gebhart/patrepeval huggingface dataset:
The 56-kilodalton major protein antigen of Rickettsia tsutsugamushi: molecular cloning and sequence analysis of the sta56 gene and precise identification of a strain-specific epitope (1990)

Lasting immunity against Rickettsia tsutsugamushi, the causative agent of scrub typhus fever, has been demonstrated to be strain specific. Two protein antigens of 110 and 56 kilodaltons (kDa) have been shown to exhibit strain-specific epitopes. The 56-kDa scrub typhus antigen (Sta56) is an abundant outer membrane protein of R. tsutsugamushi and is an antigen often recognized by humans infected with this obligate intracellular bacterium. In this study the complete gene encoding Sta56 (strain Karp) was cloned into pBR322 on a 2.3-kilobase genomic HindIII DNA fragment and the complete 56-kDa polypeptide was expressed in Escherichia coli. DNA sequence analysis of the 2.3-kilobase HindIII fragment revealed an open reading frame large enough to encode a 56-kDa polypeptide. A putative signal sequence was identified at the deduced amino terminus of the Sta56 polypeptide, and pulse-chase analysis of maxicells labeled with [35S]methionine demonstrated that a higher-molecular-weight precursor matures into the 56-kDa polypeptide. Epitope scanning analysis with synthetic peptides derived from the deduced amino acid sequence identified an octapeptide (located from amino acid residues 117 to 124) that was reactive with a Karp strain-specific monoclonal antibody (K13F88A). Other epitopes recognized by different monoclonal antibodies, including another Karp strain-specific monoclone (K1E106), were localized to different regions of the protein based on their reactivities with lambda gt11 recombinants expressing various portions of the sta56 gene.
Expression of the Arabidopsis HMG2 Gene, Encoding 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase, Is Restricted to Meristematic and Floral Tissues (1995)

Montserrat Enjuto, Victoria Lumbreras, , Albert Boronat, Expression of the Arabidopsis HMG2 Gene, Encoding 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase, Is Restricted to Meristematic and Floral Tissues, The Plant Cell, Vol. 7, No. 5 (May, 1995), pp. 517-527
Cell Surface Glycans: The Why and How of Their Functionality as Biochemical Signals in Lectin-Mediated Information Transfer (2006)

Calculations of the coding capacity of biomolecules come up with the striking result that carbohydrates excel nucleotides and amino acids by far in this respect. Consequently, glycans are ideally suited to equip cell surfaces with a maximum of signals in a minimum of space and form the cellular glycome. The ensuing concept of the sugar code interprets glycans as a platform for encoding messages and shifts in the glycome as a means to swiftly add/remove signals. Next, it implies the presence of effectors that read the signals in situ. Fittingly, recent work on natural decoding devices in mammals (endogenous lectins) has revealed not only their presence but a level of complexity that matches the structural diversity of glycans. The emerging importance of lectin-ligand interaction in immune regulation calls for an introduction to this concept for nonspecialists. This primer to the fundamentals of the sugar code, with telling examples from the realm of immunology, also illustrates the strategic and hitherto unsuspected fine-tuning between glycan structure and lectin design/expression.
Performance analysis of 3-D monolithic integrated circuits (2010)

3-D monolithic integration (3DMI), also termed as sequential integration, is a potential technology for future gigascale circuits. Since the device layers are processed in sequential order, the size of the vertical contacts is similar to traditional contacts unlike in the case of parallel 3-D integration with through silicon vias (FSVs). Given the advantage of such small contacts, 3DMI supports stacking active layers such that fine-grain integration of 3-D circuits can be implemented. This paper extends the idea of constructing the standard cells across two active layers, forming 3-D cells, to reduce the overall area and interconnect wirelength of a circuit. To demonstrate the effect of the 3DMI technology on these important parameters of circuit design, two important communication blocks are evaluated. Specifically, a low-density-parity-check (LDPC) decoder as a sample of interconnect-dominated circuit and a data-encryption-standard (DES) block, which is good instance of a gate dominated circuit, are investigated. By employing 3-D cells in the conventional design flow chain, there is more than 10% decrease in wirelength for both circuits (in wirelength driven placement mode). However, when subjected to timing driven placement a slight reduction in delay (1.6%) is observed for an LDPC decoder, whereas for the DES block considerable delay reduction (14.22%) is achieved.
Downregulation of Inflammatory MicroRNAs by Ig-like Transcript 3 Is Essential for the Differentiation of Human CD8+ T Suppressor Cells (2012)

We have investigated the mechanism underlying the immunoregulatory function of membrane Ig-like transcript 3 (ILT3) and soluble ILT3Fc. microRNA (miRNA) expression profile identified genes that were downregulated in ILT3-induced human CD8(+) T suppressor cells (Ts) while upregulated in T cells primed in the absence of ILT3. We found that miR-21, miR-30b, and miR-155 target the 3'-untranslated region of genes whose expression was strongly increased in ILT3Fc-induced Ts, such as dual specificity phosphatase 10, B cell CLL/lymphoma 6, and suppressor of cytokine signaling 1, respectively. Transfection of miRNA mimics or inhibitors and site-specific mutagenesis of their 3'-untranslated region binding sites indicated that B cell CLL/lymphoma 6, dual specificity phosphatase 10, and suppressor of cytokine signaling 1 are direct targets of miR-30b, miR-21, and miR-155. Primed CD8(+) T cells transfected with miR-21&30b, miR-21&155, or miR-21&30b&155 inhibitors displayed suppressor activity when added to autologous CD3-triggered CD4 T cells. Luciferase reporter assays of miR-21 and miR-155 indicated that their transcription is highly dependent on AP-1. Analysis of activated T cells showed that ILT3Fc inhibited the translocation to the nucleus of the AP-1 subunits, FOSB and c-FOS, and the phosphorylation of ZAP70 and phospholipase C-γ 1. In conclusion, ILT3Fc inhibits T cell activation and induces the generation of Ts targeting multiple inflammatory miRNA pathways.
Apoptosis Initiated When BH3 Ligands Engage Multiple Bcl-2 Homologs, Not Bax or Bak (2007)

A central issue in the regulation of apoptosis by the Bcl-2 family is whether its BH3-only members initiate apoptosis by directly binding to the essential cell-death mediators Bax and Bak, or whether they can act indirectly, by engaging their pro-survival Bcl-2-like relatives. Contrary to the direct-activation model, we show that Bax and Bak can mediate apoptosis without discernable association with the putative BH3-only activators (Bim, Bid, and Puma), even in cells with no Bim or Bid and reduced Puma. Our results indicate that BH3-only proteins induce apoptosis at least primarily by engaging the multiple pro-survival relatives guarding Bax and Bak.
Perioperative Glucose Control in the Diabetic or Nondiabetic Patient (2006)

Patients with diabetes are more likely to undergo surgery than nondiabetics, and maintaining glycemic control in subjects with diabetes can be challenging during the perioperative period. Surgery in diabetic patients is associated with longer hospital stay, higher health care resource utilization, and greater perioperative mortality. In addition, several observational and interventional studies have indicated that hyperglycemia is associated with adverse clinical outcomes in surgical and critically ill patients. This paper reviews the pathophysiology of hyperglycemia during trauma and surgical stress and will provide practical recommendations for the preoperative, intraoperative, and postoperative care of diabetic patients.
Interdomain zinc site on human albumin (2003)

Albumin is the major transport protein in blood for Zn(2+), a metal ion required for physiological processes and recruited by various drugs and toxins. However, the Zn(2+)-binding site(s) on albumin is ill-defined. We have analyzed the 18 x-ray crystal structures of human albumin in the PDB and identified a potential five-coordinate Zn site at the interface of domains I and II consisting of N ligands from His-67 and His-247 and O ligands from Asn-99, Asp-249, and H(2)O, which are the same amino acid ligands as those in the zinc enzymes calcineurin, endonucleotidase, and purple acid phosphatase. The site is preformed in unliganded apo-albumin and highly conserved in mammalian albumins. We have used (111)Cd NMR as a probe for Zn(2+) binding to recombinant human albumin. We show that His-67 --> Ala (His67Ala) mutation strongly perturbs Cd(2+) binding, whereas the mutations Cys34Ala, or His39Leu and Tyr84Phe (residues which may H-bond to Cys-34) have no effect. Weak Cl(-) binding to the fifth coordination site of Cd(2+) was demonstrated. Cd(2+) binding was dramatically affected by high fatty acid loading of albumin. Analysis of the x-ray structures suggests that fatty acid binding to site 2 triggers a spring-lock mechanism, which disengages the upper (His-67Asn-99) and lower (His-247Asp-249) halves of the metal site. These findings provide a possible mechanism whereby fatty acids (and perhaps other small molecules) could influence the transport and delivery of zinc in blood.
Edge-avoiding À-Trous wavelet transform for fast global illumination filtering (2010)

We present a fast and simple filtering method designed for ray traced Monte Carlo global illumination images which achieves real-time rates. Even on modern hardware only few samples can be traced for interactive applications, resulting in very noisy outputs. Taking advantage of the fact that Monte Carlo computes hemispherical integrals that may be very similar for neighboring pixels we derive a fast edge-avoiding filtering method in screen space using the A-Trous wavelet transform that operates on the full noisy image and produces a result that is close to a solution with many more samples per pixel.
Risk Prediction Models for Hospital Readmission: A Systematic Review [Internet] (2011)

An increasing body of literature attempts to describe and validate hospital readmission risk prediction tools. Interest in such models has grown for two reasons. First, transitional care interventions may reduce readmissions among chronically ill adults. Readmission risk assessment could be used to help target the delivery of these resource-intensive interventions to the patients at greatest risk. Ideally, models designed for this purpose would provide clinically relevant stratification of readmission risk and give information early enough during the hospitalization to trigger a transitional care intervention, many of which involve discharge planning and begin well before hospital discharge. Second, there is interest in using readmission rates as a quality metric. Recently, the Centers for Medicare & Medicaid Services (CMS) began using readmission rate as a publicly reported metric, with plans to lower reimbursement to hospitals with excess risk-standardized readmission rates. Valid risk adjustment methods are required for calculation of risk-standardized readmission rates which could, in turn, be used for hospital comparison, public reporting, and reimbursement determinations. Models designed for these purposes should have good predictive ability; be deployable in large populations; use reliable data that can be easily obtained; and use variables that are clinically related to, and validated in, the populations in which use is intended.This systematic review was performed to synthesize the available literature on validated readmission risk prediction models, describe their performance, and assess their suitability for clinical or administrative use.
The effect of oxygen tension on haemopoietic and fibroblast cell proliferation in vitro (1978)

The effects of providing low oxygen tension in the gas phase of two different types of cell culture systems were investigated. The clonal growth of granulocyte-macrophage progenitor cells in an agar culture system was improved markedly by incubation within a low oxygen tension gas phase (48 mmHg--6.8%) instead of the conventional air (135 mmHg--19%), the effects being measured by increases in numbers of colony forming cells detected and in the colony sizes. The increased efficiency of colony formation was observed both with mouse and human marrow cells. A similar effect was observed in a liquid adherence culture system with primary cultures of foetal mouse fibroblasts both at clonal and higher cell densities.
B7‐H3‐mediated tumor immunology: Friend or foe? (2013)

B7-H3 (CD276), a newly identified member of the B7 family of molecules, is often induced in human tumors and its overexpression is closely correlated with survival, prognosis or tumor grade. Although cancer immunotherapy has not been completely translated into clinical successes, interest has been further enhanced by the realization of these costimulatory molecules' potential as targets to modulate clinical immune responses. Despite ample evidence implicating B7-H3 in tumor immune escape, a steady flow of reports have suggested that it may also have antitumor effects under certain circumstances. The safety and efficacy of targeting B7-H3 with a monoclonal antibody for the treatment of advanced-stage central nervous system cancer in children has been proven, making B7-H3 an attractive therapeutic target for this kind of tumor. In addition, B7-H3 was shown to promote invasion and accelerate carcinogenesis in tumor progression according to its nonimmunological regulatory roles. In this review, we discuss current understanding of the diverse functions of B7-H3 in carcinogenesis and cancer progression, and consider future directions for designing cancer immunotherapeutic agents targeting B7-H3.
An object oriented DSM framework (1996)

This paper briefly outlines the motivations for, and the development of an Object Oriented DSM system which provided a framework for programming with DSM. It provides customizable consistency, coherence, and communication modes via appropriate class hierarchies. This papers specifically considers the consistency models. The intention is to provide a DSM interface which can be used to develop a wide range of applications in a portable and consistent manner, across a wide variety of hardware platforms.
TIMERx®: novel polysaccharide composites for controlled/programmed release of drugs in the gastrointestinal tract (2005)

Over the last 100 years tablets have grown from first invention to becoming the world's leading medicinal form, by any measure. This article considers some of the reasons for the pre-eminence of pharmaceutical tablets. Particular attention has been given to the role of controlled-release tablets and to a very versatile hydrogel-based controlled-release technology, called TIMERx((R)). The unique nature of TIMERx intermolecular physical chemistry is described in relation to the technology's potential to provide any one of a number of different release profiles, ranging from zero order to chronotherapeutic release. The unusual nature of TIMERx technology lies in its ability to provide different release kinetics by the manipulation of molecular interactions. This 'molecular engine' replaces the need for complex processing or novel excipients and allows desired drug release profiles to be 'factory set' following a simple formulation development process. The article describes the physico-chemical interactions of TIMERx technology at a molecular level and how they can be manipulated by formulation considerations. The article describes how TIMERx technology has been developed to the point where today it underpins a number of marketed pharmaceutical CR products as well as products under development by Penwest Pharmaceuticals.
Growth and carcass traits of open beef heifers versus beef heifers that have calved (1986)

La vitesse de croissance est modifiee mais la qualite des carcasses et de la viande n'est pas alteree apres velage
Mechanisms of Superior Anti-Tumor Cytotoxic Response of Interleukin 15-Induced Lymphokine-Activated Killer Cells (2004)

Interleukin (IL) 15 is one of the main cytokines controlling cytotoxic lymphocyte survival and growth. Despite its receptor and functional similarity to IL-2, IL-15 affects a wider target cell population and utilizes different mechanisms in cell activation. The role of IL-15 in lymphokine-activated killer (LAK) cell generation in vitro and potential mechanisms of cytotoxicity compared with equivalent low concentration of IL-2 with or without mitogens (phytohemoglutinin (PHA) and anti-CD3 antibody) have been investigated in this study. IL-15 treatment resulted in moderate cell proliferation over 7 days, whereas IL-2 treatment was associated with decreased cell numbers. Unlike IL-2 in combination with mitogens, IL-15 caused increases in both cytotoxic T lymphocytes (CTL) and CD56 LAK cells, particularly cytokine-induced killer and cytolytic natural killer T-cell (CNK-T) subpopulations, which are known to be highly effective in cytotoxicity. IL-15 also increased overall perforin and tumor necrosis factor-alpha expression and more prominently in CTLs. Consequently, IL-15 resulted in superior cytotoxicity against two different NK-sensitive (human K-562 and murine YAC-1) and LAK-sensitive (human Daudi and Raji) cell lines compared with other cytokine combinations. There was also no contribution of mitogens to IL-2-induced cytotoxicity. In conclusion, IL-15 at the concentration of 10 ng/mL used in this study causes moderate proliferation and superior cytotoxicity of LAK cells in vitro that was associated with induction of a specific LAK cell subpopulation profile and related cellular killing mechanisms. These results are encouraging for potential use of IL-15 as part of immunotherapy.
The Fgl2/fibroleukin prothrombinase contributes to immunologically mediated thrombosis in experimental and human viral hepatitis (2003)

Fibrin deposition and thrombosis within the microvasculature is now appreciated to play a pivotal role in the hepatocellular injury observed in experimental and human viral hepatitis. Importantly, the pathways by which fibrin generation is elicited in viral hepatitis may be mechanistically distinct from the classical pathways of coagulation induced by mechanical trauma or bacterial lipopolysaccharide (LPS). In the setting of murine hepatitis virus strain-3 (MHV-3) infection, a member of the Coronaviridae, activated endothelial cells and macrophages express distinct cell-surface procoagulants, including a novel prothrombinase, Fgl2/fibroleukin, which are important for both the initiation and localization of fibrin deposition. To assess the role of Fgl2/fibroleukin in murine viral hepatitis we generated a Fgl2/fibroleukin-deficient mouse. Peritoneal macrophages isolated from Fgl2/fibroleukin-/- mice did not generate a procoagulant response when infected with MHV-3. Fibrin deposition and liver necrosis were markedly reduced, and survival was increased in mice infected with MHV-3. To address the relevance of Fgl2/fibroleukin in human chronic viral hepatitis we studied patients with minimal and marked chronic hepatitis B. We detected robust expression of Fgl2/fibroleukin mRNA transcripts and protein in liver tissue isolated from patients with marked chronic hepatitis B. Fibrin deposition was strongly associated with Fgl2/fibroleukin expression. Collectively, these data indicate a critical role for Fgl2/fibroleukin in the pathophysiology of experimental and human viral hepatitis.
Fibroblast-Like Synoviocytes from Rheumatoid Arthritis Patients Express Functional IL-15 Receptor Complex: Endogenous IL-15 in Autocrine Fashion Enhances Cell Proliferation and Expression of Bcl-xL and Bcl-2 (2002)

The hallmarks of rheumatoid arthritis (RA) are leukocytic infiltration of the synovium and expansiveness of fibroblast-like synoviocytes (FLS). The abnormal proliferation of FLS and their resistance to apoptosis is mediated, at least in part, by present in RA joints proinflammatory cytokines and growth factors. Because IL-15 exerts properties of antiapoptotic and growth factors, and is produced by RA FLS, we hypothesized that IL-15 participates in RA FLS activation. To test this hypothesis, we first examined whether RA FLS express chains required for high affinity functional IL-15R. Indeed, RA FLS express IL-15Ralpha at mRNA and protein levels. Moreover, we confirmed the presence of IL-2Rbeta and common gamma-chains. Interestingly, TNF-alpha or IL-1beta triggered significant elevation of IL-15Ralpha chain at mRNA and protein levels. Next, we investigated the effects of exogenous or endogenous IL-15 on Bcl-2 and Bcl-x(L) expression, FLS proliferation, and apoptosis. Exogenous IL-15 enhanced RA FLS proliferation and increased the level of mRNA-encoding Bcl-x(L). To test the role of endogenous IL-15 in the activation of RA FLS, an IL-15 mutant/Fcgamma2a protein exerting properties of specific antagonist to the IL-15Ralpha chain was used. We found that blocking IL-15 biological activities using this protein substantially reduced endogenous expression of Bcl-2 and Bcl-x(L), and RA FLS proliferation that was reflected by increased apoptosis. Thus, we have demonstrated that a distinctive phenotype of RA FLS, i.e., persistent activation, proliferation, and resistance to apoptosis, is related to the autocrine activation of IL-15Rs by FLS-derived IL-15.
Polyethylene Glycol-Modified GM-CSF Expands CD11bhighCD11chigh But Not CD11blowCD11chigh Murine Dendritic Cells In Vivo: A Comparative Analysis with Flt3 Ligand (2000)

Dendritic cells (DC) are potent APCs that can be characterized in the murine spleen as CD11b(high)CD11c(high) or CD11b(low)CD11c(high). Daily injection of mice of Flt3 ligand (FL) into mice transiently expands both subsets of DC in vivo, but the effect of administration of GM-CSF on the expansion of DC in vivo is not well defined. To gain further insight into the role of GM-CSF in DC development and function in vivo, we treated mice with polyethylene glycol-modified GM-CSF (pGM-CSF) which has an increased half-life in vivo. Administration of pGM-CSF to mice for 5 days led to a 5- to 10-fold expansion of CD11b(high)CD11c(high) but not CD11b(low)CD11c(high) DC. DC from pGM-CSF-treated mice captured and processed Ag more efficiently than DC from FL-treated mice. Although both FL- and pGM-CSF-generated CD11b(high)CD11c(high) DC were CD8alpha-, a greater proportion of these DC from pGM-CSF-treated mice were 33D1+ than from FL-treated mice. CD11b(low)CD11c(high) DC from FL-treated mice expressed high levels of intracellular MHC class II. DC from both pGM-CSF- and FL-treated mice expressed high levels of surface class II, low levels of the costimulatory molecules CD40, CD80, and CD86 and were equally efficient at stimulating allogeneic and Ag-specific T cell proliferation in vitro. The data demonstrate that treatment with pGM-CSF in vivo preferentially expands CD11b(high)CD11c(high) DC that share phenotypic and functional characteristics with FL-generated CD11b(high)CD11c(high) DC but can be distinguished from FL-generated DC on the basis of Ag capture and surface expression of 33D1.
Integrated optics for optical head applications (1994)

A waveguide sttucture for use in optical head systems is presented. The fabricated structures are 10 × 2 × 2mm3 and are &lt;0.2 g in mass. The waveguides propagate data and feedback signals for tracking and focusing. The proper generation of these signals and their sensitivity to the accompanying imaging optics are demonstrated.
Relationship of Circulating Tumor Cells to Tumor Response, Progression-Free Survival, and Overall Survival in Patients With Metastatic Colorectal Cancer (2008)

The number of CTCs before and during treatment is an independent predictor of PFS and OS in patients with metastatic colorectal cancer. CTCs provide prognostic information in addition to that of imaging studies.