gebhart/patrepeval huggingface dataset:
Enzymatic properties, evidence for in vivo expression, and intracellular localization of shewasin D, the pepsin homolog from Shewanella denitrificans (2016)

Abstract The widespread presence of pepsin-like enzymes in eukaryotes together with their relevance in the control of multiple biological processes is reflected in the large number of studies published so far for this family of enzymes. By contrast, pepsin homologs from bacteria have only recently started to be characterized. The work with recombinant shewasin A from Shewanella amazonensis provided the first documentation of this activity in prokaryotes. Here we extend our studies to shewasin D, the pepsin homolog from Shewanella denitrificans , to gain further insight into this group of bacterial peptidases that likely represent ancestral versions of modern eukaryotic pepsin-like enzymes. We demonstrate that the enzymatic properties of recombinant shewasin D are strongly reminiscent of eukaryotic pepsin homologues. We determined the specificity preferences of both shewasin D and shewasin A using proteome-derived peptide libraries and observed remarkable similarities between both shewasins and eukaryotic pepsins, in particular with BACE-1, thereby confirming their phylogenetic proximity. Moreover, we provide first evidence of expression of active shewasin D in S. denitrificans cells, confirming its activity at acidic pH and inhibition by pepstatin. Finally, our results revealed an unprecedented localization for a family A1 member by demonstrating that native shewasin D accumulates preferentially in the cytoplasm.
From Basic Science to Blockbuster Drug: The Discovery of Lyrica (2008)

The anticonvulsant drug (S)-(+)-3-isobutyl-γ-aminobutyric acid ((S)-(+)-3-isobutyl-GABA, Lyrica; see structure) was developed from a study of fundamental science, which took an unexpected course. The activity of Lyrica was found to be unrelated to the originally anticipated activation of L-glutamic acid decarboxylase and the increase in the inhibitory neurotransmitter GABA; instead, it antagonizes a calcium ion channel, which inhibits the release of the excitatory neurotransmitter L-glutamate. The ultimate effect, however, is the same.
Synthesis of a novel polyester building block from pentoses by tin-containing silicates (2017)

C<sub>5</sub>-Sugars form a new bio-monomer (<italic>trans</italic>-2,5-dihydroxy-3-pentenoic acid methyl ester), which can undergo enzymatic copolymerization with E6-HH to form multifunctional polymers.
Multi-Objective Tradeoffs in the Design Optimization of a Brushless Permanent-Magnet Machine With Fractional-Slot Concentrated Windings (2014)

In this paper, a robust parametric model of a brushless permanent magnet machine with fractional-slot concentrated windings, which was developed for automated design optimization is presented. A computationally efficient finite-element analysis method was employed to estimate the dq-axes inductances, the induced voltage and torque ripple waveforms, and losses of the machine. A method for minimum effort calculation of the torque angle corresponding to the maximum torque per ampere load condition was developed. A differential evolution algorithm was implemented for the global design optimization with two concurrent objectives of minimum losses and minimum material cost. An engineering decision process based on the Pareto-optimal front for 3,500 candidate designs is presented together with discussions on the tradeoffs between cost and performance. One optimal design was finally selected, prototyped and successfully tested.
Expression of Class I and Class II Major Histocompatibility Complex (MHC) Antigens in Renal Cell Carcinoma (RCC) (1987)

No AccessJournal of Urology1 Jun 1987Expression of Class I and Class II Major Histocompatibility Complex (MHC) Antigens in Renal Cell Carcinoma (RCC) Joel Sheinfeld, Carlos Cordon-Cardo, Victor Reuter, Helen Lim, and Neil Bander Joel SheinfeldJoel Sheinfeld More articles by this author , Carlos Cordon-CardoCarlos Cordon-Cardo More articles by this author , Victor ReuterVictor Reuter More articles by this author , Helen LimHelen Lim More articles by this author , and Neil BanderNeil Bander More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)75958-7AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Expression of Class I and Class II Major Histocompatibility Complex (MHC) Antigens in Renal Cell Carcinoma (RCC)." The Journal of Urology, 137(6), p. 306A © 1987 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 137Issue 6June 1987Page: 306A Advertisement Copyright & Permissions© 1987 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Joel Sheinfeld More articles by this author Carlos Cordon-Cardo More articles by this author Victor Reuter More articles by this author Helen Lim More articles by this author Neil Bander More articles by this author Expand All Advertisement Loading ...
MICROFLUIDIC SINGLE-MOLECULE NUCLEASE DIGESTION REVEALS RATE-ENHANCING OFF-AND-ON MOLECULAR ENCOUNTERING FUNCTION FOR SITE-SPECIFIC DNA BREAK (2013)

An intermittent molecular encounter leading to a site-specific DNA-break was unveiled under a limited protein’s sliding-free condition. It reflects a transient molecular action by which the reaction rate and efficiency of restriction enzyme in bacterial cells is enhanced. This was experimentally verified for the first time in the world by using our microfluidic device.
Pressure-Induced Octahedral Rotation in RbMn[Fe(CN)6] (2008)

Hydrostatic pressure effect on Prussian blue type network in RbMn[Fe(CN) 6 ] has been investigated by high-pressure vibrational spectroscopy. Frequencies of the CN stretching modes increase as pressure increases: \(\mathrm{d}\hbar\omega/\mathrm{d}P = 6.4\) cm -1 /GPa for A 1g mode and 4.3 cm -1 /GPa for E g mode. With further increase of pressure beyond ≈2 GPa, slope of the \(\hbar\omega\)– P curve becomes fairly gradual. We ascribed the behavior to the in-plane rotation of FeC 6 /MnN 6 octahedra, since it compensates the pressure-induced contraction in volume.
Secure Communications Using Quantum Cryptography (1997)

The secure distribution of the secret random bit sequences known as &amp;quot;key&amp;quot; material, is an essential precursor to their use for the encryption and decryption of confidential communications. Quantum cryptography is an emerging technology for secure key distribution with single-photon transmissions: Heisenberg&amp;apos;s uncertainty principle ensures that an adversary can neither successfully tap the key transmissions, nor evade detection (eavesdropping raises the key error rate above a threshold value). We have developed experimental quantum cryptography systems based on the transmission of non-orthogonal single-photon states to generate shared key material over multi-kilometer optical fiber paths and over line-of-sight links. In both cases, key material is built up using the transmission of a single-photon per bit of an initial secret random sequence. A quantum-mechanically random subset of this sequence is identified, becoming the key material after a data reconciliation stage with the sender. ...
Fracture of Glass/Poly(vinyl butyral) (Butacite®) Laminates in Biaxial Flexure (1999)

Glass‐polymer laminates designed as safety glazing for automotive and architectural applications demonstrate a rich variety of deformation and failure modes due to the complex stress fields developed on loading and the statistical nature of glass fracture. This complexity in stress development results from the large modulus mismatch between float glass and typical polymers used in safety glazing ( E glass / E polymer similar/congruent 10 3 ‐10 5 ). We investigate stress development and the sequence of glass‐ply fracture in model two‐ply glass‐poly(vinyl butyral) (PVB; Butacite®) laminates during loading in biaxial flexure using a circular (upper) punch on three‐point (lower) support. The experiment is analyzed using a three‐dimensional finite‐element model with a viscoelastic constitutive model of plasticized PVB deformation. Our stress analysis shows that the maximum biaxial stress shifts location from one glass ply to the other as a function of loading rate and/or temperature and the loading‐support dimensions. We identify two primary modes for the initiation of failure associated with changes in maximum stress location: (1) first crack initiated in upper, ring‐loaded, glass ply (at the internal glass‐polymer interface) and (2) first crack initiated in lower, supported, glass ply (outer glass surface). The sequence of glass ply fracture is seen to depend strongly on loading rate and temperature: high temperatures, relative to the polymer‐glass transition temperature, and/or slow loading rates bias first cracking to the upper ply; low temperatures and/or high loading rates promote lower ply first cracking. We present a method to compute the probability of first cracking by combining our finite‐element‐based stress analysis with a Weibull statistical description of glass fracture. The test protocol and stress analysis presented can form the basis of a laboratory‐scale test for laminates and can be readily extended to describe load‐bearing capacity of laminate plates used in large‐scale commercial applications.
A Synthesis of 1,4-Disubstituted Imidazolidin-2-ones from Fused-Ring Aziridines (2012)

As part of an antibacterial drug discovery project, we were interested in preparing bioisosteric replacement analogues of 4,5-disubstituted oxazolidinones. One such isosteric replacement is the imidazolidinone ring system. Here, we report the development of a general synthesis of 1,4-disubstituted imidazolidinones that takes advantage of the base-catalyzed rearrangement of amino­methyl-substituted oxazolidinones.
Developing a Robust Recombination Contact to Realize Monolithic Perovskite Tandems With Industrially Common p-Type Silicon Solar Cells (2018)

Although two-terminal perovskite-silicon tandem solar cells have rapidly increased in efficiency, they have only been demonstrated with n-type silicon, which currently constitutes less than 5% of the global photovoltaics market. In this paper, we realize the first two-terminal perovskite tandem with p-type silicon by developing a recombination contact that enables voltage addition without damaging either subcell. We find that silicon interband recombination contacts are limited by a SiOx charge-extraction barrier, which forms during oxidative top-cell fabrication. A sputtered 30-nm indium tin oxide layer is found to protect the silicon cell surface from oxidation, while forming a recombination contact with the p-type nickel oxide hole transport layer for the perovskite top cell. Using this recombination contact we achieve voltage addition between the perovskite top cell and aluminum back-surface field p-type silicon bottom cell. We also find that minimizing moisture on the nickel oxide surface is important for achieving a stable open-circuit voltage under illumination. The recombination contact developed herein could play an important role in near-future developments.
Supplementary Data from Adoptive Cellular Therapy with Autologous Tumor-Infiltrating Lymphocytes and T-cell Receptor–Engineered T Cells Targeting Common p53 Neoantigens in Human Solid Tumors (2023)

Supplementary Data from Adoptive Cellular Therapy with Autologous Tumor-Infiltrating Lymphocytes and T-cell Receptor–Engineered T Cells Targeting Common p53 Neoantigens in Human Solid Tumors
Demonstrating the scalability of a molecular dynamics application on a Petaflop computer (2001)

The IBM Blue Gene project has endeavored into the development of a cellular architecture computer with millions of concurrent threads of execution. One of the major challenges of this project is demonstrating that applications can successfully exploit this massive amount of parallelism. Starting from the sequential version of a well known molecular dynamics code, we developed a new application that exploits the multiple levels of parallelism in the Blue Gene cellular architecture. We perform both analytical and simulation studies of the behavior of this application when executed on a very large number of threads. As a result, we demonstrate that this class of applications can execute efficiently on a large cellular machine.
Anti‐virulence appraoches to antimicrobial therapy (2007)

We are currently entering a challenging new era where microbial resistance to antibiotics will complicate the treatment of nearly all common bacterial infections. The ability to develop new antimicrobials has lagged behind the development of resistance for many life‐threatening bacterial species. Novel ways to combat infection and discover new antibiotics will be paramount to winning the war against microbial resistance. One novel approach is to target in vivo essential gene functions such as virulence rather than the conventional approach of targeting gene functions required simply for in vitro viability. In order do so however, it is critical to identify and understand bacterial requirements for the host‐pathogen interaction. While much about bacterial pathogenesis has been elucidated from in vitro studies, it has been far more challenging to study true bacterial behavior during in vivo infection. We are currently developing chemical biological and genomic approaches to allow systematic and comprehensive study of the role of all bacterial genes within the context of the host‐pathogen interaction. Current work focuses on the pathogens Vibrio cholerae , which causes the severe diarrhea disease cholera, and Pseudomonas aeruginosa , which is the leading Gram‐negative resistant organism in immunocompromised, hospital, and Cystic Fibrosis populations.
Characterization of Nanometer- to Micron-Sized Aluminum Powders by Thermogravimetric Analysis (2000)

Abstract : The reactivity of aluminum powders was studied by thermogravimetric analysis in air, oxygen, and nitrogen. Weight gains from complete oxidation of the aluminum were used to calculate particle sizes in the range of 30 nm to 500 nm. These particle sizes correlated well with particle sizes derived from surface area measurement. Particle size was also examined by scanning electron microscopy and atomic force microscopy, and compared to crystallite size determined by x-ray diffraction. Weight gains from complete oxidation were also used to determine the amount of active metal and aluminum oxide present in the submicron powders. Nitridation of aluminum powders was studied for extended times at 600 deg C. A 2 micrometer powder was nearly completely nitrided in 1 h, indicating that the nitride product has little inhibiting effect on the reaction.
Androgen content and BET bromodomain proteins influence enzalutamide agonism of mutant F876L androgen receptor. (2016)

e16538 Background: One emergent resistance mechanism to medical castration is intratumoral androgen synthesis that activates the androgen receptor (AR). This insight led to the development of the AR antagonist enzalutamide. One enzalutamide resistance mechanism is AR F876L mutations that lead to enzalutamide agonism in some cases. However, mechanisms that contribute to the agonist switch have not been fully clarified, and there are no therapies to block AR F876L. Methods: We usedenzalutamide-resistant cell lines harboring AR F876L mutations to determine mechanisms that contribute to enzalutamide activation of mutant F876L AR. Results: Using these cell line models, we determined that cellular androgen content influences enzalutamide agonism of mutant F876L AR. Further, enzalutamide treatment of AR F876L expressing cell lines recapitulated the effects of androgen activation of F876L AR or wild-type AR. Because the BET bromodomain inhibitor JQ1 was previously shown to block androgen activation of wild-type AR, we tested JQ1 in AR F876L-expressing CRPC models. We determined that JQ1 suppressed androgen or enzalutamide activation of mutant F876L AR and suppressed growth of mutant F876L AR CRPC tumors in vivo, demonstrating a new strategy to treat tumors harboring this mutation. Conclusions: Our data demonstrate that androgens interfere with enzalutamide-induced agonism of F876L mutant AR. Because androgens persist in enzalutamide-resistant CRPC, AR activation by androgens, rather than enzalutamide, may explain why enzalutamide discontinuation does not lead to anti-androgen withdrawal effects clinically. Further, our results provide a cautionary note on therapeutic efforts to deplete androgens concomitantly with enzalutamide treatment as this may accentuate AR agonism by enzalutamide in tumors harboring AR F876L mutations. Finally, targeting BET bromodomain proteins is a promising strategy to suppress mutant AR F876L function irrespective of whether the AR agonist is androgens or enzalutamide.
Radical surgery for malignant pleural mesothelioma: have we identified the appropriate selection tools? (2012)

The extensive utilization of asbestos in the previous century in industrialized countries, the rapid surge of asbestos use in developing countries and the omnipresence of asbestos containing materials in most man-made environments continue to contribute to the constantly increasing epidemic of malignant pleural mesothelioma (MPM) (1-3). Chronic inflammation elicited by inhaled asbestos fibers is considered the principal etiologic factor for this almost universally lethal malignancy originating in the pleura. It is assumed that 20-60 years (median around 40 years) of chronic inflammation is needed before this disease manifests itself (4). The direct consequence of this long latency period is that MPM is most frequently diagnosed at an older age (5).

MPM is usually confined to one hemithorax at the time of diagnosis, but the disease has a strong tendency to spread and involve the entire pleura and interlobular space. Infiltration into adjacent structures is characteristic of advanced MPM and despite attempts to completely resect the affected pleura, MPM will recur in most cases.
Recording and Analyzing Nucleic Acid Distance Distributions with X‐Ray Scattering Interferometry (XSI) (2018)

Most structural techniques provide averaged information or information about a single predominant conformational state. However, biological macromolecules typically function through series of conformations. Therefore, a complete understanding of macromolecular structures requires knowledge of the ensembles that represent probabilities on a conformational free energy landscape. Here we describe an emerging approach, X-ray scattering interferometry (XSI), a method that provides instantaneous distance distributions for molecules in solution. XSI uses gold nanocrystal labels site-specifically attached to a macromolecule and measures the scattering interference from pairs of heavy metal labels. The recorded signal can directly be transformed into a distance distribution between the two probes. We describe the underlying concepts, present a detailed protocol for preparing samples and recording XSI data, and provide a custom-written graphical user interface to facilitate XSI data analysis. © 2018 by John Wiley & Sons, Inc.
An Analytical Method for Disturbance Propagation Investigation Based on the Electromechanical Wave Approach (2020)

Accurate estimates of the electromechanical disturbance propagation in a power system play an important role in taking preventive, corrective, and in-extremis control actions. This paper proposes an analytical method for disturbance propagation investigation based on the electromechanical wave theory. A frame structure model is developed that allows us to derive an analytical relationship between the disturbance propagation and the turbine-generator inertia, the line reactance, bus voltage, and disturbance source frequency. In addition, the disturbance attenuation and the degree of disturbance propagation are studied. Numerical results performed on a multi-machine chain network and the IEEE 118-bus test system demonstrate the effectiveness of the developed method.
The Science of Footwear (2012)

Although we now have sophisticated algorithms and techniques for determining the shapes and sizes and for matching the fit between shoes and feet, few, if any, of the books currently available cover these new technologies until now. Bringing together high-quality and state-of-the-art contributions from designers, biomechanists, ergonomists, engineers, podiatrists, and scientists from industry and academia, The Science of Footwear provides an in-depth understanding of the technology and techniques involved in the design and development of a popular and demanding consumer product. This book introduces the design, development, manufacturing, and marketing of footwear. The chapters contain data from past research and the state-of-the art methodologies. They not only cover every aspect of the product design, but also how the footwear industry caters to the wide-ranging needs of sophisticated and demanding customers. The footwear industry has rapidly changed over the last 10 years. Mass production has changed to personalization and mass customization, areas that are not well-understood. This book explores these different concepts in a coherent way, drawing on differing views that give a holistic view of the science behind footwear. Collating information from different disciplines, the book provides the tools to develop the next generation of footwear. © 2013 by Taylor &amp; Francis Group, LLC.
Hardware synthesis (2010)

This chapter provides a brief summary of the stages in the hardware synthesis design flow. It is designed to give unfamiliar readers a high-level understanding of the hardware design process. The material in subsequent chapters describes different hardware implementations of polynomial expressions and linear systems. Therefore, we feel that it is important, though not necessarily essential, to have an understanding of the hardware synthesis process.
Double Suture Technique to Delineate PASTA Lesions (2006)

A common method of treating PASTA (partial articular surface tendon avulsion) lesions involves completing the tear followed by arthroscopic repair. Frequently, the boundaries of the tear are difficult to determine from the bursal side with the use of a single marking stitch. Therefore, we describe a simple technique that allows the surgeon to reproducibly define the boundaries of the partial tear. Following a standard arthroscopic examination of the articular portion of the shoulder joint, the PASTA lesion is identified. A spinal needle is introduced and the most anterior and posterior aspects of the tear are marked by passing 2 sutures. Following a bursectomy, the 2 sutures that clearly define the boundaries of the tear are identified. The tear is then completed by "connecting the dots" outlined by the sutures and an arthroscopic repair is performed in the standard manner.
Grafting on polysilanes using atom transfer radical polymerisation (2002)

Abstract Atom transfer radical polymerisation (ATRP) was used in an attempt to prepare a graft polymer based on poly(methylphenylsilane) (PMPS). A partially bromomethylated PMPS was subjected to ATRP conditions in order to grow poly(methyl methacrylate) (PMMA) grafts onto that backbone. Following the grafting reaction, a substantial increase in molecular weight was observed by size exclusion chromatography, analysis using refractive index detection. However, a bimodal product molecular weight distribution was observed using a UV detector set at wavelengths at which only the PMPS backbone can be detected. The lower molecular weight fraction was identified as homopolymeric PMPS although it appears to include some material with short grafts, while the higher molecular weight fraction corresponds to PMPS with long grafts. These observations are interpreted as the formation of a substantial amount of PMMA that is not grafted onto PMPS through a radical process initiated independently of the ATRP. However, since MMA is barely susceptible to thermal polymerisation, this is not easily rationalised. © 2002 Society of Chemical Industry