gebhart/patrepeval huggingface dataset:
A Single Phosphotyrosine Residue of Stat91 Required for Gene Activation by Interferon-γ (1993)

Interferon-γ (IFN-γ) stimulates transcription of specific genes by inducing tyrosine phosphorylation of a 91-kilodalton cytoplasmic protein (termed STAT for signal transducer and activator of transcription). Stat91 was phosphorylated on a single site (Tyr 701 ), and phosphorylation of this site was required for nuclear translocation, DNA binding, and gene activation. Stat84, a differentially spliced product of the same gene that lacks the 38 carboxyl-terminal amino acids of Stat91, did not activate transcription, although it was phosphorylated and translocated to the nucleus and bound DNA. Thus, Stat91 mediates activation of transcription in response to IFN-γ.
Molecular Beacons as Diagnostic Tools: Technology and Applications (2003)

Molecular beacons are single-stranded, fluorophore-labeled nucleic acid probes that are capable of generating a fluorescent signal in the presence of target, but are dark in the absence of target. Molecular beacons allow multiplex detection of PCR products in real time in a homogeneous assay format. Real time detection is inherently quantitative and affords a greater dynamic range than end-point detection methods. Reactions in a homogeneous assay format are sealed before amplification takes place, providing improved contamination control. A single cycler/reader instrument, coupled with automated sample preparation, results in higher throughput and greater ease of use. A multiplex qualitative assay that detects Chlamydia trachomatis and Neisseria gonorrhoeae, along with an internal control, has been developed. High specificity is achieved through careful selection of primers, probes and assay conditions. Quantitative HIV, HCV, and HBV viral load assays, with sensitivities of 50 copies/ml, 20 IU/ml, and 50 copies/ml, respectively, are achievable. The viral load assays are designed to quantitate all subtype and genotype specimens equivalently. A molecular beacon assay has been designed to detect a single nucleotide polymorphism in the beta2 adrenergic receptor gene.
Hierarchical disk sharing for multimedia systems (2005)

Systems that use or serve multimedia data require timely access to data on hard drives. To ensure adequate performance users must either prevent overload of disk resources, or use real-time algorithms that rely on intricate knowledge of disk internals to meet deadline requirements. We have developed Hierarchical Disk Sharing (HDS) to allow disks to be fully utilized while sustaining a bandwidth reservation, without requiring detailed knowledge of the drive internals. HDS uses a hierarchy of token bucket filters to isolate disk access among clients and groups of clients, and to allow for reclaiming of unused bandwidth. We discuss the design of HDS and present our implementation in a Linux block device driver, demonstrating the effectiveness (and limitations) of this approach.
The Effects of Basic Fibroblast Growth Factor and suramin on Cell Motility and Growth of Rat Prostate Cancer Cells (1991)

Suramin, a new type of cancer chemotherapeutic agent with growth factor antagonist properties, has been reported to affect growth of prostate cancer metastatic lesions. Partin et al. have previously reported that prostate cancer cell motility was essential for tumor cell metastasis. We have studied the effects of suramin on cell motility and cell growth in a prostate cancer cell model. We have demonstrated that suramin has differential effects on rat prostate cancer cells in vitro. The effects of suramin on cell growth were biphasic. At low concentrations of 0.01 mM and 0.1 mM, suramin stimulated growth while it was inhibitory at a higher concentration of 1.0 mM, and 10 mM suramin resulted in cell death. Cell motility was inhibited at a suramin concentration above 0.1 mM. The inhibition of cell motility by suramin may be through the blockage of growth factor effects. Reducing serum growth factor concentration reduced cell motility and the motility was restored by the addition of basic fibroblast growth factor (bFGF) to the media. Motility which had been restored by bFGF could then be blocked by the presence of suramin. The inhibition of cell motility by suramin is reversible on washout of the drug. Suramin inhibits cell motility in both the human prostate cancer cells (LNCaP) and the rat (MLL).
A New Substituent Constant, π, Derived from Partition Coefficients (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA New Substituent Constant, π, Derived from Partition CoefficientsToshio. Fujita, Junkichi. Iwasa, and Corwin. HanschCite this: J. Am. Chem. Soc. 1964, 86, 23, 5175–5180Publication Date (Print):December 1, 1964Publication History Published online1 May 2002Published inissue 1 December 1964https://pubs.acs.org/doi/10.1021/ja01077a028https://doi.org/10.1021/ja01077a028research-articleACS PublicationsRequest reuse permissionsArticle Views2663Altmetric-Citations1180LEARN 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-Alertsclose Get e-Alerts
Synthesis and structure-activity relationships of a series of aminopyridazine derivatives of .gamma.-aminobutyric acid acting as selective GABA-A antagonists (1987)

We have recently shown that an arylaminopyridazine derivative of GABA, SR 95103 [2-(3-carboxypropyl)-3-amino-4-methyl-6-phenylpyridazinium chloride], is a selective and competitive GABA-A receptor antagonist. In order to further explore the structural requirements for GABA receptor affinity, we synthesized a series of 38 compounds by attaching various pyridazinic structures to GABA or GABA-like side chains. Most of the compounds displaced [3H]GABA from rat brain membranes. All the active compounds antagonized the GABA-elicited enhancement of [3H]diazepam binding, strongly suggesting that all these compounds are GABA-A receptor antagonists. None of the compounds that displaced [3H]GABA from rat brain membranes interacted with other GABA recognition sites (GABA-B receptor, GABA uptake binding site, glutamate decarboxylase, GABA-transaminase). They did not interact with the Cl- ionophore associated with the GABA-A receptor and did not interact with the benzodiazepine, strychnine, and glutamate binding sites. Thus, these compounds appear to be specific GABA-A receptor antagonists. In terms of structure-activity, it can be concluded that a GABA moiety bearing a positive charge is necessary for optimal GABA-A receptor recognition. Additional binding sites are tolerated only if they are part of a charge-delocalized amidinic or guanidinic system. If this delocalization is achieved by linking a butyric acid moiety to the N(2) nitrogen of a 3-aminopyridazine, GABA-antagonistic character is produced. The highest potency (approximately equal to 250 times bicuculline) was observed when an aromatic pi system, bearing electron-donating substituents, was present on the 6-position of the pyridazine ring.
A PDA-based face recognition system (2003)

In this paper, we present a PDA-based face recognition system as well as some of the associated challenges of developing a PDA-based face recognition system. We describe a prototype system built from an off the shelf PDA, and introduce algorithms for image preprocessing to enhance the quality of the image by sharpening focus, and normalizing both lighting condition and head rotation. We use a unified LDA/PCA algorithm for face recognition. The algorithm maximizes the LDA criterion directly without a separate PCA step, which eliminates the possibility of losing discriminative information due to a separate PCA step. We demonstrate effectiveness of these algorithms and the feasibility of this system by experimental results. This system has many applications including information retrieval and law enforcement.
Expression of the Uteroglobin Promoter in Epithelial Cell Lines from Endometriuma (1991)

To understand the molecular mechanism of endometrial differentiation we have initiated an analysis of the uteroglobin promoter. Uteroglobin is normally expressed in endometrial tissues under the control of ovarian hormones. In gene transfer experiments with the Ishikawa cell line, derived from a human endometrial adenocarcinoma, we have identified several regions in the promoter of the uteroglobin gene that are responsible for its endometrium-specific expression. To evaluate the generality of these findings, we have begun cloning the promoter regions of potential endometrial markers, including the rat, mouse, and human uteroglobin gene. In the rat, expression of the uteroglobin-like gene, CC10, is dominant in the lung but is also observed in the endometrium of progesterone treated animals. A comparison of the 5'-flanking sequence of the rat and rabbit uteroglobin gene resulted in the detection of similarities and differences that could explain their differential expression in vivo. To substantiate these findings we have established several cell lines from rat endometrium using murine retroviral vectors containing a positive selection marker and various viral oncogenes, such as SV40 large T antigen, adenovirus E1A, and Ha-ras. Cell lines immortalized by SV40 T-antigen were subsequently transformed with the Ha-ras oncogene. Several cell lines exhibit properties of epithelial endometrial cells. Two cell lines generated with a temperature sensitive mutant of the SV40 large T-antigen grow as transformed cells at the permissive temperature, but differentiate upon shifting to the non-permissive temperature. These rat endometrial cell lines should be useful for the analysis of endometrium-specific gene expression and as model systems for endometrial carcinoma.
Characterization of the oxidation products of paralytic shellfish poisoning toxins by liquid chromatography/mass spectrometry (1993)

Periodate oxidation of the toxins responsible for paralytic shellfish poisoning (PSP) yields fluorescent products that are useful for trace analysis by reversed-phase liquid chromatography. Some toxins are oxidized to the same product, while others are transformed to a mixture of products; in all cases, the products are too unstable to be isolated preparatively. A mobile phase containing heptafluorobutyric acid as an ion-pair agent was developed to improve compatibility with liquid chromatography/mass spectrometry (LC/MS) analysis. Several LC/MS techniques were investigated: chemical ionization with the moving belt interface, atmospheric-pressure chemical ionization, thermospray, continuous-flow fast-atom bombardment, and ion-spray. Only LC/ion-spray MS was able to provide spectra of the oxidized products. The products were characterized as purines resulting from: (a) breakage of the C4-C12 bond and aromatization of the remaining rings (loss of 4 hydrogens); (b) partial elimination of a carbamoyl or N-sulfocarbamoyl side-chain (this is promoted by the presence of an N-1-hydroxy group); and (c) partial hydrolysis of an N-sulfocarbamoyl side-chain to a carbamoyl group.
Somniloquy: Maintaining Network Connectivity While Your Computer Sleeps (2007)

Reducing the energy consumption of computers is becoming increasingly important with rising energy costs and environmental concerns. It is especially important for mobile devices such as laptops where battery lifetime is always an issue. Sleep states such as S3 (suspend to RAM) save energy but prevent the device from responding to incoming network events, for example remote desktop logins and file transfer requests. Thus many people do not use S3 and instead leave their computers plugged in and active. Mobile users do not have this flexibility, and as a result their machines are unreachable during the periods when they are in S3. Somniloquy allows computers in S3 to be woken based on incoming network traffic such as incoming VoIP calls or remote file access requests, or other events such as the presence of particular access points. This is done by adding a secondary embedded processor attached to a network interface, forming a low-power domain that remains active even when the rest of the computer is in S3. This secondary processor acts transparently on behalf of the computer, sharing the same MAC address, IP address, host name, etc. Remote servers and network hardware remain completely unaware of the low-power state. We present a prototype implementation of Somniloquy using a USB peripheral, which is therefore easily retrofitted to existing computers. Our prototype achieves a ten-fold increase in battery lifetime compared to an idle computer not in S3, while only adding 4-7s of latency to respond to applicationlayer events. Our system allows computers to appear alwayson when they are in fact talking in their sleep.
When good instructions go bad (2008)

This paper reconsiders the threat posed by Shacham's -- a technique by which W-xor-X-style hardware protections are evaded via carefully crafted stack frames that divert control flow into the middle of existing variable-length x86 instructions -- creating short new instructions streams that then return. We believe this attack is both more general and a greater threat than the author appreciated. In fact, the vulnerability is not limited to the x86 architecture or any particular operating system, is readily exploitable, and bypasses an entire category of malware protections. In this paper we demonstrate general return-oriented programming on the SPARC, a fixed instruction length RISC architecture with structured control flow. We construct a Turing-complete library of code gadgets using snippets of the Solaris libc, a general purpose programming language, and a compiler for constructing return-oriented exploits. Finally, we argue that the threat posed by return-oriented programming, across all architectures and systems, has negative implications for an entire class of security mechanisms: those that seek to prevent malicious computation by preventing the execution of malicious code.
Pace recognition: eigenface, elastic matching, and neural nets (1997)

This paper is a comparative study of three recently proposed algorithms for face recognition: eigenface, autoassociation and classification neural nets, and elastic matching. After these algorithms were analyzed under a common statistical decision framework, they were evaluated experimentally on four individual data bases, each with a moderate subject size, and a combined data base with more than a hundred different subjects. Analysis and experimental results indicate that the eigenface algorithm, which is essentially a minimum distance classifier, works well when lighting variation is small. Its performance deteriorates significantly as lighting variation increases. The elastic matching algorithm, on the other hand, is insensitive to lighting, face position, and expression variations and therefore is more versatile. The performance of the autoassociation and classification nets is upper bounded by that of the eigenface but is more difficult to implement in practice.
Dosage Escalation Study of S-1 and Irinotecan in Metronomic Chemotherapy against Advanced Colorectal Cancer (2009)

The anti-angiogenic efficacy of chemotherapy would seem to be optimized by administering comparatively lower doses of drugs on a more frequent (daily, several times a week, or weekly) or continuous schedule, with no extended interruptions - sometimes referred to as 'metronomic' chemotherapy. This phase I study was performed to determine the recommended dosage (RD) of metronomic chemotherapy using oral fluoropyrimidine S-1 plus weekly irinotecan (CPT-11) in patients with previously untreated advanced or recurrent colorectal cancer. Patients received first-line chemotherapy consisting of 80 mg/m(2) of S-1 given on days 3 to 7, 10 to 14, and 17 to 21 with escalating dosages of CPT-11 (from 40 mg/m(2)) administered intravenously on day 1, 8, and 15 of a 28-day cycle. Standard patient eligibility criteria were used. Based on the concept of metronomic chemotherapy, dose limiting toxicity (DLT) was defined any toxicity that resulted in skipping of CPT-11 administration, or more than 5 days suspension in S-1 administration, in addition to the conventional criteria. If the maximum tolerated dosage (MTD) was defined as the maximum dosage at which no suspension of CPT-11 or S-1 administration occurred, the RD was considered to be the dosage one rank lower than the MTD. On the other hand, in the present study the MTD was defined as the dosage at which at least one suspension of CPT-11 or S-1 administration occurred, the MTD was considered to be the RD. Two of the first 3 patients at level 4 received 60 mg/m(2) of CPT-11 and 80 mg/m(2) of S-1 experienced a suspension in CPT-11 administration, thus level 4 was defined as the MTD and RD. Sixty mg/m(2) of CPT-11 and 80 mg/m(2) of S-1 were the indicated RD for the following phase II study of metronomic chemotherapy.
StreamRay (2009)

The wide availability of commodity graphics processors has made real-time graphics an intrinsic component of the human/computer interface. These graphics cores accelerate the z-buffer algorithm and provide a highly interactive experience at a relatively low cost. However, many applications in entertainment, science, and industry require high quality lighting effects such as accurate shadows, reflection, and refraction. These effects can be difficult to achieve with z-buffer algorithms but are straightforward to implement using ray tracing. Although ray tracing is computationally more complex, the algorithm exhibits excellent scaling and parallelism properties. Nevertheless, ray tracing memory access patterns are difficult to predict and the parallelism speedup promise is therefore hard to achieve. This paper highlights a novel approach to ray tracing based on stream filtering and presents StreamRay, a multicore wide SIMD microarchitecture that delivers interactive frame rates of 15-32 frames/second for scenes of high geometric complexity and exhibits high utilization for SIMD widths ranging from eight to 16 elements. StreamRay consists of two main components: the ray engine, which is responsible for stream assembly and employs address generation units that generate addresses to form large SIMD vectors, and the filter engine, which implements the ray tracing operations with programmable accelerators. Results demonstrate that separating address and data processing reduces data movement and resource contention. Performance improves by 56% while simultaneously providing 11.63% power savings per accelerator core compared to a design which does not use separate resources for address and data computations.
Radiation-induced normal tissue injury: Role of adhesion molecules in leukocyte-endothelial cell interactions (1999)

The late onset of necrosis and fibrosis in normal tissues can be a serious consequence of radiotherapy in cancer patients. Because radiation-induced vascular injury precedes the tissue damage, vascular injury is regarded as crucial in the pathogenesis of tissue damage. An understanding of the processes responsible is essential to develop strategies for the amelioration of radiation-induced normal tissue damage. Leukocyte infiltration is commonly observed at sites of irradiation and is likely to lead to the acceleration and/or induction of parenchymal atrophy, fibrosis and necrosis in normal tissues following radiotherapy. The molecular mechanisms mediating leukocyte infiltration of tissues during inflammation have been studied extensively. It is now well established that cell adhesion molecules (CAMs) expressed on leukocytes and endothelial cells control the trafficking of leukocytes from the blood vessel lumen in these conditions. CAMs including E (endothelial), P (platelet) and L (leukocyte)-selectins, intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), beta1 and beta2 integrins and CD31 are involved in the cascade of events resulting in rolling, arrest and transmigration of leukocytes through the inflamed endothelium. Whether a similar sequence of molecular events induces leukocyte sequestration in irradiated normal tissues is not known. This review is focussed on the role of CAMs in radiation-induced leukocyte infiltration of normal tissues and the therapeutic implications of these findings.
Identification and cloning of a novel type I sering / threonine kinase receptor of the TGF‐β / BMP superfamily in rat prostate (1996)

A cDNA clone encoding a new member of the type I serine/threonine kinase receptors of the TGF-beta/BMP superfamily was isolated from a rat prostate cDNA library. The predicted sequence of the encoded protein is 493 amino acids with a molecular weight of 55 kDa. It contains a putative cysteine rich extracellular domain, a transmembrane domain, a conserved type I receptor GS domain and a cytoplasmic serine/threonine kinase domain. The kinase domain shares 80% homology with that of ALK-4 and ALK-5 whose ligands are activin and TGF-beta. Northern blot analysis revealed that this prostate serine/threonine kinase receptor I (PSKR-I) is highly expressed in rat dorsolateral prostate, coagulating gland (anterior prostate), cerebellum and adipose tissue.
A protocol to provide verifiable proof of identity and unforgeable transaction receipts (1989)

An identity verification scheme that uses a public authentication channel to validate a private authentication channel belonging to the individual who wishes to prove his identity is described. The user can prove his identity by demonstrating that he can authenticate (suitably chosen) messages in the private channel. It also provides certified receipts for transactions whose legitimacy can later be verified by impartial arbiters who do not need to be designated in advance or be involved in the transaction at the time it takes place.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Melanin Production and Use as a Soluble Electron Shuttle for Fe(III) Oxide Reduction and as a Terminal Electron Acceptor by Shewanella algae BrY (2002)

Dissimilatory metal-reducing bacteria (DMRB) utilize numerous compounds as terminal electron acceptors, including insoluble iron oxides. The mechanism(s) of insoluble-mineral reduction by DMRB is not well understood. Here we report that extracellular melanin is produced by Shewanella algae BrY. The extracted melanin served as the sole terminal electron acceptor. Upon reduction the reduced, soluble melanin reduced insoluble hydrous ferric oxide in the absence of bacteria, thus demonstrating that melanin produced by S. algae BrY is a soluble Fe(III)-reducing compound. In the presence of bacteria, melanin acted as an electron conduit to Fe(III) minerals and increased Fe(III) mineral reduction rates. Growth of S. algae BrY occurred in anaerobic minimal medium supplemented with melanin extracted from previously grown aerobic cultures of S. algae BrY. Melanin produced by S. algae BrY imparts increased versatility to this organism as a soluble Fe(III) reductant, an electron conduit for iron mineral reduction, and a sole terminal electron acceptor that supports growth.