gebhart/patrepeval huggingface dataset:
iWarp: an integrated solution to high-speed parallel computing (1988)

iWarp is a system architecture for high speed signal, image and scientific computing. The heart of an iWarp system is the iWarp component: a single chip processor that requires only the addition of memory chips to form a complete system building block, called the iWarp cell. Each iWarp component contains both a powerful computation engine (20 MFLOPS) and a high throughput (320 MBytes/sec), low latency (100-150 ns) communication engine for interfacing with other iWarp cells. Because of its strong computation and communication capabilities, the iWarp component is a versatile building block for various high performance parallel systems. These systems range from special purpose systolic arrays to general purpose distributed memory computers. They are able to support both fine-grain parallel and coarse-grain distributed computation models simultaneously in the same system. An iWarp system can include a large number of cells; the initial iWarp demonstration system consists of an 8x8 torus of iWarp cells, delivering more than 1.2 GFLOPS. It can be expanded to include up to 1,024 cells. This paper describes the iWarp architecture and how it supports various communication models and system configurations.
Genetic and biochemical analysis of the adenylyl cyclase-associated protein, cap, in Schizosaccharomyces pombe. (1992)

We have identified, cloned, and studied a gene, cap, encoding a protein that is associated with adenylyl cyclase in the fission yeast Schizosaccharomyces pombe. This protein shares significant sequence homology with the adenylyl cyclase-associated CAP protein in the yeast Saccharomyces cerevisiae. CAP is a bifunctional protein; the N-terminal domain appears to be involved in cellular responsiveness to RAS, whereas loss of the C-terminal portion is associated with morphological and nutritional defects. S. pombe cap can suppress phenotypes associated with deletion of the C-terminal CAP domain in S. cerevisiae but does not suppress phenotypes associated with deletion of the N-terminal domain. Analysis of cap disruptants also mapped the function of cap to two domains. The functional loss of the C-terminal region of S. pombe cap results in abnormal cellular morphology, slow growth, and failure to grow at 37 degrees C. Increases in mating and sporulation were observed when the entire gene was disrupted. Overproduction of both cap and adenylyl cyclase results in highly elongated large cells that are sterile and have measurably higher levels of adenylyl cyclase activity. Our results indicate that cap is required for the proper function of S. pombe adenylyl cyclase but that the C-terminal domain of cap has other functions that are shared with the C-terminal domain of S. cerevisiae CAP.
Laparoscopic resections for colorectal carcinoma (1996)

This early experience seems to indicate that laparoscopic surgery for colorectal carcinoma does not per se compromise surgical oncologic principles and encourages us to continue our critical appraisal of this technique.
Characterization of Genetic and Biochemical Mechanisms of Fludioxonil and Pyrimethanil Resistance in Field Isolates of <i>Penicillium digitatum</i> (2008)

Genetic and biochemical mechanisms of fludioxonil and pyrimethanil resistance in isolates of Penicillium digitatum were evaluated and compared to those characterized in other fungi. Resistant isolates were naturally occurring in packinghouses and were not associated with crop losses. For the phenylpyrrole fludioxonil, EC50 values were 0.02 to 0.04 microg/ml for sensitive, 0.08 to 0.65 microg/ml for moderately resistant (MR), and > 40 microg/ml for highly resistant (HR) isolates. Two fludioxonil-sensitive isolates evaluated were also significantly more sensitive to the unrelated dicarboximide fungicide iprodione, that also disrupts osmotic regulation, than the MR and HR isolates. There was no consistent relationship, however, between the HR and MR isolates and their sensitivity to iprodione or osmotic stress. Although, two nucleotide substitutions were found in a sequence analysis of the N-terminal amino acid repeat region of the os-1-related histidine kinase gene among isolates of P. digitatum, these were not correlated with fludioxonil resistance. In mycelia not exposed to fludioxonil, the amount of phosphorylated OS-2-related protein (PdOS-2) was higher in fludioxonil-sensitive isolates and lowest in the HR isolate. An increase in PdOS-2 was observed for sensitive and resistant isolates after exposure to fludioxonil. In addition, glycerol content in untreated mycelia of the fludioxonil-sensitive isolate was significantly higher than in resistant isolates. After exposure to fludioxonil, glycerol concentrations significantly increased in the sensitive and MR isolates, but not in the HR isolate. Thus, our studies indicate that the mode of action of fludioxonil in P. digitatum is probably the mitogen-activated protein kinase pathway that stimulates glycerol synthesis in sensitive and MR isolates. The general suppression of this pathway in resistant isolates was supported by the fact that growth and sporulation of MR and HR isolates were significantly reduced from that of sensitive isolates. In studies on the mode of action of anilinopyrimidines (AP), EC50 values for mycelial growth of P. digitatum and the previously characterized Botrytis cinerea were determined for cyprodinil and pyrimethanil using a defined culture medium without and with the addition of selected amino acids and homocysteine. The addition of amino acids resulted in a reduced toxicity of the two AP fungicides in both fungi, but the effect of each additive was significantly lower for P. digitatum than for B. cinerea. This suggests that methionine biosynthesis is not the primary target site of APs in P. digitatum.
A spanning tree based recursive refinement algorithm for fast task mapping (2002)

The early version of recursive refinement, an algorithm, for fast task mapping is reported in this paper. An intended application for this algorithm is dynamic load balancing on a parallel/distributed system, including a network of workstations. Since this requires a fast mapping, the algorithm restricts the range of tasks movement during optimization and maps groups of tasks to groups of PE's in each iteration. Tasks are allowed to be swapped only between the two partitions that comprise the parent partition from the previous iteration. More freedom of task movement is unnecessary because structural characteristics of the problem graph are used to guide the mapping. The groups are derived from a spanning tree that is constructed from the original problem graph and is used to identify the structural characteristics required for the algorithm. Experimental results show that the algorithm is able to achieve a mapping quality as good as that by another mapping scheme characteristic of a class of algorithms that require an order of magnitude more time.
Clinical validation of renin monoclonal antibody-based sandwich assays of renin and prorenin, and use of renin inhibitor to enhance prorenin immunoreactivity (1996)

Newly developed IRMAs to measure the plasma concentrations of renin and prorenin were validated for clinical use and compared with a classical enzyme kinetic assay. The IRMAs involve two monoclonal antibodies, one that reacts equally well with renin and prorenin and one that recognizes renin well but prorenin only minimally. Prorenin reactivity with the second antibody was enhanced by adding the renin inhibitor, Remikiren, to plasma. The complex of prorenin with this active-site ligand undergoes a conformational change, whereby prorenin is converted into a form that cannot be differentiated from renin by the IRMA. The linear working range of the assay was 4.0-3000 mU/L. The concentration of prorenin was calculated by subtracting the assay result obtained without Remikiren (i.e., renin) from the result obtained with Remikiren (i.e., renin plus prorenin). No more than 2% of prorenin present in plasma was detected as renin. The interassay CVs for renin quantification were 18%, 13%, and 8% at low, medium, and high concentrations, respectively. The interassay CV for calculated prorenin was 8% at both low and high concentrations. The IRMA results were highly correlated with those of an enzyme kinetic assay in healthy subjects; in patients with such conditions as primary hyperaldosteronism, renovascular hypertension, and low-, medium-, and high-renin essential hypertension; and in women undergoing gonadotropin stimulation.
Temperature-independent narrow-band filter by athermal waveguide (1996)

Temperature independent narrow-band filter was realized for the first time. A ring resonator was fabricated at 1.3 /spl mu/m wavelength by using an athermal waveguide in which optical path length is independent of temperature, and the temperature coefficient of central wavelength was successfully decreased to 7/spl times/10/sup -4/ nm/K (7% of conventional filter).
Microsatellite instability and protein expression of the DNA mismatch repair gene,hMLH1, of lung cancer in chromate-exposed workers (2004)

Our previous studies of lung cancer in chromate-exposed workers (chromate lung cancer) have revealed that the frequency of replication error (RER) in chromate lung cancer is very high. We examined whether the RER phenotype of chromate lung cancer is due to an abnormality of DNA mismatch repair protein. We investigated the expression of a DNA mismatch repair gene, hMLH1, and hMSH2 proteins using immunohistochemistry and microsatellite instability (MSI) in 35 chromate lung cancers and 26 nonchromate lung cancers. Lung cancer without MSI or with MSI at one locus was defined as "RER(-)," lung cancer with MSI at two loci was defined as "RER(+)," and lung cancer with MSI at three or more loci was defined as "RER(++)." The repression rate of hMLH1 and hMSH2 proteins in chromate lung cancer was significantly more than that of nonchromate lung cancer (hMLH1: 56% vs. 20%, P = 0.006, hMSH2: 74% vs. 23%, P < 0.0001). In chromate lung cancer, the repression rate for hMLH1 was 43% in RER(-), 40% in RER(+), and 90% in the RER(++) group. The repression rate of hMLH1 protein in the RER(++) group was significantly higher than that in the RER(-) and RER(+) groups (P = 0.039). The inactivation of hMLH1 expression strongly correlated with the microsatellite high instability phenotype in chromate lung cancer. The genetic instability of chromate lung cancer is due to the repression of hMLH1 protein.
Physical and magnetic properties of submicron lithographically patterned magnetic islands (1995)

We have developed a procedure for high-resolution patterning of magnetic thin films using direct-write electron beam lithography and a multistep sputter etching process [New et al., J. Vac. Sci. Technol. B 12, 3196 (1994)]. Using this patterning procedure we have defined large arrays of 0.2 by 0.4 μm magnetic islands out of a 200-Å-thick polycrystalline film of cobalt. The physical and magnetic structure of these islands has been examined using atomic and magnetic force microscopy, as well as transmission electron microscopy. Hysteresis loop measurements have been taken from large arrays of weakly interacting islands. The particles are not single domain and show considerable nonuniformity of magnetization when they are completely demagnetized. However, after application and removal of a large field along the long axes of the islands, most of the particles do relax into an almost uniform magnetization state.
Manufacturing enhancements for CoSi/sub 2/ self-aligned silicide at the 0.12-μm CMOS technology node (2003)

As integrated circuit manufacturing moves to the 0.12-/spl mu/m and finer-line technologies, a more comprehensive understanding of the manufacturability of the cobalt silicide (CoSi/sub 2/) module is needed. In this paper, a detailed study of the manufacturability of cobalt self-aligned silicide (Salicide) for the 0.12-/spl mu/m and finer technology nodes is discussed. Experimental design for the CoSi/sub 2/ processing steps included cobalt (Co), titanium (Ti), and titanium nitride (TiN) depositions; the first and second rapid thermal anneals (RTA1 and RTA2) and the selective metal etch. Grain structure (by X-ray diffraction), surface roughness (by atomic force microscopy), sheet resistance, thickness uniformity and leakage current measurements were taken to characterize the SAlicide process module. The results show that by using a TiN rather than Ti capping layer: a) the CoSi/sub 2/ sheet resistance nonuniformity has been improved; b) the CoSi/sub 2/ thickness is independent of the capping layer thickness; and c) CoSi/sub 2/ to silicon interface roughness is reduced, thus reducing junction leakage currents. Anneal studies indicate the RTA1 temperature dominates the CoSi/sub 2/ grain structure and grain size with higher annealing temperatures resulting in rougher CoSi/sub 2/ surfaces and higher junction leakage currents.
Metal-free, regioselective and stereoregular alternating copolymerization of monosubstituted epoxides and tricyclic anhydrides (2018)

A metal-free, highly regioselective and stereoregular ring-opening alternating copolymerization of monosubstituted epoxides with tricyclic anhydrides was achieved to yield well-defined polyesters.
Procedure-Specific Hardware Removal After Evans Osteotomy (2020)

Females are twice as likely as males to develop symptoms after locking plate application over an Evans osteotomy and may require hardware removal. Despite the low-profile nature of the locking plate to fixate the Evans osteotomy, the hardware can be a source of significant pain. Patients, especially females, should be cautioned about potential hardware-related pain and a possible follow-up procedure to remove the hardware.
In Vitro Assay for Site-Specific Proteases Using Bead-Attached GFP Substrate (2001)

Site-specific proteases, which catalyze cleavage of peptide bonds in specific amino acid sequences of target proteins, play important roles in various biological events of many living organisms. In humans, disruption in regulation of these site-specific proteases can lead to pathological consequences. Here, we report a simple in vitro assay for enzymatic activities of site-specific proteases. This assay system employs a protein substrate molecule that is comprised of (i) His-tag binding module, (ii) cleavage sites, and (iii) green fluorescent protein (GFP) detection module. In this study, prostate-specific antigen (PSA) and Thrombin-specific cleavage sites were introduced into the substrate molecules. The overexpressed GFP substrate protein was purified with the aid of Ni++-charged magnetic beads. On cleavage by either PSA or Thrombin, GFP was released from the bound magnetic beads, enabling a direct measurement of the cleaved product by fluorescence. Detection sensitivity, as well as the kinetics of reaction of PSA cleavage with the GFP substrate, was similar or better than commercially available PSA fluorogenic peptide substrate. This bead-attached GFP substrate was also used for an inhibition assay using a competitive inhibitor of Thrombin. In conclusion, this assay offers a simple fluorescent method for monitoring the activity of the site-specific proteases. Furthermore, this system provides flexible means of incorporating varying sizes of flanking sequences adjacent to the cleavage site, which can be essential for studying the regulatory macromolecular interactions between proteases and their substrates.
The spectrum of glottal flow models (1999)

A unified framework for studying the time and frequency domains properties of glottal flow models is proposed. It is shown that all the models can be represented by a common set of five time-domain parameters: three scale parameters (fundamental period, amplitude of voicing , open quotient), a shape parameter (asymmetry coefficient), and a closure continuity parameter (return phase time constant). The spectrum of glottal flow models is low-pass, and its derivative can be characterized by a spectral peak. The closure continuity parameter corresponds to a spectral tilt component. The scale parameters are interpreted using scaling properties of the Fourier transform. Then, the
<scp>AMP</scp> ‐activated Protein Kinase ( <scp>AMPK</scp> ) (2014)

Abstract AMP‐activated protein kinase (AMPK) is a heterotrimeric protein kinase complex that is expressed in essentially all eukaryotes. It acts as a sensor of cellular energy status by monitoring the levels of adenine nucleotides, especially adenosine‐5′‐monophosphate (AMP) , adenosine‐5′‐diphosphate (ADP) and adenosine‐5′‐triphosphate (ATP) . When activated by falling cellular energy status, AMPK acts to restore energy balance by switching on ATP‐producing catabolic pathways (such as the uptake and oxidation of glucose and fatty acids), while switching off any energy‐requiring processes (such as biosynthesis, cell growth and division) that are not essential for short‐term cell survival. AMPK is also regulated by hormones and cytokines that control energy balance at the whole body level, and it is involved in several common disorders in humans, including type 2 diabetes and cancer. Key Concepts: An analogy can be drawn between cellular ATP and ADP and the chemicals in a rechargeable battery. Catabolism (and/or photosynthesis) ‘charges the cellular battery’ by converting ADP to ATP. Almost all other cellular processes require energy and are driven by conversion of ATP to ADP, thus ‘flattening the battery’. All living cells must maintain a balance between ATP production and ATP consumption at all times, thus maintaining energy homoeostasis. In eukaryotic cells, one key system that maintains energy homoeostasis is the AMP‐activated protein kinase (AMPK). The gamma subunit of AMPK binds AMP, ADP and ATP, and increases in AMP:ATP and ADP:ATP ratios (signals of compromised cellular energy status) activate AMPK. Once activated, AMPK switches on alternate catabolic pathways that generate ATP, while switching off energy‐consuming processes, thus conserving ATP. Although it appears to have evolved to maintain energy homoeostasis in a cell‐autonomous manner, in multicellular eukaryotes AMPK is also regulated by hormones and cytokines that regulate whole body energy balance. AMPK is a key drug target in the treatment of common human disorders such as type 2 diabetes, cancer and inflammatory disorders.
Open barrier discharge as Xe laser pumping source (2003)

A wide aperture (120 cm<sup>2</sup>) electron beam generator with peak current density up to several A/cm<sup>2</sup> based on the small-gap barrier discharge was developed. The stability of generator operation at pressure up to 1 atm was observed. Fast electrons with energy up to 20 keV were produced and injected into neutral gas. The efficiency of electron beam excitation of gas volume and the laser operation at infrared transitions of atomic Xe were investigated.
A hybrid scheduling and control system architecture for warehouse management (2003)

In recent years, the hybrid control framework has received attention from the research community. Variations of this control framework are available in the literature. In this paper, a hybrid intelligent agent-based scheduling and control system architecture is presented for an actual industrial warehouse order-picking problem, where goods are stored at multiple locations and the pick location of goods can be selected dynamically in near-real time. The presented architecture includes a higher level optimizer, a middle-level guide agent, and lower level agents. The need for a higher level optimizer and communication between higher and lower level controllers is demonstrated. A mathematical model and a genetic algorithm for the resource assignment problem are presented. Simulation results demonstrating efficiency of the new approach are also presented.
Structural Insights into the Conformation and Oligomerization of E2∼Ubiquitin Conjugates (2012)

Post-translational modification of proteins by ubiquitin (Ub) regulates a host of cellular processes, including protein quality control, DNA repair, endocytosis, and cellular signaling. In the ubiquitination cascade, a thioester-linked conjugate between the C-terminus of Ub and the active site cysteine of a ubiquitin-conjugating enzyme (E2) is formed. The E2~Ub conjugate interacts with a ubiquitin ligase (E3) to transfer Ub to a lysine residue on a target protein. The flexibly linked E2~Ub conjugates have been shown to form a range of structures in solution. In addition, select E2~Ub conjugates oligomerize through a noncovalent "backside" interaction between Ub and E2 components of different conjugates. Additional studies are needed to bridge the gap between the dynamic monomeric conjugates, E2~Ub oligomers, and the mechanisms of ubiquitination. We present a new 2.35 Å crystal structure of an oligomeric UbcH5c~Ub conjugate. The conjugate forms a staggered linear oligomer that differs substantially from the "infinite spiral" helical arrangement of the only previously reported structure of an oligomeric conjugate. Our structure also differs in intraconjugate conformation from other structurally characterized conjugates. Despite these differences, we find that the backside interaction mode is conserved in different conjugate oligomers and is independent of intraconjugate relative E2-Ub orientations. We delineate a common intraconjugate E2-binding surface on Ub. In addition, we demonstrate that an E3 CHIP (carboxyl terminus of Hsp70 interacting protein) interacts directly with UbcH5c~Ub oligomers, not only with conjugate monomers. These results provide insights into the conformational diversity of E2~Ub conjugates and conjugate oligomers, and into their compatibility and interactions with E3s, which have important consequences for the ubiquitination process.
Effects on Bone Repair of Osteotomy With Drills or With Erbium, Chromium: Yttrium‐Scandium‐Gallium‐Garnet Laser: Histomorphometric and Immunohistochemical Study (2015)

The repair process of osteotomies created by the Er,Cr:YSGG laser, despite producing thermal damage to bone tissue, is comparable to that with conventional drills.
Low frequency stimulation of ventral hippocampal commissures reduces seizures in a rat model of chronic temporal lobe epilepsy (2011)

Low frequency stimulation applied at a frequency of 1 Hz significantly reduced both the excitability of the neural tissue as well as the seizure frequency in a rat model of human temporal lobe epilepsy. The results support the hypothesis that LFS of fiber tracts can be an effective method for the suppression of spontaneous seizures in a temporal lobe model of epilepsy in rats and could lead to the development of a new therapeutic modality for human patients with temporal lobe epilepsy.
Structured Sparsity in Structured Prediction (2018)

Linear models have enjoyed great success in structured prediction in NLP. While a lot of progress has been made on efficient training with several loss functions, the problem of endowing learners with a mechanism for feature selection is still unsolved. Common approaches employ ad hoc filtering or <em>L</em><sub>1</sub>- regularization; both ignore the structure of the feature space, preventing practicioners from encoding structural prior knowledge. We fill this gap by adopting regularizers that promote structured sparsity, along with efficient algorithms to handle them. Experiments on three tasks (chunking, entity recognition, and dependency parsing) show gains in performance, compactness, and model interpretability.