gebhart/patrepeval huggingface dataset:
Chirality of Peptide Bond-Forming Condensation Domains in Nonribosomal Peptide Synthetases:  The C<sub>5</sub> Domain of Tyrocidine Synthetase Is a <sup>D</sup>C<sub>L</sub> Catalyst (2003)

Nonribosomal peptides (NRP) such as the antibiotic tyrocidine have D-amino acids, introduced by epimerase (E) domains embedded within modules of the enzymatic assembly lines. We predict that the peptide bond-forming condensation (C) domains immediately downstream of E domains are D-specific for the peptidyl donor and L-specific for the aminoacyl acceptor ((D)C(L)). To validate this prediction and establish that the C(5) domain of tyrocidine synthetase is indeed (D)C(L), the apoT (thiolation) forms of module 4 (TycB(3) AT(4)E) and module 5 (TycC(1) C(5)AT(5)) were expressed. T(5) was posttranslationally primed with CoASH to introduce the HS-pantetheinyl group and autoaminoacylated with radiolabeled L-Asn* or L-Asp*. Alternate donor substrates were introduced by priming apo AT(4)E with synthetically prepared tetrapeptidyl-CoA's differing in the chirality of Phe-4, D-Phe-L-Pro-L-Phe-L-Phe-CoA, and D-Phe-L-Pro-L-Phe-D-Phe-CoA. The tetrapeptidyl-S-T(4) and L-Asp-S-T(5) were studied for peptide bond formation and chain translocation by C(5) to yield pentapeptidyl-S-T(5), whose chirality (D-L-L-D-L- vs D-L-L-L-L-) was assayed by thioester cleavage and chiral chromatography of the released pentapeptides. Only the D-Phe-4 pentapeptidyl-S-T(5) was generated, implying that only D-L-L-D-S-T(4) was utilized, proving C(5) is indeed a (D)C(L) catalyst. Furthermore, a mutant with an inactive E domain transferred tetrapeptide only when loaded with D-Phe-4 tetrapeptidyl donor, not L-Phe-4, confirming that in the wild-type assembly line C(5) only transfers D-L-L-L-tetrapeptidyl-S-T(4) after in situ epimerization by the E domain. These results contrast the observation that C(5) can make both L-Phe-L-Asn and D-Phe-L-Asn when assayed with Phe as the donor substrate. Hence, utilizing an aminoacyl-S-T(4) versus the natural peptidyl-S-T(4) donor produced misleading information regarding the specificity of the condensation domain.
Analyzing differences between Internet information system software architectures (2002)

The history of software development is a steady progression of complexity. In response to increasingly complex software, software engineers have provided ever higher levels of abstraction with which to design, code, and analyze systems. The next logical step in this progression is to consider systems at the level of their architecture. We present a scenario-based method for analyzing systems based on their software architecture. We demonstrate this method, the software architecture analysis method (SAAM), by applying it to Internet information systems. The greatest benefits of such an analysis are people and process-oriented: it encourages communication both within a development team and between the team and customers, and it promotes a common understanding of design goals and mechanisms. Because this analysis can be done at low cost and early in the software life cycle, its benefits are enormous.
Polyelectrolyte Multilayers Impart Healability to Highly Electrically Conductive Films (2012)

Healable, electrically conductive films are fabricated by depositing Ag nanowires on water-enabled healable polyelectrolyte multilayers. The easily achieved healability of the polyelectrolyte multilayers is successfully imparted to the Ag nanowire layer. These films conveniently restore electrical conductivity lost as a result of damage by cuts several tens of micrometers wide when water is dropped on the cuts.
Comparison of Generic Fluorescent Markers for Detection of Extracellular Vesicles by Flow Cytometry (2018)

None of the generic markers detected all and only EVs in plasma. Side scatter triggering detected the highest concentration of plasma EVs on our A60-Micro, followed by lactadherin. The choice between scatter or lactadherin primarily depends on the analytical sensitivity of the flow cytometer used.
Androgens alter T-cell immunity by inhibiting T-helper 1 differentiation (2014)

The hormonal milieu influences immune tolerance and the immune response against viruses and cancer, but the direct effect of androgens on cellular immunity remains largely uncharacterized. We therefore sought to evaluate the effect of androgens on murine and human T cells in vivo and in vitro. We found that murine androgen deprivation in vivo elicited RNA expression patterns conducive to IFN signaling and T-cell differentiation. Interrogation of mechanism showed that testosterone regulates T-helper 1 (Th1) differentiation by inhibiting IL-12-induced Stat4 phosphorylation: in murine models, we determined that androgen receptor binds a conserved region within the phosphatase, Ptpn1, and consequent up-regulation of Ptpn1 then inhibits IL-12 signaling in CD4 T cells. The clinical relevance of this mechanism, whereby the androgen milieu modulates CD4 T-cell differentiation, was ascertained as we found that androgen deprivation reduced expression of Ptpn1 in CD4 cells from patients undergoing androgen deprivation therapy for prostate cancer. Our findings, which demonstrate a clinically relevant mechanism by which androgens inhibit Th1 differentiation of CD4 T cells, provide rationale for targeting androgens to enhance CD4-mediated immune responses in cancer or, conversely, for modulating androgens to mitigate CD4 responses in disorders of autoimmunity.
Bioactive Compounds from the Gorgonian <i>Briareum </i><i>polyanthes</i>. Correction of the Structures of Four Asbestinane-Type Diterpenes (2006)

Our extended chemical investigation of the crude MeOH-CHCl3 extract of the gorgonian octocoral Briareum polyanthes from Puerto Rico has led to the isolation of three eunicellin-type diterpenoids, 1-3, along with five (4-8) diterpenoids of the asbestinane-type and one (9) of the briarane-type of polycyclized diterpenes. The structures and relative stereochemistry of the new compounds 1-9 were established on the basis of spectroscopic analysis (1H NMR, 13C NMR, HMQC, HMBC, NOESY). The biological activity of these compounds against pathogenic microbes responsible for various human infectious diseases was investigated. In addition, new data recorded for four known asbestinin diterpenes also isolated during this investigation and further analysis through chemical reactions have prompted us to revise our original structural assignments for these compounds.
Muscular Atrophy in the Hemiplegic Thigh in Patients After Stroke (2003)

Muscle volume decreases in the hemiplegic side in stroke patients.
An evaluation of speculative instruction execution on simultaneous multithreaded processors (2003)

Modern superscalar processors rely heavily on speculative execution for performance. For example, our measurements show that on a 6-issue superscalar, 93% of committed instructions for SPECINT95 are speculative. Without speculation, processor resources on such machines would be largely idle. In contrast to superscalars, simultaneous multithreaded (SMT) processors achieve high resource utilization by issuing instructions from multiple threads every cycle. An SMT processor thus has two means of hiding latency: speculation and multithreaded execution. However, these two techniques may conflict; on an SMT processor, wrong-path speculative instructions from one thread may compete with and displace useful instructions from another thread. For this reason, it is important to understand the trade-offs between these two latency-hiding techniques, and to ask whether multithreaded processors should speculate differently than conventional superscalars.This paper evaluates the behavior of instruction speculation on SMT processors using both multiprogrammed (SPECINT and SPECFP) and multithreaded (the Apache Web server) workloads. We measure and analyze the impact of speculation and demonstrate how speculation on an 8-context SMT differs from superscalar speculation. We also examine the effect of speculation-aware fetch and branch prediction policies in the processor. Our results quantify the extent to which (1) speculation is critical to performance on a multithreaded processor because it ensures an ample supply of parallelism to feed the functional units, and (2) SMT actually enhances the effectiveness of speculative execution, compared to a superscalar processor by reducing the impact of branch misprediction. Finally, we quantify the impact of both hardware configuration and workload characteristics on speculation's usefulness and demonstrate that, in nearly all cases, speculation is beneficial to SMT performance.
Test generation for sequential circuits using parallel fault simulation with random inputs (1995)

Abstract This paper presents a simple test generation method for sequential circuits using a parallelesimulator with random inputs. The proposed test generation method generates sequences by simulating as many states as possible, without using a cost function for a target fault. To generate effective test sequences, dynamic switching is done between I‐Mode and S‐Mode parallel simulators. Here the I‐Mode simulates 32 patterns for one state in parallel and the S‐Mode simulates 32 patterns for 32 states in parallel. Experimental results for ISCAS'89 benchmark sequential circuits show that our method achieves test sequences with high coverage in acceptable CPU time.
Inactivation of <i>Listeria monocytogenes</i> using Water Bath Heat Treatment in Vacuum Packed Ricotta Salata Cheese Wedges (2015)

Abstract Ricotta salata cheese is frequently contaminated on the surface with Listeria monocytogenes . Water bath heat treatment in vacuum packed whole ricotta salata cheese wheels demonstrated to be effective in inactivating L. monocytogenes . However, the risk of cross‐contamination in ricotta salata wedges is increased during cheese cutting. Therefore, the effectiveness of heat treatment in ricotta salata wedges has to be demonstrated conducting a new validation study. In this study, 9 different time temperature combinations, 75, 85, and 90 °C applied for 10, 20, and 30 min each, were tested on artificially contaminated ricotta salata cheese wedges. The extent of the lethal effect on L. monocytogenes was assessed 1 and 30 d after the application of the hot water bath treatment. Five of 9 combinations, 75 °C for 30 min, 85 °C for 20, and 30 min, and 90°C for 20 and 30 min, demonstrated to meet the process criteria of at least 5 log reduction. Sensory analyses were also conducted in order to account for the potential impact on sensory features of ricotta salata wedges, which showed no significant differences between treatments.
Product accumulate codes: properties and performance (2002)

A new class of codes, named product accumulate codes, which are the concatenation of an outer product code and an inner rate-1 differential encoder (or accumulator) is proposed. We show that these codes can perform within a few tenths of a dB from the Shannon limit for rates/spl ges/1/2. For practical block lengths, these codes provide similar performance to turbo codes but with significantly lower decoding complexity.
Aspergillosis (2001)

An increasing number of immunocompromised patients are contracting opportunistic infections caused by Aspergillus, resulting in a significant rise in morbidity and mortality. Difficult to diagnose and to treat, aspergillosis may be fatal.
Online Route Prediction for Automotive Applications (2006)

An information and communication technology infrastructure is rapidly emerging that enables the delivery of location-based services to vast numbers of mobile users. Services will benefit from being aware of not only the user’s location, but also the user’s current destination and route towards the destination. This paper describes a component that enables the use of geocontext. Using GPS data, the component gathers a driver’s routes and associates them with usage meta-data. Other services may then provide the component with a driver ID, the time of the day, and a location, in return obtaining the likely routes for the driver.
A Pharmacological Paradigm for Urinary Incontinence and Enuresis (1984)

The qualitative aspects of drugs used in enuresis control or associated with enuresis or urinary incontinence and the pathological disorders associated with enuresis or urinary incontinence are reviewed. The literature to date does not clarify the factors that account for tricyclic antidepressant effectiveness in enuresis. However, it does reveal that enuresis and urinary incontinence are common symptoms of basal ganglion disorders. Furthermore, pharmacological agents that depress or block dopamine activity produce urinary incontinence or enuresis, while those drugs augmenting the noradrenergic system facilitate continence. It is postulated that urinary incontinence and enuresis are secondary to an imbalance of catecholamine neurotransmitters within basal ganglion structures. A hypothesis is proposed suggesting that dopamine agonists could be viable therapeutic alternatives to tricyclics in treating enuresis and urinary incontinence. Additional clinical drug trials are needed to assess the characteristic responses of specific catecholamine agents in urinary incontinence and enuresis.
Itch WW Domains Inhibit Its E3 Ubiquitin Ligase Activity by Blocking E2-E3 Ligase Trans-thiolation (2015)

Nedd4-family E3 ubiquitin ligases regulate an array of biologic processes. Autoinhibition maintains these catalytic ligases in an inactive state through several mechanisms. However, although some Nedd4 family members are activated by binding to Nedd4 family-interacting proteins (Ndfips), how binding activates E3 function remains unclear. Our data reveal how these two regulatory processes are linked functionally. In the absence of Ndfip1, the Nedd4 family member Itch can bind an E2 but cannot accept ubiquitin onto its catalytic cysteine. This is because Itch is autoinhibited by an intramolecular interaction between its HECT (homologous to the E6-AP carboxy terminus domain) and two central WW domains. Ndfip1 binds these WW domains to release the HECT, allowing trans-thiolation and Itch catalytic activity. This molecular switch also regulates the closely related family member WWP2. Importantly, multiple PY motifs are required for Ndfip1 to activate Itch, functionally distinguishing Ndfips from single PY-containing substrates. These data establish a novel mechanism for control of the function of a subfamily of Nedd4 E3 ligases at the level of E2-E3 trans-thiolation.
Extensions: Extrapolation Methods for CAD (2000)

Many operations within a solid modeling application, notably applying thickness (shelling) or blending edges (filleting,encounter difficulties during topology resolution. In order to create a solid object, certain faces have to be intersected but the geometry is such that no intersection curve can be computed. The solution is to 'extend' one or both faces. This means that one has to extrapolate the underlying curves or surfaces. This operation causes instability since extrapolation is inherently an unstable process. An additional difficulty is the selection of a strategy to compute the extension amount. Furthermore, there are additional restrictions relating to continuity across the extension boundary. In this paper I will illustrate by examples some modeling situations where extensions are necessary. I present the methods currently used, and illustrate their advantages and disadvantages. Subsequently, I will demonstrate a solution for primitives such as cylinders, cones, spheres and tori. I will conclude by suggesting approaches which could avoid some of the current pitfalls.
Distinct Subsets of Somatostatin Receptors on Cultured Human Lymphocytes (1989)

Somatostatin (SOM) is a neuroendocrine tetradecapeptide that suppresses specific functions of differentiated T-cells and antibody-producing cells. The Jurkat line of human leukemic T-cells and U266 IgE-producing human myeloma cells bound [I-Tyr11]SOM specifically. The maximal level of specific binding was attained by 1-2 h at 22 degrees C for both types of cells and reversed by 70-85% within 2-3 h after the addition of excess nonradioactive SOM. Computer-assisted Scatchard analysis of the competition curves revealed two classes of binding sites for both cells. An average of 144 and 1295 high affinity receptors per Jurkat and U266 cells had a Kd value of 3 pM and 5 pM, respectively, whereas a large number of low affinity sites had Kd values of 66 nM and 100 nM. The affinity of the analogs somatostatin 28, [I-Tyr11]SOM, and [D-Trp8, D-Cys14]SOM for Jurkat and U266 cell lines, relative to SOM, suggested a degree of specificity similar to receptors on neuroendocrine cells.
Gaze tracking system at a distance for controlling IPTV (2010)

Gaze tracking is used for detecting the position that a user is looking at. In this research, a new gaze-tracking system and method are proposed to control a large-screen TV at a distance. This research is novel in the following four ways as compared to previous work: First, this is the first system for gaze tracking on a large-screen TV at a distance. Second, in order to increase convenience, the user's eye is captured by a remote gaze-tracking camera not requiring a user to wear any device. Third, without the complicated calibrations among the screen, the camera and the eye coordinates, the gaze position on the TV screen is obtained by using a simple 2D method based on a geometric transform with pupil center and four cornea specular reflections. Fourth, by using a near-infrared (NIR) passing filter on the camera and NIR illuminators, the pupil region becomes distinctive in the input image irrespective of the change in the environmental visible light. Experimental results showed that the proposed system could be used as a new interface for controlling a TV with a 60-inch-wide screen (16:9).
Isostructural Series of Nine-Coordinate Chiral Lanthanide Complexes Based on Triazacyclononane (2012)

Nonadentate ligands based on triazacyclononane incorporating pyridyl-2-phosphinate groups form an isostructural series of complexes with Ln ions in the solid state and in solution. The Ln ion is effectively shielded from the solvent environment. Crystal structures reveal a rigid C(3)-symmetric tricapped trigonal-prismatic coordination geometry that is maintained in solution for the methyl and phenylphosphinate series, as shown by multinuclear NMR analysis. Variable-temperature measurements of the field dependence of the water proton relaxivity in gadolinium complexes indicate that these systems exclude solvent from the primary coordination environment and minimize the second sphere of solvation. The electronic relaxation time for the gadolinium methylphosphinate complex has been estimated to be 550 (±150) ps by EPR and NMR methods, compared to values of around 0.30-0.05 ps for the terbium-ytterbium series, deduced by analyzing the field dependence (4.7-16.5 T) of the (31)P NMR longitudinal relaxation times. Values are compared with analogous azacarboxylate ligand complexes, supporting a key role for donor atom polarizability in determining the electronic relaxation. Spectral emission behavior in solution of samarium, europium, terbium, and dysprosium complexes is compared, and the resolved RRR-Λ and SSS-Δ complexes show strong circularly polarized luminescence. The molecular quadratic hyperpolarizability 〈β(HLS)〉 has been measured in solution using hyper-Raleigh light-scattering methods, for the whole series of lanthanide complexes of one ligand. The values of 〈β(HLS)〉 reach a maximum around the center of the series and are not simply dependent on the number of f electrons, suggesting a dominant contribution from the octupolar rather than the dipolar term.
Effective vortex mass from microscopic theory (2005)

We calculate the effective mass of a single quantized vortex in the Bardeen--Cooper--Schrieffer superconductor at finite temperature. Based on effective action approach, we arrive at the effective mass of a vortex as integral of the spectral function $J(\ensuremath{\omega})$ divided by ${\ensuremath{\omega}}^{3}$ over frequency. The spectral function is given in terms of the quantum-mechanical transition elements of the gradient of the Hamiltonian between two Bogoliubov--deGennes (BdG) eigenstates. Based on self-consistent numerical diagonalization of the BdG equation we find that the effective mass per unit length of vortex at zero temperature is of order $m{({k}_{f}{\ensuremath{\xi}}_{0})}^{2}$ (${k}_{f}=\text{Fermi}$ momentum, ${\ensuremath{\xi}}_{0}=\text{coherence}$ length), essentially equaling the electron mass displaced within the coherence length from the vortex core. Transitions between the core states are responsible for most of the mass. The mass reaches a maximum value at $T\ensuremath{\approx}0.5{T}_{c}$ and decreases continuously to zero at ${T}_{c}$.
Thermochemical bond dissociation energies of carbon–magnesium bonds (1981)

The heats of formation of 29 alkylmagnesium bromides, isobutyl bromide, and neopentyl bromide have been determined, and bond dissociation energies have been derived for the Grignard reagents. For saturated alkyl derivatives the C–Mg bond strength decreases with an increasing number of β-hydrogens in the series methyl, neopentyl, isobutyl, butyl, 1-ethylpropyl, 1-methylpropyl, isopropyl, and t-butyl. Bonding in alkyl bromides and alkylmagnesium bromides is discussed.
Motor Unit Properties and Selective Involvement In Movement (1975)

LABORATORY OF NEURAL CONTROL, NATIONAL INSTITUTE OF NEUROLOGICAL DISEASES AND STROKE, BETHESDA, MARYLAND BRAIN RESEARCH INSTITUTE, UNIVERSITY OF CALIFORNIA, LOS ANGELES, CALIFORNIA
Tautomeric states of the active‐site histidines of phosphorylated and unphosphorylated III<sup>Glc</sup>, a signal‐transducing protein from <i>escherichia coli</i>, using two‐dimensional heteronuclear NMR techniques (1993)

IIIGlc is an 18.1-kDa signal-transducing phosphocarrier protein of the phosphoenolpyruvate:glycose phosphotransferase system from Escherichia coli. The 1H, 15N, and 13C histidine ring NMR signals of both the phosphorylated and unphosphorylated forms of IIIGlc have been assigned using two-dimensional 1H-15N and 1H-13C heteronuclear multiple-quantum coherence (HMQC) experiments and a two-dimensional 13C-13C-1H correlation spectroscopy via JCC coupling experiment. The data were acquired on uniformly 15N-labeled and uniformly 15N/13C-labeled protein samples. The experiments rely on one-bond and two-bond J couplings that allowed for assignment of the signals without the need for the analysis of through-space (nuclear Overhauser effect spectroscopy) correlations. The 15N and 13C chemical shifts were used to determine that His-75 exists predominantly in the N epsilon 2-H tautomeric state in both the phosphorylated and unphosphorylated forms of IIIGlc, and that His-90 exists primarily in the N delta 1-H state in the unphosphorylated protein. Upon phosphorylation of the N epsilon 2 nitrogen of His-90, the N delta 1 nitrogen remains protonated, resulting in the formation of a charged phospho-His-90 moiety. The 1H, 15N, and 13C signals of the phosphorylated and unphosphorylated proteins showed only minor shifts in the pH range from 6.0 to 9.0. These data indicate that the pK alpha values for both His-75 and His-90 in IIIGlc and His-75 in phospho-IIIGlc are less than 5.0, and that the pK alpha value for phospho-His-90 is greater than 10. The results are presented in relation to previously obtained structural data on IIIGlc, and implications for proposed mechanisms of phosphoryl transfer are discussed.
The skiving stock problem as a counterpart of the cutting stock problem (2003)

Abstract The cutting stock problem (CSP) is a particular case of the set‐covering problem. Similarly we introduce another class of combinatorial optimization problems called the skiving stock problem (SSP) as a particular case of the set‐packing problem. The SSP shares many properties and solving techniques with the CSP. When these two problem spaces are contrasted they illuminate one another in that they form a ‘dual’ relationship where techniques once thought to be applicable in one domain can be applied in the other. Furthermore the SSP, like the CSP, may have numerous applications in business and industry.