gebhart/patrepeval huggingface dataset:
Supervised Molecular Dynamics (SuMD) Insights into the mechanism of action of SARS-CoV-2 main protease inhibitor PF-07321332 (2021)

The chemical structure of PF-07321332, the first orally available Covid-19 clinical candidate, has recently been revealed by Pfizer. No information has been provided about the interaction pattern between PF-07321332 and its biomolecular counterpart, the SARS-CoV-2 main protease (M<sup>pro</sup>). In the present work, we exploited Supervised Molecular Dynamics (SuMD) simulations to elucidate the key features that characterise the interaction between this drug candidate and the protease, emphasising similarities and differences with other structurally related inhibitors such as Boceprevir and PF-07304814. The structural insights provided by SuMD will hopefully be able to inspire the rational discovery of other potent and selective protease inhibitors.
Cutting Edge: CXCR4-Lo: Molecular Cloning and Functional Expression of a Novel Human CXCR4 Splice Variant (1999)

Human CXCR4 is a specific receptor for the CXC chemokine stromal cell-derived factor-1 (SDF-1) and a coreceptor for T cell line tropic strains of HIV-1. Genetic knockouts of CXCR4 and SDF-1 have delineated their critical role during embryonic cardiogenesis, leukopoiesis, and vasculogenesis. Herein, we used bioinformatics and differential strategies like isoform-specific RT-PCR and Northern blots to identify and clone a novel unspliced isoform of human CXCR4, termed CXCR4-Lo. CXCR4-Lo corresponds to a larger approximately 4. 0-kb mRNA transcript and differs from the known human CXCR4 by the first 9 aa in the functionally important NH2-terminal extracellular domain of the receptor. CXCR4-Lo-transfected rat basophil leukemia-2H3 cells responded to SDF-1 with a transient rise of intracellular Ca2+ concentration and by undergoing chemotaxis. Expression of CXCR4-Lo is noteworthy, as it may have differential affinity as a coreceptor for HIV strains in comparison with CXCR4. Furthermore, CXCR4-Lo may also provide a functional backup to CXCR4 during embryogenesis.
Biometric Template Security: An Overview (2012)

With the widespread deployment of biometric systems in various applications, there are increasing concerns about the security and privacy of biometric technology. Public acceptance of biometrics technology will depend on the ability of system designers to demonstrate that these systems are robust, have low error rates, and are tamper proof. In particular, we focus on biometric template security which is an important issue because, unlike passwords and tokens, compromised biometric templates cannot be revoked and reissued. Protecting the template is a challenging task due to intrauser variability in the acquired biometric traits. We present an overview of various biometric template protection schemes and their potential attacks. Biometric cryptosystems and cancelable biometrics represent emerging technologies of biometric template protection addressing these concerns and improving public confidence and acceptance of biometrics. In addition, biometric cryptosystems provide mechanisms for biometric-dependent key-release. In the last years a significant amount of approaches to both technologies have been published. A comprehensive literature of biometric cryptosystems and cancelable biometrics is presented and biometric potential attacks are discussed.
Efficient Catalytic Conversion of Fructose into 5‐Hydroxymethylfurfural in Ionic Liquids at Room Temperature (2009)

A green process for the efficient conversion of fructose into 5-hydroxymethylfurfural at room temperature is described. High selectivities for 5-HMF at fructose conversions of ca. 95 % are obtained at 25 oC for 6 h in the ionic liquid [BMIM][Cl], through addition of acetone or other cosolvents.
Inverse treatment planning with adaptively evolving voxel‐dependent penalty scheme (2004)

In current inverse planning algorithms it is common to treat all voxels within a target or sensitive structure equally and use structure specific prescriptions and weighting factors as system parameters. In reality, the voxels within a structure are not identical in complying with their dosimetric goals and there exists strong intrastructural competition. Inverse planning objective function should not only balance the competing objectives of different structures but also that of the individual voxels in various structures. In this work we propose to model the intrastructural tradeoff through the modulation of voxel-dependent importance factors and deal with the challenging problem of how to obtain a sensible set of importance factors with a manageable amount of computing. Instead of letting the values of voxel-dependent importance to vary freely during the search process, an adaptive algorithm, in which the importance factors were tied to the local radiation doses through a heuristically constructed relation, was developed. It is shown that the approach is quite general and the EUD-based optimization is a special case of the proposed framework. The new planning tool was applied to study a hypothetical phantom case and a prostate case. Comparison of the results with that obtained using conventional inverse planning technique with structure specific importance factors indicated that the dose distributions from the conventional inverse planning are at best suboptimal and can be significantly improved with the help of the proposed nonuniform penalty scheme.
ASIC automatic layout generation using large standard cell libraries (2002)

We present an automatic layout generation methodology for ASICs utilizing large standard cell libraries. We also present a complete study of layout area and circuit performance as a result of utilizing a large library of standard cells. We built libraries of all possible static CMOS cells having a chain length of up to 7. We refer to a library of all possible cells having a chain length limit of n as sn. Although Library s7 has billions of possible cells in it, our technology mapper only selected on the order of 100 of these cells to implement each of the MCNC logic synthesis benchmark circuits. We drew the following conclusions from this study. (1) For three or more layers of metal, using very large libraries (e.g., s7) is optimal in terms of area and delay. (2) For two layers of metal, limiting the library size to s5, but at least s4, is optimal in terms of area and delay. Given that the number of distinct combinational cells in industrial libraries today never exceeds 200 (and usually considerably fewer) and given that even library s4 has 3503 distinct cells, tremendous area savings (without increase in worst case path delay) are readily available by utilizing much larger cell libraries. Specifically, given that library s3 has 87 distinct cells (current industrial libraries typically have no more than this), we surmise that area savings of about 30% can be achieved by using library s7 for three or more metal layers versus any current industrial library.
Generation of annexin V‐positive platelets and shedding of microparticles with stimulus‐dependent procoagulant activity during storage of platelets at 4°C (2000)

Propyl gallate induces platelet procoagulant activity and annexin V binding. Stored platelets differ from fresh platelets in a lower reactivity to propyl gallate activation and a higher rate of microparticle shedding.
Nanostructured biocides for means of rehabilitation. (2010)

In this work, the description of technology of intercalation of montmorillonite by ions of biometals is submitted. Laboratory techniques of definition of a mass fraction of silver and copper in montmorillonite are resulted The manufacturing regulations of obtaining of nanodispersed powders of intercalated montmorillonite are submitted. Bases of technology of obtaining and manufacturing of cosmetic means on a basis of nanomaterials; technologies of antibacterial processing of textile materials, obtaining of antimicrobic properties by medical polymers are described in the report. Bases of technology of obtaining of biocidal and fungicidal coatings (paints, varnishes) on a basis of nanomaterials are described. The estimation of biocidal and properties of nanomaterials on a basis of intercalated montmorillonite by an integral disk-diffusion method is resulted. High efficiency of application of nanosystems on a basis of intercalated montmorillonite for obtaining of antimicrobic properties in paint and varnish materials is shown.
1991 Volvo Award in basic sciences. Collagen types around the cells of the intervertebral disc and cartilage end plate: an immunolocalization study. (1991)

Several types of collagen are known to exist in the intervertebral disc in addition to the fibrillar collagens, Types I and II. Although they constitute only a small percentage of the total collagen content, these minor collagens may have important functions. This study was designed to investigate the presence of Types I, II, III, IV, VI, and IX collagens in the intervertebral disc and cartilage end plate by immunohistochemistry, thereby establishing their location within the tissues. Types III and VI collagen have a pericellular distribution in animal and human tissue. No staining for Type IX collagen was present in normal human disc, but in rat and bovine intervertebral disc, it was also located pericellularly. These results show that cells of the intervertebral disc and cartilage end plate sit in fibrous capsules, forming chondrons similar to those described in articular cartilage. In pathologic tissue the amount and distribution of the collagen types, and the organization of the pericellular capsule, differ from that seen in control material.
Generation of Myostatin Gene-Edited Channel Catfish (Ictalurus punctatus) via Zygote Injection of CRISPR/Cas9 System (2017)

The myostatin (MSTN) gene is important because of its role in regulation of skeletal muscle growth in all vertebrates. In this study, CRISPR/Cas9 was utilized to successfully target the channel catfish, Ictalurus punctatus, muscle suppressor gene MSTN. CRISPR/Cas9 induced high rates (88-100%) of mutagenesis in the target protein-encoding sites of MSTN. MSTN-edited fry had more muscle cells (p < 0.001) than controls, and the mean body weight of gene-edited fry increased by 29.7%. The nucleic acid alignment of the mutated sequences against the wild-type sequence revealed multiple insertions and deletions. These results demonstrate that CRISPR/Cas9 is a highly efficient tool for editing the channel catfish genome, and opens ways for facilitating channel catfish genetic enhancement and functional genomics. This approach may produce growth-enhanced channel catfish and increase productivity.
Silicon Integrated Nanophotonic Devices for On-Chip Multi-Mode Interconnects (2020)

Mode-division multiplexing (MDM) technology has drawn tremendous attention for its ability to expand the link capacity within a single-wavelength carrier, paving the way for large-scale on-chip data communications. In the MDM system, the signals are carried by a series of higher-order modes in a multi-mode bus waveguide. Hence, it is essential to develop on-chip mode-handling devices. Silicon-on-insulator (SOI) has been considered as a promising platform to realize MDM since it provides an ultra-high-index contrast and mature fabrication processes. In this paper, we review the recent progresses on silicon integrated nanophotonic devices for MDM applications. We firstly discuss the working principles and device configurations of mode (de)multiplexers. In the second section, we summarize the multi-mode routing devices, including multi-mode bends, multi-mode crossings and multi-mode splitters. The inverse-designed multi-mode devices are then discussed in the third section. We also provide a discussion about the emerging reconfigurable MDM devices in the fourth section. Finally, we offer our outlook of the development prospects for on-chip multi-mode photonics.
The Delivery Pipeline (2019)

The delivery pipeline refers to the sequence of automated processes that manage the build, test, and release process for your project. The term was popularized by the book Continuous Delivery, which says:
<title>Use of document structure analysis to retrieve information from documents in digital libraries</title> (1997)

This paper describes an approach to retrieving information from document images stored in a digital library by means of knowledge-based layout analysis and logical structure derivation techniques. Queries on document image content are categorized in terms of the type of information that is desired, and are parsed to determine the type of document from which information is desired, the syntactic level of the information desired, and the level of analysis required to extract the information. Using these clauses in the query, a set of salient documents are retrieved, layout analysis and logical structure derivation are performed on the retrieved documents, and the documents are then analyzed in detail to extract the relevant logical components. A 'document browser' application, being developed based on this approach, allows a user to interactively specify queries on the documents in the digital library using a graphical user interface, provides feedback about the candidate documents at each stage of the retrieval process, and allows refinements of the query based on the intermediate results of the search. Results of a query are displayed either as an image or as formatted text.
Cholesteric and Nematic Liquid Crystalline Phase Behavior of Double-Stranded DNA Stabilized Single-Walled Carbon Nanotube Dispersions (2011)

The first lyotropic cholesteric single-walled carbon nanotube (SWNT) liquid crystal phase was obtained by dispersing SWNTs in an aqueous solution of double-stranded DNA (dsDNA). Depending on the dispersion methodology, the polydomain nematic phase previously reported for other lyotropic carbon nanotube dispersions could also be obtained. The phase behavior and dispersion microstructure were affected by the relative concentrations of dsDNA and SWNT and whether small bundles were removed prior to concentrating the dispersions. This readily controlled phase behavior opens new routes for producing SWNT films with controlled morphology.
Banking the Poor (2005)

Low-income households often lack access to banking accounts and face high costs for transacting basic financial services through check cashers and other alternative financial service providers. These families find it more difficult to save and plan financially for the future. Living paycheck to paycheck leaves them vulnerable to medical or job emergencies that may endanger their financial stability, and lack of longer-term savings undermines their ability to improve skills, purchase a home, or send their children to college. Additionally, high cost financial services and inadequate access to bank accounts may undermine widely shared societal goals of reducing poverty, moving families from welfare to work, and rewarding work through incentives such as the Earned Income Tax Credit. This Article calls for the transformation of financial services for the poor. The Article first explores the dual financial services market in which insured depository institutions largely serve middle- and upper-income persons, and check cashers and other alternative service providers largely serve low- and moderate-income households. The Article argues that the social benefits of breaking down barriers between these markets exceed the costs of doing so. The Article also contends that network externalities in electronic payment systems help explain why some technologies that would help low-income consumers have not been as rapidly adopted as would be socially beneficial. In response to this problem, the Article recommends governmental incentives for private sector financial and technological innovation to help lower banking and savings barriers for the poor. Better access to financial services is critical for low-income persons seeking to enter the economic mainstream.
Palladium-Catalyzed Coupling Reactions of 1-Bromoadamantane with Styrenes and Arenes (1998)

The palladium-catalyzed reaction of 1-bromoadamantane (1-Br) with styrene and donor-substituted styrenes gave the corresponding Heck-type coupling products 3 a and b, and 5 a and b in moderate yields (15-41%), while the reaction of 1-Br with various arenes 6 a - p under palladium catalysis gave the corresponding adamantyl-substituted arenes 7 a - p in good to excellent yields (35-98%).
Type I Diabetes and Multiple Sclerosis Patients Target Islet Plus Central Nervous System Autoantigens; Nonimmunized Nonobese Diabetic Mice Can Develop Autoimmune Encephalitis (2001)

Type I diabetes and multiple sclerosis (MS) are distinct autoimmune diseases where T cells target either islet or CNS self-proteins. Unexpectedly, we found that autoreactive T cells in diabetic patients, relatives with high diabetes risk, nonobese diabetic (NOD) mice, and MS patients routinely target classical islet as well as CNS autoantigens. The pathogenic potential of CNS autoreactivity was testable in NOD mice. Pertussis holotoxin, without additional Ags or adjuvants, allowed development of an NOD mouse-specific, autoimmune encephalitis with variable primary-progressive, monophasic, and relapsing-remitting courses. T cells from diabetic donors transferred CNS disease to pertussis toxin-pretreated NOD.scid mice, with accumulation of CD3/IFN-gamma transcripts in the brain. Diabetes and MS appear more closely related than previously perceived. NOD mouse-specific, autoimmune encephalitis provides a new MS model to identify factors that determine alternative disease outcomes in hosts with similar autoreactive T cell repertoires.
Investigations of Repetition Rate Stability of a Mode-Locked Quantum Dot Semiconductor Laser in an Auxiliary Optical Fiber Cavity (2010)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> We have investigated experimentally the pulse train (mode beating) stability of a monolithic mode-locked multi-section quantum-dot laser with an added passive auxiliary optical fiber cavity. Addition of the weakly coupled (<formula formulatype="inline"><tex Notation="TeX">${\approx}-24$</tex></formula> dB) cavity reduces the current-induced shift <formula formulatype="inline"><tex Notation="TeX">$d\nu/dI$</tex></formula> of the principal peak in the RF spectrum (the effective pulse repetition frequency) by more than an order of magnitude, from <formula formulatype="inline"><tex Notation="TeX">${-}39.5$</tex></formula> to <formula formulatype="inline"><tex Notation="TeX">${-}2.3$</tex></formula> kHz/mA. The rms timing jitter of the pulse train is simultaneously reduced from 1.4 to 0.9 ps. </para>
Register requirements of pipelined processors (1992)

To enable concurrent instruction execution, scientific computers generally rely on pipelining, which combines with faster system clocks to achieve greater throughput. Each concurrently executing instruction requires buffer space, usually implemented as a register, to receive its result. This paper focuses on the issue of how many registers are required to achieve optimal performance in pipelined scientific computers. Four machine models are considered: single, double, and triple issue scalar machines, and vector machines with various register lengths. A model is presented that accurately relates the register requirements for optimum performance cyclically scheduled loops with tree-dependence graphs to the degree of function unit pipelining, the instruction issue bandwidth, and code properties. A method for finding upper and lower bounds on the minimum register requirements is also presented.The result of this work is a theory for assessing register requirements that can be used to reveal fundamental differences among machines within a space of architectural and implementation design choices. Some experimental data is also provided to support the theory.
Cobalt, chromium, and nickel concentrations in body fluids of patients with porous‐coated knee or hip prostheses (1989)

Abstract Co, Cr, and Ni concentrations were determined by electrothermal atomic absorption spectrophotometry in serum and urine specimens collected from a group of 28 patients at intervals of from 1 day to 2.5 years after total knee or hip arthroplasty with porous‐coated prostheses fabricated of Co‐Cr alloy (ASTM F‐75‐82). Two control groups were also tested: (a) 42 healthy adults and (b) 16 orthopaedic patients after total knee or hip arthroplasty with porous‐coated prostheses fabricated predominantly of Ti‐Al‐V alloy (ASTM F‐136‐84). All prostheses contained polyethylene components to avoid metal‐to‐metal contact. Mean Co concentrations in serum and urine were slightly increased in patients with Co‐Cr knee implants at 6–120 weeks after surgery, compared with (a) preoperative values, (b) corresponding values in patients with Co‐Cr hip implants, and (c) corresponding values in control patients with Ti‐Al‐V knee and hip prostheses. Substantially increased Co levels were observed in serum and urine of two patients at 7 weeks and 22 months postarthroplasty, associated with loosening of the prostheses; one of the patients also had elevated Cr levels in serum and urine. Although ASTM F‐75‐82 and F‐136‐84 alloys contain very little Ni (<1.0 and <0.2% Ni, respectively, by wt), mean Ni concentrations in serum and urine were greatly increased at 1–2 days after implantation of Ti‐Al‐V and Co‐Cr prostheses, diminishing by 2 weeks. The postoperative hypernickelemia and nickeluresis may reflect contamination of the operative field with Ni‐containing particles from the drills, cutting jigs, and drilling jigs, or it may represent a previously unrecognized pathophysiological response to surgery.
Inhibition of Mold Growth by Sourdough Bread Cultures (2007)

Sourdough bread cultures are mixtures of wild yeasts and Lactobacillus bacteria living in flour and water, where they form an interesting symbiosis that makes the culture quite stable. The presence of lactic acid bacteria (LAB) in sourdough bread cultures increases the shelf life of the sourdough bread and other sweet baked goods made with these cultures, due to the inhibitory effect of organic acids on spoilage molds. In addition, it has been found that when sourdough LAB are cultivated they produce antifungal substances, such as organic acids (in particular, lactic acid and acetic acid), carbon dioxide, ethanol, and hydrogen peroxide, and other, as yet unidentified inhibitory substances, that prevent mold growth. The inhibitory effect of four American sourdough cultures were tested for antifungal activity against the common spoilage molds, Aspergillus flavus, Aspergillus niger, Penicillium expansum, Penicullium roqueforti, and Cladosporium cladosporioides. In these experiments, actively growing sourdough cultures were inoculated into modified deMan Rogosa and Sharpe (mMRS) broth and incubated. After incubation, the cultures were centrifuged and filtered through 0.2µm membrane filters, the supernatants were collected and mixed with Potato Dextrose Agar (PDA). This mixture was used as culture medium for the growth of the spoilage molds. The growth rates of molds growing in the presence of the sourdough culture supernatants were compared with controls, where the molds were cultivated only in PDA. The results showed that Aspergillus flavus and Cladosporium cladosporioides were inhibited the most by the sourdough cultures. Therefore, the use of sourdough cultures shows promise for preserving food products from spoilage, as they could be a source of natural antimicrobial and antimycotic agents for use in the food industry.