gebhart/patrepeval huggingface dataset:
Hepatitis C virus: Clades and properties (2002)

Hepatitis C virus (HCV) is a member of the virus family Flaviviridae. At present HCV is classified into a discrete hepacivirus genus and is represented by six clades according to genome sequencing. Each clade is further divisible into subtypes, which may prove important for the study of clinical differences and epidemiological studies. Limited homology also exists with hepatitis G/GB viruses, despite the fact that the hepatotropic nature of the latter agents remains contentious. The variability amongst the six HCV clades is less than that observed between the four serotypes of dengue, suggesting that each clade may represent a distinct virus were tests such as plaque neutralization to become available for delineating HCV isolates. The distribution worldwide varies, with Clades 1 and 2 predominating in most regions-an important consideration for the development of any vaccine. In addition, the clade distribution among cohorts may vary according to age. Point source outbreaks of HCV, for example in large numbers of women inadvertently infected with HCV-contaminated anti-D globulin, offers an opportunity to study the evolution of HCV genotypes over several decades. Parallel studies in chimpanzees have shown that the hypervariable region of E2 may play a role in HCV immunity, with quasispecies rapidly replacing the predominant subtype as immunity develops to the initiating virus strain. There is some evidence that an IFN-sensitive motif exists in the NS5 gene which may have some predictive value in determining the likely outcome of IFN treatment. A database is available for all HCV sequences, together with information about their properties and guidance for the evaluation of new isolates (http://s2as02.genes.nig.ac.jp).
Atorvastatin Promotes Presenilin-1 Expression and Notch1 Activity and Increases Neural Progenitor Cell Proliferation After Stroke (2007)

These data indicate that atorvastatin increases the NPC pool in older rats and that it also upregulates PS1 expression and Notch1 signaling activity, which in turn, facilitate an increase in SVZ NPC proliferation.
Heat shock protein-based therapeutic strategies against human immunodeficiency virus type 1 infection (1999)

Heat shock proteins (hsps) and cyclophilins (CypA) are intracellular chaperone molecules that facilitate protein folding and assembly. These proteins are selectively expressed in cells following exposure to a range of stress stimuli, including viral infection. Hsp species are highly immunogenic, eliciting humoral, cytotoxic T lymphocyte (CTL), and natural killer (NK) cell responses against viruses, tumours, and infectious diseases. This review discusses the roles of stress proteins in immunity and viral life cycles, vis-à-vis the development of Hsp-based therapeutic strategies against human immunodeficiency virus type-1 (HIV-1) infection. Cumulative findings are cited implicating the requirement of CypA in HIV-1 replication and formation of infectious virions. Studies by our group show the upregulated expression of hsp27 and hsp70 during single-cycle HIV infections. These species redistribute to the cell surface following HIV-infection and heat stress, serving as targets for NK and antibody-dependent cellular cytotoxicity. Co-immunoprecipitation and Western blot studies show that hsp27, hsp70, and hsp78 complex with HIV-1 viral proteins intracellularly. Hsp70, hsp56, and CypA are assembled into HIV-1 virions. The ability of hsps to interact with HIV-1 viral proteins, combined with their inherent adjuvant and immunogenic properties, indicates that hsps may serve as vehicles for antigen delivery and the design of vaccines against acquired immunodeficiency syndrome. Infect. Dis. Obstet. Gynecol. 7:80–90, 1999. © 1999 Wiley-Liss, Inc.
Interpretation Of Prostatic Biopsies: A Review (2005)

The incidence of prostatic carcinoma is on the rise in the Indian subcontinent. A definitive diagnosis of this disease is obtained on a TRUS guided needle biopsy. Interpretation of these small biopsies therefore plays a vital role in the management and prognosis of the disease. However every investigation has its limitations. This review is intended to convey the complexities of biopsy interpretation with special emphasis on the problems encountered and need for clinicopathological correlation.
Inhibitory leukocyte immunoglobulin-like receptors: Immune checkpoint proteins and tumor sustaining factors (2015)

Inhibitory leukocyte immunoglobulin-like receptors (LILRBs 1-5) transduce signals via intracellular immunoreceptor tyrosine-based inhibitory motifs (ITIMs) that recruit protein tyrosine phosphatase non-receptor type 6 (PTPN6 or SHP-1), protein tyrosine phosphatase non-receptor type 11 (PTPN11 or SHP-2), or Src homology 2 domain-containing inositol phosphatase (SHIP), leading to negative regulation of immune cell activation. Certain of these receptors also play regulatory roles in neuronal activity and osteoclast development. The activation of LILRBs on immune cells by their ligands may contribute to immune evasion by tumors. Recent studies found that several members of LILRB family are expressed by tumor cells, notably hematopoietic cancer cells, and may directly regulate cancer development and relapse as well as the activity of cancer stem cells. LILRBs thus have dual concordant roles in tumor biology - as immune checkpoint molecules and as tumor-sustaining factors. Importantly, the study of knockout mice indicated that LILRBs do not affect hematopoiesis and normal development. Therefore LILRBs may represent ideal targets for tumor treatment. This review aims to summarize current knowledge on expression patterns, ligands, signaling, and functions of LILRB family members in the context of cancer development.
Matrix-assisted Laser Desorption/Ionization for Sequencing Single-stranded and Double-stranded DNA (1997)

The DNA sequence of a single-stranded and double-stranded template was determined. The templates were sequenced using the chain termination method and cycle sequencing method and detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The sequencing products were analyzed successfully without the laborious and expensive methods for removal of the template. Direct sequencing of the double-stranded template was achieved with minimal post-reaction purifications, which could be extremely important for mutation analysis and clinical diagnosis. A systematic study of the mechanisms and kinetics of sequencing reactions was also performed. The details of this analysis and directions for future improvements of the quality of sequencing are presented.
Strain-induced polarization in wurtzite III-nitride semipolar layers (2006)

This paper presents growth orientation dependence of the piezoelectric polarization of InxGa1−xN and AlyGa1−yN layers lattice matched to GaN. This topic has become relevant with the advent of growing nitride based devices on semipolar planes [A. Chakraborty et al., Jpn. J. Appl. Phys., Part 2 44, L945 (2005)]. The calculations demonstrate that for strained InxGa1−xN and AlyGa1−yN layers lattice matched to GaN, the piezoelectric polarization becomes zero for nonpolar orientations and also at another point ≈45° tilted from the c plane. The zero crossover has only a very small dependence on the In or Al content of the ternary alloy layer. With the addition of spontaneous polarization, the angle at which the total polarization equals zero increases slightly for InxGa1−xN, but the exact value depends on the In content. For AlyGa1−yN mismatched layers the effect of spontaneous polarization becomes important by increasing the crossover point to ∼70° from c-axis oriented films. These calculations were performed using the most recent and convincing values for the piezoelectric and elasticity constants, and applying Vegard’s law to estimate the constants in the ternary InxGa1−xN and AlyGa1−yN layers.
A novel class of zinc finger/leucine zipper genes identified from the molecular cloning of the t(10;11) translocation in acute leukemia (1995)

A novel class of conserved transcription factors has been identified from the molecular cloning of AF10, the gene involved in the t(10;11)(p12;q23) translocation of acute myeloid leukemias. AF10 encodes a 109-kD protein of 1,027 amino acids and contains an N-terminal zinc finger region and a C-terminal leucine zipper. These structures have been found to be conserved in sequence and position in three other proteins, AF17, BR140, and a previously unrecognized Caenorhabditis elegans gene, provisionally named CEZF. The overall structure, level of sequence conservation, and expression pattern suggest that these genes encode a new class of transcription factors, some of which are targets for chromosomal translocation in acute leukemia.
Long-Lifetime Power Inverter for Photovoltaic AC Modules (2008)

This paper presents a power inverter tailored for low-power photovoltaic (PV) systems. The inverter features high reliability, thanks to a circuit topology that obviates aluminum electrolytic capacitors from the circuit. Moreover, all components, including logic and control, have been designed to exhibit high reliability at high temperatures. Three conversion stages form the power topology. First, a full bridge connected to a high-frequency transformer and a full-bridge rectifier amplifies the voltage of the PV panel to approximately 475 V. This stage is controlled by using a phase-shift pulsewidth-modulation controller that permits zero-voltage switching, thereby minimizing losses. Second, a buck converter is connected in series with the rectifier and is controlled by using current mode in order to shape the current injection into a rectified sine wave. Last, a full bridge is operated at line frequency to unfold the current injection. The amplification stage has a proportional compensator that maintains the voltage at the PV terminals constant. The current injection stage has a proportional-derivative compensator that controls the amplitude of the grid current so that the dc-link average voltage is maintained constant. Experimental results show that the peak efficiency of the system is 89%, and the total current harmonic distortion is below 5%. Finally, analyses show a designed lifetime of approximately ten years.
Advancement of MEMS into RF-filter applications (2003)

RF-MEMS filters will substitute conventional filters in mobile communication under certain technical and commercial conditions. Key performance parameters and requirements are discussed in detail. Two different approaches for RF-MEMS filters are reviewed and compared: Electric field driven MEMS-resonators and piezoelectric MEMS resonators. State-of-the-art RF-MEMS filters based on bulk-acoustic-wave (BAW) resonators are presented.
First Total Synthesis of ent-Gelsedine via a Novel Iodide-Promoted Allene N-Acyliminium Ion Cyclization (2000)

The first total synthesis of the oxindole alkaloid gelsedine (1) starting from (S)-malic acid is described. The key step is a novel iodide-promoted intramolecular reaction of an allene with an N-acyliminium ion intermediate which provided in a single step the bicyclic vinyl iodide 11. Other important steps are the highly stereoselective Pd-catalyzed Heck cyclization of N-methylanilide 23a which led to the desired spiro-oxindole 24a, the fully regioselective intramolecular oxymercuration of 25a to the desired cyclic ether, and the remarkable oxindole N-demethylation of 29 via a radical mechanism by using dibenzoyl peroxide. The total synthesis was concluded by the stereoselective introduction of the ethyl group from the bis-Boc compound 41 followed by methoxylation of the oxindole nitrogen. This total synthesis leads to the unnatural (+)-enantiomer of gelsedine in 21 steps and 0.10% overall yield.
TRANSPORTATION - TECHNOLOGY 1999 ANALYSIS & FORECAST (1999)

The author discusses technological advances taking place in a number of areas, including automobiles, high-speed trains, and maglev trains. Other topics discussed include: automated toll collection; computer-controlled automobile navigation and audio systems; high-speed rail in Taiwan, Spain and the U.S.; Maglev trains in Germany; driverless subway cars in Paris.
The expanding evidence base for rTMS treatment of depression (2012)

These recent studies suggest that daily left prefrontal TMS over several weeks as a treatment for depression not only appears to have efficacy in rigorous randomized controlled trials, but is effective in real-world settings, with remission in 30-40% of patients. The TMS antidepressant effect, once achieved, appears to be as durable as with other antidepressant medications or interventions. Much more research is needed, particularly with issues such as the TMS coil location, stimulation intensity and frequency, and dosing strategy.
Functional proteomic analysis of promyelocytic leukaemia nuclear bodies in irradiation-induced MCF-7 cells (2010)

It is well established that promyelocytic leukaemia nuclear bodies (PML NBs) play important roles in DNA damage responses (DDR). After irradiation, PML NBs dynamically recruit or release important proteins involved in cell-cycle regulation, DNA repair and apoptosis. As PML protein is the key molecule of PML NBs' dynamic assembling, we aimed to characterize the PML-interacting proteins in (60)Co-irradiated MCF-7 cells. A proteomic approach using CoIP, mono-dimensional electrophoresis and tandem mass spectrometry, allowed us to identify a total of 124 proteins that may associate with PML after irradiation. Bioinformatic analysis of the identified proteins showed that most of them were related to characterized PML functions, such as transcriptional regulation, cell-cycle regulation, cell-death regulation and response to stress. Four proteins, B23, MVP, G3BP1 and DHX9, were verified to co-localize with PML differentially before and after ionizing radiation (IR) treatment. The proteins identified in this study will significantly improve our understanding of the dynamic organization and multiple functions of PML NBs in DDR.
Fast sort on CPUs and GPUs (2010)

Sort is a fundamental kernel used in many database operations. In-memory sorts are now feasible; sort performance is limited by compute flops and main memory bandwidth rather than I/O. In this paper, we present a competitive analysis of comparison and non-comparison based sorting algorithms on two modern architectures - the latest CPU and GPU architectures. We propose novel CPU radix sort and GPU merge sort implementations which are 2X faster than previously published results. We perform a fair comparison of the algorithms using these best performing implementations on both architectures. While radix sort is faster on current architectures, the gap narrows from CPU to GPU architectures. Merge sort performs better than radix sort for sorting keys of large sizes - such keys will be required to accommodate the increasing cardinality of future databases. We present analytical models for analyzing the performance of our implementations in terms of architectural features such as core count, SIMD and bandwidth. Our obtained performance results are successfully predicted by our models. Our analysis points to merge sort winning over radix sort on future architectures due to its efficient utilization of SIMD and low bandwidth utilization. We simulate a 64-core platform with varying SIMD widths under constant bandwidth per core constraints, and show that large data sizes of 240 (one trillion records), merge sort performance on large key sizes is up to 3X better than radix sort for large SIMD widths on future architectures. Therefore, merge sort should be the sorting method of choice for future databases.
A framework for the development of personalized, distributed web-based configuration systems (2003)

For the last two decades, configuration systems relying on AI techniques have successfully been applied in industrial environments. These systems support the configuration of complex products and services in shorter time with fewer errors and, therefore, reduce the costs of a mass-customization business model. The European Union-funded project entitled CUSTOMER-ADAPTIVE WEB INTERFACE FOR THE CONFIGURATION OF PRODUCTS AND SERVICES WITH MULTIPLE SUPPLIERS (CAWICOMS) aims at the next generation of web-based configuration applications that cope with two challenges of today's open, networked economy: (1) the support for heterogeneous user groups in an open-market environment and (2) the integration of configurable subproducts provided by specialized suppliers.This article describes the CAWICOMS WORKBENCH for the development of configuration services, offering personalized user interaction as well as distributed configuration of products and services in a supply chain. The developed tools and techniques rely on a harmonized knowledge representation and knowledge-acquisition mechanism, open XML-based protocols, and advanced personalization and distributed reasoning techniques. We exploited the workbench based on the real-world business scenario of distributed configuration of services in the domain of information processing-based virtual private networks.
Brain Infarction and the Clinical Expression of Alzheimer Disease<subtitle>The Nun Study</subtitle> (1997)

<h3>Objective.</h3> —To determine the relationship of brain infarction to the clinical expression of Alzheimer disease (AD). <h3>Design.</h3> —Cognitive function and the prevalence of dementia were determined for participants in the Nun Study who later died. At autopsy, lacunar and larger brain infarcts were identified, and senile plaques and neurofibrillary tangles in the neocortex were quantitated. Participants with abundant senile plaques and some neurofibrillary tangles in the neocortex were classified as having met the neuropathologic criteria for AD. <h3>Setting.</h3> —Convents in the Midwestern, Eastern, and Southern United States. <h3>Participants.</h3> —A total of 102 college-educated women aged 76 to 100 years. <h3>Main Outcome Measures.</h3> —Cognitive function assessed by standard tests and dementia and AD assessed by clinical and neuropathologic criteria. <h3>Results.</h3> —Among 61 participants who met the neuropathologic criteria for AD, those with brain infarcts had poorer cognitive function and a higher prevalence of dementia than those without infarcts. Participants with lacunar infarcts in the basal ganglia, thalamus, or deep white matter had an especially high prevalence of dementia, compared with those without infarcts (the odds ratio [OR] for dementia was 20.7,95% confidence interval [95% CI], 1.5-288.0). Fewer neuropathologic lesions of AD appeared to result in dementia in those with lacunar infarcts in the basal ganglia, thalamus, or deep white matter than in those without infarcts. In contrast, among 41 participants who did not meet the neuropathologic criteria for AD, brain infarcts were only weakly associated with poor cognitive function and dementia. Among all 102 participants, atherosclerosis of the circle of Willis was strongly associated with lacunar and large brain infarcts. <h3>Conclusion.</h3> —These findings suggest that cerebrovascular disease may play an important role in determining the presence and severity of the clinical symptoms of AD.
A Markov decision process approach to temporal modulation of dose fractions in radiation therapy planning (2009)

The current state of the art in cancer treatment by radiation optimizes beam intensity spatially such that tumors receive high dose radiation whereas damage to nearby healthy tissues is minimized. It is common practice to deliver the radiation over several weeks, where the daily dose is a small constant fraction of the total planned. Such a 'fractionation schedule' is based on traditional models of radiobiological response where normal tissue cells possess the ability to repair sublethal damage done by radiation. This capability is significantly less prominent in tumors. Recent advances in quantitative functional imaging and biological markers are providing new opportunities to measure patient response to radiation over the treatment course. This opens the door for designing fractionation schedules that take into account the patient's cumulative response to radiation up to a particular treatment day in determining the fraction on that day. We propose a novel approach that, for the first time, mathematically explores the benefits of such fractionation schemes. This is achieved by building a stylistic Markov decision process (MDP) model, which incorporates some key features of the problem through intuitive choices of state and action spaces, as well as transition probability and reward functions. The structure of optimal policies for this MDP model is explored through several simple numerical examples.
Diverse Flavonoids Stimulate NodD1 Binding tonodGene Promoters inSinorhizobium meliloti (2006)

NodD1 is a member of the NodD family of LysR-type transcriptional regulators that mediates the expression of nodulation (nod) genes in the soil bacterium Sinorhizobium meliloti. Each species of rhizobia establishes a symbiosis with a limited set of leguminous plants. This host specificity results in part from a NodD-dependent upregulation of nod genes in response to a cocktail of flavonoids in the host plant's root exudates. To demonstrate that NodD is a key determinant of host specificity, we expressed nodD genes from different species of rhizobia in a strain of S. meliloti lacking endogenous NodD activity. We observed that nod gene expression was initiated in response to distinct sets of flavonoid inducers depending on the source of NodD. To better understand the effects of flavonoids on NodD, we assayed the DNA binding activity of S. meliloti NodD1 treated with the flavonoid inducer luteolin. In the presence of luteolin, NodD1 exhibited increased binding to nod gene promoters compared to binding in the absence of luteolin. Surprisingly, although they do not stimulate nod gene expression in S. meliloti, the flavonoids naringenin, eriodictyol, and daidzein also stimulated an increase in the DNA binding affinity of NodD1 to nod gene promoters. In vivo competition assays demonstrate that noninducing flavonoids act as competitive inhibitors of luteolin, suggesting that both inducing and noninducing flavonoids are able to directly bind to NodD1 and mediate conformational changes at nod gene promoters but that only luteolin is capable of promoting the downstream changes necessary for nod gene induction.
A specific quadrilateral synthesized from DNA branched junctions (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA specific quadrilateral synthesized from DNA branched junctionsJung Huei Chen, Neville R. Kallenbach, and Nadrian C. SeemanCite this: J. Am. Chem. Soc. 1989, 111, 16, 6402–6407Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://doi.org/10.1021/ja00198a063RIGHTS & PERMISSIONSArticle Views376Altmetric-Citations42LEARN 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 (2 MB) Get e-Alerts Get e-Alerts
Marine natural products: metabolites of marine invertebrates (1984)

D. J. Faulkner, Nat. Prod. Rep., 1984, 1, 551 DOI: 10.1039/NP9840100551