the laboratory mouse using phenotypic selection, genetic techniques and/or environmental manipulations. It is hoped that such models with enhanced construct validity will provide improved ways of studying the neurobiology and treatment of pathological anxiety. Examples of findings from mouse models of enhanced anxiety-related behavior will be discussed, as well as their relation to findings in anxiety disorder patients regarding neuroanatomy, neurobiology, genetic involvement and epigenetic modifications. Finally, we highlight novel targets for potential anxiolytic pharmacotherapeutics that have been established with the help of research involving mice. Since the use of psychopathological mouse models is only just beginning to increase, it is still unclear as to the extent to which such approaches will enhance the success rate of drug development in translating identified therapeutic targets into clinical trials and, thus, helping to introduce the next anxiolytic class of drugs.
In Vitro Assembly Properties of Purified Bacterially Expressed Capsid Proteins of Human Immunodeficiency Virus (1997)

The Gag polyprotein of retroviruses is sufficient for assembly and budding of virus-like particles from the host cell. In the case of human immunodeficiency virus (HIV), Gag contains the domains matrix, capsid (CA), nucleocapsid (NC) and p6 which are separated by the viral proteinase inside the nascent virion, leading to morphological maturation to yield an infectious virus. In the mature virus, CA forms a capsid shell surrounding the ribonucleoprotein core consisting of NC and the genomic RNA. To define requirements for particle assembly and functional contributions of individual domains, we expressed domains of HIV Gag in Escherichia coli and purified the products to near homogeneity. In vitro assembly of CA, with or without the C-terminally adjacent spacer peptide, yielded tubular structures with a diameter of approximately 55 nm and heterogeneous length. Efficient particle formation required high protein concentration, high salt and neutral to alkaline pH. In contrast, in vitro assembly of CA-NC occurred at a 20-fold lower protein concentration and in low salt, but required addition of RNA. These results suggest that hydrophobic interactions of capsid proteins are sufficient for particle formation while the RNA-binding nucleocapsid domain may concentrate and align structural proteins on the viral genome.
Studies on enzymatic production of oligosaccharides. Part III. An amylase producing maltotriose from Bacillus subtilis. (1985)

An amylase which produces maltotriose from starch as the main product was found in the culture filtrate of a strain of Bacillus subtilis newly isolated from soil. The enzyme was purified to almost complete homogeneity, as judged by disc electrophoresis in polyacrylamide gel, by means of ammonium sulfate fractionation, DEAE-Sepharose column chromatography and Sephadex gel filtration. The optimum pH and temperature of the enzyme were around 6-7 and 50°C, respectively. Metal ions such as Hg2+, Cu2+, Zn2+, Ni2+ and Fe2+ strongly inhibitied the enzyme activity. The molecular weight was found to be about 25, 000 by gel filtration. The yields of maltotriose from short-chain amylose (DP 17), amylopectin, soluble starch and glycogen were about 69, 56, 56 and 40%, respectively.
Debye–Edwards electron recombination kinetics (1979)

The decay of recombination luminescence intensity I with time t, given by the Debye–Edwards law I ∝ t−m, with m?1 and time independent, applies to Coulombically correlated charge pairs in rigid low-dielectric media. For observation times much greater than preparation times it is remarkably successful, e.g., for a range of 10−6–102 s for some media. These results provide a minimal experimental basis for examining improved procedures for measurement and presentation of results. A simple extension of the D–E law for electron decay or luminescence intensity describes results quantitatively for continuous excitation at low constant dose rate with in-phase measurement, extending the range and improving the precision.
Tumor-specific expression of αvβ3 integrin promotes spontaneous metastasis of breast cancer to bone (2006)

These results demonstrate for the first time that tumor-specific alphavbeta3 contributes to spontaneous metastasis of breast tumors to bone and suggest a critical role for this receptor in mediating chemotactic and haptotactic migration towards bone factors.
ALKANE METABOLISM BY CYTOCHROME P450 BM3 (1993)

Conference Article| November 01 1993 ALKANE METABOLISM BY CYTOCHROME P450 BM3 Andrew W. Munro; Andrew W. Munro 1Department of Biochemistry, University of Glasgow, Glasgow. G12 8QQ. U.K. Search for other works by this author on: This Site PubMed Google Scholar J. Gordon Lindsay; J. Gordon Lindsay 1Department of Biochemistry, University of Glasgow, Glasgow. G12 8QQ. U.K. Search for other works by this author on: This Site PubMed Google Scholar John R. Coggins John R. Coggins 1Department of Biochemistry, University of Glasgow, Glasgow. G12 8QQ. U.K. Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1993) 21 (4): 412S. https://doi.org/10.1042/bst021412s Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation Andrew W. Munro, J. Gordon Lindsay, John R. Coggins; ALKANE METABOLISM BY CYTOCHROME P450 BM3. Biochem Soc Trans 1 November 1993; 21 (4): 412S. doi: https://doi.org/10.1042/bst021412s Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1993 Biochemical Society1993 Article PDF first page preview Close Modal You do not currently have access to this content.
Making Deep Neural Networks Robust to Label Noise: a Loss Correction Approach (2016)

We present a theoretically grounded approach to train deep neural networks, including recurrent networks, subject to class-dependent label noise. We propose two procedures for loss correction that are agnostic to both application domain and network architecture. They simply amount to at most a matrix inversion and multiplication, provided that we know the probability of each class being corrupted into another. We further show how one can estimate these probabilities, adapting a recent technique for noise estimation to the multi-class setting, and thus providing an end-to-end framework. Extensive experiments on MNIST, IMDB, CIFAR-10, CIFAR-100 and a large scale dataset of clothing images employing a diversity of architectures --- stacking dense, convolutional, pooling, dropout, batch normalization, word embedding, LSTM and residual layers --- demonstrate the noise robustness of our proposals. Incidentally, we also prove that, when ReLU is the only non-linearity, the loss curvature is immune to class-dependent label noise.
Spinal anesthesia for lengthy lower limb orthopedic surgeries: dexmedetomidine plus fentanyl versus dexmedetomidine (2019)

Spinal anesthesia is efficient but of limited duration. Intrathecal dexmedetomidine prolongs the sensory and motor blockade of bupivacaine. Dexmedetomidine-opioids combination displayed a clinically controversial interaction. Our proposal is that fentanyl may augment the block characteristics of dexmedetomidine using proper doses. This is a randomized double-blinded study. The included patients were scheduled for orthopedic procedures expected to extend more than 4 h. Patients were allocated into two groups each of 23. Group D received intrathecal bupivacaine 20 mg 0.5% + dexmedetomidine 10 μg. Group DF received bupivacaine 20 mg 0.5% + dexmedetomidine 10 μg + fentanyl 25 μg. The spinal block characteristics and adverse effects were determined. Data were compared by t test, Mann-Whitney, and chi-square tests as appropriate. There was no significant difference between the two groups as regards spinal block and hemodynamic characteristics. The addition of fentanyl provided earlier time to T10 sensory block, lower midazolam and ephedrine utilization, but occasional mild itching. Postoperatively, the time to the first analgesic request, morphine consumption, and patient’s satisfaction were not different. The addition of fentanyl does not prolong the sensory and motor block characteristics of dexmedetomidine. In favor of dexmedetomidine-fentanyl combination was the less hypotension and less sedative requirement. Pan African Clinical Trials Registry Trial number: PACTR201703002122189 on 28 March 2017.
Temperature independent strain measurement with a fiber grating tapered cavity sensor (1999)

A novel fiber grating tapered cavity sensor used for encoding strain into its spectral profile independently and its experimental demonstration are presented. The sensor possesses two spectral peaks within its main reflection band and the normalized power difference between the two peaks changes linearly with applied strain while it is independent of temperature variation. The accuracy of this particular sensor in measuring strain is estimated to be /spl plusmn/29 μ/spl epsi/ in a range of 1200 μ/spl epsi/.
A Paracrine Loop Between Adipocytes and Macrophages Aggravates Inflammatory Changes (2005)

We postulate that a paracrine loop involving FFAs and TNF-alpha between adipocytes and macrophages establishes a vicious cycle that aggravates inflammatory changes in the adipose tissue.