gebhart/patrepeval huggingface dataset:
Method for introducing site-specific mutations into adenovirus 2 genome: construction of a small deletion mutant in VA-RNAI gene. (1981)

We have developed a method for introducing mutations into the adenovirus type 2 genome at predetermined sites. Specific mutations are introduced into segments of the viral genome cloned in bacteria by using plasmid vectors. The chimeric DNA is used to construct viral mutants by cotransfection with two viral DNA segments derived from both ends of the viral genome, each of which has overlapping sequence homology with the cloned viral DNA segment. To illustrate this procedure, we cloned a large restriction fragment [EcoRI fragment A, map position (mp) 0--58.5] by using plasmid vector pBR322, and a small deletion mutation was introduced at the BamHI cleavage site located within the VA-RNAI gene (mp 29 at residue +75 on VA-RNAI gene). The mutated DNA was then used to construct viral mutants by cotransfection into human cells with the adenovirus type 2 DNA--protein complex digested with Sal I. In vivo recombination occurred via overlapping sequences between the cloned EcoRI fragment A and Sal I-digested DNA--protein complex at two sites, mp 0--25 (i.e., within Sal I fragment B) and mp 45--58.5 (i.e., overlapping sequences between Sal I fragment A and EcoRI fragment A), generating infectious DNA molecules with intact ends. The viral mutant grows as well as the wild type in KB cells and induces the synthesis of smaller VA-RNAI but normal-size VA-RNAII.
HIV: AIDS: a quarter of a century later (2009)

The Limulus amoebocyte lysate (LAL) test is inhibited or enhanced by many substances. In order to overcome this problem, a specific endotoxin assay method using a membrane filter unit, a chromogenic LAL reagent, and immobilized histidine (which is a specific adsorbent for endotoxins) was developed. Endotoxins are quantitatively adsorbed on immobilized histidine. The adsorbed endotoxins are separated from LAL-inhibiting or -enhancing substances by the membrane filter unit, and their activities are directly assayed with the LAL reagent in a filter cup without any inhibition or enhancement. The reproducibility and the accuracy of this method are high. This new endotoxin assay method using immobilized histidine can be used for the determination of endotoxins in a solution containing LAL-inhibiting or -enhancing substances such as amino acids and antibiotics, as an alternative to the more common gel-clot technique.
Multicenter study of oxygen-insensitive handheld glucose point-of-care testing in critical care/hospital/ambulatory patients in the United States and Canada (1998)

The performance of GD-based, oxygen-insensitive, handheld glucose testing was technically suitable for arterial specimens in critical care patients, cord blood and heelstick specimens in neonates, and capillary and venous specimens in other patients. Multicenter findings benchmark the performance of bedside glucose testing devices. With the new +/-15 mg/dL --> 100 mg/dL --> +/-15% accuracy criterion, point-of-care systems for handheld glucose testing should score 95% (or better), as compared with the recommended reference method. Physiologic changes, preanalytical factors, confounding variables, and treatment goals must be taken into consideration when interpreting glucose results, especially in critically ill patients, for whom arterial blood glucose measurements will reflect systemic glucose levels.
Superhydrophobic coatings based on boron nitride nanotubes: The mechanism of superhydrophobicity and self-regeneration of highly hydrophobic properties (2011)

The mechanism of superhydrophobicity is discussed for coatings based on boron nitride nanotubes, i.e., on a material with high surface energy. It is shown that the thermodynamic stability of the superhydrophobic state is related to a surface roughness determined by nanotube packing and a decrease in surface energy due to the adsorption of hydrocarbon contaminants. The phenomenon of self-regeneration of highly hydrophobic properties is observed after the removal of organic impurities from the surface using different methods. The possibility for the cyclic switching of wettability from superhydrophobicity to hydrophilicity and back is demonstrated by successive coating treatment in plasma at a variation of its composition from atomic hydrogen plasma to methane plasma.
Analysis of circulating immune complexes from leprosy patients for Mycobacterium leprae antigens. (1992)

Circulating immune complexes (CICs) from 31 leprosy patients (16 tuberculoid, 15 lepromatous) and 12 healthy volunteers, precipitated by 3.5% polyethylene glycol, were individually subjected to SDS-PAGE and immunoblotting using a variety of monoclonal and polyclonal antibodies against Mycobacterium leprae. A common mycobacterial antigen of an apparent molecular size of 65 kDa was identified in CICs from about 40% of the patients. No correlation was observed between the positivity for this antigen and any of the following parameters: bacterial index, M. leprae-specific antibody titers, motor nerve involvement, duration of disease or treatment. Nevertheless, patients with a relatively recent and massive infection were more frequently positive for antigen than the others.
Design and synthesis of paclitaxel conjugated with an ErbB2‐recognizing peptide, EC‐1 (2007)

The selective delivery of therapeutic agents to receptors overexpressed in cancer cells without harming the rest of the body is a major challenge in clinical oncology today. In this study, we report the design and synthesis of paclitaxel (PTX) conjugated with an erbB2-recognizing peptide (EC-1). The cyclic peptide EC-1 specifically binds to the extracellular domain of ErbB2 and selectively inhibits proliferation of breast cancer cells overexpressing ErbB2. PTX is a potent antitumor agent commonly used in the treatment of advanced metastatic breast cancer, yet patients have to suffer some side effects caused by its systemic toxicity. The aim of our conjugate is to specifically deliver antitumor agent PTX to breast cancer cells that overexpress oncogenic ErbB2 with the purpose to reduce toxicity and enhance selective killing of cancer cells. In this study, a concise and efficient synthetic route for the preparation of the PTX-EC-1 conjugate has been developed in 6% overall yield. This synthetic approach provides a general method for conjugating a highly functionalized and disulfide-bridge containing cyclopeptide to Taxol or other antitumor agents.
Abnormal Behavior Detection to Identify Infected Systems Using the<i> APChain</i> Algorithm and Behavioral Profiling (2018)

Recent cyber-attacks have used unknown malicious code or advanced attack techniques, such as zero-day attacks, making them extremely difficult to detect using traditional intrusion detection systems. Botnet attacks, for example, are a very sophisticated type of cyber-security threat. Malicious code or vulnerabilities are used to infect endpoints. Systems infected with this malicious code connect a communications channel to a command and control (C&C) server and receive commands to perform attacks on target servers. To effectively protect a corporate network’s resources against such threats, we must be able to detect infected systems before an attack occurs. In this paper, an attack pattern chain algorithm ( APChain ) is proposed to identify infected systems in real-time network environments, and a methodology for detecting abnormal behavior through network-based behavioral profiling is explained. APChain analyzes the attribute information of real-time network traffic, connects chains over time, and conducts behavioral profiling of different attack types to detect abnormal behavior. The dataset used in the experiment employed real-time traffic accumulated over a period of six months, and the proposed algorithm was developed into a prototype for the experiment. The C&C channel detection accuracy was measured at 0.996, the true positive rate at 1.0, and the false positive rate at 0.003. This study proposes a methodology that can overcome the limitations of conventional security mechanisms and suggests an approach to the detection of abnormal behavior in a real-time network environment.
Monitoring of oral anticoagulant therapy in lupus anticoagulant positive patients with the anti‐phospholipid syndrome (1997)

Introduction of the International Normalized Ratio (INR) has improved the standardization of laboratory control of oral anticoagulant therapy (OAT). However, it has been reported that misleading INR results can be obtained from OAT patients with lupus anticoagulant (LA). To investigate this claim, we studied 35 OAT patients, 14 of whom had anti-phospholipid syndrome (APS) with a documented LA. Attainment of anticoagulation was confirmed by chromogenic assay of factor VII and factor X. Prothrombin times were performed using eight thromboplastins (five derived from rabbit brain, two recombinant human tissue factor and one made from human placenta) with an International Sensitivity Index (ISI) of <1.40. When using the thromboplastin manufacturers' ISI there was a significant difference (ANOVA, P<0.0001) between INR results obtained with the eight reagents for both APS (average CV = 12.4%) and non-APS (average CV = 12.5%) patient groups. Variation using the eight thromboplastins was assessed by calculating the CV for each sample; these values were then pooled for each patient group to give the average CV for all samples with all reagents for the two patient groups. Results for both patient groups exhibited markedly reduced variation (APS group average CV = 6.5%, non-APS group average CV = 5.8%) when locally assigned ISI values were employed in the calculation of INRs. Our data does not support the suggestion that the INR may not reflect the true level of anticoagulation in the long-term warfarin-treated patient, in whom lupus anticoagulant was detected. However, there was strong evidence that thromboplastin use should be restricted to those clot detection systems for which the reagent's manufacturer has assigned an ISI, or local ISI assignment must be undertaken. The inappropriate use of a generic (i.e. optical or mechanical clot detection system without regard to specific analyser type) ISI value can lead to ambiguous results.
Dealing with sleep problems during home confinement due to the COVID‐19 outbreak: Practical recommendations from a task force of the European CBT‐I Academy (2020)

In the current global home confinement situation due to the COVID-19 outbreak, most individuals are exposed to an unprecedented stressful situation of unknown duration. This may not only increase daytime stress, anxiety and depression levels, but also disrupt sleep. Importantly, because of the fundamental role that sleep plays in emotion regulation, sleep disturbance can have direct consequences upon next day emotional functioning. In this paper, we summarize what is known about the stress-sleep link and confinement as well as effective insomnia treatment. We discuss those effects of the current home confinement situation that can disrupt sleep but also those that could benefit sleep quality. We suggest adaptions of cognitive behavioural therapy elements that are feasible to implement for those facing changed work schedules and requirements, those with health anxiety and those handling childcare and home-schooling, whilst also recognizing the general limitations imposed on physical exercise and social interaction. Managing sleep problems as best as possible during home confinement can limit stress and possibly prevent disruptions of social relationships.
Rapid multiexposure in vivo brain imaging system using vertical cavity surface emitting lasers as a light source (2013)

We demonstrate an imaging technique implementing vertical cavity lasers with extremely low transient times for a greatly simplified realization of a multiexposure laser speckle contrast imaging system. Data from multiexposure laser speckle imaging was observed to more closely agree with absolute velocity measurements using time of flight technique, when compared to long-exposure laser speckle imaging. Furthermore, additional depth information of the vasculature morphology was inferred by accounting for the change in the static scattering from tissue above vessels with respect to the total scattering from blood flow and tissue.
Layer‐Type Transition Metal Dichalcogenides — a New Class of Electrodes for Electrochemical Solar Cells (1977)

Abstract The problem of the rapid anodical photoelectrochemical desintegration of visible‐light‐sensitive semiconductor electrodes (e.g. CdS, GaAs) in presently investigated continuously operating electrochemical solar cells is tackled by two improvements: a) The use of covalent layer‐type transition metal dichalcogenides as electrode material, in which photon absorption involves d‐d transitions and does not produce a splitting of chemical bonds and b) the operation of the transition metal dichalcogenides as photo‐cathodes, which is possible with p‐conducting material. The first photocell of this kind is constructed with p‐conducting natural MoS 2 layer crystals and Fe 2+/3+ as redox‐couple. It proved to be stable during longtime experiments. A power output of up to 1% was obtained. The limiting factor was found to be the insufficient solid state behaviour of the available natural crystals (high recombination losses through traps, weak p‐character). A considerable improvement is to be expected from better quality p‐type electrode‐material. Some development possibilities for solar cells, based on covalent semiconducting layer‐type transition metal dichalcogenides are outlined.
Mussel-Inspired Adhesive and Tough Hydrogel Based on Nanoclay Confined Dopamine Polymerization (2017)

Adhesive hydrogels are attractive biomaterials for various applications, such as electronic skin, wound dressing, and wearable devices. However, fabricating a hydrogel with both adequate adhesiveness and excellent mechanical properties remains a challenge. Inspired by the adhesion mechanism of mussels, we used a two-step process to develop an adhesive and tough polydopamine-clay-polyacrylamide (PDA-clay-PAM) hydrogel. Dopamine was intercalated into clay nanosheets and limitedly oxidized between the layers, resulting in PDA-intercalated clay nanosheets containing free catechol groups. Acrylamide monomers were then added and in situ polymerized to form the hydrogel. Unlike previous single-use adhesive hydrogels, our hydrogel showed repeatable and durable adhesiveness. It adhered directly on human skin without causing an inflammatory response and was easily removed without causing damage. The adhesiveness of this hydrogel was attributed to the presence of enough free catechol groups in the hydrogel, which were created by controlling the oxidation process of the PDA in the confined nanolayers of clay. This mimicked the adhesion mechanism of the mussels, which maintain a high concentration of catechol groups in the confined nanospace of their byssal plaque. The hydrogel also displayed superior toughness, which resulted from nanoreinforcement by clay and PDA-induced cooperative interactions with the hydrogel networks. Moreover, the hydrogel favored cell attachment and proliferation, owning to the high cell affinity of PDA. Rat full-thickness skin defect experiments demonstrated that the hydrogel was an excellent dressing. This free-standing, adhesive, tough, and biocompatible hydrogel may be more convenient for surgical applications than adhesives that involve in situ gelation and extra agents.
THE PHOTO CD SYSTEM: AN OVERVIEW FOR CONSUMER AND PHOTOFINISHING APPLICATIONS (1991)

The Photo CD system links traditional still photography with post-capture electronic still and computer based imaging. Three environments are considered; photofinishing, home viewing, and computerized image processing. A technical overview of system components and their interrelationships is presented. SUMMARY:
Reactive Nitrogen Species Contribute to Innate Host Defense against<i>Campylobacter jejuni</i> (2008)

Campylobacter jejuni, a gram-negative, invasive organism, is a common cause of food-borne bacterial diarrheal disease. However, the relationship between C. jejuni and the innate immune system is not well described. To better characterize host defense against C. jejuni, we investigated the ability of nitric oxide/reactive nitrogen species to kill two strains of C. jejuni. C. jejuni viability was measured after exposure to reactive nitrogen species produced biochemically as acidified nitrite and by bone marrow-derived macrophages. We report that acidified nitrite caused a 3-log-increased kill of C. jejuni (P < 0.05) at doses that did not affect the viability of Salmonella enterica serovar Typhimurium. Expression of NOS2, the gene responsible for the production of inducible nitric oxide, was increased >100-fold in murine macrophages after incubation with C. jejuni (P < 0.001). These macrophages effected a 2-log-increased kill of C. jejuni over 24 h compared to that by NOS2-/- macrophages unable to produce nitric oxide (P < 0.05). These findings suggest that the mammalian host upregulates the production of nitric oxide in response to exposure to C. jejuni and that nitric oxide and reactive nitrogen species comprise part of the innate defense mechanisms that contribute to the resolution of C. jejuni infection.
Glutathione Transferase Omega 1 Catalyzes the Reduction of <i>S</i>-(Phenacyl)glutathiones to Acetophenones (2006)

S-(Phenacyl)glutathione reductase (SPG-R) plays a significant role in the biotransformation of reactive alpha-haloketones to nontoxic acetophenones. Comparison of the apparent subunit size, amino acid composition, and catalysis of the reduction of S-(phenacyl)glutathiones indicated that a previously described rat SPG-R (Kitada, M., McLenithan, J. C., and Anders, M. W. (1985) J. Biol. Chem. 260, 11749-11754) is homologous to the omega-class glutathione transferase GSTO1-1. The available data show that the SPG-R reaction is catalyzed by GSTO1-1 and not by other GSTs, including the closely related GSTO2-2 isoenzyme. In the proposed reaction mechanism, the active-site cysteine residue of GSTO1-1 reacts with the S-(phenacyl)glutathione substrate to give an acetophenone and a mixed disulfide with the active-site cysteine; a second thiol substrate (e.g., glutathione or 2-mercaptoethanol) reacts with the active-site disulfide to regenerate the catalytically active enzyme and to form a mixed disulfide. A new spectrophotometric assay was developed that allows the rapid determination of SPG-R activity and specific measurement of GSTO1-1 in the presence of other GSTs. This is the first specific reaction attributed to GSTO1-1, and these results demonstrate the catalytic diversity of GSTO1-1, which, in addition to SPG-R activity, catalyzes the reduction of dehydroascorbate and monomethylarsonate(V) and also possesses thioltransferase and GST activity.
Perfusion preservation of rodent kidneys in a portable preservation device based on fluidics technology (2002)

Background. Technology that can implement the basic requirements for successful organ preservation in a portable configuration has yet to be realized. Methods. This work evaluates kidney preservation in a new class of portable organ preservation technology based on fluidics principles. During hypothermic pulsatile perfusion preservation (HPPP), oxygen consumption, renal vascular resistance (RVR), pH, pCO2, and perfusion pressure were measured. After 24 hr of preservation, perfusate distribution was assessed, and oxygen consumption, RVR, and glomerular filtration rate (GFR) were compared in perfused, statically stored, and freshly harvested kidneys. Results. During HPPP, perfusion pressure was 5.8±3.3 mmHg with oxygen delivery to the organs in excess of 3.5 times the organ metabolic requirement. During function measurements, RVR was not statistically different in the three groups; however, both oxygen consumption and GFR in the statically stored organs were significantly lower than in HPPP stored or freshly harvested kidneys. Conclusions. Our findings suggest that full portability in a hypothermic perfusion preservation device seems feasible utilizing fluidics-based technology.
Treatment of Non-alcoholic Fatty Liver Disease with Curcumin: A Randomized Placebo-controlled Trial (2016)

Non-alcoholic fatty liver disease (NAFLD) is a global health problem. Although many aspects of NAFLD pathogenesis have been understood, there is a paucity of effective treatments to be used as the second line when lifestyle modification is insufficient. Curcumin, a natural polyphenol from turmeric, has been shown to be effective against development of hepatic steatosis and its progression to steatohepatitis, yet these beneficial effects have not been explored in clinical practice. The aim of this study is to investigate the effects of curcumin on hepatic fat content as well as biochemical and anthropometric features of patients with NAFLD. In this randomized double-blind placebo-controlled trial, patients with ultrasonographic evidence of NAFLD were randomly assigned to receive an amorphous dispersion curcumin formulation (500 mg/day equivalent to 70-mg curcumin) or matched placebo for a period of 8 weeks. Liver fat content (assessed through ultrasonography), glycemic and lipid profile, transaminase levels, and anthropometric indices were evaluated at baseline and at the end of follow-up period. The clinical trial protocol was registered under the Iranian Registry of Clinical Trials ID: IRCT2014110511763N18. Compared with placebo, curcumin was associated with a significant reduction in liver fat content (78.9% improvement in the curcumin vs 27.5% improvement in the placebo group). There were also significant reductions in body mass index and serum levels of total cholesterol, low-density lipoprotein cholesterol, triglycerides, aspartate aminotransferase, alanine aminotransferase, glucose, and glycated hemoglobin compared with the placebo group. Curcumin was safe and well tolerated during the course of trial. Findings of the present proof-of-concept trial suggested improvement of different features of NAFLD after a short-term supplementation with curcumin. Copyright © 2016 John Wiley & Sons, Ltd.
Platelet-lowering Therapy with Anagrelide as an Adjuvant Therapy for Treatment of Primary Pulmonary Neoplasm-associated Extreme Thrombocytosis (2012)

Thrombocytosis is a common paraneoplastic syndrome in patients with lung cancer. However, complications associated with malignancy-related thrombocytosis, including thrombosis and hemorrhage, have rarely been reported. In this case, we describe a 57-year-old man with unresectable adenocarcinoma of the lung who presented with a platelet count over 100 × 10(4)/mm(3). In addition, deep venous thrombosis of the left femoral vein was found during admission. The circumference of the left lower leg and platelet count progressed during the period without chemotherapy and anticoagulants; however, with the addition of anagrelide they improved. We provided an adjuvant therapy with platelet-lowering therapy to treat cancer-induced thrombocytosis during the period without chemotherapy.
Metal–Organic Vapor Phase Epitaxy of GaN and InGaN Using Triethylamine with Ammonia as a Nitrogen Source (2008)

Metal–organic vapor phase epitaxy (MOVPE) of GaN and InGaN was investigated using a combination of triethylamine (TEA) and ammonia (NH3) as the nitrogen source. The reaction of TEA and NH3 in the gas phase was verified by quadrupole mass spectrometry. By using this nitrogen source, a GaN epitaxial layer was grown at 600 °C with a peak photoluminescence at 375 nm. An InxGa1-xN (x=0.6) eptaxial layer was also grown at 600 °C. The indium to gallium concentration ratio was verified by secondary ion-microprobe mass spectrometry (SIMS) and X-ray diffraction. It is confirmed that this is an effective nitride source for the efficient growth of GaN and InGaN.