gebhart/patrepeval huggingface dataset:
Phosphotyrosine-Containing Dipeptides as High-Affinity Ligands for the p56<i><sup>lck</sup></i> SH2 Domain (1999)

Src homology-2 (SH2) domains are noncatalytic motifs containing approximately 100 amino acid residues that are involved in intracellular signal transduction. The phosphotyrosine-containing tetrapeptide Ac-pYEEI binds to the SH2 domain of p56lck (Lck) with an affinity of 0.1 microM. Starting from Ac-pYEEI, we have designed potent antagonists of the Lck SH2 domain which are reduced in peptidic character and in which the three carboxyl groups have been eliminated. The two C-terminal amino acids (EI) have been replaced by benzylamine derivatives and the pY + 1 glutamic acid has been substituted with leucine. The best C-terminal fragment identified, (S)-1-(4-isopropylphenyl)ethylamine, binds to the Lck SH2 domain better than the C-terminal dipeptide EI. Molecular modeling suggests that the substituents at the 4-position of the phenyl ring occupy the pY + 3 lipophilic pocket in the SH2 domain originally occupied by the isoleucine side chain. This new series of phosphotyrosine-containing dipeptides binds to the Lck SH2 domain with potencies comparable to that of tetrapeptide 1.
ChemInform Abstract: Reinvestigation of a Cyclization Reaction of 2‐Hydrazino‐3‐(1H‐pyrrol‐ 1‐yl)pyridine. (1987)

Abstract The reaction of the hydrazine (III) with acetylacetone (V) yields the pyrazole (VI) and not the triazepine (IV).
Perforation Resistance of Precoated Steels in an Accelerated Automotive Test (1986)

<div class="htmlview paragraph">Samples of electrogalvanized, hot-dipped galvanized, galvannealed, single and dual layer Zn-Fe (19-25%) and Zn-Ni (13%) alloy electroplated, zinc-rich primed and cold-rolled steel were cathodic e-coat primed and exposed for 250 cycles in an accelerated automotive-corrosion test environment. By extending the test period, it became possible to determine the number of cycles to perforation for all materials and to collect comparable data on scribe creepback corrosion, under paint corrosion, and overall material degradation with time. During the first 100 cycles, results were primarily indicative of the cosmetic corrosion behavior of test materials, showing that Zn-Fe and dual layer coatings with a chromium plus chromium oxide top-coating to be the best coatings. However, after 250 cycles, results clearly show that electrolytic pure zinc coatings offer the best perforation protection, i.e., better than heavier hot-dipped coatings or electrolytic Zn-Fe alloy coatings of equal coating weights. A correlation was evident between available zinc in the electrolytic coatings and time to perforation, but with an apparent diminishing return above 40 g/m<sup>2</sup>. Zinc-rich primed and Zn-Ni (13%) alloy coatings did not offer a substantial increase in time to perforation in comparison to cold-rolled steel.</div>
Feasibility of using citations as document summaries (2003)

The purpose of this research is to establish whether it is feasible to use citations as document summaries. People are good at creating and selecting summaries and are generally the standard for evaluating computer generated summaries. Citations can be characterized as concept symbols or short summaries of the document they are citing. Similarity metrics have been used in retrieval and text summarization to determine how alike two documents are. Similarity metrics have never been compared to what human subjects think are similar between two documents. If similarity metrics reflect human judgment, then we can mechanize the selection of citations that act as short summaries of the document they are citing. The research approach was to gather rater data comparing document abstracts to citations about the same document and then to statistically compare those results to several document metrics; frequency count, similarity metric, citation location and type of citation. There were two groups of raters, subject experts and non-experts. Both groups of raters were asked to evaluate seven parameters between abstract and citations: purpose, subject matter, methods, conclusions, findings, implications, readability, andunderstandability. The rater was to identify how strongly the citation represented the content of the abstract, on a five point likert scale. Document metrics were collected for frequency count, cosine, and similarity metric between abstracts and associated citations. In addition, data was collected on the location of the citations and the type of citation. Location was identified and dummy coded for introduction, method, discussion, review of the literature and conclusion. Citations were categorized and dummy coded for whether they refuted, noted, supported, reviewed, or applied information about the cited document. The results show there is a relationship between some similarity metrics and human judgment of similarity.%%%%Ph.D., Information Studies  – Drexel University, 2003
Flexible embedded control system architecture for power electronics applications (2010)

The paper presents a new flexible architecture of an embedded control system for power electronics applications. The hardware part of the system is divided between a CPU module and a baseboard dedicated for target system arrangement, depending on application requirements. Flexibility of the configration was achieved by using DSP/ARM/CPLD/FPGA components. The development line of unified CPUs and a baseboard family for various power converter topologies and applications is introduced. Some research, educational and industrial applications are briefly presented and discussed.
Citrullinated Vimentin Presented on MHC-II in Tumor Cells Is a Target for CD4+ T-Cell–Mediated Antitumor Immunity (2016)

Stressful conditions in the harsh tumor microenvironment induce autophagy in cancer cells as a mechanism to promote their survival. However, autophagy also causes post-translational modification of proteins that are recognized by the immune system. In particular, modified self-antigens can trigger CD4(+) T-cell responses that might be exploited to boost antitumor immune defenses. In this study, we investigated the ability of CD4 cells to target tumor-specific self-antigens modified by citrullination, which converts arginine residues in proteins to citrulline. Focusing on the intermediate filament protein vimentin, which is frequently citrullinated in cells during epithelial-to-mesenchymal transition of metastasizing epithelial tumors, we generated citrullinated vimentin peptides for immunization experiments in mice. Immunization with these peptides induced IFNγ- and granzyme B-secreting CD4 T cells in response to autophagic tumor targets. Remarkably, a single immunization with modified peptide, up to 14 days after tumor implant, resulted in long-term survival in 60% to 90% of animals with no associated toxicity. This antitumor response was dependent on CD4 cells and not CD8(+) T cells. These results show how CD4 cells can mediate potent antitumor responses against modified self-epitopes presented on tumor cells, and they illustrate for the first time how the citrullinated peptides may offer especially attractive vaccine targets for cancer therapy.
Sintering of Copper Particles for Die Attach (2012)

First steps are taken toward a low-cost alternative to silver sintering as a highly reliable die attach technology for deep drilling applications and future power electronic modules. In this feasibility analysis, we evaluate sintering of copper particles for die attach. Particulate copper pastes are pretreated in H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> atmosphere (50 mbar) in order to gain oxide-free particles. Subsequently, particles are sintered at a pressure of 40 N/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a temperature of 350°C for 2 min. Porosity, Young's modulus as well as electrical and thermal conductivities of sintered layers are analyzed. Moreover, shear tests at ambient temperature are performed for evaluating the adhesion of monometallic as well as Cu-Au bonds according to the American military standard for chip-substrate contacts (MIL-STD-883H, method 2019.8).
Radioactive Isotope Labeled Diffusible Components of a Bone Morphogenetic Substratum (1977)

Bone matrix gelatin labeled with radioactive glucose, cysteine, proline, tyrosine or tryptophan was enclosed in one chamber while an adjoined second chamber was left empty to become filled with interstitial fluid. The paired diffusion chambers were implanted into the anterior abdominal wall of allogeneic rats for 14 days. Release of the matrix gelatin (BMG) from the loaded chamber was followed by a bone formation on the outer membrane of the unloaded chamber. 3H-cysteine labeled components of BMG were disseminated into the interstitial fluids and throughout the host tissues 5 times more rapidly than 3H-proline labeled BMG. The relative rates of loss of radioactivity from the residue was cysteine greater than tryptophan greater than tyrosine greater than proline. Electron microscopic autoradiography revealed random dissemination of collagenous and non-collagenous derivatives of BMG. 3H-glucose distribution was coordinated with ruthenium red staining coarse granules and may have originated from BMG. A component of interstitial fluid staining positively with Coomassie brilliant blue and PAS methods was identified by SDS polyacrylamide gel electrophoresis of interstitial fluid aspirated from empty chambers attached to chambers loaded with bone matrix gelatin. The character of the bone morphogenetic property in bone gelatin has not yet been defined in physico-chemical terms but present evidence points to the view that it is associated with a protein molecule.
Pattern-Identified Online Task Scheduling in Multitier Edge Computing for Industrial IoT Services (2018)

In smart manufacturing, production machinery and auxiliary devices, referred to as industrial Internet of things (IIoT), are connected to a unified networking infrastructure for management and command deliveries in a precise production process. However, providing autonomous, reliable, and real-time offloaded services for such a production is an open challenge since these IIoT devices are assumed lightweight embedded platforms with limited computing performance. In this paper, we propose a pattern-identified online task scheduling (PIOTS) mechanism for the networking infrastructure, where multitier edge computing is provided, in order to handle the offloaded tasks in real time. First, historical IIoT task patterns in every timeslot are used to train a self-organizing map (SOM), which represents the features of the task patterns within defined dimensions. Consequently, offline task scheduling among edge computing-enabled entities is performed on the set of all SOM neurons using the Hungarian method to determine the expected optimal task assignments. In real-time context, whenever a task arrives at the infrastructure, the expected optimal assignment for the task is scheduled to the appropriate edge computing-enabled entity. Numerical simulation results show that the proposed PIOTS mechanism overcomes existing solutions in terms of computation performance and service capability.
Gaze Tracking Control Using Active Stereo Camera (2008)

The full automation of 3-D spatial data reference and revision requires spatial registration between existing spatial data and newly acquired data. In addition, it must be able to recognize an object’s shapes and behaviors. Therefore, the authors propose a real-time gaze tracking system capable of 3-D object recognition, in which an active stereo camera recognizes 3-D objects without markers. The real-time gaze tracking system was developed, and scenario-based experiments with the system were conducted. The results confirmed that our system could gaze and track moving objects successfully. Moreover, the proposed system achieves high-resolution 3-D spatial data acquisition and recognition, relative object behavior detection, and wide range covering.
Nanofilter array chip for fast gel-free biomolecule separation (2005)

We report here a microfabricated nanofilter array chip that can size-fractionate SDS-protein complexes and small DNA molecules based on the Ogston sieving mechanism. Nanofilter arrays with a gap size of 40-180nm were fabricated and characterized. Complete separation of SDS-protein complexes and small DNA molecules were achieved in several minutes with a separation length of 5mm. The fabrication strategy for the nanofilter array chip allows further increasing of the nanofilter density and decreasing of the nanofilter gap size, leading, in principle, to even faster separation.
Tele-3D-developing a handheld scanner using structured light projection (2005)

Three-dimensional surface reconstruction from twodimensional images is a process with great potential for use on different fields of research, commerce and industrial production. In this article we will describe the evolution of a project comprising the study and development of systems which implement the aforementioned process, exploring several techniques with the final aim of devising the best possible compromise between flexibility, performance and cost-effectiveness. We will firstly focus our attention on past work, namely the description of the implementation and results of a fixed system involving a camera and a laser-stripe projector mounted on a pan-tilt unit which sweeps the surface vertically with a horizontal stripe. Then we will describe our current work on the development of a fully portable, handheld system using cameras, projected structured light and inertial/magnetic positioning and attitude sensors — the Tele-3D scanner.
Association between Respiratory Disease and Bacterial and Viral Infections in British Racehorses (2005)

Respiratory disease is important in horses, particularly in young Thoroughbred racehorses, and inflammation that is detected in the trachea and bronchi (termed inflammatory airway disease [IAD]) is more significant in this population in terms of impact and frequency than other presentations of respiratory disease. IAD, which is characterized by neutrophilic inflammation, mild clinical signs, and accumulation of mucus in the trachea, may be multifactorial, possibly involving infections and environmental and immunological factors, and its etiology remains unclear. This 3-year longitudinal study of young Thoroughbred racehorses was undertaken to characterize the associations of IAD and nasal discharge with viral and bacterial infections. IAD was statistically associated with tracheal infection with Streptococcus pneumoniae (capsule type 3), Streptococcus zooepidemicus, Actinobacillus spp., and Mycoplasma equirhinis and equine herpesvirus 1 and 4 infections, after adjustment for variation between training yards, seasons, and age groups. The association with S. pneumoniae and S. zooepidemicus was independent of prior viral infection and, critically, was dependent on the numbers of organisms isolated. S. pneumoniae was significant only in horses that were 2 years old or younger. The prevalence and incidence of IAD, S. zooepidemicus, and S. pneumoniae decreased in parallel with age, consistent with increased disease resistance, perhaps by the acquisition of immunity. The study provided evidence for S. zooepidemicus and S. pneumoniae playing an important etiological role in the pathogenesis of IAD in young horses.
A Reassessment of the Groundwater Inverse Problem (1996)

This paper presents a functional formulation of the groundwater flow inverse problem that is sufficiently general to accommodate most commonly used inverse algorithms. Unknown hydrogeological properties are assumed to be spatial functions that can be represented in terms of a (possibly infinite) basis function expansion with random coefficients. The unknown parameter function is related to the measurements used for estimation by a “forward operator” which describes the measurement process. In the particular case considered here, the parameter of interest is the large‐scale log hydraulic conductivity, the measurements are point values of log conductivity and piezometric head, and the forward operator is derived from an upscaled groundwater flow equation. The inverse algorithm seeks the “most probable” or maximum a posteriori estimate of the unknown parameter function. When the measurement errors and parameter function are Gaussian and independent, the maximum a posteriori estimate may be obtained by minimizing a least squares performance index which can be partitioned into goodness‐of‐fit and prior terms. When the parameter is a stationary random function the prior portion of the performance index is equivalent to a regularization term which imposes a smoothness constraint on the estimate. This constraint tends to make the problem well‐posed by limiting the range of admissible solutions. The Gaussian maximum a posteriori problem may be solved with variational methods, using functional generalizations of Gauss‐Newton or gradient‐based search techniques. Several popular groundwater inverse algorithms are either special cases of, or variants on, the functional maximum a posteriori algorithm. These algorithms differ primarily with respect to the way they describe spatial variability and the type of search technique they use (linear versus nonlinear). The accuracy of estimates produced by both linear and nonlinear inverse algorithms may be measured in terms of a Bayesian extension of the Cramer‐Rao lower bound on the estimation error covariance. This bound suggests how parameter identifiability can be improved by modifying the problem structure and adding new measurements.
Principal component analysis with missing data and its application to object modeling (1994)

Observation-based modeling can reduce the cost and effort of model constructions for tasks such as virtual reality environment. Object modeling from a sequence of range images has been formulated as a problem of principal component analysis with missing data (PCAMD), which can be generalized as a weighted least square (WLS) minimization problem. After all visible regions appeared over the whole sequence are segmented and tracked, a normal measurement matrix of surface normals and a distance measurement matrix of normal distances to the origin are constructed respectively. These two measurement matrices, with possibly many missing elements due to occlusion and mismatching, enable us to formulate multiple view merging as a combination of two WLS problems. The solution to the first WLS problem, which employs the quaternion representation of the rotation matrix, yields surface normals and rotation matrices. Subsequently the normal distances and translation vectors are computed by solving the second WLS problem. Experiments using synthetic data and real range images show that our approach is robust against noise and mismatch because it produces a statistically optimal object model by making use of redundancy from multiple views. A toy house model from a sequence of real range images is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Addressing the Challenge of Changing the Specificity of RNase T1 with Rational and Evolutionary Approaches (2004)

Although ribonuclease T1 (RNase T1) is one of the best-characterized proteins with respect to structure and enzymatic action, numerous attempts at altering the specificity of the enzyme to cleave single-stranded RNA at the 3'-side of adenylic instead of guanylic residues by rational approaches have failed so far. Recently we generated and characterized the RNase T1 variant RV with a 7200-fold increase in adenylyl-3',5'-cytidine (ApC)/guanylyl-3',5'-cytidine (GpC) preference, with the guanine-binding loop changed from 41-KYNNYE-46 (wt) to 41-EFRNWN-46. Now we have introduced the asparagine residue at position 46 of the wild-type enzyme as a single-point mutation in variant E46N and in combination with the Y45W exchange also occurring in RV. Both variants show an improved ApC/GpC preference with a 1450-fold increase for E46N and a 2100-fold increase for Y45W/E46N in comparison to wild-type activity. We also addressed the challenge of altering enzyme specificity with an evolutionary approach. We have randomly introduced point mutations into the RNase T1 wild-type gene and into the gene of the variant RV with different mutation rates. Altogether we have screened about 100,000 individual clones for activity on RNase indicator plates; 533 of these clones were active. A significant change in substrate specificity towards an ApC preference could not be observed for any of these active variants; this demonstrated the magnitude of the challenge to alter the specificity of this evolutionary perfected enzyme.
Breeding of Dardford Warbler Sylvia undata in Mallorca (1997)

Nidificación de la curruca rabilarga Sylvia undata a Mallorca. Se presenta la existencia de una población reproductora (y posiblemente sedentaria) de currruca rabilarga Sylvia undata en dos áreas del NE de Mallorca. Las evidencias presentadas son las observaciones de machos territoriales durante las primaveras de 1997 y 1998, observaciones de un juvenil (verano de 1997), un grupo familiar y un nido con tres pollos (primavera de 1998), y la captura de ejemplares adultos con la muda postnupcial activa entre septiembre y noviembre de 1997. La coloración de estos individuos coincide con la descrita para la subespecie nominal. La aparente baja densidad, y la falta de registros estivales durante las últimas décadas, sugieren una colonización muy reciente, quizá a partir de la población sedentaria de Menorca.
RNAi Applications in Therapy Development for Neurodegenerative Disease (2009)

RNA-mediated interference (RNAi) is a powerful tool for experimental manipulation of gene expression and is widely used to investigate gene function both in vitro and in vivo. RNAi refers to an evolutionarily conserved cellular mechanism for sequence-specific post-transcriptional gene silencing, in which double-stranded RNAs promote selective degradation of homologous cellular mRNAs. Because RNAi-based techniques can be employed to reduce expression of specific genes, this approach holds great promise as a therapy for diverse diseases, including devastating neurodegenerative disorders such as Alzheimer's, Parkinson's, and Huntington's diseases and amyotrophic lateral sclerosis (ALS). Importantly, in recent years RNAi has also emerged as a key tool in target identification and validation studies designed to complement traditional (i.e., small molecule-based) drug development strategies. These studies harness the power of RNAi-mediated reverse genetics to probe disease-associated pathways in both cell-based and animal models, and thus may provide critical data needed to focus drug development efforts around disease-relevant targets. This review highlights recent progress in the preclinical development of RNAi-based therapeutics for neurodegenerative disease and discusses the particular challenges that disorders of the central nervous system (CNS) pose for this approach. It further describes current applications of RNAi techniques for target identification and validation studies and underscores the importance of this methodology to developing treatments for neurological diseases.
Deep-oxide curved resonator for low-threshold AlGaAs–GaAs quantum well heterostructure ring lasers (1995)

Data are presented on curved-resonator AlGaAs–GaAs quantum well heterostructure laser diodes employing a deep-oxide guiding structure formed by a combination of impurity-induced layer disordering and native oxidation. Room-temperature, continuous wave (cw) threshold currents as low as ∼13 mA are measured for a ∼5 μm wide, 100 μm radius half-ring laser employing a deep-oxide structure. For similar 150 μm radius devices, cw threshold currents as low as ∼19 mA are observed (∼7 μm width), with total output powers exceeding 30 mW. Spectral data indicate single-mode operation over a large current range (25–100 mA). The low-threshold characteristics are attributed to the excellent current and optical confinement of the deep-oxide structure, combined with low edge scattering loss.