gebhart/patrepeval huggingface dataset:
Mechanism-based affinity capture of sirtuins (2010)

The ability to probe for catalytic activities of enzymes and to detect their abundance in complex biochemical contexts has traditionally relied on a combination of kinetic assays and techniques such as western blots that use expensive reagents such as antibodies. The ability to simultaneously detect activity and isolate a protein catalyst from a mixture is even more difficult and currently impossible in most cases. In this manuscript we describe a chemical approach that achieves this goal for a unique family of enzymes called sirtuins using novel chemical tools, enabling rapid detection of activity and isolation of these protein catalysts. Sirtuin deacetylases are implicated in the regulation of many physiological functions including energy metabolism, DNA-damage response, and cellular stress resistance. We synthesized an aminooxy-derivatized NAD(+) and a pan-sirtuin inhibitor that reacts on sirtuin active sites to form a chemically stable complex that can subsequently be crosslinked to an aldehyde-substituted biotin. Subsequent retrieval of the biotinylated sirtuin complexes on streptavidin beads followed by gel electrophoresis enabled simultaneous detection of active sirtuins, isolation and molecular weight determination. We show that these tools are cross reactive against a variety of human sirtuin isoforms including SIRT1, SIRT2, SIRT3, SIRT5, SIRT6 and can react with microbial derived sirtuins as well. Finally, we demonstrate the ability to simultaneously detect multiple sirtuin isoforms in reaction mixtures with this methodology, establishing proof of concept tools for chemical studies of sirtuins in complex biological samples.
An Improved Stokes Parameter Method for Determination of the Cell Thickness and Twist Angle of Twisted Nematic Liquid Crystal Cells (1998)

Based on the method previously proposed by us, an improved Stokes parameter method (ISPM), which is independent of the liquid crystal (LC) molecular alignment direction at the front substrate of the cell, is presented here to determine the cell thickness and twist angle of twisted nematic liquid crystal (TNLC) cells. The function equations of the Stokes parameters with the cell thickness and twist angle are deduced, and the experimental method is introduced. The preliminary experimental results verify the ISPM's validity. This method is very simple basically, only four transmission intensities of the TNLC cell are required to be measured. Furthermore, the theoretical analyses indicate that a high level of accuracy can be obtained by means of this method.
Partial Decision Overrides in a Declarative Policy Framework (2020)

The ability to specify various policies with different overriding criteria allows for complex sets of sharing policies. This is particularly useful in situations in which data privacy depends on various properties of the data, and complex policies are needed to express the conditions under which data is protected. However, if overriding policy decisions constrain the affected data, decisions from overridden policies should not be suppressed completely, because they can still apply to subsets of the affected data. This article describes how a privacy policy framework can be extended with a mechanism to partially override decisions based on specified constraints. Our solution automatically generates complementary sets of decisions for both the overridden and the complementary, non-overridden subsets of the data, and thus, provides a means to specify a complex policies tailored to specific properties of the protected data.
Extending document management systems with user-specific active properties (2000)

Document properties are a compelling infrastructure on which to develop document management applications. A property-based approach avoids many of the problems of traditional heierarchical storage mechanisms, reflects document organizations meaningful to user tasks, provides a means to integrate the perspectives of multiple individuals and groups, and does this all within a uniform interaction framework. Document properties can reflect not only categorizations of documents and document use, but also expressions of desired system activity, such as sharing criteria, replication management, and versioning. Augmenting property-based document management systems with active properties that carry executable code enables the provision of document-based services on a property infrastructure. The combination of document properties as a uniform mechanism for document management, and active properties as a way of delivering document services, represents a new paradigm for document management infrastructures. The Placeless Documents system is an experimental prototype developed to explore this new paradigm. It is based on the seamless integration of user-specific, active properties. We present the fundamental design approach, explore the challenges and opportunities it presents, and show our architectures deals with them.
Identifying User Issues and Request Types in Forum Question Posts Based on Discourse Analysis (2016)

In this paper we propose the detection of user issues and request types in technical forum question posts with a twofold purpose: supporting up-to-date knowledge generation in organizations that provide (semi-) automated customer-care services, and enriching forum metadata in order to enhance the effectiveness of search. We present a categorization system for detecting the proposed question post types based on discourse analysis, and show the advantage of using discourse patterns compared to a baseline relying on standard linguistic features. Besides the detailed description of our method, we also release our annotated corpus to the community.
In/sub 0.53/Ga/sub 0.47/As/InP floating guard ring avalanche photodiodes fabricated by double diffusion (1990)

In/sub 0.53/Ga/sub 0.47/As/InP separate absorption and multiplication region avalanche photodiodes (SAM-APDs) with doubly diffused floating guard rings have been demonstrated. The planar, front-side illuminated devices are easily fabricated and incorporate strong guarding against edge and surface breakdown. Edge gain is suppressed both by the action of the floating guard rings and by the grading of the p-n junction at the outer edges of the active region that results from the second diffusion. Uniform gains as high as 85 have been measured at multiplied dark currents <100 nA. Multiplied dark currents below 5 nA have been measured at 90% of breakdown, with capacitances below 400 fF for front-side illuminated devices. The low values of dark current and capacitance, as well as the ease of fabrication, make the devices well suited for fiber-optic applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
External cavity wavelength tunable laser with on-chip VOA using etched mirror based integration technology (2006)

An external cavity wavelength tunable laser using a novel gain chip with a monolithically integrated variable optical attenuator is demonstrated. An output power tuning range of 55 dB and output powers in excess of 15 dBm were obtained over the whole C-band.
Synthesis and characterization of novel biodegradable unsaturated poly(ester amide)s (2005)

Abstract A series of novel biodegradable unsaturated poly(ester amide)s (UPEAs) were synthesized through the solution polycondensation of two unsaturated monomers, di‐ p ‐nitrophenyl fumarate and L ‐phenylalanine 2‐butene‐1,4‐diol diester p ‐toluene sulfonate, and four other saturated monomers in different combinations. The UPEAs were obtained in fairly good yields with N,N ‐dimethylacetamide (DMA) as the solvent. The number‐average and weight‐average molecular weights of the UPEAs, measured by gel permeation chromatography, ranged from 10 to 30 kg/mol, they had a rather narrow molecular weight distribution of 1.40. The chemical structures of the novel biodegradable UPEAs were confirmed by both IR and NMR spectra. The UPEAs had higher glass‐transition temperatures than saturated PEAs of similar structures, and their glass‐transition temperatures were affected more by the CC double bond located in the diamide part than by those in the diester part. The solubility of the polymers was poor in water but better in DMA and dimethyl sulfoxide. With the availability of these inherent CC double bonds in the UPEA backbones, these UPEAs have the functionality of CC bonds, such as photochemical reactivity or the ability to react with or be modified by other bioactive or other environmentally sensitive compounds, and this can easily extend their applications to biomedical and pharmaceutical areas. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 1463–1477, 2005
ChemInform Abstract: SYNTHESIS OF ISOCOUMARINS VIA THALLATION‐OLEFINATION OF BENZOIC ACIDS (1984)

Abstract In einer Eintopfreaktion werden die Benzoesäuren (I) zunächst zu den ortho‐Derivaten (II) thalliert, welche sich dann mit einer Reihe ungesättigter Verbindungen, wie einfachen Olefinen (III), Allylhalogeniden (VII), Vinylhalogeniden und ‐acetaten (X), (XI), 1,2‐ (XVI) sowie 1,3‐Dienen (XV) und Vinylcyclopropanen (XIX), (XX) zu Isocumarinen cyclisieren lassen.
Nanotopography-mediated Reverse Uptake for siRNA Delivery into Neural Stem Cells to Enhance Neuronal Differentiation (2013)

RNA interference (RNAi) for controlling gene expression levels using siRNA or miRNA is emerging as an important tool in stem cell biology. However, the conventional methods used to deliver siRNA into stem cells result in significant cytotoxicity and undesirable side-effects. To this end, we have developed a nanotopography-mediated reverse uptake (NanoRU) delivery platform to demonstrate a simple and efficient technique for delivering siRNA into neural stem cells (NSCs). NanoRU consists of a self-assembled silica nanoparticle monolayer coated with extracellular matrix proteins and the desired siRNA. We use this technique to efficiently deliver siRNA against the transcription factor SOX9, which acts as a switch between neuronal and glial fate of NSCs. The knockdown of SOX9 enhanced the neuronal differentiation and decreased the glial differentiation of the NSCs. Our NanoRU platform demonstrates a novel application and the importance of nanotopography-mediated siRNA delivery into stem cells as an effective method for genetic manipulation.
Ion implantation enhanced metal–Si–metal photodetectors (1994)

The quantum efficiency and frequency response of simple Ni-Si-Ni metal-semiconductor-metal (MSM) photodetectors at long wavelengths are significantly enhanced with a simple, ion-implantation step to create a highly absorbing region /spl sim/1 /spl mu/m below the Si surface. The internal quantum efficiency is improved by a factor of /spl sim/3 at 860 nm (to 64%) and a full factor of ten at 1.06 /spl mu/m (to 23%) as compared with otherwise identical unimplanted devices. Dark currents are only slightly affected by the implantation process and are as low as 630 pA for a 4.5-/spl mu/m gap device at 10-V bias. Dramatic improvement in the impulse response is observed, 100 ps vs, 600 ps, also at 10-V bias and 4.5-/spl mu/m gap, due to the elimination of carrier diffusion tails in the implanted devices. Due to its planar structure, this device is fully VLSI compatible. Potential applications include optical interconnections for local area networks and multi-chip modules. >
Constitutive expression of the<i>Period1</i>gene impairs behavioral and molecular circadian rhythms (2006)

Three mammalian Period (Per) genes, termed Per1, Per2, and Per3, have been identified as structural homologues of the Drosophila circadian clock gene, period (per). The three Per genes are rhythmically expressed in the suprachiasmatic nucleus (SCN), the central circadian pacemaker in mammals. The phases of peak mRNA levels for the three Per genes in the SCN are slightly different. Light sequentially induces the transcripts of Per1 and Per2 but not of Per3 in mice. These data and others suggest that each Per gene has a different but partially redundant function in mammals. To elucidate the function of Per1 in the circadian system in vivo, we generated two transgenic rat lines in which the mouse Per1 (mPer1) transcript was constitutively expressed under the control of either the human elongation factor-1alpha (EF-1alpha) or the rat neuron-specific enolase (NSE) promoter. The transgenic rats exhibited an approximately 0.6-1.0-h longer circadian period than their wild-type siblings in both activity and body temperature rhythms. Entrainment in response to light cycles was dramatically impaired in the transgenic rats. Molecular analysis revealed that the amplitudes of oscillation in the rat Per1 (rPer1) and rat Per2 (rPer2) mRNAs were significantly attenuated in the SCN and eyes of the transgenic rats. These results indicate that either the level of Per1, which is raised by overexpression, or its rhythmic expression, which is damped or abolished in over expressing animals, is critical for normal entrainment of behavior and molecular oscillation of other clock genes.
Sequence Analysis of <i>Mus dunni</i> Endogenous Virus Reveals a Hybrid VL30/Gibbon Ape Leukemia Virus-Like Structure and a Distinct Envelope (1998)

Mus dunni endogenous virus (MDEV) can be activated from M. dunni cells by exposing the cells to hydrocortisone or 5-iodo-2'-deoxyuridine. Interference analysis has revealed that MDEV uses a receptor for cell entry that is different from those used by other murine retroviruses. The entire genome has now been sequenced, revealing a long terminal repeat (LTR)-gag-pol-env-LTR structure typical of simple retroviruses of the murine leukemia virus genus, with no additional open reading frames between env and the 3' LTR. The LTRs and other noncoding regions of MDEV are most closely related to those of VL30 elements, while the majority of the coding sequences are most closely related to those of gibbon ape leukemia virus. MDEV represents the first example of a naturally occurring, replication-competent virus with sequences closely related to VL30 elements. The U3 region of MDEV contains six nearly perfect 80-bp repeats and the beginning of a seventh, and the region expected to contain the packaging sequence contains approximately four imperfect 33-bp repeats. The receptor specificity domains of the envelope are unique among retroviruses and show no apparent similarity to regions of known proteins.
β1 Integrin: Critical Path to Antiangiogenic Therapy Resistance and Beyond (2013)

Angiogenesis is an important tissue-level program supporting the growth of highly aggressive cancers and early-stage metastases. However, rapid emergence of resistance to antiangiogenic therapies, such as bevacizumab, greatly limits the clinical utility of these promising approaches. The mechanisms of resistance to antiangiogenic therapy remain incompletely understood. The tumor microenvironment has been demonstrated to be a source of broad therapeutic resistance in multiple cancers. Much of the interaction between the cells comprising a tumor and their microenvironment is driven by integrins. Notably, signaling downstream of integrins in tumor cells promotes fundamental programs vital to aggressive cancer biology, including proliferation, growth, invasion, and survival signaling. These functions then can contribute to malignant phenotypes, including metastasis, therapy resistance, epithelial-to-mesenchymal transition, and angiogenesis. Accordingly, we found β1 integrin to be functionally upregulated in tumor specimens from patients after bevacizumab failure and in xenograft models of bevacizumab resistance. Inhibition of β1 in tumor cells with stable gene knockdown or treatment with OS2966, a neutralizing β1 integrin monoclonal antibody, attenuated aggressive tumor phenotypes in vitro and blocked growth of bevacizumab-resistant tumor xenografts in vivo. Thus, β1 integrins promote resistance to antiangiogenic therapy through potentiation of multiple malignant programs facilitated by interactions with the tumor microenvironment. The elucidation of this mechanism creates an outstanding opportunity for improving patient outcomes in cancer.
Acoustic diaphragm for speakers and method of producing the same (1982)

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Genomic and transcriptomic insights into the efficient entomopathogenicity of Bacillus thuringiensis (2015)

Bacillus thuringiensis has been globally used as a microbial pesticide for over 70 years. However, information regarding its various adaptions and virulence factors and their roles in the entomopathogenic process remains limited. In this work, we present the complete genomes of two industrially patented Bacillus thuringiensis strains (HD-1 and YBT-1520). A comparative genomic analysis showed a larger and more complicated genome constitution that included novel insecticidal toxicity-related genes (ITRGs). All of the putative ITRGs were summarized according to the steps of infection. A comparative genomic analysis showed that highly toxic strains contained significantly more ITRGs, thereby providing additional strategies for infection, immune evasion, and cadaver utilization. Furthermore, a comparative transcriptomic analysis suggested that a high expression of these ITRGs was a key factor in efficient entomopathogenicity. We identified an active extra urease synthesis system in the highly toxic strains that may aid B. thuringiensis survival in insects (similar to previous results with well-known pathogens). Taken together, these results explain the efficient entomopathogenicity of B. thuringiensis. It provides novel insights into the strategies used by B. thuringiensis to resist and overcome host immune defenses and helps identify novel toxicity factors.
Detecting heap smashing attacks through fault containment wrappers (2002)

Buffer overflow attacks are a major cause of security breaches in modern operating systems. Not only are overflows of buffers on the stack a security threat, overflows of buffers kept on the heap can be too. A malicious user might be able to hijack the control flow of a root-privileged program if the user can initiate an overflow of a buffer on the heap when this overflow overwrites a function pointer stored on the heap. The paper presents a fault-containment wrapper which provides effective and efficient protection against heap buffer overflows caused by C library functions. The wrapper intercepts every function call to the C library that can write to the heap and performs careful boundary checks before it calls the original function. This method is transparent to existing programs and does not require source code modification or recompilation. Experimental results on Linux machines indicate that the performance overhead is small.
Single-mask double-patterning lithography (2009)

This paper proposes shift-trim double patterning lithography (ST-DPL), a cost-effective method for achieving 2× pitchrelaxation with a single photomask (especially at polysilicon layer). The mask is re-used for the second exposure by applying a translational mask-shift. Extra printed features are then removed using a non-critical trim exposure. The viability of ST-DPL is demonstrated. The proposed method has many advantages with virtually no area overhead (< 0.3% standard-cell area): (1) cuts mask-cost to nearly half that of standard-DPL, (2) reduces overlay errors between the two patterns and can virtually eliminate it in some process implementations, (3) alleviates the bimodal problem in doublepatterning, and (4) enhances throughput of first-rate scanners. We implement a small 45nm standard-cell library and small benchmark designs with ST-DPL to illustrate its viability.
Reduced switching delay in wavelength-division-multiplexed 2D multiple-plane optical interconnections using multiple-wavelength vertical-cavity surface-emitting laser (VCSEL) arrays (1995)

We calculate the expected number of internodal hops for a network established with a wavelength-division-multiplexed (WDM) 2-D multiple-plane optical interconnection. This WDM optical interconnection incorporates WDM pixels consisting of multiple-wavelength vertical-cavity surface-emitting laser (VCSEL) arrays and wavelength-selective detectors. The WDM interconnection can support simultaneous and reconfigurable communication among a network of nodes. Using the expected number of hops as a measure of internodal switching delay, we show that the integration of WDM into the interconnection results in a significantly reduced delay as compared to single-wavelength systems. Substantial delay reduction results even when the number of wavelengths is small relative to the number of 2-D planes. We analyze the bus, dual-bus, and ring architectures since they define the means of communication between pixels. For each architecture, we analyze three configurations which provide each node access to: (1) an entire plane of pixels, (2) a row (or column) of pixels, or (3) an individual pixel. When each network node has access to an entire plane of pixels, the proposed WDM interconnection incurs substantially shorter delay than single-wavelength optical solutions. By allowing a node to access an entire row or column of pixels, the interconnection benefits from the incorporation of spatial-division-multiplexing (SDM) and the number of interconnections can grow substantially with negligible added delay. Finally, when a node can access only a single pixel, a large number of independent processors can be interconnected exhibiting far less switching delay than other electronic or optical interconnections of comparable size.
Compression Efficiency Improvement over HEVC Main 10 Profile for HDR and WCG Content (2016)

The paper presents the joint proposal by Arris, Dolby and InterDigital as a response to the Call-for-Evidence of the High Dynamic Range and Wide Color Gamut (HDR/WCG) video compression in MPEG. The joint proposal introduces a set of new HDR coding technologies, including the IPT-PQ color space, the adaptive reshaping process, the color enhancement filters, and the adaptive transfer function. These new coding technologies are applied to the decoded output of an HEVC decoder. Hence, no changes to the lower level logics of the HEVC decoder are required to implement the proposal. Formal subjective tests conducted by MPEG confirmed that the proposal could achieve significant subjective quality improvements over the HEVC Main10 anchors at similar bit rates for HDR/WCG video content.