gebhart/patrepeval huggingface dataset:
Mutagenic Organized Recombination Process by Homologous In Vivo Grouping (MORPHING) for Directed Enzyme Evolution (2014)

Approaches that depend on directed evolution require reliable methods to generate DNA diversity so that mutant libraries can focus on specific target regions. We took advantage of the high frequency of homologous DNA recombination in Saccharomyces cerevisiae to develop a strategy for domain mutagenesis aimed at introducing and in vivo recombining random mutations in defined segments of DNA. Mutagenic Organized Recombination Process by Homologous IN vivo Grouping (MORPHING) is a one-pot random mutagenic method for short protein regions that harnesses the in vivo recombination apparatus of yeast. Using this approach, libraries can be prepared with different mutational loads in DNA segments of less than 30 amino acids so that they can be assembled into the remaining unaltered DNA regions in vivo with high fidelity. As a proof of concept, we present two eukaryotic-ligninolytic enzyme case studies: i) the enhancement of the oxidative stability of a H2O2-sensitive versatile peroxidase by independent evolution of three distinct protein segments (Leu28-Gly57, Leu149-Ala174 and Ile199-Leu268); and ii) the heterologous functional expression of an unspecific peroxygenase by exclusive evolution of its native 43-residue signal sequence.
Insights into the binding modes of CC chemokine receptor 4 (CCR4) inhibitors: a combined approach involving homology modelling, docking, and molecular dynamics simulation studies (2014)

CC chemokine receptor 4 (CCR4), a G protein-coupled receptor (GPCR), plays a vital role in the progression of asthma, T-cell lymphoma, inflammation, and Alzheimer's disease. To date, the structure of CCR4 has not been determined. Therefore, the nature of the interactions between inhibitors and CCR4 is not well known. In this study, we used CCR5 as a template to model the structure of CCR4. Docking studies were performed for four naphthalene-sulphonamide derivatives and crucial ligand-protein interactions were analysed. Molecular dynamics (MD) simulations of these complexes (100 ns each) were carried out to gain insights into the interactions between ligands and CCR4. MD simulations revealed that the residues identified by the docking were displaced and new residues were inserted near the ligands. Results of a principal component analysis (PCA) suggested that CCR4 unfolds at the extracellular site surrounding the ligands. Our simulations identified crucial residues involved in CCR4 antagonism, which were supported by previous mutational studies. Additionally, we identified Ser3.29, Leu3.33, Ser5.39, Phe6.47, Ile7.35, Thr7.38, Thr7.40, and Ala7.42 as residues that play crucial roles in CCR4 antagonism. Mutational studies will help elucidate the significance of these residues in CCR4 antagonism. An understanding of ligand-CCR4 interactions might aid in the design of novel CCR4 inhibitors.
Rapid modulation of interband optical properties of quantum wells by intersubband absorption (1992)

Intersubband absorption of radiation by a two-dimensional electron gas can be used to control the electron temperature and effect a significant modulation of the interband optical properties of the semiconductor in the quantum well. We discuss the implementation of a fast modulator of infrared radiation for fiber-optical communications as well as the formation of powerful and short single-mode infrared pulses.
Problems Associated with Collecting Breath Condensate for the Measurement of Exhaled Hydrogen Peroxide from Neonates on Respiratory Support (2003)

We developed a bedside method for collecting exhaled breath condensate (EBC) from neonates who were ventilated or receiving nasal continuous positive airway pressure (CPAP) and analyzed their EBC for hydrogen peroxide levels. A sufficient volume for analysis could be collected over 25-40 min from neonates on the ventilator and nasal CPAP (medians 5.3 and 2.7 ml, respectively). There was no significant difference between hydrogen peroxide levels from neonates on a ventilator or CPAP (median 0.28 vs. 0.38 microM, p = 0.06) and these were no different from a background with the ventilator or CPAP system alone (median for each 0.31 microM). The dilution of breath condensate by humidified gases plus the existence of background hydrogen peroxide resulted in this collecting setup being insufficiently sensitive to use for the detection of exhaled hydrogen peroxide in infants who were ventilated or on nasal CPAP.
Cooperative enhancement of F-cell formation in baboons treated with erythropoietin and hydroxyurea (1988)

Chronically anemic baboons on a continuous hydroxyurea regimen were treated with pulsed doses of recombinant human erythropoietin (rHuEpo) to test whether the combination of these two compounds, which individually induce F-cell production, can enhance further F-cell output. A low-F-cell-responding animal under chronic hydroxyurea treatment was given three separate pulses of Epo and responded with F- reticulocyte increments that were similar to the sum increments caused by either hydroxyurea alone or rHuEpo alone. The same results were obtained in a high-F-responding animal similarly treated. These findings suggest that rHuEpo and hydroxyurea can increase F cell numbers in an additive fashion. It is speculated that both compounds act through perturbation of erythroid differentiation kinetics.
Stereospecific Polymerization of Isoprene with Molecular and MCM‐48‐Grafted Lanthanide(<scp>III</scp>) Tetraalkylaluminates (2004)

Hard graft: Heterobimetallic peralkylated complexes [Ln{(μ-R)2(AlR2)}3] (R=Me, Et) can be exploited to study metal-size effects in “Ziegler Mischkatalysatoren”. Binary precatalyst system [Nd(AlMe3)4]/Et2AlCl and heterogenized single-component variants, such as [Nd(AlMe3)4]@Et2AlCl@MCM-48 (see picture) efficiently transform isoprene to a high-cis polymer (>99 %).
Type IX collagen from sternal cartilage of chicken embryo contains covalently bound glycosaminoglycans. (1985)

Type IX collagen was isolated as a native protein from chicken embryo sternal cartilages and purified to homogeneity. Chondroitin and/or dermatan sulfate were bound covalently to one of the three polypeptide chains present in this protein containing collagenous and noncollagenous domains. Type IX collagen could be metabolically labeled with both radioactive sulfate and glycine. The protein containing either of these labels was sensitive to digestion by bacterial collagenase as well as chondroitinase ABC. Besides the glycosaminoglycans, type IX collagen contains asparagine-linked carbohydrate chains because the protein could be labeled with radioactive mannose and no glycosaminoglycans other than those mentioned above were present. The melting curve indicated that, in contrast to interstitial collagens, this molecule contains at least two disulfide-bonded collagenous domains with distinct thermal stabilities.
Regioselective F‐18 radiolabeling of AM694, a CB<sub>1</sub> cannabinoid receptor ligand (2003)

Abstract [ 18 F]AM694, [1‐(5‐[ 18 F]fluoropentyl)‐1H‐indol‐3‐yl]‐(2‐iodophenyl)methanone, 1b , a potential radiotracer for imaging of cerebral cannabinoid receptor (CB 1 ), has been synthesized by no‐carrier‐added regioselective radiofluorination of the corresponding tosylate. [ 18 F]AM694 was obtained in 20% radiochemical yield (non‐decay‐corrected) with a specific activity of 14 500 mCi/µmol, a radiochemical purity of > 99%, and a chemical purity of 95.5%. Copyright © 2003 John Wiley & Sons, Ltd.
Preparation of 13-Substituted 8<i>H</i>-Dibenzo[<i>a</i>,<i>g</i>]quinolizin-8-ones by Intramolecular Wittig-Horner Reaction of Dialkyl 2-(<i>o</i>-Acylbenzoyl)-1,2-dihydro-1-isoquinolylphosphonates (1984)

Abstract Dialkyl 2-(o-acylbenzoyl)-1,2-dihydro-1-isoquinolyl-phosphonates (1) were prepared by reactions of isoquinoline, o-acylbenzoyl chloride, and trialkyl phosphites. Treatment of 1 with lithium diisopropylamide gave 13-substituted 8H-dibenzo[a,g]quinolizin-8-ones by intramolecular Wittig-Horner reaction. Especially, 13-alkoxy and dimethylamino derivatives were obtained in good yields. A similar reaction of dimethyl 1-[o-(methoxycarbonyl)benzoyl]-1,2-dihydro-2-quinolylphosphonate was also described.
Accuracy of Implanted Port Placement with the use of the Electromagnetic CathTrack<sup>®</sup> catheter locator system (2005)

The CathTrack electromagnetic locator system can be used to reliably position catheters for the establishment of long-term central venous access. Decreased cost and elimination of radiation exposure are distinct advantages of this system over fluoroscopy.
Sorption‐enhanced reaction process for hydrogen production (1999)

Abstract A novel concept called Sorption Enhanced Reaction Process (SERP) for hydrogen production by steam‐methane reformation (SMR) reaction uses a fixed packed column of an admixture of an SMR catalyst and a chemisorbent to remove carbon dioxide selectively from the reaction zone. The chemisorbent is periodically regenerated by using the principles of pressure swing adsorption. The SERP process steps allow direct production of high‐purity hydrogen (>95 mol %) at high methane to hydrogen conversion (>80%) with dilute methane (<5 mol%) and trace carbon oxide (∼50 ppm) impurities at the reaction pressure by operating the reactor at a low temperature of 450°C. A conventional plug‐flow reactor packed with catalyst alone not only needs to be operated at a much higher temperature (>650°C) to achieve the same methane to hydrogen conversion, but produces a much lower purity of hydrogen product (∼75 mol %) with a large quantity of carbon oxide (∼20 mol %) impurities. A novel chemisorbent, which reversibly sorbs carbon dioxide in the presence of excess steam at a temperature of 300–500°C, was developed for application in the SERP and the process is experimentally demonstrated in a bench‐scale apparatus.
Frame synchronization for noncoherent demodulation on flat fading channels (2002)

We consider the problem of locating a known periodically embedded synchronization pattern in random data, which is subject to flat fading and additive white Gaussian noise. We derive the maximum likelihood rule and its high-SNR approximation for the case of noncoherent demodulation and show experimental results for the slow-fading Rayleigh channel. It is shown that the well-known correlation rule performs substantially worse than maximum-likelihood rule derived here.
An Enhanced Application Gateway for some Web services to Personal Mobile Systems (2006)

A strategy and some practical examples are proposed to enhance functionally an application gateway located between clients and some kinds of servers and to utilize it for multiple purposes in order to take advantages on some Web services and communication and/or computation between clients and servers. In such an enhanced application gateway, some suitable interfaces can be selected, offered for each request from client, and an effective communication method between client and target server can be also provided according to request from client. And some practical examples are demonstrated, such as remote monitoring system and e-mail handling system. With our proposed style of enhancing application gateway, an integration of Web function and other special-purpose facilities can be effectively realized as one high-performance application gateway. With our enhanced application gateway, therefore, several kinds of clients utilizing mobile devices will be able to enjoy such efficient environment of some Web services for communication, data handling, and/or specific computation
Integrated therapy for HIV and cryptococcosis (2016)

Cryptococcosis has been one of the most common opportunistic infections and causes of mortality among HIV-infected patients, especially in resource-limited countries. Cryptococcal meningitis is the most common form of cryptococcosis. Laboratory diagnosis of cryptococcosis includes direct microscopic examination, isolation of Cryptococcus from a clinical specimen, and detection of cryptococcal antigen. Without appropriate treatment, cryptococcosis is fatal. Early diagnosis and treatment is the key to treatment success. Treatment of cryptococcosis consists of three main aspects: antifungal therapy, intracranial pressure management for cryptococcal meningitis, and restoration of immune function with antiretroviral therapy (ART). Optimal integration of these three aspects is crucial to achieving successful treatment and reducing the mortality. Antifungal therapy consists of three phases: induction, consolidation, and maintenance. A combination of two drugs, i.e. amphotericin B plus flucytosine or fluconazole, is preferred in the induction phase. Fluconazole monotherapy is recommended during consolidation and maintenance phases. In cryptococcal meningitis, intracranial pressure rises along with CSF fungal burden and is associated with morbidity and mortality. Aggressive control of intracranial pressure should be done. Management options include therapeutic lumbar puncture, lumbar drain insertion, ventriculostomy, or ventriculoperitoneal shunt. Medical treatment such as corticosteroids, mannitol, and acetazolamide are ineffective and should not be used. ART has proven to have a great impact on survival rates among HIV-infected patients with cryptococcosis. The time to start ART in HIV-infected patients with cryptococcosis has to be deferred until 5 weeks after the start of antifungal therapy. In general, any effective ART regimen is acceptable. Potential drug interactions between antiretroviral agents and amphotericin B, flucytosine, and fluconazole are minimal. Of most potential clinical relevance is the concomitant use of fluconazole and nevirapine. Concomitant use of these two drugs should be cautious, and patients should be monitored closely for nevirapine-associated adverse events, including hepatotoxicity. Overlapping toxicities of antifungal and antiretroviral drugs and immune reconstitution inflammatory syndrome are not uncommon. Early recognition and appropriate management of these consequences can reinforce the successful integrated therapy in HIV-infected patients with cryptococcosis.
The influence of amateur radio on the development of the commercial market for quartz piezoelectric resonators in the United States (2002)

In the mid and late 1920s, amateur radio operators were experimenting in great numbers with crystal control of radio transmitters. At the time, most amateurs used home built transmitters made from a combination of purchased and home made parts. The use of quartz crystals by amateurs predated the first U.S. commercial broadcast station to use crystal control. Amateur radio operators were the first sizable commercial market for crystals. Many of the crystal companies of the 1920s and 1930s were founded by amateur radio operators to supply other amateurs.
The Fingerprint Method: Using Over-bark and Under-bark Log Measurement Data Generated by Three-dimensional Log Scanners in Combination with Radiofrequency Identification Tags to Achieve Traceability in the Log Yard at the Sawmill (2004)

In the forestry–wood chain the concept and the technologies of traceability are in a mature development phase. Important advances in marking and reading techniques have been made in different parts along the forestry–wood chain. For Swedish sawmills the most critical information gap is located between the log sorting station and the saw intake, where the forest log batch identity disappears and the logs are mixed according to different sorting criteria. This study utilizes radiofrequency identification tags for automatic log marking/reading to develop a traceability system for logs, which is free of marking/reading, between the log sorting station and the saw intake, i.e. the fingerprint method. The originality of the fingerprint approach rests on the hypothesis that logs are separate entities with individual features. The results show that the log parameters and the search algorithm developed, combined with the negative influence of the measurement uncertainty due to bark thickness and bark damage, made it possible to achieve an individual separation for 57% of the tested logs.
Mutagenesis and Laue Structures of Enzyme Intermediates: Isocitrate Dehydrogenase (1995)

Site-directed mutagenesis and Laue diffraction data to 2.5 A resolution were used to solve the structures of two sequential intermediates formed during the catalytic actions of isocitrate dehydrogenase. Both intermediates are distinct from the enzyme-substrate and enzyme-product complexes. Mutation of key catalytic residues changed the rate determining steps so that protein and substrate intermediates within the overall reaction pathway could be visualized.
Highly uniform SERS substrates formed by wrinkle-confined drying of gold colloids (2010)

SERS substrates were fabricated through self-assembly of gold nanoparticles upon solution-drying in a periodic confining structure. The technique leads to uniform, parallel linear nanoparticle arrays with the precise arrangement defined through the dimensions of the particles and the grooves, which provide high and uniform SERS enhancement over extended areas.
Isolation and characterization of a soluble lactose‐binding lectin from postnatal chicken retina (1994)

We investigated the presence of endogenous lectins in postnatal chicken retinal tissue assaying the hemagglutinating activity of crude soluble extracts of the tissue that was homogenized in a buffer supplemented with different sugars. Lactose was the most effective sugar to extract an hemagglutinating activity. Using similar extraction conditions, other sugars, such as glucose, N-acetylglucosamine, mannose, fucose, glucuronic and sialic acid, were ineffective to extract any significant hemagglutinating activity. The lectin was purified by affinity chromatography on lactosyl-Sepharose. SDS-PAGE and isoelectric focusing analyses showed that it has a subunit molecular weight of 16 kDa and a pI about 4.5. The retinal lectin cross-reacted immunologically with a rabbit antiserum raised against a lectin purified from adult chicken liver, which is a CLL-I (Beyer et al.: J Biol Chem 255:4236-4239, 1980) or C-16 (Sakakura et al.: J Biol Chem 265:21573-21579, 1990) form of chicken endogenous soluble lactose-binding lectins. Gel filtration studies showed that the oligomeric structure of the retinal lectin is dependent on the ionic strength of the elution buffer. The lectin hemagglutinating activity and the amount of lectin protein reached their highest levels at late developmental stages of the retinal tissue, suggesting that retinal lectin might have a functional role during terminal differentiation of retinal cells.
Dependence of aptamer activity on opposed terminal extensions: improvement of light-regulation efficiency (2009)

Aptamers that can be regulated with light allow precise control of protein activity in space and time and hence of biological function in general. In a previous study, we showed that the activity of the thrombin-binding aptamer HD1 can be turned off by irradiation using a light activatable 'caged' intramolecular antisense-domain. However, the activity of the presented aptamer in its ON state was only mediocre. Here we studied the nature of this loss in activity in detail and found that switching from 5'- to 3'-extensions affords aptamers that are even more potent than the unmodified HD1. In particular we arrived at derivatives that are now more active than the aptamer NU172 that is currently in phase 2 clinical trials as an anticoagulant. As a result, we present light-regulatable aptamers with a superior activity in their ON state and an almost digital ON/OFF behavior upon irradiation.
Implementing ultra-high-value floating tunable CMOS resistors (2008)

A compact high-value floating resistor utilising PMOS devices in the subthreshold region is introduced. A test chip has been fabricated in 0.18 µm CMOS technology to verify the proposed concept. This technique has been applied to design a reconfigurable sixth-order very-low-cutoff-frequency MOSFET-C filter.
Pharmacokinetics of cis-diamminedichloroplatinum(II) after administration in hypertonic saline. (1986)

Nephrotoxicity, the dose-limiting toxicity of cis-diamminedichloroplatinum(II) (CDDP), is ameliorated when administered in hypertonic saline with normal saline hydration. To determine whether the diminished nephrotoxicity is associated with alteration of the pharmacokinetics of CDDP, we examined the pharmacokinetics of free and total platinum, platinum renal excretion, and urine electrolytes in patients given CDDP in hypertonic saline and in patients given CDDP in a conventional manner. The pharmacokinetics of free and total platinum for equal doses of CDDP were similar regardless of the vehicle of administration and the method of hydration. CDDP given in a vehicle of high chloride concentration with normal saline hydration resulted in a statistically significant increase in both urine volume and chloruresis compared to the conventional regimen. The decreased nephrotoxicity associated with administration of CDDP in hypertonic saline with saline diuresis may be related to increased chloruresis, urinary volume, or a combination of both, but did not appear to be related to an alteration in the pharmacokinetics.
Confirmation of Fanconiʼs Anemia and Detection of a Chromosomal Aberration (1Q12–32 Triplication) Via BRDU/Hoechst Flow Cytometry (1987)

Journal of Pediatric Hematology/Oncology (JPHO) reports on major advances in the diagnosis and treatment of cancer and blood diseases in children. The journal publishes original research, commentaries, historical insights, and clinical and laboratory observations.
MobileAppScrutinator: A Simple yet Efficient Dynamic Analysis Approach for Detecting Privacy Leaks across Mobile OSs (2016)

Smartphones, the devices we carry everywhere with us, are being heavily tracked and have undoubtedly become a major threat to our privacy. As "tracking the trackers" has become a necessity, various static and dynamic analysis tools have been developed in the past. However, today, we still lack suitable tools to detect, measure and compare the ongoing tracking across mobile OSs. To this end, we propose MobileAppScrutinator, based on a simple yet efficient dynamic analysis approach, that works on both Android and iOS (the two most popular OSs today). To demonstrate the current trend in tracking, we select 140 most representative Apps available on both Android and iOS AppStores and test them with MobileAppScrutinator. In fact, choosing the same set of apps on both Android and iOS also enables us to compare the ongoing tracking on these two OSs. Finally, we also discuss the effectiveness of privacy safeguards available on Android and iOS. We show that neither Android nor iOS privacy safeguards in their present state are completely satisfying.
Simulations of Modulation of the Current in a Field Emitter Caused by a CW or Pulsed Laser (1996)

Solutions of the time-dependent Schrödinger equation show that the tunneling current in a field emitter may be modulated by means of a laser. The steady-state response is calculated with Floquet methods, and the transient response is determined with a product formulation that does not require the use of absorbing boundary conditions or wave packets. The steady-state response contains a series of resonances, but when the full distribution of energies in a metal is considered the resulting effect is a broad peak that is typically centered in the blue end of the visible spectrum, but may be shifted by varying the applied static field. The transient solutions show that the response of the electrons to the optical fields is delayed by the semiclassical tunneling time, which is defined as the time for traversing the inverted barrier.