gebhart/patrepeval huggingface dataset:
Man to Machine, Applications in Electromyography (2012)

The study of electrical signals due to muscle activation has been evolving since Francesco Redi found electrical generation in the muscles of the electric ray fish in 1666 (Fishman, Wilkins, 2011), Dubois discovered electrical activation in voluntary muscles in 1849 Evolving over the following decades, electromyography has found widespread use in clinical settings as well as extensive use in ergonomic assessment and biomechanics research laboratories. As with many technologies, the discovery of electromyography occurred long before inexpensive and robust hardware was developed to utilize the vast amount of information available from myoelectric signals. Until recently, existing technology could not support efficient generation of repeatable robust signals for even highly sophisticated research laboratories, let alone the widespread availability of affordable, robust hardware required to propagate electromyography through the research communities. New high-speed computation tools make real-time analysis feasible. With the emergence of low cost hardware, high speed wireless communication technology, and low cost, high speed computing/signal processing equipment, Electromyography is becoming available to a whole new set of experimenter. With these advances making electromyography a feasible option in many situations, we see the emergence of a key period in the evolution of the technology. Surface electromyography (sEMG) provides a convenient and relatively noninvasive avenue for determining muscle activation, particularly as highly portable devices become available. Of course with the benefits of wider availability, we must consider the risks inherent in this spread, as the practitioners involved move from electromyography specialists, to technologists in other fields, using electromyography either part time, or only occasionally. Electromyography is a detailed art, and can easily lead to erroneous conclusions if not practiced carefully. With new applications, particularly where electromyography is employed as a means for humans to control electromechanical systems, care must be taken to insure that these systems are developed with robust safety systems, and improper assumptions about electromyography do not cause harm, injury, or even death.
[Purification and several properties of dihydroxyacetone kinase from the methylotrophic yeast Candida boidinii]. (1983)

A procedure for isolation of a homogeneous dihydroxyacetone kinase including fractionation by polyethylene glycol and ion-exchange chromatography on polyethylenimine-Biogel has been developed. The enzyme is a dimer with Mr = 139 000 (2.71 000 according to SDS disc electrophoresis) and has a pI of 4.64 and pH optimum of 7.8-8.2. The enzyme phosphorylates dihydroxyacetone and, in a lesser degree, glyceraldehyde. ATP is the most efficient phosphate group donor for the enzyme. When ITP, GTP, CTP and UTP are used, the dihydroxyacetone kinase activity is about 30%.
An androgen-dependent mouse mammary tumor. (1965)

An entirely androgen-dependent tumor derived from a spontaneous hormone-independent mammary tumor in a female mouse was established. Many interesting biological properties of the tumor are described and discussed from the point of view of the tumor-host relationship.
Effect of spacer chemistry on the formation and properties of linear reversible polymers (2013)

ABSTRACT A series of four pairs of bismaleimide and bisfuran monomers were combined to make thermally reversible linear polymers. The monomers were prepared using diamines having different spacer chemistries, n ‐octyl, cyclohexyl, phenyl, and ethylenedioxy, such that a relatively constant spacer dimension among the four monomers was achieved. Heating of the bismaleimide/bisfuran couples resulted in low‐viscosity, easily processable liquids. Subsequent cooling to room temperature resulted in the formation of hard films, with the rate of hardening varying significantly within the series of compounds. The rate and degree of polymerization were determined using 1 H NMR spectroscopy and were both found to be dependent on the chemistry of the spacer group, as was the film rheology, which was measured using nanoindentation. Adhesion of the polymers was quantified by measurement of their tensile adhesive strength, and this was also found to be spacer dependent. Polymerization reversibility was verified using 1 H NMR spectroscopy. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013 , 51 , 5056–5066
Chemical and enzymatic stability of amino acid derived phosphoramidates of antiviral nucleoside 5′-monophosphates bearing a biodegradable protecting group (2010)

Ribavirin and 2'-O-methylcytidine 5'-phosphoramidates derived from L-alanine methyl ester bearing either an O-phenyl or a biodegradable O-[3-(acetyloxy)-2,2-bis(ethoxycarbonyl)propyl] or O-[3-(acetyloxymethoxy)-2,2-bis(ethoxycarbonyl)propyl] protecting group were prepared. The kinetics of the deprotection of these pro-drugs by porcine liver esterase and by a whole cell extract of human prostate carcinoma was studied by HPLC-ESI-MS/MS. The 3-(acetyloxymethoxy)-2,2-bis(ethoxycarbonyl)propyl and 3-(acetyloxy)-2,2-bis(ethoxycarbonyl)propyl groups were readily removed releasing the l-alanine methyl ester phosphoramidate nucleotide, the deprotection of the 3-(acetyloxymethoxy) derivative being approximately 20 times faster. The chemical stability of the 2'-O-methylcytidine pro-drugs was additionally determined over a pH range from 7.5 to 10.
A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis (2008)

QCs (glutaminyl cyclases; glutaminyl-peptide cyclotransferases, EC 2.3.2.5) catalyse N-terminal pyroglutamate formation in numerous bioactive peptides and proteins. The enzymes were reported to be involved in several pathological conditions such as amyloidotic disease, osteoporosis, rheumatoid arthritis and melanoma. The crystal structure of human QC revealed an unusual H-bond (hydrogen-bond) network in the active site, formed by several highly conserved residues (Ser(160), Glu(201), Asp(248), Asp(305) and His(319)), within which Glu(201) and Asp(248) were found to bind to substrate. In the present study we combined steady-state enzyme kinetic and X-ray structural analyses of 11 single-mutation human QCs to investigate the roles of the H-bond network in catalysis. Our results showed that disrupting one or both of the central H-bonds, i.e., Glu(201)...Asp(305) and Asp(248)...Asp(305), reduced the steady-state catalysis dramatically. The roles of these two COOH...COOH bonds on catalysis could be partly replaced by COOH...water bonds, but not by COOH...CONH(2) bonds, reminiscent of the low-barrier Asp...Asp H-bond in the active site of pepsin-like aspartic peptidases. Mutations on Asp(305), a residue located at the centre of the H-bond network, raised the K(m) value of the enzyme by 4.4-19-fold, but decreased the k(cat) value by 79-2842-fold, indicating that Asp(305) primarily plays a catalytic role. In addition, results from mutational studies on Ser(160) and His(319) suggest that these two residues might help to stabilize the conformations of Asp(248) and Asp(305) respectively. These data allow us to propose an essential proton transfer between Glu(201), Asp(305) and Asp(248) during the catalysis by animal QCs.
Rhodium-Stabilized Vinylcarbenoid Intermediates in Organic Synthesis (1998)

Abstract: This article will give an overview of the reactions and synthetic utility of rhodium-stabilized vinylcarbenoids, which have been shown in recent years to be versatile synthetic intermediates. They undergo highly diastereoselective cyclopropanations with a wide array of alkenes and dienes, and the resulting vinylcyclopropanes are readily converted to other ring systems. Most notable is the reaction between vinylcarbenoids and dienes, which is a general method for the stereoselective construction of seven-membered carbocycles by means of a tandem cyclopropanation/Cope rearrangement sequence. Efficient insertions into Si-H, C-H, N-H and 0-H bonds can also be achieved by rhodium-stabilized vinylcarbenoids. The synthetic utility of vinylcarbenoid chemistry has been greatly enhanced by the recent development of chiral catalysts and auxiliaries that enable this chemistry to be achieved with high asymmetric induction.
Clinical genomic profiling to identify actionable alterations for investigational therapies in patients with diverse sarcomas (2017)

Incorporating CGP into sarcoma management may allow for more precise diagnosis and sub-classification of this diverse and rare disease, as well as personalized matching of patients to targeted therapies such as those available in basket clinical trials.
A Review of the Biocompatibility of Implantable Devices: Current Challenges to Overcome Foreign Body Response (2008)

In recent years, a variety of devices (drug-eluting stents, artificial organs, biosensors, catheters, scaffolds for tissue engineering, heart valves, etc.) have been developed for implantation into patients. However, when such devices are implanted into the body, the body can react to these in a number of different ways. These reactions can result in an unexpected risk for patients. Therefore, it is important to assess and optimize the biocompatibility of implantable devices. To date, numerous strategies have been investigated to overcome body reactions induced by the implantation of devices. This review focuses on the foreign body response and the approaches that have been taken to overcome this. The biological response following device implantation and the methods for biocompatibility evaluation are summarized. Then the risks of implantable devices and the challenges to overcome these problems are introduced. Specifically, the challenges used to overcome the functional loss of glucose sensors, restenosis after stent implantation, and calcification induced by implantable devices are discussed.
Comparative Structural and Functional Studies of 4-(Thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile CDK9 Inhibitors Suggest the Basis for Isotype Selectivity (2012)

Cyclin-dependent kinase 9/cyclin T, the protein kinase heterodimer that constitutes positive transcription elongation factor b, is a well-validated target for treatment of several diseases, including cancer and cardiac hypertrophy. In order to aid inhibitor design and rationalize the basis for CDK9 selectivity, we have studied the CDK-binding properties of six different members of a 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile series that bind to both CDK9/cyclin T and CDK2/cyclin A. We find that for a given CDK, the melting temperature of a CDK/cyclin/inhibitor complex correlates well with inhibitor potency, suggesting that differential scanning fluorimetry (DSF) is a useful orthogonal measure of inhibitory activity for this series. We have used DSF to demonstrate that the binding of these compounds is independent of the presence or absence of the C-terminal tail region of CDK9, unlike the binding of the CDK9-selective inhibitor 5,6-dichlorobenzimidazone-1-β-d-ribofuranoside (DRB). Finally, on the basis of 11 cocrystal structures bound to CDK9/cyclin T or CDK2/cyclin A, we conclude that selective inhibition of CDK9/cyclin T by members of the 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile series results from the relative malleability of the CDK9 active site rather than from the formation of specific polar contacts.
Identification of Structural Domains Involved in Astrovirus Capsid Biology (2005)

Coat proteins of non-enveloped, icosahedral viruses must perform a variety of functions during their life cycle such as assembly of the coat protein subunits into a closed shell, specific encapsidation of the viral nucleic acid, maturation of the capsid, interaction with host receptors, and disassembly to deliver the genetic information into the newly infected cell. A thorough understanding of the multiple capsid properties at the molecular level is required in order to identify potential targets for antiviral therapy and the prevention of viral disease. The system we have chosen for study is the astrovirus, a family of icosahedral, single-stranded RNA viruses that cause disease in mammals and birds. Very little is known about what regions of the coat protein contribute to the diverse capsid functions. This review will present novel structural predictions for the coat protein sequence of different astrovirus family members. Based on these predictions, we hypothesize that the assembly and RNA packaging functions of the astrovirus coat protein constitutes an individual domain distinct from the determinants required for receptor binding and internalization. Information derived from these structural predictions will serve as an important tool in designing experiments to understand astrovirus biology.
Challenges for Capillary Self-Assembly of Microsystems (2010)

Within the currently rising trend of heterogeneous microsystem integration and packaging, capillary self-assembly emerges as an innovative technique to enhance, complement and eventually replace pick-and-place assembly. Vast literature and experimental data support such claim. Still, the technique needs to overcome some important limitations in order to fully express its potential and earn wide industrial recognition. In this paper, we review and illustrate what are in our opinion the challenges ahead for making part-to-substrate capillary self-assembly reliable and seriously competitive with long-established assembly techniques. After setting self-assembly methods in the context of microsystem assembly and integration technologies, we focus on the standard embodiment of capillary self-assembly, and we describe in details the main, often novel technological steps required for its effective and reproducible performance. This preludes to an outline of what are presently, in our view, the major failure modes affecting the overall yield of the capillary self-assembly technique. Consequently, we propose solutions to face and overcome these challenges, which need to be met to foster the success of this technique.
Cytokines (IFNs, TNF-alpha, IL-2 and IL-12) and animal models of cancer. (1999)

Cytokines are a complex family of mediators that influence many aspects of tumour cell biology. Whether they are used as a therapy or produced locally during the process of tumorigenesis, they are able to act on tumour cells, on the tumour stroma and on the host itself. Animal models have played key roles in optimizing doses and schedules, and have been useful in determining net effects in the tissue microenvironment. Whilst early studies used xenogeneic and syngeneic systems, more recently gene and protein delivery systems have been used to introduce ectopically expressed high and continuous levels of cytokines. This review will discuss the application of some animal model systems that have been investigated to further understand the role cytokines play in cancer, and will concentrate on those cytokines for which there are the most experimental animal model data.
Repair of alkylated DNA in Escherichia coli. Physical properties of O6-methylguanine-DNA methyltransferase. (1982)

An inducible methyltransferase of Escherichia coli acts on O6-methylguanine in DNA by conveying the methyl group to one of its own cysteine residues. The protein has now been purified to apparent homogeneity from a constitutively expressing strain. The homogeneous methyltransferase exhibits no DNA glycosylase or endonuclease activity on alkylated DNA. Further, the methyltransferase activity is strikingly resistant to heat inactivation under reducing conditions. The protein has Mr = 18,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, while the sedimentation coefficient and Stokes radius of the native enzyme yield Mr = 18,400. The amino acid composition of the purified protein shows 4 to 5 cysteine residues/transferase molecule. The methylated, inactive form of the transferase has an unaltered molecular weight.
A fast algorithm for reduced-complexity programmable DSP implementation of the IFFT/FFT in DMT systems (2002)

The discrete multitone (DMT) modulation/demodulation scheme is the standard transmission technique in the application of asymmetric digital subscriber lines (ADSL). Although the DMT can achieve higher data rate compared with other modulation/demodulation schemes, its computational complexity is too high for cost-efficient implementations. For example, it requires 512-point IFFT/FFT as the modulation/demodulation kernel. The large block size results in a heavy computational load in running programmable digital signal processors (DSPs). We derive a computationally efficient fast algorithm for the IFFT/FFT. The proposed algorithm requires a minimum number of multiplication operations compared with existing approaches. Also, it can avoid complex-domain operations that are inevitable in conventional IFFT/FFT computation. The resulting software function requires less MIPS count. Hence, it is very suitable for DSP-based DMT implementation. The proposed algorithm can also be applied to the technology of orthogonal frequency division multiplexing (OFDM) which is the processing kernel of the digital audio/video broadcasting (DAB/DVB) systems.
Topology and Active Site of PlsY (2007)

The most widely distributed biosynthetic pathway to initiate phosphatidic acid formation in bacterial membrane phospholipid biosynthesis involves the conversion of acyl-acyl carrier protein to acylphosphate by PlsX and the transfer of the acyl group from acylphosphate to glycerol 3-phosphate by an integral membrane protein, PlsY. The membrane topology of Streptococcus pneumoniae PlsY was determined using the substituted cysteine accessibility method. PlsY has five membrane-spanning segments with the amino terminus and two short loops located on the external face of the membrane. Each of the three larger cytoplasmic domains contains a highly conserved sequence motif. Site-directed mutagenesis revealed that each conserved domain was critical for PlsY catalysis. Motif 1 had an essential serine and arginine residue. Motif 2 had the characteristics of a phosphate-binding loop. Mutations of the conserved glycines in motif 2 to alanines resulted in a Km defect for glycerol 3-phosphate binding leading to the conclusion that this motif corresponded to the glycerol 3-phosphate binding site. Motif 3 contained a conserved histidine and asparagine that were important for activity and a glutamate that was critical to the structural integrity of PlsY. PlsY was noncompetitively inhibited by palmitoyl-CoA. These data define the membrane architecture and the critical active site residues in the PlsY family of bacterial acyltransferases.
Emergence of resistance as a consequence of antimicrobial prophylaxis in immunocompromised patients. (1986)

Many authors in the literature have investigated the use of antibiotics in prophylaxis against infections in granulocytopenic patients. Two general methods have been used: one consists in trying to decontaminate the digestive tract in the hope of reducing the amount of microorganisms responsible for systemic infections. Another method is to use well-absorbed oral antibiotics, like trimethoprim-sulphamethoxazole, throughout the neutropenic period. It is considered critical to preserve as much as possible of the anaerobic flora, which is believed to provide protection against colonization by aerobic microorganisms or by fungi. Experimental and clinical evidence for this is critically reviewed. The efficacy of such methods has been variable, but there is also widespread fears that they could enhance selection of resistant organisms. We have reviewed the literature, specifically looking for data on the emergence of such resistant organisms, as well as data on changes in bacterial and fungal faecal flora.
Subchronic Stimulation Performance of Transverse Intrafascicular Multichannel Electrodes in the Median Nerve of the Göttingen Minipig (2014)

Abstract This work evaluated the subchronic stimulation performance of an intraneural multichannel electrode (transverse intrafascicular multichannel electrode, TIME ) in a large human‐sized nerve. One or two TIME s were implanted in the right median nerve above the elbow joint in four pigs for a period of 32 to 37 days (six TIME s in total). The ability of the contact sites to recruit five muscles in the forelimb was assessed via their evoked electromyographic responses. Based on these responses, a selectivity index was defined. Four TIME s were able to selectively recruit a subset of muscles throughout the implantation period. The required recruitment current significantly increased, while there was a tendency for the recruitment selectivity to decrease over time. Histological assessment showed that all TIME s remained inside the nerve and that they were located between fascicles. The average thickness of the encapsulation of the electrode was estimated to be 115.4 ± 51.5 μm (mean ± SD ). This study demonstrates the feasibility of keeping the TIME electrodes fixed and functional inside a large polyfascicular human‐sized nerve in a subchronic setting.
Room-temperature lasing operation of a quantum-dot vertical-cavity surface-emitting laser (1996)

Self-assembled growth of quantum dots by molecular-beam epitaxy is used to form the active region of a vertical-cavity surface-emitting laser (VCSEL). Ten layers of InGaAs quantum dots are stacked in order to increase the gain. This quantum-dot VCSEL has a continuous-wave operating current of 32 mA at room temperature. Emission spectra at various current injections demonstrate that the lasing action is associated with a higher-order transition in the quantum dots.
Expanding the Catalytic Repertoire of Nucleic Acid Catalysts: Simultaneous Incorporation of Two Modified Deoxyribonucleoside Triphosphates Bearing Ammonium and Imidazolyl Functionalities (1999)

Two nucleoside triphosphates, a pyrimidine modified with an ammonium functionality and a purine modified with an imidazolyl functionality are compatible with all conditions for a combinatorial selection of nucleic-acid catalysts. We believe that this work is the first to demonstrate the potential for using not one but two modified nucleotides in tandem. The potential for an enriched catalytic repertoire is envisioned.
Intrauterine Transmission of Cytomegalovirus to Infants of Women with Preconceptional Immunity (2001)

In women who are seropositive for CMV, reinfection with a different strain of CMV can lead to intrauterine transmission and symptomatic congenital infection.
The Putative Glutamate Receptors from Plants Are Related to Two Superfamilies of Animal Neurotransmitter Receptors via Distinct Evolutionary Mechanisms (2001)

Animal ionotropic glutamate receptors (iGLRs) and members of subfamily C (Kolakowski 1994) or IV
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-Å resolution (2000)

The crystal structure of Escherichia coli ribosomal protein L25 bound to an 18-base pair portion of 5S ribosomal RNA, which contains "loop E," has been determined at 1.8-A resolution. The protein primarily recognizes a unique RNA shape, although five side chains make direct or water-mediated interactions with bases. Three beta-strands lie in the widened minor groove of loop E formed by noncanonical base pairs and cross-strand purine stacks, and an alpha-helix interacts in an adjacent widened major groove. The structure of loop E is largely the same as that of uncomplexed RNA (rms deviation of 0.4 A for 11 base pairs), and 3 Mg(2+) ions that stabilize the noncanonical base pairs lie in the same or similar locations in both structures. Perhaps surprisingly, those residues interacting with the RNA backbone are the most conserved among known L25 sequences, whereas those interacting with the bases are not.