gebhart/patrepeval huggingface dataset:
Mechanisms of Opsin Activation (1996)

Rhodopsin is constrained in an inactive conformation by interactions with 11-cis-retinal including formation of a protonated Schiff base with Lys296. Upon photoisomerization, major structural rearrangements that involve protonation of the active site Glu113 and cytoplasmic acidic residues, including Glu134, lead to the formation of the active form of the receptor, metarhodopsin II b, which decays to opsin. However, an activated receptor may be generated without illumination by addition of all-trans-retinal or its analogues to opsin, as measured in this study by the increased phosphorylation of opsin by rhodopsin kinase. The potency of stimulation depended on the chemical and isomeric nature of the analogues and the length of the polyene chain with all-trans-C17 aldehyde and all-trans-retinal being the most active and trans-C12 aldehyde being the least active. Certain cis-isomers, 11-cis-13-demethyl-retinal and 9-cis-C17 aldehyde, were also active. Most of the retinal analogues tested did not regenerate a spectrally identifiable pigment, and many were incapable of Schiff base formation (ketone, stable oximes, and Schiff base-derivatives of retinal). Thus, receptor activation resulted from formation of non-covalent complexes with opsin. pH titrations suggested that an equilibrium exists between partially active (protonated) and inactive (deprotonated) forms of opsin. These findings are consistent with a model in which protonation of one or more cytoplasmic carboxyl groups of opsin is essential for activity. Upon addition of retinoids, the partially active conformation of opsin is converted to a more active intermediate similar to metarhodopsin II b. The model provides an understanding of the structural requirements for opsin activation and an interpretation of the observed activities of natural and experimental opsin mutants.
A Convenient Two-Step Procedure for the Synthesis of Substituted Allylic Amines from Allylic Alcohols (1995)

The synthesis of several isomerically pure allylic amines, including farnesyl amine, is achieved in excellent yields using a modified Gabriel synthesis.
Induction of Competence Regulons as a General Response to Stress in Gram-Positive Bacteria (2006)

Bacterial transformation, a programmed mechanism for genetic exchange originally discovered in Streptococcus pneumoniae, is widespread in bacteria. It is based on the uptake and integration of exogenous DNA into the recipient genome. This review examines whether induction of competence for genetic transformation is a general response to stress in gram-positive bacteria. It compares data obtained with bacteria chosen for their different lifestyles, the soil-dweller Bacillus subtilis and the major human pathogen S. pneumoniae. The review focuses on the relationship between competence and other global responses in B. subtilis, as well as on recent evidence for competence induction in response to DNA damage or antibiotics and for the ability of S. pneumoniae to use competence as a substitute for SOS. This comparison reveals that the two species use different fitness-enhancing strategies in response to stress conditions. Whereas B. subtilis combines competence and SOS induction, S. pneumoniae relies only on competence to generate genetic diversity through transformation.
A Malicious Code Immune Model Based on Program Encryption (2008)

Signature scanning and access control have been the major approaches for malicious code defenses in the past decades. The former can't defend against unknown attacks effectively and the latter may be circumvented if its implementation lacks high security assurance. In this paper, a methodology for malicious code immune is proposed at first. The key idea of it is encrypting program files to make their formats be unrecognizable by unintended entities, by this way to prevent un-trusted programs from running and to protect trusted programs from being infected by computer virus. Based on the methodology, a malicious code immune model is then proposed. It defines three security rules to make sure only trusted programs can be loaded and run by operating system. The model doesn't rely on an additional white list. It can be implemented as internal logic of the system call which creates processes. Therefore, circumvention of it is much more difficult than that of access control models. A prototype of the model for Windows XP is also illustrated. It uses the technologies of kernel mode file system filter driver and on-the-fly decryption, requiring neither binary level nor source code level modifications to the Windows OS.
In Silico Design of Small RNA Switches (2007)

The discovery of natural RNA sensors that respond to a change in the environment by a conformational switch can be utilized for various biotechnological and nanobiotechnological advances. One class of RNA sensors is the riboswitch: an RNA genetic control element that is capable of sensing small molecules, responding to a deviation in ligand concentration with a structural change. Riboswitches are modularly built from smaller components. Computational methods can potentially be utilized in assembling these building block components and offering improvements in the biochemical design process. We describe a computational procedure to design RNA switches from building blocks with favorable properties. To achieve maximal throughput for genetic control purposes, future designer RNA switches can be assembled based on a computerized preprocessing buildup of the constituent domains, namely the aptamer and the expression platform in the case of a synthetic riboswitch. Conformational switching is enabled by the RNA versatility to possess two highly stable states that are energetically close to each other but topologically distinct, separated by an energy barrier between them. Initially, computer simulations can produce a list of short sequences that switch between two conformers when trigerred by point mutations or temperature. The short sequences should possess an additional desirable property; when these selected small RNA switch segments are attached to various aptamers, the ligand binding mechanism should replace the aforementioned event triggers, which will no longer be effective for crossing the energy barrier. In the assembled RNA sequence, energy minimization folding predictions should then show no difference between the folded structure of the entire sequence relative to the folded structure of each of its constituents. Moreover, energy minimization methods applied on the entire sequence could aid at this preprocessing stage by exhibiting high mutational robustness to capture the stability of the formed hairpin in the expression platform. The above computer-assisted assembly procedure together with application specific considerations may further be tailored for therapeutic gene regulation. Index Terms-Design of RNA switches, energy minimization methods, RNA folding predictions.
Synthesis, Chromatographic Separation, and Characterization of Near-Infrared Labeled DNA Oligomers for Use in DNA Sequencing (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis, Chromatographic Separation, and Characterization of Near-Infrared Labeled DNA Oligomers for Use in DNA SequencingDana B. Shealy, Malgorzata. Lipowska, Jacek. Lipowski, Narasimhachari. Narayanan, Scott. Sutter, Lucjan. Strekowski, and Gabor. PatonayCite this: Anal. Chem. 1995, 67, 2, 247–251Publication Date (Print):January 15, 1995Publication History Published online1 May 2002Published inissue 15 January 1995https://doi.org/10.1021/ac00098a002RIGHTS & PERMISSIONSArticle Views385Altmetric-Citations65LEARN 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 InReddit PDF (1 MB) Get e-Alertsclose Get e-Alerts
[ 18 F]‐fluorocholine positron‐emission/computed tomography for lymph node staging of patients with prostate cancer: preliminary results of a prospective study (2010)

This small series supports the use of FCH PET/CT as a tool for lymph node staging of patients with prostate cancer. Values of SUV(max) at early and late imaging did not differ. However, larger prospective studies are needed to validate these findings.
Low Complexity LDPC Code Decoders for Next Generation Standards (2007)

This paper presents the design of low complexity LDPC codes decoders for the upcoming WiFi (IEEE 802.11n), WiMax (IEEE802.16e) and DVB-S2 standards. A complete exploration of the design space spanning from the decoding schedules, the node processing approximations up to the top-level decoder architecture is detailed. According to this search state-of-the-art techniques for a low complexity design have been adopted in order to meet feasible high throughput decoder implementations. An analysis of the standardized codes from the decoder-aware point of view is also given, presenting, for each one, the implementation challenges (multi rates-length codes) and bottlenecks related to the complete coverage of the standards. Synthesis results on a present 65nm CMOS technology are provided on a generic decoder architecture
Config: A Mechanism for Installing and Tracking System Configurations (1994)

<i>Background and Objectives</i>: Percutaneous nephrolithotomy (PCNL) is still the gold-standard treatment for large and/or complex renal stones. Endoscopic combined intrarenal surgery (ECIRS) was developed with the goal of minimizing the number of access tracts of PCNL while simultaneously improving the one-step stone-free rate (SFR). The aim of this study was to share the experience of the consecutive 200 cases of ECIRS in one institute and analyze surgical outcomes of mini-ECIRS and standard ECIRS. <i>Materials and Methods</i>: We performed ECIRS for 200 adult patients between July 2017 and January 2020. An ECIRS was performed with the patient under general anesthesia in the intermediate-supine position. Surgeries were finished using a tubeless technique with a simple ureteral stent insertion. <i>Results</i>: There were significant differences in the mean maximal stone length (MSL), the variation coefficient of stone density (VCSD), the linear calculus density (LCD), the Seoul National University Renal Stone Complexity (S-ReSC), and the modified S-ReSC scores in stone characteristics, and estimated blood loss (EBL) and operation time in peri-operative outcomes between conventional and mini-ECIRS. After propensity-score matching, there was only a difference in EBL between the two groups. In logistic regression models, MSL [odds ratio (OR) 0.953; 95% confidence interval (CI) 0.926-0.979; <i>p</i> < 0.001], LCD (OR 4.702; 95% CI 1.613-18.655; <i>p</i> = 0.013) were significant factors for the success rate after ECIRS. <i>Conclusions</i>: In patients who underwent a mini-ECIRS, the stones were relatively smaller and less complex, and the operation time was shorter. However, if the size of stones was similar, there was no difference in the success rate, but EBL was lower in mini-ECIRS than in standard surgery.
9.8 An 860&#x03BC;W 2.1-to-2.7GHz all-digital PLL-based frequency modulator with a DTC-assisted snapshot TDC for WPAN (Bluetooth Smart and ZigBee) applications (2014)

Ultra-low-power (ULP) transceivers enable short-range networks of autonomous sensor nodes for wireless personal-area-network (WPAN) applications. RF PLLs for frequency synthesis and modulation consume a significant share of the total transceiver power, making sub-mW PLLs key to realize ULP WPAN radios. Compared to analog PLLs [1], all-digital PLLs (ADPLLs) are preferred in nanoscale CMOS as they offer benefits of smaller area, programmability, capability of extensive self-calibrations, and easy portability [2]. However, analog PLLs dominate the field of ULP WPAN radios [1], since the time-to-digital-converter (TDC) of an ADPLL has traditionally been power hungry. We present a 2.1-to-2.7GHz 860μW fractional-N ADPLL in 40nm CMOS for WPAN applications, which breaks the 1mW barrier and consumes at least 5× lower power compared to state-of-the-art ADPLLs.
Size-Dependent Bacterial Growth Inhibition and Mechanism of Antibacterial Activity of Zinc Oxide Nanoparticles (2011)

The antibacterial properties of zinc oxide nanoparticles were investigated using both gram-positive and gram-negative microorganisms. These studies demonstrate that ZnO nanoparticles have a wide range of antibacterial activities toward various microorganisms that are commonly found in environmental settings. The antibacterial activity of the ZnO nanoparticles was inversely proportional to the size of the nanoparticles in S. aureus. Surprisingly, the antibacterial activity did not require specific UV activation using artificial lamps, rather activation was achieved under ambient lighting conditions. Northern analyses of various reactive oxygen species (ROS) specific genes and confocal microscopy suggest that the antibacterial activity of ZnO nanoparticles might involve both the production of reactive oxygen species and the accumulation of nanoparticles in the cytoplasm or on the outer membranes. Overall, the experimental results suggest that ZnO nanoparticles could be developed as antibacterial agents against a wide range of microorganisms to control and prevent the spreading and persistence of bacterial infections.
Polymers Move in Response to Light (2006)

Abstract Significant advances have recently been made in the development of functional polymers that are able to undergo light‐induced shape changes. The main challenge in the development of such polymer systems is the conversion of photoinduced effects at the molecular level to macroscopic movement of working pieces. This article highlights some selected polymer architectures and their tailored functionalization processes. Examples include the contraction and bending of azobenzene‐containing liquid‐crystal elastomers and volume changes in gels. We focus especially on light‐induced shape‐memory polymers. These materials can be deformed and temporarily fixed in a new shape. They only recover their original, permanent shape when irradiated with light of appropriate wavelengths. Using light as a trigger for the shape‐memory effect will extend the applications of shape‐memory polymers, especially in the field of medical devices where triggers other than heat are highly desirable.
WAF1/CIP1 is induced in p53-mediated G1 arrest and apoptosis. (1994)

The tumor growth suppressor WAF1/CIP1 was recently shown to be induced by p53 and to be a potent inhibitor of cyclin-dependent kinases. In the present studies, we sought to determine the relationship between the expression of WAF1/CIP1 and endogenous regulation of p53 function. WAF1/CIP1 protein was first localized to the nucleus of cells containing wild-type p53 and undergoing G1 arrest. WAF1/CIP1 was induced in wild-type p53-containing cells by exposure to DNA damaging agents, but not in mutant p53-containing cells. The induction of WAF1/CIP1 protein occurred in cells undergoing either p53-associated G1 arrest or apoptosis but not in cells induced to arrest in G1 or to undergo apoptosis through p53-independent mechanisms. DNA damage led to increased levels of WAF1/CIP1 in cyclin E-containing complexes and to an associated decrease in cyclin-dependent kinase activity. These results support the idea that WAF1/CIP1 is a critical downstream effector in the p53-specific pathway of growth control in mammalian cells.
Recent Advances in Classical and Non-Classical Antifolates as Antitumor and Antiopportunistic Infection Agents: Part I (2007)

Antifolates that inhibit the key enzymes thymidylate synthase (TS) and dihydrofolate reductase (DHFR) have found clinical utility as antitumor and antiopportunistic agents. Methotrexate {MTX, (1)} and 5-fluorouracil (5-FU) were among the first clinically useful DHFR and TS inhibitors, respectively. The development of resistance to 5-FU, its occasional unpredictable activity and toxicity resulted in the search of novel antifolates. Pemetrexed (4) and raltitrexed (5) specifically inhibit TS, and are clinically useful as antitumor agents. A major mechanism of tumor resistance to clinically useful antifolates is based on their need for polyglutamylation via the enzyme folylpoly-gamma-glutamate synthetase (FPGS). Novel antifolates have been developed that do not need to be polyglutamylated and include plevitrexed (6) and GW1843 (7). Nonclassical antifolates for antitumor and parasitic chemotherapy, such as nolatrexed (8), trimethoprim {TMP, (11)} and piritrexim {PTX, (12)}, can passively diffuse into cells and hence do not have to depend on FPGS or the reduced folate carrier (RFC). Variations in the structures of antifolates have helped delineate the structural influence on the interaction with TS, DHFR, FPGS, and RFC utilization. The differences in the active site of human and pathogen DHFR have also been exploited. The literature contains excellent reviews on the design and synthesis of antifolates prior to 1996. This two-part review discusses the design, synthesis and structural requirements for TS and DHFR inhibition and their relevance to antitumor and parasitic chemotherapy, since 1996. Monocyclic and 6-5 fused bicyclic antifolates will be discussed in Part I, while 6-6 bicyclic and tricyclic antifolates will be discussed in Part II.
Expression and prognostic significance of survivin in de novo acute myeloid leukaemia (2000)

Survivin is an inhibitor of apoptosis (programmed cell death) overexpressed in various human cancers, but undetectable in normal differentiated tissues. A potential distribution and prognostic significance of survivin in patients with de novo acute myeloid leukaemia (AML) was investigated. By immunofluorescence of bone marrow specimens and peripheral blood mononuclear cells, survivin was detected in 75 out of 125 interpretable AML cases (60%), with reactivity in 50-90% of AML cells. Survivin expression correlated with a lower white blood cell count (WBC) (P = 0.008 by the Mann-Whitney test) and was associated, in the 55 cases of FAB M0/M1/M2, with leukaemic granulocytic maturation (one out of five M/L0, 11 out of 22 M/L1 and 23 out of 28M/L2; P = 0.007 by the Fisher test). In 69 patients treated with the Acute Leukaemia French Association (ALFA) 9000 protocol, survivin expression was significantly associated with a lower WBC (P = 0.03 by the Mann-Whitney test) and favourable/intermediate cytogenetics (P= 0.03 by the Fisher test). There was no significant difference in complete remission rate or overall survival between survivin-positive and survivin-negative AML patients (P = 0.15 by the log-rank test). However, survivin expression became an independent negative prognostic factor for survival when adjusted with the Cox model for established prognostic factors in AML (cytogenetics, age and WBC) or for the ALFA 9000 treatment arm (RR = 2.8 and P = 0.026, by the likelihood-ratio test). These data suggest that survivin expression may be considered as a new unfavourable prognostic factor of de novo AML and suggest a role for apoptosis inhibition in influencing disease outcome.
The Emerging Role of HLA-E-Restricted CD8+T Lymphocytes in the Adaptive Immune Response to Pathogens and Tumors (2010)

Human leukocyte antigen (HLA)-E is a nonclassical major histocompatibility complex (MHC) class I molecule of limited sequence variability that is expressed by most tissues albeit at low levels. HLA-E has been first described as the ligand of CD94/NKG2 receptors expressed mainly by natural killer (NK) cells, thus confining its role to the regulation of NK-cell function. However, recent evidences obtained by our and other groups indicate that HLA-E complexed with peptides can interact with alphabeta T-cell receptor (TCR) expressed on CD8(+) T cells. Although, HLA-E displays a selective preference for nonameric peptides, derived from the leader sequence of various HLA class I alleles, several reports indicate that it can present also "noncanonical" peptides derived from both stress-related and pathogen-associated proteins. Because HLA-E displays binding specificity for innate CD94/NKG2 receptors, as well as all the features of an antigen-presenting molecule, its role in both natural and acquired immune responses has recently been re-evaluated.
Human responses to bacterial endotoxin. (1994)

The literature concerning human responses to bacterial endotoxin, in particular to the purified lipopolysaccharide derivative, has been critically reviewed and summarized. Papers selected for review are those that reported studies of human subjects in a normal state of health administered defined doses of either intravenous or aerosol inhaled material. Emphasis was placed on cardiovascular, pulmonary, metabolic, and inflammatory parameters. The information detailed here can be applied to understanding the pathophysiology of human consequences to spontaneous, clinical diseases induced by this highly inflammatory and ubiquitous substance.
Answering complex, list and context questions with LCC's Question-Answering Server (2001)

This paper presents the architecture of the Question-Answering Server (QAS) developed at the Language Computer Corporation (LCC) and used in the TREC-10 evaluations. LCC&amp;apos;s QAS extracts answers for (a) factual questions of variable degree of difficulty; (b) questions that expect lists of answers; and (c) questions posed in the context of previous questions and answers. One of the major novelties is the implementation of bridging inference mechanisms that guide the search for answers to complex questions. Additionally, LCC&amp;apos;s QAS encodes an efficient way of modeling context via reference resolution. In TREC-10, this system generated an RAR, of 0.58 on the main task and 0.78 on the context task.
Expression and activation of the farnesoid X receptor in the vasculature (2004)

The farnesoid X receptor/bile acid receptor (FXR) is a recently discovered member of the nuclear hormone superfamily. FXR ligands have been proposed as targets in cardiovascular disease, regulating cholesterol metabolism and bile acid transport and metabolism in the liver and gastrointestinal tract. When we used a human cardiovascular tissue array, we found that FXR is expressed in a variety of normal and pathological human tissue. Particularly high levels of FXR were found in the vasculature and in a number of different metastatic cancers, as well as the previously identified target tissues of the liver, small intestine, and kidney. In vitro, FXR is present in rat and human vascular smooth muscle cells. When treated with a range of FXR ligands, vascular smooth muscle cells undergo apoptosis in a manner that correlates with the ligands' ability to activate FXR. Furthermore, FXR activators induce mRNA for the FXR target genes, phospholipid transfer protein, and the small heterodimer partner. FXR therefore is a functional protein in the vasculature that may provide a direct target for the treatment of proliferative and dyslipidaemic diseases.