gebhart/patrepeval huggingface dataset:
Some 6-Aza-5-substituted-2'-deoxyuridines Show Potent and Selective Inhibition of Herpes Simplex Virus Type 1 Thymidine Kinase (1998)

The synthesis and X-ray crystal structures of a series of 5-substituted-6-aza-2'-deoxyuridines is reported. These nucleoside analogues inhibit the phosphorylation of thymidine by HSV-1 TK but have no effect on the corresponding human enzyme. Detailed examination of one analogue proves it to be a competitive inhibitor of thymidine with a Ki of 0.34 microM and is a very poor substrate. The analogues are not substrates for the enzyme and also do not inhibit the degradation of thymidine by thymidine phosphorylase. Molecular modelling showed that the inhibitors fit well in the active site of HSV-1 TK, provided the conformation of the sugar moiety is the same for thymidine in the complex.
“RAISIN” – a national programme for early warning, investigation and surveillance of healthcare-associated infection in France (2009)

Binary file ES_Abstracts_Final_ECDC.txt matches
Identification of group B rotavirus as an etiological agent in the gastroenteritis outbreak in Maharashtra, India (2017)

Acute gastroenteritis outbreak occurred at Pargaon, Maharashtra, India in 1789 cases with an attack rate of 32.5% between November to December 2015. The stool specimens (n = 32) were investigated for different enteric viral agents using conventional methods. Transmission electron microscopy and RNA polyacrylamide gel electrophoresis respectively identified morphologically distinct rotavirus particles in 28% and RNA migration pattern of Group B Rotavirus (GBR) in 72% of the specimens. Reverse transcription polymerase chain reaction and nucleotide sequencing confirmed presence of GBR in 97% of the samples analyzed. The predominance of GBR infections and absence or insignificant presence of other agents confirmed GBR as an etiological agent of the gastroenteritis outbreak occurred in Maharashtra, India.
Provenance in Scientific Workflow Systems (2007)

The automated tracking and storage of provenance information promises to be a major advantage of scientific workflow systems. We discuss issues related to data and workflow provenance, and present techniques for focusing user attention on meaningful provenance through “user views,” for managing the provenance of nested scientific data, and for using information about the evolution of a workflow specification to understand the difference in the provenance of similar data products.
LDPC Coded Iterative Signal Detection Based on QRD-M with CRC Check (2006)

Maximum likelihood detection with QR decomposition and M-algorithm (QRD-M) is one of the detection methods in multiple-input multiple-output (MIMO) multiplexing. We recently proposed a Turbo coded iterative modified QRD-M with decision directed channel estimation and showed that the packet error rate (PER) performance close to the ideal channel estimation case can be obtained. In the iterative modified QRD-M, signal ranking is performed based on both received signal-to- interference plus noise power ratio (SINR) and results of cyclic redundancy check (CRC) decoding and then, signal detection is performed by modified M-algorithm based on the results of CRC decoding. In this paper, we apply irregular low density parity check (irregular LDPC) codes to the previously proposed iterative modified QRD-M. The a posteriori probability of each bit (including parity bit) is necessary for decision directed channel estimation and modified M-algorithm in the iterative modified QRD-M. Unlike Turbo decoding, the a posteriori probability of each bit can be obtained in LDPC decoding. Thus, by using LDPC codes, more accurate signal detection is possible than using Turbo codes. To achieve more powerful detection of decoding errors, CRC codes can be jointly used with parity check equation of LDPC codes. It is shown by the computer simulation that the performance of the LDPC coded iterative modified QRD-M is superior to that of the Turbo coded iterative modified QRD-M.
Oracle real application testing (2008)

This paper presents the Oracle solution for database testing delivered in the Oracle 11g Database Real Application Testing option. The first feature, the SQL Performance Analyzer, performs unit testing of the SQL of a production workload. The second feature, Database Replay, makes it possible to subject a test system to a real production system workload. Both features base their effectiveness on the fact that the best possible workload for testing is the actual production workload, which is unparalleled to our knowledge. By running the real application workload on a test system, these features can predict the impact of changes to a production system accurately and without risk. Combined with Oracle's performance manageability offerings, such as the Automatic Database Diagnostic Monitor (ADDM) and SQL Tuning Advisor, these features provide a compelling end-to-end approach for introducing change into production environments without risk of performance regression.
Localized and stationary dynamic gratings via stimulated Brillouin scattering with phase modulated pumps (2012)

A novel technique for the localization of stimulated Brillouin scattering (SBS) interaction is proposed, analyzed and demonstrated experimentally. The method relies on the phase modulation of two counter-propagating optical waves by a common pseudo-random bit sequence (PRBS), these waves being spectrally detuned by the Brillouin frequency shift. The PRBS symbol duration is much shorter than the acoustic lifetime. The interference between the two modulated waves gives rise to an acoustic grating that is confined to narrow correlation peaks, as short as 1.7 cm. The separation between neighboring peaks, which is governed by the PRBS length, can be made arbitrarily long. The method is demonstrated in the generation and applications of dynamic gratings in polarization maintaining (PM) fibers. Localized and stationary acoustic gratings are induced by two phase modulated pumps that are polarized along one principal axis of the PM fiber, and interrogated by a third, readout wave which is polarized along the orthogonal axis. Using the proposed technique, we demonstrate the variable delay of 1 ns-long readout pulses by as much as 770 ns. Noise due to reflections from residual off-peak gratings and its implications on the potential variable delay of optical communication data are discussed. The method is equally applicable to the modulation of pump and probe waves in SBS over standard fibers.
The maturing of telemedicine technology. Part 1. (1994)

A part of the solution to scarce medical resources is telemedicine--a bundling of high- and low-tech equipment with distinct advantages for both rural and urban providers. Here is Part One of a two-part series on the state-of-the-art and its practical uses.
A top-down hardware/software co-simulation method for embedded systems based upon a component logical bus architecture (2002)

We propose a top-down hardware/software co-simulation method for embedded systems and introduce a component logical bus architecture as an interface between software components and hardware components. Co-simulation using a component logical bus architecture is possible in the same environment from the stage at which the processor is not yet determined to the stage at which the processor is modeled in register transfer language. A model whose design is based on a component logical bus architecture is replaceable and reusable. By combining such replaceable models, it is possible to quickly realize seamless co-simulation. We further describe experimental results of our approach.
Biomedical text retrieval in languages with a complex morphology (2002)

Document retrieval in languages with a rich and complex morphology - particularly in terms of derivation and (single-word) composition - suffers from serious performance degradation with the stemming-only query-term-to-text-word matching paradigm. We propose an alternative approach in which morphologically complex word forms are segmented into relevant subwords (such as stems, named entities, acronyms), and subwords constitute the basic unit for indexing and retrieval. We evaluate our approach on a large biomedical document collection.
Identification and Characterization of a Neuroretina-Specific Enhancer Element in the Quail<i>Pax-6</i>(<i>Pax-QNR</i>) Gene (1995)

Using nuclear run-on assays, we showed that the tissue-specific expression of quail Pax-6 (Pax-QNR) P0-initiated mRNAs is due in part to regulation of the gene at the transcriptional level. Regulatory sequences governing neuroretina-specific expression of the P0-initiated mRNAs were investigated. By using reporter-based expression assays, we characterized a region within the Pax-QNR gene, located 7.5 kbp downstream from the P0 promoter, that functions as an enhancer in neuroretina cells but not in nonexpressing P0-initiated mRNA cells (quail embryo cells and quail retinal pigment epithelial cells). This enhancer element functioned in a position- and orientation-independent manner both on the Pax-QNR P0 promoter and the heterologous thymidine kinase promoter. Moreover, this enhancer element exhibited a developmental stage-specific activity during embryonic neuroretina development: in contrast to activity at day E7, the enhancer activity was very weak at day E5. This paralleled the level of expression of P0-initiated mRNAs observed at the same stages. Using footprinting, gel retardation, and Southwestern (DNA-protein) analysis, we demonstrated the existence of four neuroretina-specific nuclear protein-binding sites, involving multiple unknown factors. In addition we showed that the quail enhancer element is structurally and functionally conserved in mice. All of these results strongly suggest that this enhancer element may contribute to the neuroretina-specific transcriptional regulation of the Pax-6 gene in vivo.
Stress Resilience Training: The Need for Circumspection (2014)

Weltman et al have presented a fascinating report on the effectiveness of a stress resilience training program on police department personnel (Global Adv Health Med. 2014;3(2):72-79). Certainly at first reading there appears to be strong evidence of the effectiveness of the program. However, careful evaluation of the methodology and results suggests the need for some circumspection.
Preparation of photonic crystals made of air pores in anodic alumina (2007)

Photonic crystals made of air pores in anodic alumina were prepared by electrochemical oxidation of aluminium and subsequent chemical etching. Optical photographs and transmission spectra prove the existence of a photonic band gap in the optical sprectrum for this porous material. The colour of the sample and the diffraction peak position in the transmission spectra could easily be adjusted in the chemical etching process. This method could provide a possible approach to producing large-area optical photonic crystals cheaply and rapidly.
Adhesion molecule expression in human hepatic graft-versus-host disease. (1992)

An immunohistological study of the distribution of three cellular adhesion molecules, ICAM-1, VCAM-1 and ELAM-1, was undertaken on normal liver and liver biopsies taken from allogeneic bone marrow transplant (BMT) recipients. In normal controls, ICAM-1 was seen on vascular endothelium and sinusoidal lining cells, and VCAM-1 on Kuppfer cells and dendritic macrophages in portal tracts. ELAM-1 staining was virtually absent. Biopsies from BMT recipients with histological evidence of hepatic graft-versus-host disease (GVHD) showed ICAM-1 expression on damaged bile duct epithelium in only one of five cases, in contrast to four of five showing epithelial HLA-DR expression. Increased numbers of VCAM-1 positive portal tract macrophages were seen in GVHD and also in non-GVHD pathology. No increase in vascular endothelial expression of VCAM-1 or ELAM-1 was seen. These findings contrast with previous studies on other target sites for GVHD, namely skin and gastrointestinal tract, where the expression of all three molecules is increased on various cells. Although the lack of adhesion molecule expression in the liver in GVHD in this study may be related to the timing of biopsies or immunosuppressive therapy, it is likely to represent to some extent variation in cell and molecular changes occurring in the different tissues affected by GVHD.
Fibrin gel – advantages of a new scaffold in cardiovascular tissue engineering (2001)

Fibrin gel combines a number of important properties of an ideal scaffold. It can be produced as a complete autologous scaffold. It is moldable and degradation is controllable by the use of aprotinin.
THE ANATOMICAL BASIS OF THE STRAUB PHENOMENON (1960)

The administration of morphine was followed in white mice by a typical Straub reaction which consisted of the tail becoming rigid and erected across the back of the animal in an S-shaped curve. This reaction was accompanied by restlessness, excitability, extension rigidity of the hindlimbs, forcible viodance of faeces and prominence of the perineum. The Straub reaction was abolished by general anaesthesia with pentobarbitone or ether, by administration of tubocurarine, by bilateral section of the muscles causing extension to the tail, and by the removal of the circulation to the lower extremity. The reaction was modified by unilateral section of the extensor muscles of the tail. Section of the spinal cord, decortication, division of the anal sphincter and perineal floor, or ablation of the pelvic splanchnic nerves did not suppress the appearance of the Straub response. It was concluded that the phenomenon described by Straub (1911) was produced mainly by the action of the sacro-coccygeus dorsalis muscle, and that it was also necessary that the lumbo-sacral cord with its peripheral nervous outflow should be intact and that these functioning units should have an adequate circulation.
Early mortality with immune checkpoint inhibitors (IOs) in solid tumors: An inconvenient truth? (2018)

12121 Background: Overall survival (OS) benefit with IOs has been demonstrated in several solid tumor types leading to their rapid adoption and use in practice. We noticed IO randomized controlled trials (RCTs) with early crossover of OS Kaplan-Meier (KM) curves favoring control therapy but with overall benefit favoring IO therapy. This suggests a subpopulation of patients at a higher risk of death on IO therapy compared to control therapy early in treatment. We performed a systematic review to examine the frequency and characteristics of IO RCTs showing this negative discordant crossover (NDC). Methods: RCTs studying IOs and non-IOs in solid tumors with published OS KM curves were identified by electronic database search and FDA approvals 2015-17. Early OS divergence was identified by blinded reviewers. NDC of OS KM curves was defined as early divergence discordant with an overall beneficial survival trend. RCT characteristics were compared using Fisher’s exact test. Results: 29 IO RCTs providing 33 comparisons and 24 non-IO RCTs providing 25 comparisons were identified. Nine IO RCTs (27%) and 1 non-IO RCT (4%) demonstrated NDC (p = 0.03). NDC occurred in NSCLC (3/9), urothelial cancer (2/2), melanoma (2/9), SCLC (1/2) and CRPC (1/2) RCTs. RCTs with NDC trended to less often study melanoma (22% v 46%) and squamous cancer (0% v 13%), and less often report OS benefit (22% v 71%). They trended to more often study urothelial cancer (22% v 0%) and 2nd-line treatment (56% v 38%), and more often have active treatment control arms (89% v 75%). Conclusions: Early NDC of overall survival curves occurs commonly in IO RCTs. This suggests a subpopulation of patients at higher risk of early death with IO therapy. Causes of this mortality are unclear but could include toxicity of IO therapy, superior antitumor effects of control therapy, and/or tumor growth promoting effects of IO therapy. We are quantitating this risk. Such crossover complicates proportional hazards modeling. Further research to identify the causes of and patients at risk for early mortality with IO therapy should be a priority and patients should be informed of this potential risk.
Electrical Accuracy of Selsyn Generator-Control Transformer System (1946)

THE military requirements for high accuracy position control systems have placed emphasis on the need for a voltage signal source which can indicate electrically a mechanical shaft position. In addition this signal source must have high accuracy, marked dependability, and the capability of continuous mechanical rotation. A modification of the conventional Selsyn generator-motor system1 has been developed and used extensively to fill this need.
Lactoferrin stimulates colony stimulating factor production in vitro and in vivo. (1989)

A physiologic role for lactoferrin (Lf) has been implicated by (1) its antibacterial effect and (2) its involvement as a negative-feedback regulator for colony stimulating factor (CSF) and, therefore, granulocyte production. The isolation and purification of endotoxin-free, species-specific mouse and human Lf have enabled a study of the role of Lf both in vitro and in vivo. Injection of Salmonella typhimurium or LPS into mice resulted in a dose-dependent increase in plasma Lf. Treating normal and neutropenic mice with LPS showed that the plasma Lf level was directly related to the number of granulocytes found in the peripheral blood. The effect of neutropenia did not inhibit release of Lf. By incubating mouse bone marrow and adherent peritoneal cells with 0.1 microM mouse or human Lf in the absence or presence of the prostaglandin synthesis inhibitor, indomethacin (1.0 microM), no evidence could be obtained in support of a negative-feedback regulation of CSF. In fact, rather than an inhibition of CSF, the production of the latter was found to be stimulated from both cell types. Injection of endotoxin-free, mouse Lf (2 mg/animal) into mice at concentrations in the same order of magnitude as that found during bacterial infection, resulted in an increase in CSF production by 12 hours and prior to the increase in bone marrow granulocyte-macrophage progenitor cells (GM-CFC) at 48 hours. The results do not support a negative-feedback regulation of CSF by macrophages. Instead, they can be incorporated into a "demand signal" model for CSF production by macrophages.
An Enhanced Remote User Authentication Scheme Providing Mutual Authentication and Key Agreement with Smart Cards (2009)

In 2005, Yoon et al. proposed a user-friendly remote user authentication scheme using smart cards. The security of their scheme is based on one-way hash function and they claimed that their scheme is secured from attacks and achievable for proving mutual authentication, freely choosing password, no verification tables, and involving very lightweight hashing operations. However, we find that Yoon et al.'s scheme suffers from the denial of service attack and performs only unilateral authentication (only user authentication). In this paper we consequently propose an enhanced version to eliminate the vulnerability. Furthermore, our enhanced scheme can also provide mutual authentication and key agreement between a remote server and login users.
Dual Effects of IκB Kinase β-Mediated Phosphorylation on p105 Fate: SCF<sup>β-TrCP</sup>-Dependent Degradation and SCF<sup>β-TrCP</sup>-Independent Processing (2003)

Processing of the p105 NF-kappaB precursor to yield the p50 active subunit is a unique and rare case in which the ubiquitin system is involved in limited processing rather than in complete destruction of its target. The mechanisms involved in this process are largely unknown, although a glycine repeat in the middle of p105 has been identified as a processing stop signal. IkappaB kinase (IKK)beta-mediated phosphorylation at the C-terminal domain with subsequent recruitment of the SCF(beta-TrCP) ubiquitin ligase leads to accelerated processing and degradation of the precursor, yet the roles that the kinase and ligase play in each of these two processes have not been elucidated. Here we demonstrate that IKKbeta has two distinct functions: (i) stimulation of degradation and (ii) stimulation of processing. IKKbeta-induced degradation is dependent on SCF(beta-TrCP), which acts through multiple lysine residues in the IkappaBgamma domain. In contrast, IKKbeta-induced processing of p105 is beta-transduction repeat-containing protein (beta-TrCP) independent, as it is not affected by expression of a dominant-negative beta-TrCP or following its silencing by small inhibitory RNA. Furthermore, removal of all 30 lysine residues from IkappaBgamma results in complete inhibition of IKK-dependent degradation but has no effect on IKK-dependent processing. Yet processing still requires the activity of the ubiquitin system, as it is inhibited by dominant-negative UbcH5a. We suggest that IKKbeta mediates its two distinct effects by affecting, directly and indirectly, two different E3s.
Structure of Ca<sup>2+</sup>-Bound S100A4 and Its Interaction with Peptides Derived from Nonmuscle Myosin-IIA (2008)

S100A4, also known as mts1, is a member of the S100 family of Ca2+-binding proteins that is directly involved in tumor invasion and metastasis via interactions with specific protein targets, including nonmuscle myosin-IIA (MIIA). Human S100A4 binds two Ca2+ ions with the typical EF-hand exhibiting an affinity that is nearly 1 order of magnitude tighter than that of the pseudo-EF-hand. To examine how Ca2+ modifies the overall organization and structure of the protein, we determined the 1.7 A crystal structure of the human Ca2+-S100A4. Ca2+ binding induces a large reorientation of helix 3 in the typical EF-hand. This reorganization exposes a hydrophobic cleft that is comprised of residues from the hinge region,helix 3, and helix 4, which afford specific target recognition and binding. The Ca2+-dependent conformational change is required for S100A4 to bind peptide sequences derived from the C-terminal portion of the MIIA rod with submicromolar affinity. In addition, the level of binding of Ca2+ to both EF-hands increases by 1 order of magnitude in the presence of MIIA. NMR spectroscopy studies demonstrate that following titration with a MIIA peptide, the largest chemical shift perturbations and exchange broadening effects occur for residues in the hydrophobic pocket of Ca2+-S100A4. Most of these residues are not exposed in apo-S100A4 and explain the Ca2+ dependence of formation of theS100A4-MIIA complex. These studies provide the foundation for understanding S100A4 target recognition and may support the development of reagents that interfere with S100A4 function.