gebhart/patrepeval huggingface dataset:
Cyclometalated Gold(III) Complexes Containing N‐Heterocyclic Carbene Ligands Engage Multiple Anti‐Cancer Molecular Targets (2017)

Abstract Metal N‐heterocyclic carbene (NHC) complexes are a promising class of anti‐cancer agents displaying potent in vitro and in vivo activities. Taking a multi‐faceted approach employing two clickable photoaffinity probes, herein we report the identification of multiple molecular targets for anti‐cancer active pincer gold(III) NHC complexes. These complexes display potent and selective cytotoxicity against cultured cancer cells and in vivo anti‐tumor activities in mice bearing xenografts of human cervical and lung cancers. Our experiments revealed the specific engagement of the gold(III) complexes with multiple cellular targets, including HSP60, vimentin, nucleophosmin, and YB‐1, accompanied by expected downstream mechanisms of action. Additionally, Pt II and Pd II analogues can also bind the cellular proteins targeted by the gold(III) complexes, uncovering a distinct pincer cyclometalated metal–NHC scaffold in the design of anti‐cancer metal medicines with multiple molecular targets.
HybNET (2013)

The emergence of Software-Defined Networking(SDN) has led to a paradigm shift in network management. SDN has the capability to provide clear and easy management of complex operational challenges in large scale networks. However, most of the existing work in SDN network management assumes a full deployment of SDN enabled network switches. Due to both practical and financial limitation real implementations are likely to transition through a partial deployment. In this paper, we describe our experience in the design of HybNET a framework for automated network management of a hybrid network infrastructure (both SDN and legacy network infrastructure). We discuss some of the challenges we encountered, and provide a best-effort solution in providing compatibility between legacy and SDN switches while retaining some of the advantages and flexibility of SDN enabled switches. We have tested our tool on small hybrid network infrastructure, and applied it to manage the OpenStack Neutron interface a well known open-source IaaS provider.
Composite Damage Detection Using Laser Vibrometry with Nonlinear Response Characteristics (2011)

Composite materials are susceptible to subsurface damage mechanisms (delaminations, disbonds, etc), which are difficult to detect visually. Current inspection techniques for composite materials used in military aircraft are time consuming and typically require removal of the component for inspection. In this paper, a technique is discussed that uses multi-amplitude frequency response measurements collected with a three-dimensional scanning laser vibrometer to detect and locate damage by observing nonlinear vibration response characteristics introduced into composite specimens by material damage. A carbon fiber composite panel with several impact damage locations is investigated. The panel is excited by a piezoelectric actuator and the surface velocity is measured with a 3-D scanning laser vibrometer. Nonlinear characteristics in the measured response at multiple amplitudes of excitation are used to locate and detect the subsurface damage introduced by the impacts. The higher energy level impacts investigated were successfully detected using this reference-free technique. In addition, the damage on the panel is further localized by investigating nonlinearities at higher frequency ranges.
MO‐E‐T‐618‐03: Dynamic Intraoperative Prostate Brachytherapy Using 3D TRUS Guidance with Robotic Assistance (2005)

Purpose: Develop a dynamic intraoperative prostate brachytherapy system, in which all phases of the procedure are performed in one session, including planning, monitoring of prostate changes, dynamic re‐planning, optimal needle insertion including oblique trajectories and automatic seed localization in US images, to deal with variabilities in the current procedure. Method and Materials: The system consists of 3D TRUS imaging, a robot and software tools for prostate segmentation, intraoperative planning, oblique needle segmentation and tracking, seed segmentation, and 3D dose planning. The robot and 3D TRUS coordinate systems are unified with robot and image calibrations. In 3D TRUS images, the prostate is segmented using discrete dynamic contour method, and optimal implantation plan is performed by applying geometric optimization followed by simulated annealing. The robot can be controlled to guide the needle to target points in 3D TRUS images along oblique trajectories accurately and consistently. The inserted needles are segmented and tracked using grey‐level change, and seed segmentation is performed using 3D line segment patterns. Results: Needle placement accuracy of the robot at “patient” skin was 0.15mm±0.06mm, and needle angulation error was 0.07°. Needle targeting accuracy was 0.79mm±0.32mm. The average difference between manual and the prostate segmentation algorithm of prostate boundaries was −0.20±0.28mm. In our needle tracking tests, errors in determining needle orientation were less than 2° in robot yaw and 0.7° in robot pitch orientations, for up to 20° needle insertion angles when the needle insertion distance was greater than 15mm. The true‐positive rates for the seed segmentation algorithm in 3D TRUS images were 100% for agar and 93% for chicken phantoms. With optimal planning tools provided, 98% of prostate volume receives 80% of dose coverage. Conclusion: The result of this work provides a tool to achieve dynamic intraoperative prostate brachytherapy using 3D TRUS imaging and robotic assistance together with efficient segmentation software.
Homogenized Fourier transform holographic data storage using phase spatial light modulators and methods for recovery of data from the phase image (2006)

We present a method for homogenizing the Fourier spectrum for holographic digital data storage by use of a phase spatial light modulator (SLM), and methods for the recovery of data from a phase image are implemented and discussed. Binary digital data are displayed on a phase SLM operating in 0 and pi phase modes to optimally remove the intense dc peak so as to obtain a homogenized Fourier spectrum. Methods based on holographic interferometry have been developed and employed for recovery of the original amplitude data page from the phase-data page. A new edge-detection-based method also has been demonstrated and analyzed for reconstruction of the original data. Experimental results are presented to confirm the feasibility of these novel techniques.
Goldilocks (2010)

research-article Share on Goldilocks: a race-aware Java runtime Authors: Tayfun Elmas Koç University, Istanbul, Turkey Koç University, Istanbul, TurkeyView Profile , Shaz Qadeer Microsoft Research, Redmond, WA Microsoft Research, Redmond, WAView Profile , Serdar Tasiran Koç University, Istanbul, Turkey Koç University, Istanbul, TurkeyView Profile Authors Info & Claims Communications of the ACMVolume 53Issue 11November 2010 pp 85–92https://doi.org/10.1145/1839676.1839698Online:01 November 2010Publication History 11citation5,136DownloadsMetricsTotal Citations11Total Downloads5,136Last 12 Months2,188Last 6 weeks917 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
<title>Low-temperature in-situ dry cleaning process for epitaxial layer multiprocessing</title> (1991)

A low-temperature (600-750C) dry surface cleaning process has been developed for in-situ removal of native oxide layers and other surface contaminants. The cleaning process chemistry consists of a mixture of germane (Ge114) and hydrogen (112) gases with very low germane-tohydrogen flow ratio (10-20 ppm). The process parameters (e. g. temperature pressure and CeH4:H2 gas flow ratio) were adjusted in order to prevent deposition or surface nucleation of germanium during the thermal cleaning process and to minimize the stacking fault densities in the epitaxial silicon layers deposited following the in-situ germane-assisted cleaning steps. The insitu dry surface cleaning processes developed in this work also include associated Ge114/112-based chemistries with a halogen-containing additive gas such as llCl and/or HF. These surface cleaning processes can be easily integrated with various thin film growth and deposition processes such as epitaxial growth gate dielectric formation and polycrystalline or amorphous silicon deposition for MOS and bipolar device fabrication.
Improved Low-Rank Filtering of Magnetic Resonance Spectroscopic Imaging Data Corrupted by Noise and &lt;i>B&lt;/i>&lt;sub>0&lt;/sub> Field Inhomogeneity (2015)

The proposed low-rank filtering method will enhance the practical utility of high-resolution MRSI, where SNR has been a limiting factor.
Document image decoding using Markov source models (1994)

Document image decoding (DID) is a communication theory approach to document image recognition. In DID, a document recognition problem is viewed as consisting of three elements: an image generator, a noisy channel and an image decoder. A document image generator is a Markov source (stochastic finite-state automaton) that combines a message source with an imager. The message source produces a string of symbols, or text, that contains the information to be transmitted. The imager is modeled as a finite-state transducer that converts the 1D message string into an ideal 2D bitmap. The channel transforms the ideal image into a noisy observed image. The decoder estimates the message, given the observed image, by finding the a posteriori most probable path through the combined source and channel models using a Viterbi-like dynamic programming algorithm. The proposed approach is illustrated on the problem of decoding scanned telephone yellow pages to extract names and numbers from the listings. A finite-state model for yellow page columns was constructed and used to decode a database of scanned column images containing about 1100 individual listings.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Stabilized-transducer driving device for underwater ultrasonic detection system (1979)

First Page
Prediction of Genetic Risk for Hypertension (2003)

Although genetic epidemiological studies have suggested that several genetic variants increase the risk for hypertension, the genes that underlie genetic susceptibility to this condition remain to be identified definitively. Large-scale association studies that examine many gene polymorphisms simultaneously are required to predict genetic risk for hypertension. The population of the present study comprised 1940 unrelated Japanese individuals, including 1067 subjects with hypertension (574 men, 493 women) and 873 controls (533 men, 340 women). The genotypes for 33 single nucleotide polymorphisms of 27 candidate genes were determined with a fluorescence- or colorimetry-based allele-specific DNA primer-probe assay system. Multivariate logistic regression analysis with adjustment for age, body mass index, and the prevalence of smoking, diabetes mellitus, hypercholesterolemia, and hyperuricemia revealed that 2 polymorphisms (825C-->T in the G protein beta3 subunit gene and 190G-->A in the CC chemokine receptor 2 gene) were significantly associated with hypertension in men and that one polymorphism (-238G-->A in the tumor necrosis factor alpha gene) was significantly associated with hypertension in women. These results suggest that 2 and 1 genes may be susceptibility loci for hypertension in Japanese men and women, respectively, and that genotyping of these polymorphisms may prove informative for prediction of the genetic risk for hypertension.
Fabrication of a rotary carbon nanotube bearing test apparatus (2015)

Carbon Nanotubes (CNTs) are attractive elements for bearings in Micro-Electro-Mechanical Systems (MEMS), because their structure comprises nested shells with no bonding and sub-nanometre spacing between them, enabling relative motion with low friction and wear. A reliable bearing technology is critical to bringing rotating MEMS machines from laboratory demonstrations to common use. We report here the design and fabrication of a test rotor, a testing apparatus and testing attempts, and integration of CNTs with MEMS. The device improves on existing CNT bearing demonstrators by establishing a vertical bearing orientation (enabling superior rotor balance and speed, and drive mechanism placement flexibility) and a manufacturable process (employing CNTs grown in place by chemical vapour deposition (CVD)). The main outstanding challenge to demonstrating rotation is available CVD CNT quality.
Security policy enforcement by automated program-rewriting (2006)

Traditional approaches to protecting computer systems from malicious or other misbehaved code typically involve (1) monitoring code for unacceptable behavior as it runs, or (2) detecting potentially misbehaved code and preventing it from running at all. These approaches are effective when unacceptable behavior can be detected in time to take remedial action, but in many settings and for many important security policies this is computationally expensive or provably impossible.
A third approach, termed in this dissertation program-rewriting , involves automatically rewriting code prior to running it in such a way that acceptable behavior is preserved but unacceptable behavior is not. Rewritten code can be run without further analysis or monitoring because it is guaranteed to exhibit only acceptable behavior. Program-rewriting has received recent attention in the literature in the form of in-lined reference monitors, which implement approach 1 above by in-lining security checks directly into the code being monitored. Program-rewriting generalizes in-lined reference monitoring, encompassing many other strategies for automatically rewriting programs as well. 
This dissertation provides a formal characterization of the class of security policies enforceable by program-rewriting and shows that it is strictly greater than the classes of policies enforceable by all other known approaches combined. The dissertation also presents the design and implementation of a certified program-rewriting system for the .NET Common Language Infrastructure, showing that program-rewriters can be developed for real architectures. The extra step of certification provides a formal proof that the program-rewriter produces code that satisfies the security policy, resulting in additional guarantees that the implementation is correct, and higher levels of assurance.
Fast multislice mapping of the myelin water fraction using multicompartment analysis of <i>T</i> decay at 3T: A preliminary postmortem study (2007)

Quantitative mapping of the myelin water content can provide significant insight into the pathophysiology of several white matter diseases, such as multiple sclerosis and leukoencephalopathies, and can potentially become a useful clinical tool for early diagnosis of these diseases. In this study, multicompartment analysis of T(2)(*) decay (MCAT(2)(*)) was used for the quantitative mapping of myelin water fraction (MWF). T(2)(*) decay of each voxel at multiple slice locations was acquired in fixed human brains using a multigradient-echo (MGRE) pulse sequence with alternating readout gradient polarities. Compared to prior techniques using Carr-Purcell-Meiboom-Gill (CPMG) acquisition, the MGRE acquisition approach has: 1) a very short first echo time ( approximately 2 ms) and echo-spacing ( approximately 1 ms), which allows for the acquisition of multiple sampling points during the fast decay of the myelin water signal; 2) a low RF duty cycle, which is especially important for achieving acceptable specific absorption rate (SAR) levels at high field strengths. Multicompartment analysis was then applied to the T(2)(*) decay in each pixel using a 3-pool model of white matter to detect the signal arising from the myelin water, myelinated axonal water, and mixed water compartments.
QTL Mapping of a Novel Genomic Region Associated with High Out-Crossing Rate Derived from Oryza longistaminata and Development of New CMS Lines in Rice, O. sativa L. (2021)

High seed cost due to poor seed yield severely limits the adoption of hybrid rice by farmers. Increasing the out-crossing rate is one of the key strategies to increase hybrid seed production. Out-crossing rate is highly influenced by the size of female floral traits, which capture pollen grains from male donor plants. In the current study, we identified 14 QTLs derived from the perennial wild rice Oryza longistaminata by composite interval mapping for five key floral traits: stigma length (five), style length (three), stigma breadth (two), stigma area (one), and pistil length (three). QTL analysis and correlation studies revealed that these stigma traits were positively correlated and pleiotropic to the stigma length trait. We selected the major-effect QTL qSTGL8.0 conferring long stigma phenotype for further fine mapping and marker-assisted selection. The qSTGL8.0 (~ 3.9 Mb) was fine mapped using newly developed internal markers and was narrowed down to ~ 2.9 Mb size (RM7356-RM256 markers). Further, the flanking markers were validated in a segregating population and in progenies from different genetic backgrounds. The markers PA08-03 and PA08-18 showed the highest co-segregation with the stigma traits. The qSTGL8.0 was introgressed into two cytoplasmic male sterile (CMS) lines, IR58025A and IR68897A, by foreground, background, and trait selection approaches. The qSTGL8.0 introgression lines in CMS backgrounds showed a significantly higher seed setting rate (2.5-3.0-fold) than the original CMS lines in test crosses with their corresponding maintainer lines. The newly identified QTLs especially qSTGL8.0, will be quite useful for increasing out-crossing rate and this will contribute to increase seed production and decrease seed cost.
Targeted delivery of Kv1.3 siRNAs with functionalized lipid nanoparticles (2013)

Hyperactive effector memory T cells (TEM) play a key role in cardiovascular complications of the autoimmune disease systemic lupus erythematosus (SLE). SLE TEM's have higher intracellular Ca2+ level, which contributes to their hyperactivity. Kv1.3 channels facilitate Ca2+ influx in T cells. Therefore silencing the Kv1.3 gene selectively in TEM's can be used as novel immunosuppressive therapy. Here we demonstrate that lipid nanoparticles (NPs) can be used to selectively deliver Kv1.3 siRNAs into TEM cells. Specificity and efficacy of Kv1.3 siRNAs was determined by RT‐qPCR and electrophysiology. NPs were made from a mixture of phosphatidylcholine, phosphoethanolamine‐PEG2000‐biotin and cholesterol. NPs were functionalized with inactive biotin‐CD45RO (TEM marker) antibodies via fluorophore‐conjugated streptavidin. Human T and MOLT‐4 (TEM cell line) cells were used to test the specific binding of NPs to TEM cells. NPs (ca. 100 nm) were characterized by dynamic light scattering and fluorescent/electron microscopy. Incubation of T/MOLT‐4 cells with CD45RO‐coated NPs resulted into the selective attachment and endocytosis of the NPs into TEM's via the internalization of the membrane CD45RO tyrosine kinase. Consequently, the Cy3‐labeled siRNA encapsulated into the NPs was released into the cytosol. These finding set the foundation for a novel therapeutic approach in autoimmunity. (NIH R21AR060966)
3-(1H-Tetrazol-5-yl)-4(3H)-quinazolinone sodium salt (MDL 427): a new antiallergic agent (1986)

Syntheses for 3-(1H-tetrazol-5-yl)-4(3H)-quinazolinone sodium salt monohydrate (9; MDL 427) and the related formamido compound, 2-(formylamino)-N-1H-tetrazol-5-ylbenzamide (10), are described. Both compounds are active in the rat passive cutaneous anaphylaxis and passive peritoneal anaphylaxis tests. A 94:6 equilibrium mixture of 9 and ionized 10, respectively, forms in aqueous buffer systems at a pH-dependent rate. In addition, analogues of 3-(1H-tetrazol-5-yl)-4(3H)-quinazolinone (8) bearing substituents on the benzene ring, substituents at the 2-position, and heteroaryl groups at the 3-position other than tetrazole were prepared. These analogue sets demonstrated that an accessible electrophilic center and an acidic functionality were requirements for good antiallergic activity.
Mouse Monoclonal Antibody 5-21-3 Recognizes a Contiguous, Conformation-Dependent Epitope and Maps to a Hydrophilic Region in HIV-1 gp41 (1990)

Mouse monoclonal antibody 5-21-3 is mapped to an epitope within a hydrophilic region of HIV-1 gp41 between amino acids 642 and 665 (numbering by Meyers et al. based on HXB2 isolate). The epitope is formed from amino acids within the sequence IHSLIEESQNQQEKNEQELLELDK; however, antibody 5-21-3 is unable to recognize the epitope-forming sequence when it is presented to the antibody in the form of a short (642-665) synthetic polypeptide. The epitope apparently is partially formed when additional native sequence of varying length is added to the amino and/or carboxy ends of the epitope-forming sequence, and 5-21-3 binds these larger synthetic polypeptides to varying degrees depending on the position and length of the flanking sequences. The 5-21-3 epitope apparently is formed from contiguous amino acids which require a specific, conformation-dependent, secondary structure for proper epitope formation. Binding preferences exhibited by 5-21-3 toward synthetic polypeptides and recombinant proteins may reflect the conformational nature of the epitope in disrupted HIV which elicited formation of the monoclonal.
Structure and dynamics of an α-fucosidase reveal a mechanism for highly efficient IgG transfucosylation (2020)

Fucosylation is important for the function of many proteins with biotechnical and medical applications. Alpha-fucosidases comprise a large enzyme family that recognizes fucosylated substrates with diverse α-linkages on these proteins. Lactobacillus casei produces an α-fucosidase, called AlfC, with specificity towards α(1,6)-fucose, the only linkage found in human N-glycan core fucosylation. AlfC and certain point mutants thereof have been used to add and remove fucose from monoclonal antibody N-glycans, with significant impacts on their effector functions. Despite the potential uses for AlfC, little is known about its mechanism. Here, we present crystal structures of AlfC, combined with mutational and kinetic analyses, hydrogen-deuterium exchange mass spectrometry, molecular dynamic simulations, and transfucosylation experiments to define the molecular mechanisms of the activities of AlfC and its transfucosidase mutants. Our results indicate that AlfC creates an aromatic subsite adjacent to the active site that specifically accommodates GlcNAc in α(1,6)-linkages, suggest that enzymatic activity is controlled by distinct open and closed conformations of an active-site loop, with certain mutations shifting the equilibrium towards open conformations to promote transfucosylation over hydrolysis, and provide a potentially generalizable framework for the rational creation of AlfC transfucosidase mutants.