gebhart/patrepeval huggingface dataset:
Integrin-linked kinase is localized to cell-matrix focal adhesions but not cell-cell adhesion sites and the focal adhesion localization of integrin-linked kinase is regulated by the PINCH-binding ANK repeats (1999)

Integrin-linked kinase (ILK) is a ubiquitously expressed protein serine/threonine kinase that has been implicated in integrin-, growth factor- and Wnt-signaling pathways. In this study, we show that ILK is a constituent of cell-matrix focal adhesions. ILK was recruited to focal adhesions in all types of cells examined upon adhesion to a variety of extracellular matrix proteins. By contrast, ILK was absent in E-cadherin-mediated cell-cell adherens junctions. In previous studies, we have identified PINCH, a protein consisting of five LIM domains, as an ILK binding protein. We demonstrate in this study that the ILK-PINCH interaction requires the N-terminal-most ANK repeat (ANK1) of ILK and one (the C-terminal) of the two zinc-binding modules within the LIM1 domain of PINCH. The ILK ANK repeats domain, which is capable of interacting with PINCH in vitro, could also form a complex with PINCH in vivo. However, the efficiency of the complex formation or the stability of the complex was markedly reduced in the absence of the C-terminal domain of ILK. The PINCH binding defective ANK1 deletion ILK mutant, unlike the wild-type ILK, was unable to localize and cluster in focal adhesions, suggesting that the interaction with PINCH is necessary for focal adhesion localization and clustering of ILK. The N-terminal ANK repeats domain, however, is not sufficient for mediating focal adhesion localization of ILK, as an ILK mutant containing the ANK repeats domain but lacking the C-terminal integrin binding site failed to localize in focal adhesions. These results suggest that focal adhesions are a major subcellular compartment where ILK functions in intracellular signal transduction, and provide important evidence for a critical role of PINCH and integrins in regulating ILK cellular function.
GENE TRANSFER BY F′ STRAINS OF <i>ESCHERICHIA COLI</i> K-12 II (1963)

Pittard, James (Yale University, New Haven, Conn.) and Edward A. Adelberg. Gene transfer by F' strains of Escherichia coli K-12. II. Interaction between F-merogenote and chromosome during transfer. J. Bacteriol. 85:1402-1408. 1963.-When F' strains harboring the F-merogenate F(14) are mated with female recipients, the transfer of the F-merogenote begins, in the majority of cases, before chromosome transfer. The markers on F(14) are transferred in the sequence met-1, arg-1, ilva-16, and sex-factor, met-1 being transferred first and sex-factor being transferred last, 9 min after met-1. In the class of zygotes that have received both the F-merogenote marker met-1 and the chromosomal marker xyl or mal, the gradient of recombination frequencies for the F-merogenote markers arg-1 and ilva-16 is much steeper than in the corresponding zygotes that have not received chromosomal markers. In F' strains which exhibit an increased frequency of transfer of chromosome markers, this gradient of recombination frequencies for merogenote markers is much steeper. An analysis of experiments involving an F' strain with a much shorter F-merogenote, F(16), and of a triparental mating in which F-merogenote and chromosome were transferred from different donor cells reveals that the effect of chromosome transfer on the recovery of distal F-merogenote markers in the zygotes is not due to any form of postzygotic elimination. It is suggested that, when F' strains which are transferring F-merogenote begin to transfer chromosome, the latter event causes breakage of the F-merogenote. A second consequence of this interaction is a delay of 8 to 10 min in the first appearance of chromosomal markers in the zygotes.
What a Long, Strange “TRIPS” it’s Been: Compulsory Licensing from the Adoption of TRIPS to the Agreement on Implementation of the Doha Declaration, 3 J. Marshall Rev. Intell. Prop. L. 331 (2004) (2004)

Startling numbers of people die every day because they do not have access to essential medicines and treatment for diseases such as HIV/AIDS, particularly in Africa and Asia. The Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS) was established by the World Trade Organization (WTO) to set a minimum level of protection of intellectual property rights across international borders, as well as promote and protect the welfare of humanity. This Comment reviews the history of the TRIPS Agreement, including the most recent adoption of the WTO relating to the issuance of compulsory licenses. Specifically, this Comment suggests that the WTO look to United States case law on the topic of governmental use of patents without authorization, in addition to the spirit and goals of the TRIPS Agreement, and amend TRIPS by setting adequate remuneration at a very modest royalty rate when a compulsory license is utilized. Implementation of such an amendment will prevent further delay to the access to critical medicines in developing countries and advance the objectives of TRIPS.
Sulfur-oxidizing bacteria as plant growth promoting rhizobacteria for canola (1991)

Canola (Brassica napus) has a high sulfur requirement during vegetative growth and exhibits symptoms of sulfur deficiency when cropped on Saskatchewan soils low in plant available sulfur. Elemental sulfur (S 0 ) is frequently used as a fertilizer to alleviate this deficiency. The potential of sulfur-oxidizing microorganisms to enhance the growth of canola in S 0 fertilized soils was assessed. Sulfur-oxidizing bacteria and fungi were isolated from the rhizosphere and rhizoplane of canola grown in four different Saskatchewan soils under growth chamber conditions. Of 273 bacterial isolates, 245 (89.7%) oxidized S 0 to thiosulfate or tetrathionate in vitro, and 133 (48.7%) oxidized S 0 to sulfate; 70 fungal isolates oxidized S 0 to sulfate. Eighteen bacterial isolates demonstrating the highest in vitro sulfur oxidation were tested as seed inoculants under growth chamber conditions, with S 0 as sulfur source. Fourteen isolates increased canola leaf size measured at the bud stage of growth, and seven isolates increased root and pod dry weights at maturity. Three of the 14 isolates were also able to stimulate canola leaf area in the presence of plant available sulfate. The shoot material from canola inoculated with two of these isolates contained more iron, sulfur, and magnesium than uninoculated canola. Three of the 14 isolates inhibited the growth of the canola fungal pathogens, Rhizoctonia solani AG2-1, R. solani AG4, and Leptosphaeria maculans "Leroy." Another isolate was antagonistic towards both R. solani strains and another inhibited the growth of R. solani AG2-1 and L. maculans "Leroy." Thus some sulfur-oxidizing isolates appear to stimulate canola growth due to the enhancement of mineral nutrient uptake, whereas in other cases antibiosis towards canola pathogens may also be involved. Key words: elemental sulfur, oxidation, canola, rhizosphere, plant growth promoting rhizobacteria.
A Long Short-Term Memory Recurrent Neural Network Framework for Network Traffic Matrix Prediction (2017)

Network Traffic Matrix (TM) prediction is defined as the problem of estimating future network traffic from the previous and achieved network traffic data. It is widely used in network planning, resource management and network security. Long Short-Term Memory (LSTM) is a specific recurrent neural network (RNN) architecture that is well-suited to learn from experience to classify, process and predict time series with time lags of unknown size. LSTMs have been shown to model temporal sequences and their long-range dependencies more accurately than conventional RNNs. In this paper, we propose a LSTM RNN framework for predicting short and long term Traffic Matrix (TM) in large networks. By validating our framework on real-world data from GEANT network, we show that our LSTM models converge quickly and give state of the art TM prediction performance for relatively small sized models.
A stochastic finite-state word-segmentation algorithm for Chinese (1994)

We present a stochastic finite-state model for segmenting Chinese text into dictionary entries and productively derived words, and providing pronunciations for these words; the method incorporates a class-based model in its treatment of personal names. We also evaluate the system's performance, taking into account the fact that people often do not agree on a single segmentation.
In Vivo Anti-Inflammatory Effect of Statins Is Mediated by Nonsterol Mevalonate Products (2001)

This study set out to clarify whether the inhibition of sterol or nonsterol derivatives arising from mevalonate biotransformation plays a major role in the in vivo anti-inflammatory action of statins. Hepatic synthesis of all these derivatives was inhibited in mice by administered statins, whereas squalestatin inhibited only sterol derivatives. Using a short-term treatment schedule, we found that statins reduced the hepatic activity of 3-hydroxy-3-methylglutaryl coenzyme A reductase without affecting blood cholesterol. This treatment inhibited lipopolysaccharide- and carrageenan-induced pouch leukocyte recruitment and the exudate production of interleukin-6, monocyte chemotactic protein-1, and RANTES. Coadministration of mevalonate reversed the effect of statin on leukocyte recruitment. The inhibition of sterol synthesis by squalestatin did not have any anti-inflammatory effect, indicating that the biosynthesis of nonsterol compounds arising from mevalonate is crucial for the in vivo regulation of cytokine and chemokine production by statins. Their inhibition by statins may account for the reported anti-inflammatory effects of these drugs and may provide a biochemical basis for the recently reported effects of statins in the prevention of cardiovascular disease and mortality.
Analysis of pressure, angle and temporal effects on tissue optical properties from  polarization-gated spectroscopic probe measurements (2010)

Noninvasive optical techniques for tissue characterization, in particular, light scattering properties and blood supply quantification of mucosa, is useful in a wide variety of applications. However, fiber-optic probes that require contact with the tissue surface can present a challenging problem in the variability of in vivo measurements due the nature of interactions, for example affects due to variations in pressure applied to the probe tip. We present an in vivo evaluation of pressure, angle, and temporal effects on tissue properties for polarization-gated spectroscopy at superficial depths (within 100 to 200 microns of tissue surface) for oral mucosa.
The Radiology of Referred Otalgia (2009)

Pain referred to the ear is a well-documented phenomenon, which can be due to a multitude of disease processes. With the recent and rapid progression of CT and MR imaging technology, radiologists have played an increasing role in solving this potentially difficult diagnostic dilemma. Essentially any pathology residing within the sensory net of cranial nerves V, VII, IX, and X and the upper cervical nerves C2 and C3 can potentially cause referred otalgia. This article will attempt to outline the various sensorineural pathways that dually innervate the ear and other sites within the head and neck, as well as discuss various disease processes that are known to result in referred otalgia.
Synthesis of Enantiomerically Pure 8-Substituted 5,6,7,8-Tetrahydroquinolines (2002)

Enantiomerically pure (S)-5,6,7,8-tetrahydroquinolin-8-ol [(S)-1] and (R)-8-acetoxy-5,6,7,8-tetrahydroquinoline [(R)-2] have been prepared by the lipase-catalyzed kinetic acetylation of racemic 5,6,7,8-tetrahydroquinolin-8-ol [(±)-1] in excellent chemical yields. The mesylation of (R)-1 followed by a substitution reaction with the azide, thioacetate, and dimethyl malonate anions and benzylamine gives the corresponding substituted products in an enantiomerically pure form with an inversion of the configuration in good yields. The methanolysis of (S)-5,6,7,8-tetrahydroquinolin-8-yl acetate in the presence of potassium carbonate and alkylation of the resulting thiol anion with alkyl halides in a one-pot reaction gives the 5,6,7,8-tetrahydroquinolin-8-yl thioether.
Scalable Analysis Techniques for Microprocessor Performance Counter Metrics (2002)

Contemporary microprocessors provide a rich set of integrated performance counters that allow application developers and system architects alike the opportunity to gather important information about workload behaviors. Current techniques for analyzing data produced from these counters use raw counts, ratios, and visualization techniques help users make decisions about their application performance. While these techniques are appropriate for analyzing data from one process, they do not scale easily to new levels demanded by contemporary computing systems. Very simply, this paper addresses these concerns by evaluating several multivariate statistical techniques on these datasets. We find that several techniques, such as statistical clustering, can automatically extract important features from the data. These derived results can, in turn, be fed directly back to an application developer, or used as input to a more comprehensive performance analysis environment, such as a visualization or an expert system.
An integrated multicomponent synthesis environment for MCMs (1993)

The multicompact synthesis (MSS) integrated design environment for multichip modules (MCMs) is discussed. The MSS environment is centered in VHDL (very-high-speed integrated circuit hardware description language), WAVES (waveform and vector exchange specification), and PDL (performance description language). MSS provides four levels of automated synthesis support all the way from the behavioral level to MCM placement and routing, three levels of simulation support including behavioral, register, and switch levels, and tools for automated test-bench compilation and design validation for all synthesized designs. Three tutorial examples illustrate MSS algorithms and results. The primary example is the Find, which performs a bubble sort followed by binary search. It is used as the running example because it is small. Such small specifications, however, do not require MCMs. Two larger examples, the Move Machine and the Viper Microprocessor, are used to illustrate the results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A phase II study of ramucirumab as first-line monotherapy in patients (pts) with advanced hepatocellular carcinoma (HCC). (2010)

4083 Background: Vascular endothelial growth factor (VEGF)-mediated angiogenesis contributes to HCC pathogenesis. Ramucirumab (IMC-1121B) is a recombinant human monoclonal antibody that binds to the extracellular domain of the VEGF receptor 2 (VEGFR-2). There is a compelling rationale for antiangiogenic (and specifically anti-VEGFR-2) therapy in HCC. Methods: Pts with advanced HCC received ramucirumab 8 mg/kg IV every (q) 2 weeks until disease progression or intolerable toxicity. Eligibility included no prior systemic therapy, Child-Pugh (C-P) A-B cirrhosis, ECOG PS 0-1, CLIP score 0-3, bilirubin ≤ 3 mg/dL, transaminases ≤ 5X ULN, Cr ≤ 2 mg/dL and platelets ≥ 75K. Tumor evaluations were q6 weeks. The primary endpoint was progression-free survival (PFS). Other endpoints were overall survival (OS), response rate, safety, pharmacokinetic (PK)/pharmacodynamic (PD) profiles, and immunogenicity of ramucirumab. Results: 43 pts were enrolled; 42 received therapy. Pts were predominantly male (81%), C-P A (74%), ECOG PS 0 (43%) or 1 (55%), and HCV-infected (49%). Most had extrahepatic disease (76%), BCLC stage C (83%), and 17% had macrovascular invasion. Median PFS was 4.3 months (m) and 4.0 m for pts with BCLC C (4.2 m for pts with C-P A, 2.8 m for pts with C-P B cirrhosis). 3 pts (7%) with extrahepatic disease and BCLC C had partial response, and 18 (43%) had stable disease (50% disease control rate). The most frequent adverse events (AEs) were fatigue (62%), headache (38%), and hypertension (HTN) (38%). Serious AEs included fatigue (10% grade [G] 3), gastrointestinal (GI) bleeding (7% G3; 2% G5), HTN (12% G3; 2% G4), infusion-related reactions (5% G3), and headache (2% G3). Cmin concentrations were above the target trough concentration (20 mg/mL) for the entire treatment period; evaluation through cycle 13 suggests no long-term accumulation of ramucirumab when administered q2 weeks. Conclusions: Ramucirumab confers moderate disease control in advanced, sorafenib-naive HCC. The treatment was well tolerated for most patients; serious AEs included GI bleeding, infusion- related reactions and HTN. Updated data on clinical efficacy and PD profiles will be presented. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration ImClone Systems Bayer, Genentech, ImClone Systems Lilly
Semi-automatic Navigation on 3D Triangle Meshes Using BVP Based Path-Planning (2011)

Efficient path-planning methods are being explored along the years to allow the movement of robots or virtual agents in planar environments. However, there is a lot of space to improve the quality of paths restricted to 3D surfaces, with holes and bends for instance. This work presents a new technique for path-planning on 3D surfaces called 3DS-BVP. This path planner is based on Boundary Value Problem (BVP), which generates potential fields whose gradient descent represents navigation routes from any point on the surface to a goal position. Resulting paths are smooth and free from local minima. The 3DS-BVP works on complex surfaces of arbitrary genus or curvature, represented by a triangle mesh, without the need of 2D parametrizations. Our results demonstrate that our technique can generate paths in arbitrary surfaces with similar quality as those generated by BVP-based methods in planar environments. Our approach can be applied in the development of new tools to automate the navigation on 3D surfaces, like the camera control in the exploratory visualization of 3D models.
Subthreshold oscillations of the membrane potential: a functional synchronizing and timing device (1993)

1. Subthreshold membrane potential oscillations have been observed in different types of CNS neurons. In this in vitro study, we examined the possible role of these oscillations by analyzing the responses of neurons from the inferior olivary nucleus to a combined stimulation of sine wave and synaptic potentials. 2. A nonlinear summation of the sine wave and the synaptic potential occurred in olivary neurons; a superlinear summation occurred when the synaptic potential was elicited at the trough of the sine wave or during the rising phase. On the other hand, a less than linear summation occurred when the synaptic potentials were evoked during the falling phase of the wave. 3. Significant changes in the delay of the synaptic responses were observed. As a result of these changes, the maximum amplitude of the response occurred at the peak of the sine wave, regardless of the exact time of stimulation. The output of the neuron was therefore synchronized with the sine wave and depended only partly on the input phase. 4. These data demonstrate that neurons from the inferior olivary nucleus are capable of operating as accurate synchronizing devices. Moreover, by affecting the delay line, they act as a logic gate that ensures that the information will be added to the system only at given times.
Extraction of group A streptococcal M protein with nitrous acid (1981)

Specific precipitating and opsonic neutralizing antigens were identified in dilute-nitrous acid extracts of group A streptococci. This was done by decreasing the temperature and time of exposure of the streptococcal cells to the nitrous acid. Ninety percent of 31 strains of group A streptococcal dilute-nitrous acid extracts formed precipitin lines of identity with conventional Lancefield extracts of the same group A streptococci.
Bridging the gap between planning and scheduling (2000)

Planning research in Artificial Intelligence (AI) has often focused on problems where there are cascading levels of action choice and complex interactions between actions. In contrast, scheduling research has focused on much larger problems where there is little action choice, but the resulting ordering problem is hard. In this paper, we give an overview of AI planning and scheduling techniques, focusing on their similarities, differences, and limitations. We also argue that many difficult practical problems lie somewhere between planning and scheduling, and that neither area has the right set of tools for solving these vexing problems.
Diffusion of boron in germanium at 800–900°C (2004)

Diffusion of B in Ge is studied in the temperature range 800–900°C using implantation doping and B doped epitaxial Ge layers. Concentration profiles before and after furnace annealing were obtained using high resolution secondary ion mass spectroscopy (SIMS). Diffusion coefficients were calculated by fitting the annealed profiles using TSUPREM. We obtained diffusivity values which are at least two orders of magnitude lower than the lowest values previously reported in the literature. Using our values an activation energy of 4.65(±0.3)eV is calculated. Present experimental results suggest that interstitial mediated mechanism should be considered for B diffusion in Ge in accordance with recent theoretical calculations. Annealed SIMS profiles also suggest that B solid solubility in Ge is ∼2×1018cm−3 at 875°C which agrees with literature values.
A novel method of tear collection: comparison of glass capillary micropipettes with porous polyester rods. (1997)

Polyester rods provide a more rapid, user-friendly alternative to glass-capillary micropipettes for the collection and analysis of tear fluid and tear proteins. Polyester rods may have greater clinical utility, facilitating routine analysis of the preocular tear film.
COOL: a language for parallel programming (1990)

We present COOL, an object-oriented parallel language derived from C++ by adding constructs to specify concurrent execution. We describe the language design, and the facilities for creating parallelism, performing synchronization, and communicating. The parallel construct is parallel functions that execute asynchronously. Synchronization support includes mutex functions and future types. A shared-memory model is assumed for parallel execution, and all communication is through shared-memory. The parallel programming model of COOL has proved useful in several small programs that we have attempted. We present some examples and discuss the primary implementation issues.