gebhart/patrepeval huggingface dataset:
Purification and reactivation of recombinant Synechococcus phytoene desaturase from an overexpressing strain of Escherichia coli (1993)

The Synechococcus phytoene desaturase has been isolated from an overexpressing strain of Escherichia coli. The plasma pPDSde135 mediated the overexpression of the full-length polypeptide directly. The recombinant protein comprised 5% of the total cellular protein and was found predominantly in the inclusion body fraction. Urea was used to solubilize the recombinant protein from the inclusion fraction and the protein was subsequently purified to homogeneity on a DEAE-cellulose column. The purification scheme yielded 4.0 mg of homogeneous desaturase protein after a 20-fold purification, recovering 40% of the original protein from a 100 ml suspension culture of E. coli. The recombinant desaturase had an apparent molecular mass of 53 kDa on SDS/PAGE and crossreacted with an antiserum raised against the expressed protein. Desaturase activity was restored upon the removal of urea. The enzyme catalysed the conversion of phytoene to zeta-carotene via phytofluene. These products of the desaturase reaction existed predominantly in a cis configuration. Lipid replenishment enhanced activity. NAD+ and NADP+ were observed to be involved, whilst FAD was an ineffective electron acceptor.
Expression of Stimulated by Retinoic Acid Gene 8 (Stra8) and Maturation of Murine Gonocytes and Spermatogonia Induced by Retinoic Acid In Vitro1 (2007)

Vitamin A deficiency in the mouse results in an arrest in the progression of undifferentiated spermatogonia to differentiating spermatogonia. The supplement of retinol to vitamin-A-deficient mice reinitiates spermatogenesis in a synchronous manner throughout the testes. It is unclear whether the effects of retinoids are the result of a direct action on germ cells or are indirectly mediated through Sertoli cells. The expression of Stimulated by retinoic acid gene 8 (Stra8), which is required for spermatogenesis, is directly related to the availability of retinoic acid (RA). Analysis of gene expression by microarrays revealed moderate levels of Stra8 transcript in gonocytes and high levels in A and B spermatogonia. Stra8 mRNA levels were greatly reduced or absent in germ cells once they entered meiosis. This study examined the effect of retinoic acid on cultured neonatal testes and isolated gonocytes/spermatogonia in vitro. THY1(+) and KIT(+) germ cells were isolated by magnetic-activated cell sorting from the testes of mice of different ages. Isolated germ cells were cultured and treated with either vehicle (ethanol) or RA without feeder cells. We found that 1) Stra8 is predominantly expressed in premeiotic germ cells, 2) RA stimulates gonocyte DNA replication and differentiation in cultured neonatal testes, 3) in the absence of feeder cells, RA directly induces the transition of undifferentiated spermatogonia to differentiating spermatogonia by stimulating Stra8 and Kit gene expression, 4) RA dramatically stimulates Stra8 expression in undifferentiated spermatogonia but has a lesser impact in differentiating spermatogonia, 5) endogenous Stra8 gene expression is higher in differentiating spermatogonia than in undifferentiated spermatogonia and could mediate the RA effects on spermatogonial maturation, and 6) RA stimulates a group of genes involved in the metabolism, storage, transport, and signaling of retinoids.
Human embryonic stem cells differentiate into oligodendrocytes in high purity and myelinate after spinal cord transplantation (2004)

Human embryonic stem cells (hESCs) demonstrate remarkable proliferative and developmental capacity. Clinical interest arises from their ability to provide an apparently unlimited cell supply for transplantation, and from the hope that they can be directed to desirable phenotypes in high purity. Here we present for the first time a method for obtaining oligodendrocytes and their progenitors in high yield from hESCs. We expanded hESCs, promoted their differentiation into oligodendroglial progenitors, amplified those progenitors, and then promoted oligodendroglial differentiation using positive selection and mechanical enrichment. Transplantation into the shiverer model of dysmyelination resulted in integration, differentiation into oligodendrocytes, and compact myelin formation, demonstrating that these cells display a functional phenotype. This differentiation protocol provides a means of generating human oligodendroglial lineage cells in high purity, for use in studies of lineage development, screening assays of oligodendroglial-specific compounds, and treating neurodegenerative diseases and traumatic injuries to the adult CNS.
Targeted delivery across the blood–brain barrier (2005)

The safest and most effective way of targeting drugs to the entire brain is via delivery systems directed at endogenous receptor-mediated uptake mechanisms present at the cerebral capillaries. Such systems have been shown to be effective in animal models including primates, but no clinical trials have been performed so far. This review focuses on the well-characterised transferrin and insulin receptor-targeted systems, as well as on the more recently described systems that use the low-density lipoprotein-related protein 1 receptor, the low-density lipoprotein-related protein 2 receptor (also known as megalin and glycoprotein 330) or the diphtheria toxin receptor (which is the membrane-bound precursor of heparin-binding epidermal growth factor-like growth factor). The possibilities and limitations of these systems are compared and their future for human application is discussed.
Marijuana Smoking: Factors That Influence the Bioavailability of Tetrahydrocannabinol (1990)

Marijuana smoking is the most commonly used method for the selfadministration of delta-9-tetrahydrocannabinol (THC) the active principle of marijuana. The inhalation of marijuana smoke induces subjective effects (“high”) that are rapidly perceived by the smokers. The perception of these effects allows smokers the capacity to achieve, within certain limits, their desired level of high by changing the puff volume, the interval between puffs, and the number of puffs taken. Therefore, the manner in which marijuana cigarettes are smoked (smoking dynamics) is probably the mast important factor in determining the bioavailability of THC. However, the following factors are also important: (1) the potency of the marijuana smoked; (2) the amount of unchanged THC present in the smoke inhaled (i.e., the amount of THC not destroyed by pyrolysis); (3) the amount of THC lost in side-stream smoke; (4) the method of smoking (cigarette vs. pipe smoking); and (5) the amount of THC trapped in the mucosa of the upper respiratory tract. A review of the experiments we have conducted that permit evaluation of the relative importance of these factors is presented in this chapter.
Sulfatases: Structure, Mechanism, Biological Activity, Inhibition, and Synthetic Utility (2004)

Abstract Sulfatases, which cleave sulfate esters in biological systems, play a key role in regulating the sulfation states that determine the function of many physiological molecules. Sulfatase substrates range from small cytosolic steroids, such as estrogen sulfate, to complex cell‐surface carbohydrates, such as the glycosaminoglycans. The transformation of these molecules has been linked with important cellular functions, including hormone regulation, cellular degradation, and modulation of signaling pathways. Sulfatases have also been implicated in the onset of various pathophysiological conditions, including hormone‐dependent cancers, lysosomal storage disorders, developmental abnormalities, and bacterial pathogenesis. These findings have increased interest in sulfatases and in targeting them for therapeutic endeavors. Although numerous sulfatases have been identified, the wide scope of their biological activity is only beginning to emerge. Herein, accounts of the diversity and growing biological relevance of sulfatases are provided along with an overview of the current understanding of sulfatase structure, mechanism, and inhibition.
Identification and application of the concepts important for accurate and reliable protein secondary structure prediction (1996)

A protein secondary structure prediction method from multiply aligned homologous sequences is presented with an overall per residue three-state accuracy of 70.1%. There are two aims: to obtain high accuracy by identification of a set of concepts important for prediction followed by use of linear statistics; and to provide insight into the folding process. The important concepts in secondary structure prediction are identified as: residue conformational propensities, sequence edge effects, moments of hydrophobicity, position of insertions and deletions in aligned homologous sequence, moments of conservation, auto-correlation, residue ratios, secondary structure feedback effects, and filtering. Explicit use of edge effects, moments of conservation, and auto-correlation are new to this paper. The relative importance of the concepts used in prediction was analyzed by stepwise addition of information and examination of weights in the discrimination function. The simple and explicit structure of the prediction allows the method to be reimplemented easily. The accuracy of a prediction is predictable a priori. This permits evaluation of the utility of the prediction: 10% of the chains predicted were identified correctly as having a mean accuracy of > 80%. Existing high-accuracy prediction methods are "black-box" predictors based on complex nonlinear statistics (e.g., neural networks in PHD: Rost & Sander, 1993a). For medium- to short-length chains (> or = 90 residues and < 170 residues), the prediction method is significantly more accurate (P < 0.01) than the PHD algorithm (probably the most commonly used algorithm). In combination with the PHD, an algorithm is formed that is significantly more accurate than either method, with an estimated overall three-state accuracy of 72.4%, the highest accuracy reported for any prediction method.
Optimal complexity correction of correlated errors in the surface code (2013)

The surface code is designed to suppress errors in quantum computing hardware and currently offers the most believable pathway to large-scale quantum computation. The surface code requires a 2-D array of nearest-neighbor coupled qubits that are capable of implementing a universal set of gates with error rates below approximately 1%, requirements compatible with experimental reality. Consequently, a number of authors are attempting to squeeze additional performance out of the surface code. We describe an optimal complexity error suppression algorithm, parallelizable to O(1) given constant computing resources per unit area, and provide evidence that this algorithm exploits correlations in the error models of each gate in an asymptotically optimal manner.
Inflammation and Chronic Oxidative Stress in Radiation-Induced Late Normal Tissue Injury: Therapeutic Implications (2008)

The threat of radiation-induced late normal tissue injury limits the dose of radiation that can be delivered safely to cancer patients presenting with solid tumors. Tissue dysfunction and failure, associated with atrophy, fibrosis and/or necrosis, as well as vascular injury, have been reported in late responding normal tissues, including the central nervous system, gut, kidney, liver, lung, and skin. The precise mechanisms involved in the pathogenesis of radiation-induced late normal tissue injury have not been fully elucidated. It has been proposed recently that the radiation-induced late effects are caused, in part, by chronic oxidative stress and inflammation. Increased production of reactive oxygen species, which leads to lipid peroxidation, oxidation of DNA and proteins, as well as activation of pro-inflammatory factors has been observed in vitro and in vivo. In this review, we will present direct and indirect evidence to support this hypothesis. To improve the long-term survival and quality of life for radiotherapy patients, new approaches have been examined in preclinical models for their efficacy in preventing or mitigating the radiation-induced chronic normal tissue injury. We and others have tested drugs that can either attenuate inflammation or reduce chronic oxidative stress in animal models of late radiation-induced normal tissue injury. The effectiveness of renin-angiotensin system blockers, peroxisome proliferator-activated receptor (PPAR) gamma agonists, and antioxidants/antioxidant enzymes in preventing or mitigating the severity of radiation-induced late effects indicates that radiation-induced chronic injury can be prevented and/or treated. This provides a rationale for the design and development of anti-inflammatory-based interventional approaches for the treatment of radiation-induced late normal tissue injury.
Amiloride inhibits macropinocytosis by lowering submembranous pH and preventing Rac1 and Cdc42 signaling (2010)

Macropinocytosis is differentiated from other types of endocytosis by its unique susceptibility to inhibitors of Na(+)/H(+) exchange. Yet, the functional relationship between Na(+)/H(+) exchange and macropinosome formation remains obscure. In A431 cells, stimulation by EGF simultaneously activated macropinocytosis and Na(+)/H(+) exchange, elevating cytosolic pH and stimulating Na(+) influx. Remarkably, although inhibition of Na(+)/H(+) exchange by amiloride or HOE-694 obliterated macropinocytosis, neither cytosolic alkalinization nor Na(+) influx were required. Instead, using novel probes of submembranous pH, we detected the accumulation of metabolically generated acid at sites of macropinocytosis, an effect counteracted by Na(+)/H(+) exchange and greatly magnified when amiloride or HOE-694 were present. The acidification observed in the presence of the inhibitors did not alter receptor engagement or phosphorylation, nor did it significantly depress phosphatidylinositol-3-kinase stimulation. However, activation of the GTPases that promote actin remodelling was found to be exquisitely sensitive to the submembranous pH. This sensitivity confers to macropinocytosis its unique susceptibility to inhibitors of Na(+)/H(+) exchange.
Vaccination with FimH Adhesin Protects Cynomolgus Monkeys from Colonization and Infection by UropathogenicEscherichia coli (2000)

Escherichia coli FimH adhesin mediates binding to the bladder mucosa. In mice, a FimH vaccine protects against bacterial challenge. In this study, 4 monkeys were inoculated with 100 microgram of FimCH adhesin-chaperone complex mixed with MF59 adjuvant, and 4 monkeys were given adjuvant only intramuscularly. After 2 doses (day 0 and week 4), a booster at 48 weeks elicited a strong IgG antibody response to FimH in the vaccinated monkeys. All 8 monkeys were challenged with 1 mL of 108 E. coli cystitis isolate NU14. Three of the 4 vaccinated monkeys were protected from bacteruria and pyuria; all control monkeys were infected. These findings suggest that a vaccine based on the FimH adhesin of E. coli type 1 pili may have utility in preventing cystitis in humans.
"Neither master nor slave...". A practical case study in the development and employment of cleaning robots (2003)

Industrially-oriented robotics research over the past decade has turned its attention to applications outside manufacturing environments. This is leading to the development of so-called "service robots". The function of a service robot necessarily entails greater focus on human factors issues. This industrial-perspective overview paper presents current floor-cleaning robots, and in particular describes the development of the Acromatic 750, made under ESPRIT Project 6051 "ACRO" (Autonomous Cleaning RObot), and its re-design and testing under ESPRIT Project 22172 "TEAM" (Test Environments for Autonomous Machines). It examines the practical barriers currently hindering commercial development and argues for a more eclectic approach to autonomous systems development, taking into account the operator's role and current industry structure.
The N.Y.I.T. Digital Sound Editor (1982)

This article describes a digital sound editor developed to meet the needs of musicians, sound engineers, video artists, and research scientists at the New York Institute of Technology's Digital Sound and Computer Graphics Laboratories. A preliminary version of the editor was described in a paper delivered at Queens College during the 1980 International Computer Music Conference (Glassner 1980). The existence of a large and diverse user group consisting of over 30 computer scientists, mathematicians, hardware engineers, artists, and composers made it necessary to design a highly adaptable and easy-to-use system for displaying, editing, and playing back audio sample data. We are of the opinion that any computer system, whether intended for research or production, is useful in inverse proportion to its complexity-or, more precisely, to its perceived complexity. The initial operating version of the N.Y.I.T. editor, as described in this article, is the result of an 18-month developmental effort aimed at providing a fast, simple, bare-bones editor. However, it also provides a sufficient number of user-definable playback and display parameters and a sufficient number of hooks for user-supplied preand postprocessors to serve equally well in a variety of roles, for example:
Phase error corrected 4-bit true time delay module using a cascaded 2 × 2 polymer waveguide switch array (2007)

A fully integrated 4-bit true time delay device using polymer optical switches and waveguide delay lines is demonstrated. The fabricated device, which contains five 2x2 thermo-optic switches, has a maximum power consumption of 143 mW and a switching time less than 3 ms. The rf phase error, which is affected by the optical switch cross talk, is also theoretically analyzed and proved to be negligible by experimental results.
In vitro biosynthesis and membrane insertion of gamma-glutamyl transpeptidase. (1984)

gamma-Glutamyl transpeptidase consists of two polypeptide chains anchored to the kidney brush-border membrane only through a short hydrophobic domain near the NH2-terminal end of the heavy subunit. The two subunits were reported to derive from a single polypeptide precursor by tissue labeling experiments. We have investigated the first steps of GGT biosynthesis and processing in a cell-free system. mRNA was prepared from kidney and enriched in specific sequences by a preparative gel electrophoresis. In vitro translation resulted in the synthesis of a single polypeptide (Mr = 63,000) specifically immunoprecipitated by antibodies raised against the mature dimeric enzyme. Incubation with microsomal membranes resulted in the appearance of a glycosylated form of the propeptide (Mr = 78,000). This latter form was cotranslationally segregated into microsomes and was sensitive to endoglycosidase H. Purified Escherichia coli leader peptidase did not process the primary gamma-glutamyl transpeptidase chain. This ectoprotein therefore appears to be inserted in the phospholipid bilayer without cleavage of a signal peptide, similar to most integral membrane proteins so far studied.
A Comparative Study of Glycerinized and Lyophilized Porine Skin in Dressings for Third-Degree Burns (1982)

A comparative study of local treatment with lyophilized and glycerinized porcine skin was performed on 100 patients with third-degree burns. We compared the efficiency, simplicity, and cost of preparation of dehydrated, sterile porcine skin for ready use in temporary dressings for burn victims. We conclude that this is a simple, efficient, and safe method, which, because of its low cost, will permit greater use of porcine skin as a temporary substitute in dressings for third-degree burns.
Anatomy of a Scalable Software Transactional Memory (2009)

Existing software transactional memory (STM) implementations often exhibit poor scalability, usually because of nonscalable mechanisms for read sharing, transactional consistency, and privatization; some STMs also have nonscalable centralized commit mechanisms. We describe novel techniques to eliminate bottlenecks from all of these mechanisms, and present SkySTM, which employs these techniques. SkySTM is the first STM that supports privatization and scales on modern multicore multiprocessors with hundreds of hardware threads on multiple chips. A central theme in this work is avoiding frequent updates to centralized metadata, especially for multi-chip systems, in which the cost of accessing centralized metadata increases dramatically. A key mechanism we use to do so is a scalable nonzero indicator (SNZI), which was designed for this purpose. A secondary contribution of the paper is a new and simplified SNZI algorithm. Our scalable privatization mechanism imposes only about 4% overhead in low-contention experiments; when contention is higher, the overhead still reaches only 35 % with over 250 threads. In contrast, prior approaches have been reported as imposing over 100 % overhead in some cases, even with only 8 threads. 1.
Microcontact Printing of Dendrimers, Proteins, and Nanoparticles by Porous Stamps (2008)

Porous stamps fabricated by one-step phase separation micromolding were used for microcontact printing of polar inks, in particular aqueous solutions of dendrimers, proteins, and nanoparticles. Permanent hydrophilicity was achieved without any additional treatment by tailored choice of the polymer components. Pores with several hundred nanometers to micrometers were obtained during the phase separation process. These pores can act as ink reservoirs. The porous stamps were thoroughly characterized by SEM, NMR, and contact angle measurement. The versatility of the porous stamps was shown in three printing schemes. First, positive microcontact printing was achieved by printing a polar thioether-modified dendrimer as the ink, followed by backfilling and wet etching. Second, the porous stamps were used for multiple printing of fluorescent proteins without reinking. Third, nanoparticles of about 60 nm in diameter, which cannot be directly transferred by oxidized PDMS stamps, were successfully printed onto substrates by using these porous stamps.
A multi-level buffering and feedback scheme for distributed multimedia presentation systems (2002)

Distributed multimedia presentation systems require flexibility and good quality of service for multimedia data presentations. To ensure flexible and satisfiable presentations of multimedia data, collaborations between servers, network, and clients must be carefully designed to retrieve the data from the disk and transfer the data to the client. In this paper we investigate a multi-level buffering and feedback scheme to guarantee the on-time retrieval and transmission of multimedia data in the distributed multimedia presentation environments. In the multi-level buffering scheme, both client and server buffers are designed and collaborated to support the end-to-end multimedia data transmission. These buffers can absorb the rate variations of media streams in different locations. Local and remote feedback messages are used to dynamically prevent buffer overflow/underflow problems. Experiments demonstrate that highly smooth and synchronized presentations of multimedia streams can be supported.
A batch-fabricated silicon accelerometer (1979)

An extremely small batch-fabricatable accelerometer has been developed using silicon IC technology. The device, 3 mm long and weighing 0.02 g, is a simple cantilevered beam and mass structure sealed into a silicon and glass package. The fabrication of the accelerometer is described, and the theory behind its operation developed. Experimental results on sensitivity, frequency response, and linearity are presented and found to agree with theory. The accelerometer is capable of measuring accelerations from 0.001 to 50 g over a 100-Hz bandwidth, while readily implemented geometry changes allow these performance characteristics to be varied over a wide range to meet the needs of differing applications.