gebhart/patrepeval huggingface dataset:
Design and implementation of a scribe line measurement transistor test array structure in 14nm FinFET CMOS technology (2015)

Submicron fin-shaped field effect transistor (FinFET) process technologies pose a variety of challenges for foundries ramping designs into production due to parameter variation.Accurate and relevant electrical transistor parametric data are required to correlate product yield and performance to the process technology throughout the manufacturing cycle.Typically, transistor data are obtained from foundry-designed and isolated transistors test structures which do not resemble the layout, physical attributes, or design style of the transistors in the standard cells of the actual design.As a result, the topographical, density, and stress effects on the transistors of a custom or synthesized design layout are not reflected in the test measurements.To address this issue, a scribe line macro (SLM) test structure with modular transistor arrays utilizing standard cells from the design library was designed for a 14nm FinFET complementary metal oxide semiconductor (CMOS) technology process.The SLM test structure fits in a 52m by 2000m footprint and can be printed at multiple locations in the scribe lines of a 300mm wafer.The SLM test structure comprises of four n-type metal oxide semiconductor (NMOS) and four p-type vi metal oxide semiconductor (PMOS) transistor arrays containing 240 FinFET transistors of 33 types that can be tested rapidly and in parallel.The SLM test structure is designed to generate silicon data for parametric transistor measurements such as IDSAT, IDLIN, IDOFF, VTSAT, and VTLIN using a parametric inline tester in the manufacturing line of a foundry.These silicon measurements will be correlated to simulation data extracted from the netlist of the SLM test structure to eventually improve the 14nm FinFET technology libraries and silicon models.The SLM test structure design will be continuously improved for future technology processes with a goal of enabling accurate and design-relevant transistor parametric measurements to help drive cycle time, cost, and yield improvements.
An investigation of RAKE receiver operation in an urban environment for various spreading bandwidth allocations (2003)

The renewed interest in the application of the spread-spectrum techniques such as CDMA to cellular mobile radio systems, in both the US, and within Europe through the RACE II and UK DTI/SERC LINK programs continues to gather momentum. To this end, an analytical performance model has been developed in order to provide a greater insight into the operation of this technique, in particular the sensitivity of the bandwidth efficiency of the network to the form of diversity signal processing used in the mobile transceiver. This theme is continued with an investigation of the wideband channel characteristics of an urban service area. Results are presented relating the statistics of the RAKE receiver branches to the spreading bandwidth used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
BAFF production by antigen-presenting cells provides T cell co-stimulation (2004)

The B cell-activating factor from the tumor necrosis factor family (BAFF) is an important regulator of B cell immunity. Recently, we demonstrated that recombinant BAFF also provides a co-stimulatory signal to T cells. Here, we studied expression of BAFF in peripheral blood leukocytes and correlated this expression with BAFF T cell co-stimulatory function. BAFF is produced by antigen-presenting cells (APC). Blood dendritic cells (DC) as well as DC differentiated in vitro from monocytes or CD34+ stem cells express BAFF mRNA. Exposure to bacterial products further up-regulates BAFF production in these cells. A low level of BAFF transcription, up-regulated upon TCR stimulation, was also detected in T cells. Functionally, blockade of endogenous BAFF produced by APC and, to a lesser extent, by T cells inhibits T cell activation. Altogether, this indicates that BAFF may regulate T cell immunity during APC-T cell interactions and as an autocrine factor once T cells have detached from the APC.
Investigating Cellular Metabolism of Synthetic Azidosugars with the Staudinger Ligation (2002)

The structure of sialic acid on living cells can be modulated by metabolism of unnatural biosynthetic precursors. Here we investigate the conversion of a panel of azide-functionalized mannosamine and glucosamine derivatives into cell-surface sialosides. A key tool in this study is the Staudinger ligation, a highly selective reaction between modified triarylphosphines and azides that produces an amide-linked product. A preliminary study of the mechanism of this reaction, and refined conditions for its in vivo execution, are reported. The reaction provided a means to label the glycoconjugate-bound azidosugars with biochemical probes. Finally, we demonstrate that the cell-surface Staudinger ligation is compatible with hydrazone formation from metabolically introduced ketones. These two strategies provide a means to selectively modify cell-surface glycans with exogenous probes.
Coexpression of CCR6 and CD146 (MCAM) is a marker of effector memory T‐helper 17 cells (2012)

Effector memory T (T(EM)) cells are a subpopulation of memory T cells that express receptors mediating migration to inflamed tissues and produce various cytokines. Effector memory T-helper (Th)17 (Th17(EM)) cells are thought to be essential for inflammation in Th17-mediated diseases, but have not been studied in detail. To identify superior surface markers to isolate a homogeneous population of Th17(EM) cells from peripheral blood, CD4(+) T cells were isolated from the peripheral blood of healthy donors based on the expression of CCR7, CCR6 and CD146 using six-color flow cytometry. After 4days of culture in the presence of anti-CD3/28 beads, intracellular cytokines were determined by flow cytometric analysis. To investigate the relevance of Th17(EM) cells in Th17-mediated disease, the frequencies of T(EM) -cell subsets in psoriasis were quantified using six-color flow cytometry. An enzyme-linked immunosorbent assay was performed to confirm the interleukin (IL)-17-producing capacity of T(EM) -cell subsets from the peripheral blood of a patient with psoriasis. CCR6(+) CD146(+) T(EM) (CD4(+) CD45RA(-) CCR7(-)) cells had a greater capacity to produce IL-17 than CCR6(+) CD146(-) or CCR6(-) CD146(+) T(EM) cells. Although the percentage of CCR6(+) CD146(+) cells in T(EM) cells was not significantly different between patients with psoriasis and controls, three of eight patients had a higher percentage of CCR6(+) CD146(+) T(EM) cells than the mean +5 standard deviations of the controls. Coexpression of CCR6 and CD146 is a useful marker for Th17(EM) cells. Increasing the number of CCR6(+) CD146(+) Th17(EM) cells in peripheral blood may facilitate estimation of systemic Th17-cell activity in Th17-mediated diseases.
Evidence for a Role of a Tumor Necrosis Factor-α (TNF-α)-converting Enzyme-like Protease in Shedding of TRANCE, a TNF Family Member Involved in Osteoclastogenesis and Dendritic Cell Survival (1999)

Tumor necrosis factor (TNF)-related activation-induced cytokine (TRANCE), a member of the TNF family, is a dendritic cell survival factor and is essential for osteoclastogenesis and osteoclast activation. In this report we demonstrate (i) that TRANCE, like TNF-alpha, is made as a membrane-anchored precursor, which is released from the plasma membrane by a metalloprotease; (ii) that soluble TRANCE has potent dendritic cell survival and osteoclastogenic activity; (iii) that the metalloprotease-disintegrin TNF-alpha convertase (TACE) can cleave immunoprecipitated TRANCE in vitro in a fashion that mimics the cleavage observed in tissue culture cells; and (iv) that in vitro cleavage of a TRANCE ectodomain/CD8 fusion protein and of a peptide corresponding to the TRANCE cleavage site by TACE occurs at the same site that is used when TRANCE is shed from cells into the supernatant. We propose that the TRANCE ectodomain is released from cells by TACE or a related metalloprotease-disintegrin, and that this release is an important component of the function of TRANCE in bone and immune homeostasis.
Clinical and Bacteriologic Studies of the Effect of Massive Doses of Penicillin G on Infections Caused by Gram-Negative Bacilli (1964)

INFECTIONS due to gram-negative bacilli are presently increasing in frequency and difficulty of management. One approach to the therapy of this type of disease has been a search for and development of more effective antimicrobial compounds. Another possibility that has received little attention is the use of some of the "old" antibiotics in doses higher than those conventionally employed. When penicillin G was first used clinically, the limited quantities available dictated its application in situations involving highly "sensitive" organisms (1 to 2 units per milliliter) such as pneumococci, Streptococcus pyogenes, penicillinase-negative staphylococci and some strains of neisseria. That other . . .
An Implantable Vascularized Protein Gel Construct That Supports Human Fetal Hepatoblast Survival and Infection by Hepatitis C Virus in Mice (2010)

The system described here thus provides the basis for a simple and robust small animal model of HFH engraftment that is applicable to the study of HCV infections in vivo.
Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry (2007)

Naturally selected T-cell receptors (TCRs) are characterised by low binding affinities, typically in the range 1-100 microM. Crystal structures of syngeneic TCRs bound to peptide major histocompatibility complex (pMHC) antigens exhibit a conserved mode of binding characterised by a distinct diagonal binding geometry, with poor shape complementarity (SC) between receptor and ligand. Here, we report the structures of three in vitro affinity enhanced TCRs that recognise the pMHC tumour epitope NY-ESO(157-165) (SLLMWITQC). These crystal structures reveal that the docking mode for the high affinity TCRs is identical to that reported for the parental wild-type TCR, with only subtle changes in the mutated complementarity determining regions (CDRs) that form contacts with pMHC; both CDR2 and CDR3 mutations act synergistically to improve the overall affinity. Comparison of free and bound TCR structures for both wild-type and a CDR3 mutant reveal an induced fit mechanism arising from restructuring of CDR3 loops which allows better peptide binding. Overall, an increased interface area, improved SC and additional H-bonding interactions are observed, accounting for the increase in affinity. Most notably, there is a marked increase in the SC for the central methionine and tryptophan peptide motif over the native TCR.
THE ORIGINS OF NEW PANDEMIC VIRUSES: The Acquisition of New Host Ranges by Canine Parvovirus and Influenza A Viruses (2005)

Transfer of viruses between hosts to create a new self-sustaining epidemic is rare; however, those new viruses can cause severe outbreaks. Examples of such viruses include three pandemic human influenza A viruses and canine parvovirus in dogs. In each case one virus made the original transfer and spread worldwide, and then further adaptation resulted in the emergence of variants worldwide. For the influenza viruses several changes were required for growth and spread between humans, and the emergence of human H2N2 and H3N2 strains in 1957 and 1968 involved the acquisition of three or two new genomic segments, respectively. Adaptation to humans involved several viral genes including the hemagglutinin, the neuraminidase, and the replication proteins. The canine adaptation of the parvoviruses involved capsid protein changes altering the recognition of the host transferrin receptors, allowing canine transferrin receptor binding and its use as a receptor for cell infection.
Dealing with disaster (2007)

Terrorism and naturally occurring catastrophic events provide fertile ground for nursing emergency preparedness, including deployment strategies. Are you ready to respond?
Herpes Simplex: Insights on Pathogenesis and Possible Vaccines (2008)

Abstract Herpes simplex viruses are evolutionarily ancient and ubiquitous. In the past 20 years, there has been increasing recognition of a worldwide pandemic of HSV-2 infection. Moreover, HSV-2 prevalence has increased despite fairly widespread use of antiviral drugs for HSV. The success of HSV-1 and HSV-2 stems from latency within long-lived neurons and frequent mucocutaneous shedding. The generally mild medical consequences of HSV infection reflect a functional equilibrium between host and microbe in most immunocompetent persons. However, significant gaps in our knowledge of the correlates of disease severity and HSV immune evasion are limiting rational advances in these areas. Human genetic studies are gradually outlining important innate responses, while recent imaging and biopsy studies have begun to show that the temporal and spatial anatomic interplay between virus reactivation and host immune response may be important in reactivations and disease expression.
Comparison of Recombinant Human Haptocorrin Expressed in Human Embryonic Kidney Cells and Native Haptocorrin (2012)

Haptocorrin (HC) is a circulating corrinoid binding protein with unclear function. In contrast to transcobalamin, the other transport protein in blood, HC is heavily glycosylated and binds a variety of cobalamin (Cbl) analogues. HC is present not only in blood but also in various secretions like milk, tears and saliva. No recombinant form of HC has been described so far. We report the expression of recombinant human HC (rhHC) in human embryonic kidney cells. We purified the protein with a yield of 6 mg (90 nmol) per litre of cell culture supernatant. The isolated rhHC behaved as native HC concerning its spectral properties and ability to recognize both Cbl and its baseless analogue cobinamide. Similar to native HC isolated from blood, rhHC bound to the asialoglycoprotein receptor only after removal of terminal sialic acid residues by treatment with neuraminidase. Interestingly, rhHC, that compared to native HC contains four excessive amino acids (…LVPR) at the C-terminus, showed subtle changes in the binding kinetics of Cbl, cobinamide and the fluorescent Cbl conjugate CBC. The recombinant protein has properties very similar to native HC and although showing slightly different ligand binding kinetics, rhHC is valuable for further biochemical and structural studies.
Fluorescence enhancement from an array of subwavelength metal apertures (2003)

We report the resonant excitation of a fluorescing molecular monolayer applied to a periodic array of subwavelength apertures in a metal film. The peak fluorescence occurs under conditions of maximum transmission of the excitation light, which indicates strong enhancement of the incident light within the apertures under resonant conditions. Fluorescence output normalized to the aperture fill fraction is enhanced by nearly 40 times, and the rate of photobleaching is increased by approximately a factor of 2, suggesting an increase in the fluorescence yield.
Normal Lymphocyte Development but Delayed Humoral Immune Response in CD81-null Mice (1997)

CD81 is a cell surface molecule expressed on many cell types and associated with the CD19/CD21/Leu13 signal-transducing complex on B cells. A recent report implies that CD81 expression on thymic stromal cells is important in the maturation of thymocytes from CD4-CD8- to CD4+CD8+. However, we have produced CD81-null mice by gene targeting, and find that they undergo normal development of thymocytes and express normal numbers of T cells. B cells are also found in normal numbers in the spleen, blood, and peritoneal cavity of CD81-null mice, but they express a lower level of CD19 compared to heterozygous littermates. Finally, early antibody responses to the protein antigen ovalbumin are weaker in CD81-null mice compared to their heterozygous littermates. This is consistent with the proposed role of the CD19/CD21/CD81-signaling complex in lowering the threshold for B cell responses. These results show that CD81 is not required for maturation of T cells, but is important for optimal expression of CD19 on B cells and optimal stimulation of antibody production.
The Tetraspanin CD63/lamp3 Cycles between Endocytic and Secretory Compartments in Human Endothelial Cells (2000)

In the present study, we show that in human endothelial cells the tetraspanin CD63/lamp3 distributes predominantly to the internal membranes of multivesicular-multilamellar late endosomes, which contain the unique lipid lysobisphosphatidic acid. Some CD63/lamp3 is also present in Weibel-Palade bodies, the characteristic secretory organelle of these cells. We find that CD63/lamp3 molecules can be transported from late endosomes to Weibel-Palade bodies and thus that CD63/lamp3 cycles between endocytic and biosynthetic compartments; however, movement of CD63/lamp3 is much slower than that of P-selectin, which is known to cycle between plasma membrane and Weibel-Palade bodies. When cells are treated with U18666A, a drug that mimics the Niemann-Pick type C syndrome, both proteins accumulate in late endosomes and fail to reach Weibel-Palade bodies efficiently, suggesting that P-selectin, like CD63/lamp3, cycles via late endosomes. Our data suggest that CD63/lamp3 partitions preferentially within late endosome internal membranes, thus causing its accumulation, and that this mechanism contributes to CD63/lamp3 retention in late endosomes; however, our data also indicate that the protein can eventually escape from these internal membranes and recycle toward Weibel-Palade bodies to be reused. Our observations thus uncover the existence of a selective trafficking route from late endosomes to Weibel-Palade bodies.
Plasma Epstein-Barr virus DNA as a biomarker for nasopharyngeal carcinoma (2014)

Nasopharyngeal carcinoma (NPC) is common in southern China and Southeast Asia. Epstein-Barr virus (EBV) infection is an important etiology for NPC, and EBV genome can be detected in almost all tumor tissues of NPC in this region. Plasma EBV DNA, when quantitatively analyzed using real-time polymerase chain reaction (PCR), has been developed as a biomarker for NPC. In this review, the different clinical applications of plasma EBV DNA in the management of NPC, including screening, monitoring, and prognostication, are discussed. In addition, the biological issues of circulating EBV DNA, including the molecular nature and clearance kinetics, are also explored.
Advances and limitations in the modeling of fabricated photonic bandgap fibers (2006)

We model fabricated silica photonic bandgap fibers and achieve good agreement between simulated and measured properties. We identify the size of the SEM bitmap image as the ultimate limit to the accurate calculation of surfaces modes within the bandgap
A linear analog of atrial natriuretic peptide (ANP) discriminates guanylate cyclase-coupled ANP receptors from non-coupled receptors. (1988)

Atrial natriuretic peptide (ANP) contains a disulfide which is generally considered to be required for biological activity. A truncated linear ANP analog, des-Cys105,Cys121-ANP-(104-126) (referred to as analog I), that lacks the 2 cysteine residues of the parent peptide was synthesized. In competition binding studies using rabbit lung membranes, ANP-(103-126) and analog I displaced bound 125I-ANP-(103-126) from specific ANP binding sites 100 and 73%, respectively. The concentrations of ANP-(103-126) and analog I that produced 50% inhibition of radioligand binding to the membranes were 0.26 +/- 0.07 and 0.31 +/- 0.09 nM, respectively. Radioiodinated ANP-(103-126) and analog I were chemically cross-linked to binding sites on rabbit lung membranes, and the labeled membrane proteins were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. 125I-Analog I specifically labeled a 65,000-dalton protein and a 135,000-dalton protein which, under reducing conditions, dissociated into 65,000-dalton subunits. In contrast, 125I-ANP-(103-126) labeled specifically a nonreducible 135,000-dalton protein, in addition to the 65,000-dalton species and the reducible 135,000-dalton species. ANP-(103-126) (100 nM) stimulated rabbit lung particulate guanylate cyclase activity, whereas analog I, at the same concentration, had no effect on cyclic GMP production and did not antagonize the effect of ANP-(103-126). From these observations, we conclude that analog I is a selective ligand which binds to approximately 73% of the total ANP binding sites present in rabbit lung membranes. Unlike ANP-(103-126), analog I does not bind to the remaining 27% of the binding sites and does not activate guanylate cyclase. Binding to the cyclase-linked ANP receptor correlates with the specific labeling by 125I-ANP-(103-126) of the nonreducible 135,000-dalton membrane protein.
An amorphous silicon solar cell having a conversion efficiency of 10.50 percent (1984)

We report on a hydrogenated amorphous silicon (a-Si:H) p-i-n solar cell having a conversion efficiency of 10.50 percent (1.05-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> area). The cell was prepared by a conventional plasma-enhanced chemical vapor deposition process using a structure back electrode n-i-p/SnO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> -ITO/glass. This conversion efficiency was obtained from the reduction and control of impurity levels in the i-layer. Photovoltaic characteristics of prepared cells were measured under AMI (100 mW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ). The impurity levels of oxygen and boron were measured by SIMS and are discussed.
Studies on neplanocin a, new antitumor antibiotic. I. Producing organism, isolation and characterization. (1981)

Neplanocin A. C11H13N5O3, is a novel carbocyclic analog of adenosine with cyclopentene. It was isolated from the culture filtrate of Ampullariella regularis A11079 by means of ion-exchange, carbon, silica gel adsorption, or partition chromatography. Neplanocin A forms crystals, and is stable at acidic or alkaline pH. Neplanocin A has cytotoxicity against L5178Y cells in culture and showed a remarkable effect on the life prolongation of mice infected with L1210 leukemia.
Unexpected low‐dose toxicity of the universal solvent DMSO (2013)

Dimethyl sulfoxide (DMSO) is an important aprotic solvent that can solubilize a wide variety of otherwise poorly soluble polar and nonpolar molecules. This, coupled with its apparent low toxicity at concentrations <10%, has led to its ubiquitous use and widespread application. Here, we demonstrate that DMSO induces retinal apoptosis in vivo at low concentrations (5 μl intravitreally dosed DMSO in rat from a stock concentration of 1, 2, 4, and 8% v/v). Toxicity was confirmed in vitro in a retinal neuronal cell line, at DMSO concentrations >1% (v/v), using annexin V, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), and AlamarBlue cell viability assays. DMSO concentrations >10% (v/v) have recently been reported to cause cellular toxicity through plasma membrane pore formation. Here, we show the mechanism by which low concentrations (2-4% DMSO) induce caspase-3 independent neuronal death that involves apoptosis-inducing factor (AIF) translocation from mitochondria to the nucleus and poly-(ADP-ribose)-polymerase (PARP) activation. These results highlight safety concerns of using low concentrations of DMSO as a solvent for in vivo administration and in biological assays. We recommend that methods other than DMSO are employed for solubilizing drugs but, where no alternative exists, researchers compute absolute DMSO final concentrations and include an untreated control group in addition to DMSO vehicle control to check for solvent toxicity.