gebhart/patrepeval huggingface dataset:
Endostatin binds to the catalytic domain of matrix metalloproteinase‐2 (2002)

We previously reported that endostatin inhibits endothelial and tumor cellular invasion by blocking activation and catalytic activity of matrix metalloproteinase (MMP)-2. Here we have examined the domain of proMMP-2 responsible for the binding of endostatin using surface plasmon resonance. ProMMP-2 and proMMP-2deltaHP lacking the hinge and hemopexin-like (HP) domains bound little to the immobilized endostatin. The active MMP-2 and MMP-2deltaHP, but not the HP domain of MMP-2, bound to endostatin at similar levels. In addition, preincubation of MMP-2 and MMP-2deltaHP with the MMP inhibitor actinonin, which binds to the active site of MMP-2, abolished their bindings to endostatin. These results indicate that endostatin binds to neither the latent proMMP-2 nor the HP domain but to the catalytic domain of MMP-2.
Use of cloned DNA methylase genes to increase the frequency of transfer of foreign genes into Xanthomonas campestris pv. malvacearum (1991)

In vitro-packaged cosmid libraries of DNA from the bacterium Xanthomonas campestris pv. malvacearum were restricted 200- to 1,000-fold when introduced into Mcr+ strains of Escherichia coli compared with restriction in the Mcr- strain HB101. Restriction was predominantly associated with the mcrBC+ gene in E. coli. A plasmid (pUFR052) encoding the XmaI and XmaIII DNA methylases was isolated from an X. campestris pv. malvacearum library by a screening procedure utilizing Mcr+ and Mcr- E. coli strains. Transfer of plasmids from E. coli strains to X. campestris pv. malvacearum by conjugation was enhanced by up to five orders of magnitude when the donor cells contained pUFR052 as well as the plasmid to be transferred. Subcloning of pUFR052 revealed that at least two regions of the plasmid were required for full modification activity. Use of such modifier plasmids is a simple, novel method that may allow the efficient introduction of genes into any organism in which restriction systems provide a potent barrier to such gene transfer.
Regulation and Prognostic Relevance of Symmetric Dimethylarginine Serum Concentrations in Critical Illness and Sepsis (2013)

In systemic inflammation and sepsis, endothelial activation and microvascular dysfunction are characteristic features that promote multiorgan failure. As symmetric dimethylarginine (SDMA) impacts vascular tension and integrity via modulating nitric oxide (NO) pathways, we investigated circulating SDMA in critical illness and sepsis. 247 critically ill patients (160 with sepsis, 87 without sepsis) were studied prospectively upon admission to the medical intensive care unit (ICU) and on day 7, in comparison to 84 healthy controls. SDMA serum levels were significantly elevated in critically ill patients at admission to ICU compared to controls and remained stably elevated during the first week of ICU treatment. The highest SDMA levels were found in patients with sepsis. SDMA levels closely correlated with disease severity scores, biomarkers of inflammation, and organ failure (renal, hepatic, and circulatory). We identified SDMA serum concentrations at admission as an independent prognostic biomarker in critically ill patients not only for short-term mortality at the ICU but also for unfavourable long-term survival. Thus, the significant increase of circulating SDMA in critically ill patients indicates a potential pathogenic involvement in endothelial dysfunction during sepsis and may be useful for mortality risk stratification at the ICU.
Land mobile SSB : Promises and problems (1981)

SSB radios for land mobile use will require more circuits and tighter tolerances than FM units. The extra circuits, which are required for purposes such as pilot extraction and automatic gain control, must be designed as compromises between various aspects of performance and cost. Tests, with phase-locked-loop receivers, of three pilot schemes (pilot carrier, tone-in-band, tone-above-band) have given very similar results. Considerations of the ease of implementation, and compatibility with existing systems, suggest that pilot carrier is to be preferred. Amplitude companding may improve the effective signal to noise ratio under some conditions but its use is optional, not essential.
Innovative management strategies for building and sustaining a digital initiatives department with limited resources (2017)

Purpose The purpose of this paper is to offer and explore innovative strategies for building and sustaining digital initiatives at information organizations. Although the examples provided are based on case studies at an academic library, the practices are rooted in project management principles and therefore applicable to all library types, museums, archives and other information organizations. The innovative strategies on staffing and funding will be particularly useful to organizations faced with monetary and staffing shortages and highlights collaborative management practices. Design/methodology/approach Concept of strategic and collaborative management practices led by an experienced project manager cross-trained in management, technical and soft skills enables the successful development and sustainability of digital initiatives. A cross-trained librarian’s management practices of leading the Digital Scholarship Initiatives at a particular university will be examined as a case study and aided with literature supporting the need for digital initiatives leaders to have training beyond the credentials of librarian, curator, archivist or historian in the technologically savvy twenty-first century ecology of information centers. Findings The innovative strategies implemented in the case study yielded increases in the number of hours of digital lab usage, digital projects developed, seminars or workshops presented, attendance of library hosted events, number of programs implemented and awareness on campus, all with limited staff and funding. The variety and level of production and marketing is instrumental to the growth and sustainability of digital initiatives. Practical implications The innovative strategies emphasized in this paper use the concept of borrowed or shared time to start staffing needs and is particularly helpful to organizations that do not have a strong line of dedicated staffing or funding to begin building digital initiatives. Offers small ways to start immediately while setting the stage to plan for big ideas for the future. Originality/value This paper suggests a credentialed information expert, such as a librarian, archivist or curator, that is, also cross-trained in project management and technology is the key to not only successfully leading digital initiatives but is instrumental for its sustainability and the marketing, growth and future of digital initiatives.
Histogram of Oriented Uniform Patterns for robust place recognition and categorization (2012)

This paper presents a novel context-based scene recognition method that enables mobile robots to recognize previously observed topological places in known environments or categorize previously unseen places in new environments. We achieve this by introducing the Histogram of Oriented Uniform Patterns (HOUP), which provides strong discriminative power for place recognition, while offering a significant level of generalization for place categorization. HOUP descriptors are used for image representation within a subdivision framework, where the size and location of sub-regions are determined using an informative feature selection method based on kernel alignment. Further improvement is achieved by developing a similarity measure that accounts for perceptual aliasing to eliminate the effect of indistinctive but visually similar regions that are frequently present in outdoor and indoor scenes. An extensive set of experiments reveals the excellent performance of our method on challenging categorization and recognition tasks. Specifically, our proposed method outperforms the current state of the art on two place categorization datasets with 15 and 5 place categories, and two topological place recognition datasets, with 5 and 27 places.
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins (2004)

STRIDE is a software tool for secondary structure assignment from atomic resolution protein structures. It implements a knowledge-based algorithm that makes combined use of hydrogen bond energy and statistically derived backbone torsional angle information and is optimized to return resulting assignments in maximal agreement with crystallographers' designations. The STRIDE web server provides access to this tool and allows visualization of the secondary structure, as well as contact and Ramachandran maps for any file uploaded by the user with atomic coordinates in the Protein Data Bank (PDB) format. A searchable database of STRIDE assignments for the latest PDB release is also provided. The STRIDE server is accessible from http://webclu.bio.wzw.tum.de/stride/.
Systematic comparative analysis of single cell RNA-sequencing methods (2019)

ABSTRACT A multitude of single-cell RNA sequencing methods have been developed in recent years, with dramatic advances in scale and power, and enabling major discoveries and large scale cell mapping efforts. However, these methods have not been systematically and comprehensively benchmarked. Here, we directly compare seven methods for single cell and/or single nucleus profiling from three types of samples – cell lines, peripheral blood mononuclear cells and brain tissue – generating 36 libraries in six separate experiments in a single center. To analyze these datasets, we developed and applied scumi, a flexible computational pipeline that can be used for any scRNA-seq method. We evaluated the methods for both basic performance and for their ability to recover known biological information in the samples. Our study will help guide experiments with the methods in this study as well as serve as a benchmark for future studies and for computational algorithm development.
Reversible Luminescence Switching of an Organic Solid: Controllable On–Off Persistent Room Temperature Phosphorescence and Stimulated Multiple Fluorescence Conversion (2015)

On–off-switchable, persistent, room-temperature phosphorescence (373 ms) is realized in organic solids based on bis(4-(9H-carbazol-9-yl)phenyl)methanone. The reversible on–off RTP switching can be controlled by repeatedly chloroform fuming and heating (or grinding). Multi­ple-color fluorescence is also feasible, and they reversibly convert to each other under the stimuli of heating, shearing, and fuming with varied solvents. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Blockchain for Business Value: A Contract and Work Flow Management to Reduce Disputes Pilot Project (2018)

Blockchain technology has seen significant growth, hype, and potential new developments over the past few years. In this article additional insights into how blockchain can add value to a business process relationship is detailed. Specifically an engineering contract workflow use application pilot including various high level system architectural aspects are presented. This application shows the integration of blockchain technology with existing legacy systems. Some management and technology issues are also overviewed for the reader.
New substrate-crosstalk reduction structure using SO1 substrate (2001)

Recently, much attention has been paid to the one-chip transceiver since it can reduce the volume and weight of mobile communication equipment. A typical one-chip transceiver IC contains RF (radio frequency), IF (intermediate frequency) and baseband circuits. and many of those consist of analog and digital circuits. For such mixed-signal IC, the coupling through the substrate is a very important factor to limit its performance[l]. The use of SO1 (silicon on insulator) technology is a promising candidate to reduce the substratecrosstalk because it allows us to manipulate substrate resistivity. In previous papers[2][3], the effect of the substrate resistivity was mainly discussed. In this paper. we propose the new isolation structure to reduce the substrate-crosstalk using the SO1 technology. New isolation structure
Addressing Food and Nutrition Security Threats in the Caribbean: Lessons from the Cassava Value Chain in Barbados (2016)

Cassava production is one of the most promising industries to deal with the main challenges that Caribbean region is currently facing. Cassava as a strategic locally-produced crop with a vast potential could contribute to addressing the issues of agricultural diversification, economic revitalization, climate change and food import bill. The main objective of this study is to evaluate the main perspectives of the cassava industry development. The paper presents the results of analysis of the profitability of the cassava value chain development in Barbados in terms of economic opportunities for local producers and processors. High production cost of cassava roots and traditional farm management system with low yields are the main constraints of cassava value chain development. Cost-benefit analysis applied to evaluate cassava production models and small-scale plants (mash, flour, chips) shows that returns and generated value can be multiplied many times, when cassava yields are increased up to 28 MT/Ha and higher. Results indicate that growing cassava and transforming it in various value-added products can be a profitable activity if local farmers decrease production costs under proposed management systems and guarantee a constant supply of fresh cassava roots at competitive prices. Policy decisions and incentives are needed to stimulate private sector investments in the development of this industry.
The sweating deficiency in diabetes mellitus (1984)

A method that measures the amount of sweat evaporating from the skin was used to quantitate the sweating deficiency that accompanies diabetic neuropathy. The decreased amount of sweat secreted after pilocarpine stimulation was proportional to the reduction in number of excitable sweat glands, and to the decrease in water measured by the summed volume of all sweat droplets secreted. The results also correlated favorably with the degree of sensory loss to painful stimuli, but not to the alpha motor nerve conduction velocity or motor axon loss evaluated by muscle action potentials evoked from foot muscles. Respiratory-cardiovascular reflexes, as measured by the Valsalva ratio, were always abnormal in patients with demonstrated sweating deficiency and often in patients with normal sweat function.
FKHR-L1 can act as a critical effector of cell death induced by cytokine withdrawal (2002)

Survival signals elicited by cytokines include the activation of phosphatidylinositol 3-kinase (PI3K), which in turn promotes the activation of protein kinase B (PKB). Recently, PKB has been demonstrated to phosphorylate and inactivate forkhead transcription factor FKHR-L1, a potent inducer of apoptosis. To explore the mechanisms underlying the induction of apoptosis after cytokine withdrawal or FKHR-L1 activation, we used a cell line in which FKHR-L1 activity could be specifically induced. Both cytokine withdrawal and FKHR-L1 activation induced apoptosis, which was preceded by an upregulation in p27KIP1 and a concomitant decrease in cells entering the cell cycle. Induction of apoptosis by both cytokine withdrawal and activation of FKHR-L1 correlated with the disruption of mitochondrial membrane integrity and cytochrome c release. This was preceded by upregulation of the pro-apoptotic Bcl-2 family member Bim. Ectopic expression of an inhibitory mutant of FKHR-L1 substantially reduced the levels of apoptosis observed after cytokine withdrawal. Activation of PKB alone was sufficient to promote cell survival, as measured by maintenance of mitochondrial integrity and the resultant inhibition of effector caspases. Furthermore, hematopoietic stem cells isolated from Bim-/- mice exhibited reduced levels of apoptosis upon inhibition of PI3K/PKB signaling. These data demonstrate that activation of FKHR-L1 alone can recapitulate all known elements of the apoptotic program normally induced by cytokine withdrawal. Thus PI3K/PKB--mediated inhibition of this transcription factor likely provides an important mechanism by which survival factors act to prevent programmed cell death.
Corneal epithelial tight junctions and their response to lipopolysaccharide challenge. (2000)

Occludin, ZO-1, and ZO-2, but not claudin-1, are components of corneal epithelial TJs. LPS induces breakdown of the epithelial barrier through disruption of TJs, and ZO-1 and ZO-2 are targets for the induction.
Charge storage in dielectrics (2003)

Work on charge-storage processes in dielectrics performed over the past few years is reviewed. Results obtained on polymers with corona, electron-beam and pressure-pulse methods and pertaining to trap filling, spatial distribution of the charge, radiation-induced conductivity, and dynamics of the charge decay are discussed. The generation of a variety of polarization distributions in polyvinylidene fluoride (PVDF) with electron-beam and other methods is reviewed. Some results on charge storage and transport in silicon dioxide are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Incorporation of attenuation into time-domain computations of seismic wave fields (1987)

Abstract The only numerically tractable way yet found to incorporate attenuation into numerical time-domain computations of seismic wave fields is to approximate the viscoelastic modulus by a low-order rational function of frequency. The coefficients of this function can be determined by the Pade approximation. Our test computations show, however, that this approximation generally is of poor quality. Therefore, we suggest a new approach which is based on the rheological model of the generalized Maxwell body, which has a modulus of the desired rational form. We choose the relaxation frequencies logarithmically equidistant in the frequency band of interest, and determine the weight factors by simple numerical curve fitting to an arbitrary Q law. This approach is superior to the method above both in accuracy and in computational efficiency. For most practical applications, approximations of orders 2 or 3 are sufficient. The computing time and memory requirements for a finite-difference calculation are then approximately twice those of a purely elastic calculation. As a first application of the method, we compute SH channel waves in discontinuous coal seams with Q = 50 within the coal. The results show that the high-frequency Airy phase is strongly attenuated. This indicates that care has to be taken in comparing the results of purely elastic model calculations of the propagation of seam waves with experimental data.
Cardiovascular Importance of the MicroRNA‐23/27/24 Family (2011)

MicroRNAs (miRNAs) are a class of highly conserved, noncoding short RNA molecules that regulate gene expression on the post-transcriptional level. MiRNAs are involved in a variety of processes such as proliferation, differentiation, and apoptosis. Deregulated expression of miRNAs has been linked to the development of diseases including cardiovascular disorders. Recently, the miR-23/27/24 cluster has been shown to be involved in angiogenesis and endothelial apoptosis in cardiac ischemia and retinal vascular development. In the present review, we summarize and discuss the role and importance of the miRNA-23/27/24 cluster during cardiovascular angiogenesis. Moreover, we illustrate a novel therapeutic application of the miRNA-23/27/24 cluster in vascular disorders and ischemic heart disease.
From Euclid's GCD to Montgomery Multiplication to the Great Divide (2001)

Euclid's method for finding the greatest common divisor (GCD) of two integers was first described around the year 300 B.C. This simple iterative method is often regarded as the grandfather of all algorithms in Number Theory today. Many advances have been made since then--for example, Berlekamp's algorithm for multiplicative inverse and Montgomery's technique for modular multiplication. These binary add-and-shift algorithms for efficient finite field arithmetic operations have played important roles in today s public-key cryptographic systems. Yet, two thousand three hundred years after Euclid's GCD, one algorithm remained missing--division. For many decades we did not tackle modular division problems directly. Instead, we relied on the Extended Euclidean algorithm for calculating inversion and we computed division in a two-step process--inversion followed by multiplication. This practice is so deeply rooted in our teachings and doings today that we have neglected to ask whether the idea underlying the binary Extended Euclidean algorithm can also be applied to finding a general solution for field division. This paper describes such a solution: a binary add-and-shift algorithm for modular division in a residue class. This technique for fast computation of divisions in GF(2m) is the key to a highly efficient implementation of elliptic curve cryptosystems.
Unit commitment by Lagrangian relaxation and genetic algorithms (2000)

This paper presents an application of a combined genetic algorithms (GAs) and Lagrangian relaxation (LR) method for the unit commitment (UC) problem. Genetic algorithms (GAs) are a general purpose optimization technique based on principle of natural selection and natural genetics. The Lagrangian relaxation (LR) method provides a fast solution but it may suffer from numerical convergence and solution quality problems. The proposed Lagrangian relaxation and genetic algorithms (LRGA) incorporates genetic algorithms into Lagrangian relaxation method to update the Lagrangian multipliers and improve the performance of Lagrangian relaxation method in solving combinatorial optimization problems such as the UC problem. Numerical results on two cases including a system of 100 units and comparisons with results obtained using Lagrangian relaxation (LR) and genetic algorithms (GAs), show that the feature of easy implementation, better convergence, and highly near-optimal solution to the UC problem can be achieved by the LRGA.
High optical quality polycrystalline indium phosphide grown on metal substrates by metalorganic chemical vapor deposition (2012)

III–V semiconductor solar cells have demonstrated the highest power conversion efficiencies to date. However, the cost of III-V solar cells has historically been too high to be practical outside of specialty applications. This stems from the cost of raw materials, need for a lattice-matched substrate for single-crystal growth, and complex epitaxial growth processes. To address these challenges, here, we explore the direct non-epitaxial growth of thin poly-crystalline films of III-Vs on metal substrates by using metalorganic chemical vapor deposition. This method minimizes the amount of raw material used while utilizing a low cost substrate. Specifically, we focus on InP which is known to have a low surface recombination velocity of carriers, thereby, making it an ideal candidate for efficient poly-crystalline cells where surface/interface properties at the grain boundaries are critical. The grown InP films are 1-3 μm thick and are composed of micron-sized grains that generally extend from the surface to the Mo substrate. They exhibit similar photoluminescence peak widths and positions as single-crystalline InP, as well as excellent crystallinity as examined through TEM and XRD analyses. This work presents poly-InP as a promising absorber layer for future photovoltaics.