gebhart/patrepeval huggingface dataset:
Of Kindlins and Cancer (2016)

Kindlins are 4.1-ezrin-ridixin-moesin (FERM) domain containing proteins. There are three kindlins in mammals, which share high sequence identity. Kindlin-1 is expressed primarily in epithelial cells, kindlin-2 is widely distributed and is particularly abundant in adherent cells, and kindlin-3 is expressed primarily in hematopoietic cells. These distributions are not exclusive; some cells express multiple kindlins, and transformed cells often exhibit aberrant expression, both in the isoforms and the levels of kindlins. Great interest in the kindlins has emerged from the recognition that they play major roles in controlling integrin function. In vitro studies, in vivo studies of mice deficient in kindlins, and studies of patients with genetic deficiencies of kindlins have clearly established that they regulate the capacity of integrins to mediate their functions. Kindlins are adaptor proteins; their function emanate from their interaction with binding partners, including the cytoplasmic tails of integrins and components of the actin cytoskeleton. The purpose of this review is to provide a brief overview of kindlin structure and function, a consideration of their binding partners, and then to focus on the relationship of each kindlin family member with cancer. In view of many correlations of kindlin expression levels and neoplasia and the known association of integrins with tumor progression and metastasis, we consider whether regulation of kindlins or their function would be attractive targets for treatment of cancer.
Deubiquitylating Enzymes and DNA Damage Response Pathways (2013)

Covalent post-translational modification of proteins by ubiquitin and ubiquitin-like factors has emerged as a general mechanism to regulate myriad intra-cellular processes. The addition and removal of ubiquitin or ubiquitin-like proteins from factors has recently been demonstrated as a key mechanism to modulate DNA damage response (DDR) pathways. It is thus, timely to evaluate the potential for ubiquitin pathway enzymes as DDR drug targets for therapeutic intervention. The synthetic lethal approach provides exciting opportunities for the development of targeted therapies to treat cancer: most tumours have lost critical DDR pathways, and thus rely more heavily on the remaining pathways, while normal tissues are still equipped with all DDR pathways. Here, we review key deubiquitylating enzymes (DUBs) involved in DDR pathways, and describe how targeting DUBs may lead to selective therapies to treat cancer patients.
Lactate discrimination incorporated into echo‐planar spectroscopic imaging (2001)

A technique for discriminating a lactate signal from overlapping lipid signals in (1)H spectroscopic imaging is presented. It is based on J-coupling between lactate protons and on the broad spectral bandwidth of lipid signal. Measurement parameters used in the technique are determined so that TE is separated from n/J (n: a natural number, J: J-coupling constant) enough to suppress the lipid signal at the time when the lactate signal is strongest. Data processing is used to calculate the lactate signal intensity from the reconstructed spectra. This technique enables lactate to be discriminated in a single measurement and enables spectra of other metabolites to be acquired simultaneously. However, it necessitates a homogeneous magnetic field, long TE, and supplementary lipid suppression. Discrimination of the lactate signal is demonstrated by applying lactate-discriminating echo-planar spectroscopic imaging (EPSI), which combines this discrimination technique with the standard EPSI, to rat focal cerebral ischemia models. Magn Reson Med 45:568-574, 2001.
Nucleic acid related compounds. 53. Synthesis and biological evaluation of 2′-deoxy-β-threo-pentofuranosyl nucleosides. "Reversion to starting alcohol" in Barton-type reductions of thionocarbonates (1988)

Treatment of selectively 3′,5′-protected β-D-xylofuranosyl nucleosides (4) with phenyl chlorothionocarbonate and DMAP followed by hydrogenolysis of the resulting (2′-O-phenoxythiocarbonyl) phenyl thionocarbonate esters (6) with tributylstannane/AIBN, and deprotection, gave 2′-deoxy-β-D-threo-pentofuranosyl nucleosides (7). Formation of a by-product bis(nucleosid-2′-yl)thionocarbonate dimer (8) was detected in the uracil nucleoside reaction sequence. Its subsequent reduction provides one explanation for "reversion to starting alcohol" in Barton-type deoxygenation reactions. Only the guanine 2′-deoxynucleoside analogue (7b) had (weak) antiviral activity (against herpes simplex virus type 1).
Metal‐Ion‐Coated Graphitic Nanotubes: Controlled Self‐Assembly of a Pyridyl‐Appended Gemini‐Shaped Hexabenzocoronene Amphiphile (2009)

Abstract Nanoröhren vom Fließband : Hexabenzocoronen(HBC)‐Amphiphile mit pyridylterminierten Triethylenglycol‐Seitenketten bilden in Kombination mit trans ‐[Pt(PhCN) 2 Cl 2 ] graphitische Nanoröhren. Die Strukturen und Abmessungen der Nanoröhren hängen dabei von den Synthesebedingungen ab. Auch Platin(II)‐verbrückte cyclische Dimere mit zwei HBC‐Einheiten bauen Nanoröhren auf. magnified image
High Speed, Optically Sectioned Fluorescence Lifetime Imaging utilizing Time-gated Nipkow Disk or Multifocal Multiphoton Time Correlated Single Photon Counting Microscopy (2008)

We report two optically sectioned fluorescence lifetime systems that exhibit better signal to noise per unit time than conventional time correlated single photon counting systems. Both systems are applied to biologically relevant samples.
Synthesis, electron spin resonance spectroscopy, and shape-determining angle analysis of superstructured copper(II) Schiff base complexes containing persistent voids (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, electron spin resonance spectroscopy, and shape-determining angle analysis of superstructured copper(II) Schiff base complexes containing persistent voidsWilliam M. Davis, Sharlene J. Dzugan, Mark W. Glogowski, Rita Delgado, and Daryle H. BuschCite this: Inorg. Chem. 1991, 30, 13, 2724–2731Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/ic00013a005https://doi.org/10.1021/ic00013a005research-articleACS PublicationsRequest reuse permissionsArticle Views75Altmetric-Citations8LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Quantitative Intellectual Property Protection Using Physical-Level Characterization (2013)

Hardware metering, the extraction of unique and persistent identifiers (IDs), is a crucial process for numerous integrated circuit (IC) intellectual property protection tasks. The currently known hardware metering approaches, however, are subject to alternations due to device aging, since they employ unstable manifestational IC properties. We, on the other hand, have developed the first robust hardware metering approach by using physical-level gate proprieties for ID generation. By using effective channel length, which is resilient to aging, and threshold voltage, which is essentially independent across gates and suitable for calculating the uniqueness of the IDs, we overcome the limitations of the existing approaches. Also, despite the increase in threshold voltage that occurs with aging, the original threshold voltage value can be extracted through intentional IC aging. Our ID generation procedure first employs two types of side channels, namely switching power and leakage power, to extract metering results for each gate. Next, we show that localized delay measurements alone are sufficient for accurate characterization of large sets of gates. Finally, by using threshold voltage for ID creation, we are able to obtain low probabilities of coincidence between legitimate and pirated ICs. The application of the approach to a set of benchmarks quantitatively establishes the effectiveness of the new hardware metering approach.
Assembly of a functional Machupo virus polymerase complex (2010)

Segmented negative-sense viruses of the family Arenaviridae encode a large polymerase (L) protein that contains all of the enzymatic activities required for RNA synthesis. These activities include an RNA-dependent RNA polymerase (RdRP) and an RNA endonuclease that cleaves capped primers from cellular mRNAs to prime transcription. Using purified catalytically active Machupo virus L, we provide a view of the overall architecture of this multifunctional polymerase and reconstitute complex formation with an RNA template in vitro. The L protein contains a central ring domain that is similar in appearance to the RdRP of dsRNA viruses and multiple accessory appendages that may be responsible for 5' cap formation. RNA template recognition by L requires a sequence-specific motif located at positions 2-5 in the 3' terminus of the viral genome. Moreover, L-RNA complex formation depends on single-stranded RNA, indicating that inter-termini dsRNA interactions must be partially broken for complex assembly to occur. Our results provide a model for arenavirus polymerase-template interactions and reveal the structural organization of a negative-strand RNA virus L protein.
Distribution of Threading Dislocations in Epitaxial Lateral Overgrowth GaN by Hydride Vapor-Phase Epitaxy Using Mixed Carrier Gas of H2and N2 (2002)

Distribution of threading dislocations (TDs) in epitaxial lateral overgrowth (ELO) GaN by hydride vapor-phase epitaxy (HVPE) has been investigated. Two types of carrier gas, i.e., N2 and H2+N2, were used in the HVPE in order to change the facet structure of the ELO layer. Results of cathodoluminescence (CL) mapping and HCl vapor-phase etching revealed lower TD density in the ELO layer grown using the H2+N2 mixed carrier gas than that using the N2 carrier gas.
Pt(II) Complexes of a Combretastatin A-4 Analogous Chalcone: Effects of Conjugation on Cytotoxicity, Tumor Specificity, and Long-Term Tumor Growth Suppression (2008)

Three dichlorido(6-aminomethylnicotinate)platinum complexes 6 comprising a combretastatin A-4 analogous chalcone were tested on a panel of 21 tumor cell lines from 9 entities. Parent chalcone 1a and the directly linked conjugate 6a exhibited excellent antiproliferative activities, similar in magnitude [average log(IC(50)) values of -7.3 (1a) and -7.0 (6a)] and cell line specificity but slightly different in the mechanism of apoptosis induction. While 1a and 6a caused an equally fast rise in caspase-9 in the tested cancer cell lines, the downstream effector caspase-3 built up faster in cells treated with 1a compared to 6a, yet reached an equal end level. They also had different long-term effects on the regrowth of cancer cells treated with a single dose. In contrast, conjugates 6b,c featuring longer spacers between the Pt complex and the chalcone moieties were less antiproliferative than 6a.
Spontaneous appearance of rocking localized current filaments in a nonequilibrium distributive system (1992)

In a ${\mathit{p}}^{+\mathrm{\ensuremath{-}}}$${\mathit{n}}^{+\mathrm{\ensuremath{-}}}$p-${\mathit{n}}^{\mathrm{\ensuremath{-}}}$ device driven by a dc-voltage source via a load resistor we experimentally observe a sequence of transitions when the total current is increased. A first transition from a stationary spatially homogeneous low-current state to a stationary localized current-density filament is followed by a second transition into a spontaneously rocking current filament oscillating with a definite frequency around a fixed position in space. For large total currents a third transition occurs. The rocking current filament transforms into a traveling current filament oscillating between the edges of the sample. A two-layer model for the device is proposed. The physical mechanism and the conditions for the appearance of rocking and traveling current filaments are considered and generalized for a wide class of nonequilibrium systems.
Role of AMPKα2 in basal, training-, and AICAR-induced GLUT4, hexokinase II, and mitochondrial protein expression in mouse muscle (2006)

We investigated the role of AMPKalpha2in basal, exercise training-, and AICAR-induced protein expression of GLUT4, hexokinase II (HKII), mitochondrial markers, and AMPK subunits. This was conducted in red (RG) and white gastrocnemius (WG) muscle from wild-type (WT) and alpha2-knockout (KO) mice after 28 days of activity wheel running or daily AICAR injection. Additional experiments were conducted to measure acute activation of AMPK by exercise and AICAR. At basal, mitochondrial markers were reduced by approximately 20% in alpha2-KO muscles compared with WT. In both muscle types, AMPKalpha2 activity was increased in response to both stimuli, whereas AMPKalpha1 activity was increased only in response to exercise. Furthermore, AMPK signaling was estimated to be 60-70% lower in alpha2-KO compared with WT muscles. In WG, AICAR treatment increased HKII, GLUT4, cytochrome c, COX-1, and CS, and the alpha2-KO abolished the AICAR-induced increases, whereas no AICAR responses were observed in RG. Exercise training increased GLUT4, HKII, COX-1, CS, and HAD protein in WG, but the alpha2-KO did not affect training-induced increases. Furthermore, AMPKalpha1, -alpha2, -beta1, -beta2, and -gamma3 subunits were reduced in RG, but not in WG, by 30-60% in response to exercise training. In conclusion, the alpha2-KO was associated with an approximately 20% reduction in mitochondrial markers in both muscle types and abolished AICAR-induced increases in protein expression in WG. However, the alpha2-KO did not reduce training-induced increases in HKII, GLUT4, COX-1, HAD, or CS protein in WG, suggesting that AMPKalpha2 may not be essential for metabolic adaptations of skeletal muscles to exercise training.
Long‐term protection against hepatitis B in pediatric liver recipients can be achieved effectively with vaccination after transplantation (2006)

Liver recipients who have antibodies to hepatitis B core antigen (anti-HBc) or received an anti-HBc positive liver graft are at risk of acquiring de novo hepatitis B infection so a life long prophylaxis is required. A post-transplant vaccination against hepatitis B virus (HBV) can offer a better alternative than either hepatitis B hyperimmune globulin (HBIG) or lamivudine. This study investigated the course of anti-HBs titer after vaccination and analyzed the factors that influence the response. Between October 1999 and February 2003, 37 pediatric patients were given a post-transplant vaccination when an anti-HBc positive graft was used, the recipient was anti-HBc positive, or when anti-HBs titer was below 20 IU/L irrespective of the serological status. Thirty-three patients responded to the vaccine and did not require further HBIG injections at a mean follow up of 33.6 months. Fifteen patients were good responder and only needed a single set of vaccines, and 18 were poor responder needing additional boosters. Two patients developed de novo hepatitis B infection and two required additional HBIG injections. Preoperative severity of liver disease, serological status of HBV of recipient or donor, use of HBIG or pulse steroid therapy, type of vaccines, and dose or time interval between doses had no influence on response rate. Recipients with a high preoperative anti-HB titer, small graft-recipient weight ratio (GRWR), greater catch up growth, heavier body weight, lower tacrolimus level at the time of vaccination, and longer time interval between transplant or steroid medication and vaccination yielded good response. If well tailored, post-transplant vaccination can be effective and offer patients prophylaxis against de novo hepatitis B infection for a prolonged period of time.
Instrumentation and algorithms for electrostatic inverse problems (2001)

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and, (S.B.)--Massachusetts Institute of Technology, Dept. of Physics, 2001.
Al-2.14 Bottom Anti-Reflective Coating (Barc) (2021)

As increasingly smaller molecular materials and material structures are devised or developed for technological applications, the demands on the processes of lithography now routinely include feature sizes that are of the order of 10 nm. In reaching such a fine level of resolution, the methods of lithography have increased markedly in sophistication and brought into play 2terminology that is unfamiliar, on the one hand, to scientists tasked with the development of new lithographic materials or, on the other, to the engineers who design and operate the complex equipment that is required in modern-day processing. Publications produced by scientists need to be understood by engineers and vice versa, and these commonly arise from collaborative research that draws heavily on the terminology of two or more of the traditional disciplines. It is developments in polymer science and material science that lead progress in areas that cross traditional boundaries, such as microlithography. This document provides the exact definitions of a selection of unfamiliar terms that researchers and practitioners from different disciplines might encounter.
Turkey Behavior Identification System with a GUI Using Deep Learning and Video Analytics (2021)

In this paper, we propose a video analytics system to identify the behavior of turkeys.Turkey behavior provides evidence to assess turkey welfare, which can be negatively impacted by uncomfortable ambient temperature and various diseases.In particular, healthy and sick turkeys behave differently in terms of the duration and frequency of activities such as eating, drinking, preening, and aggressive interactions.Our system incorporates recent advances in object detection and tracking to automate the process of identifying and analyzing turkey behavior captured by commercial grade cameras.We combine deep-learning and traditional image processing methods to address challenges in this practical agricultural problem.Our system also includes a webbased user interface to create visualization of automated analysis results.Together, we provide an improved tool for turkey researchers to assess turkey welfare without the time-consuming and labor-intensive manual inspection.
Geographic analysis & visualization of climate extremes for the Quadrennial Defense Review (2009)

We have developed demonstrable capabilities in the area of geographic analysis and visualization for climate extremes, uncertainty and impacts. The capabilities were used for to provide climate science support to an international climate change war game, where real-world policy makers, as well as business, political and science leaders from around the world, engaged in a mock policy negotiations. We have since further developed the capabilities for supporting the development of the Quadrennial Defense Review (QDR) by the Office of the Secretary of Defense within the United States Department of Defense (DOD).
POCA: First Power-on Chip Authentication in Untrusted Foundry and Assembly (2021)

The increased complexity, extensive verification requirement, shortened time-to-market, and increased manufacturing and test costs have made fabless design houses adopt the horizontal business model where system-on-chips (SoCs) are shipped to outsourced semiconductor assembly and test facilities. However, such a model renders offshore facilities complete control over the manufacturing and test of integrated circuits (ICs), potentially enabling them to perform attacks like IC overproduction, intellectual property (IP) piracy, shipping defective chips into the supply chain, and stealing security assets (e.g., locking keys). In this paper, we propose a novel protocol called POCA, enabling the first power-on chip authentication during wafer sort to securely provision design assets inside the chip. Using POCA, the design house can authenticate the chips on the untrusted manufacturing/test floor and generate a shared secret key with the chip. This key is then utilized to encrypt the secret assets and securely provision them inside the chip after decryption. To the best of our knowledge, POCA is the first protocol that performs authentication at an untrusted foundry and ensures secure communication with the chip during the test. POCA has been implemented for ASIC and FPGA environments and is proven resistant to all possible attacks known to us as of today.
Antibodies to Glutamic Acid Decarboxylase in Young Chinese Diabetic Patients (1998)

Antibodies to glutamic acid decarboxylase (GAD) are a useful autoimmune marker for type 1 diabetes mellitus in Caucasians. We examined antibodies to GAD and their relationships with clinical features and pancreatic beta cell function in 140 young Chinese diabetic patients. Over an 18-month period beginning in 1995, 140 young Chinese diabetic subjects with age of onset of disease < or = 35 years and age < 40 years were recruited consecutively, irrespective of their modes of presentation. Clinical features, antibodies to GAD and pancreatic beta cell function (using a glucagon stimulation test) were examined. Increased levels of antibodies to GAD (> 18 units) were detected in 12.1% (n = 17) of these subjects. Forty-three (31%) patients had a classical type 1 presentation and 65 (46%) patients were insulin-deficient based on post-glucagon plasma C-peptide levels. Patients who were insulin-deficient and had a type 1 presentation had the highest prevalence of antibodies to GAD (29.0%) compared with patients who had a type 2 presentation and were non-insulin deficient (6.4%, P = 0.003). Patients who had antibodies to GAD had lower body mass index and waist-hip ratio, earlier onset of disease, lower blood pressure, plasma triglyceride and C-peptide, and higher concentrations of plasma high-density lipoprotein cholesterol and glycated haemoglobin, and were more likely to require drug treatment, compared with those without antibodies to GAD. In conclusion, there was a low prevalence of antibodies to GAD in Chinese young diabetic patients although such antibodies remained a relatively specific marker for insulin deficiency and acute presentation. Causes other than autoimmunity should be sought to explain the high prevalence of insulin deficiency in these young Chinese patients.
Interest of the association clonidine-spironolactone in cirrhotic patients with ascites and activation of sympathetic nervous system. (2002)

In cirrhotic patients with ascites and marked activation of sympathetic nervous system, spironolactone (200 mg/day) is unable to mobilize ascites. In these patients, after 8 days, clonidine decreases sympathetic activity, increases glomerular filtration rate and after 18 days, decreases plasma renin and aldosterone concentrations allowing a better action of spironolactone. The association clonidine-spironolactone enhances natriuresis and body weight loss.