gebhart/patrepeval huggingface dataset:
Control of Threshold Voltage of AlGaN/GaN HEMTs by Fluoride-Based Plasma Treatment: From Depletion Mode to Enhancement Mode (2006)

This paper presents a method with an accurate control of threshold voltages (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) of AlGaN/GaN high-electron mobility transistors (HEMTs) using a fluoride-based plasma treatment. Using this method, the V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> of AlGaN/GaN HEMTs can be continuously shifted from -4 V in a conventional depletion-mode (D-mode) AlGaN/GaN HEMT to 0.9 V in an enhancement-mode AlGaN/GaN HEMT. It was found that the plasma-induced damages result in a mobility degradation of two-dimensional electron gas. The damages can be repaired and the mobility can be recovered by a post-gate annealing step at 400 degC. At the same time, the shift in V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> shows a good thermal stability and is not affected by the post-gate annealing. The enhancement-mode HEMTs show a performance (transconductance, cutoff frequencies) comparable to the D-mode HEMTs. Experimental results confirm that the threshold-voltage shift originates from the incorporation of F ions in the AlGaN barrier. In addition, the fluoride-based plasma treatment was also found to be effective in lowering the gate-leakage current, in both forward and reverse bias regions. A physical model of the threshold voltage is proposed to explain the effects of the fluoride-based plasma treatment on AlGaN/GaN HEMTs
Interaction of genetics and epidemiology in the literature (1986)

To evaluate the extent of interaction between genetics and epidemiology in studies reported in the literature, we reviewed all the "familial/genetic" papers published in a standard epidemiology journal (American Journal of Epidemiology, AJE) and all the "epidemiology" papers published in a standard human genetics journal (American Journal of Human Genetics, AJHG) between 1966 and 1984. A variety of medline subject headings were used in this search. Computerized listings of titles, subject headings, and abstracts were reviewed. It could be shown that familial/genetic papers constituted 4.3% of all papers published in AJE and epidemiology papers constituted 16.4% of papers published in AJHG. Over time, familial/genetic studies published in AJE increased both in number and in proportion of all papers, and more family studies are using complex statistical genetic techniques. On the other hand, epidemiology papers published in AJHG did not increase in number over time, and actually decreased in relation to all papers. These papers were mostly either descriptive (eg, defining frequencies of Mendelian traits in populations) or analytical (eg, defining risk factors for chromosomal abnormalities, and other reproductive outcomes). This analysis suggests that epidemiologic methods have been widely used in the genetic literature, and that genetic methods are gaining more access to the recent epidemiology literature. Because of increasing recognition of the role of genetic factors in disease, there is a growing need to incorporate both genetic and epidemiologic methods in etiologic studies of complex disorders.
Plant Cuticular Lipid Export Requires an ABC Transporter (2004)

A waxy protective cuticle coats all primary aerial plant tissues. Its synthesis requires extensive export of lipids from epidermal cells to the plant surface. Arabidopsis cer5 mutants had reduced stem cuticular wax loads and accumulated sheetlike inclusions in the cytoplasm of wax-secreting cells. These inclusions represented abnormal deposits of cuticular wax and resembled inclusions found in a human disorder caused by a defective peroxisomal adenosine triphosphate binding cassette (ABC) transporter. We found that the CER5 gene encodes an ABC transporter localized in the plasma membrane of epidermal cells and conclude that it is required for wax export to the cuticle.
Size-Tailored Synthesis of Silver Quasi-Nanospheres by Kinetically Controlled Seeded Growth (2013)

This paper describes a simple and convenient procedure to synthesize monodisperse silver (Ag) quasi-nanospheres with size tunable in a range of 19-140 nm through a one-step seeded growth strategy. Acetonitrile was employed as a coordinating ligand of a Ag(I) salt in order to achieve a low concentration of elemental Ag after reduction and thus suppression of new nucleation events. Since the addition of the seeds significantly accelerates the reduction reaction of Ag(I) by ascorbic acid, the reaction kinetics was further delicately balanced by tuning the reaction temperature, which proved to be critical in producing Ag quasi-nanospheres with uniform size and shape. This synthesis is highly scalable, so that it provides a simple yet very robust process for producing Ag quasi-nanospheres for many biological, analytical, and catalytic applications which often demand samples in large quantity and widely tunable particle sizes.
Biology of HER2 and Its Importance in Breast Cancer (2001)

Human epidermal growth factor receptor-2 (HER2/erbB-2) belongs to a family of four transmembrane receptors involved in signal transduction pathways that regulate cell growth and differentiation. Overexpression/amplification of HER2 is associated with malignancy and a poor prognosis in breast cancer. HER2 acts as a networking receptor that mediates signaling to cancer cells, causing them to proliferate. HER receptors exist as monomers but dimerize on ligand binding. HER ligands are bivalent growth factor molecules whose low-affinity site binds to HER2. No HER2-specific ligand has been identified but HER2 is the preferred heterodimerization partner for other HER receptors. HER2-containing heterodimers are relatively long-lived and potent. HER3 has no inherent activity and is the major and most potent dimerization partner of HER2. HER2 overexpression biases the formation of HER2-containing heterodimers, leading to enhanced responsiveness to stromal growth factors and oncogenic transformation. Removal of HER2 from the cell surface or inhibition of its intrinsic enzymatic activity may reduce oncogenicity. Our research suggests that the antitumor efficacy of HER2-specific antibodies such as Herceptin relates to their ability to direct HER2 to a Cbl- dependent endocytosis and degradation pathway. The reported clinical therapeutic efficacy of anti-HER2 monoclonal antibodies in breast cancer highlights the importance of understanding the biology of HER2.
Noninvasive imaging of immune responses (2015)

At their margins, tumors often contain neutrophils, dendritic cells, and activated macrophages, which express class II MHC and CD11b products. The interplay between stromal cells, tumor cells, and migratory cells such as lymphocytes creates opportunities for noninvasive imaging of immune responses. We developed alpaca-derived antibody fragments specific for mouse class II MHC and CD11b products, expressed on the surface of a variety of myeloid cells. We validated these reagents by flow cytometry and two-photon microscopy to obtain images at cellular resolution. To enable noninvasive imaging of the targeted cell populations, we developed a method to site-specifically label VHHs [the variable domain (VH) of a camelid heavy-chain only antibody] with (18)F or (64)Cu. Radiolabeled VHHs rapidly cleared the circulation (t1/2 ≈ 20 min) and clearly visualized lymphoid organs. We used VHHs to explore the possibility of imaging inflammation in both xenogeneic and syngeneic tumor models, which resulted in detection of tumors with remarkable specificity. We also imaged the infiltration of myeloid cells upon injection of complete Freund's adjuvant. Both anti-class II MHC and anti-CD11b VHHs detected inflammation with excellent specificity. Given the ease of manufacture and labeling of VHHs, we believe that this method could transform the manner in which antitumor responses and/or infectious events may be tracked.
Nucleic Acid Extraction, Amplification, and Detection on Si-Based Microfluidic Platforms (2007)

This paper gives a brief overview of silicon-based microfluidic platforms developed over the years by our group for the extraction, amplification, and detection of nucleic acids. Extraction of both genomic and viral nucleic acids from whole blood has been demonstrated on Si-based microfluidics. Rapid amplification has been achieved by polymerase chain reaction in Si-based thermal reactors (micro-PCR). Detection has been realized by a chip-to-chip integration of the micro-PCR and micro capillary electrophoresis (micro-CE).
Editor's Note (1979)

This issue contains articles written in late 1977 and early 1978 which document the dramatic changes in education after the fall of the gang of four in late 1976.
Carbon nanotube electronics and photonics (2009)

Their geometry, mechanical flexibility, and unique charge-transport properties make carbon nanotubes ideally suited to supplant silicon in the next generation of FETs.
New equivalent circuits for elementary piezoelectric transducers (1970)

New equivalent circuits, having several advantages over previous circuits, are presented for three types of piezoelectric transducer: the thickness-expander plate, the end-electroded bar and the side-electroded bar. Each of the circuits involves an electrical network of frequency-dependent components connected to the centre of an acoustic transmission line.
REGULATION OF PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP) GENE EXPRESSION (1997)

Phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) (PEPCK) is a key enzyme in the synthesis of glucose in the liver and kidney and of glyceride-glycerol in white adipose tissue and the small intestine. The gene for the cytosolic form of PEPCK (PEPCK-C) is acutely regulated by a variety of dietary and hormonal signals, which result in alteration of synthesis of the enzyme. Major factors that increase PEPCK-C gene expression include cyclic AMP, glucocorticoids, and thyroid hormone, whereas insulin inhibits this process. PEPCK-C is absent in fetal liver but appears at birth, concomitant with the capacity for gluconeogenesis. Regulatory elements that control transcription of the PEPCK-C gene in liver, kidney, and adipose tissue have been delineated, and many of the transcription factors that bind to these elements have been identified. Transgenic mice have been especially useful in elucidating the physiological roles of specific sequence elements in the PEPCK-C gene promoter and in demonstrating the key role played at these sites by the isoforms of CAAT/enhancer binding protein in patterning of PEPCK-C gene expression during the perinatal period. The PEPCK-C gene provides a model for the metabolic control of gene transcription.
A Highly Convenient, Efficient, and Selective Process for Preparation of Esters and Amides from Carboxylic Acids Using Fe3+-K-10 Montmorillonite Clay1 (2003)

In the presence of Fe(3+)-K-10 montmorillonite clay as a catalyst, aliphatic carboxylic acids selectively produced the corresponding esters in the presence of aromatic carboxylic acids by treatment with alcohols. Both the aliphatic and aromatic carboxylic acids formed the amides by reacting with the aliphatic amines, but only the aliphatic carboxylic acids yielded the anilides by treatment with aromatic amines. The catalyst is recoverable and recyclable.
Organic Solar Cells Using Nanoimprinted Transparent Metal Electrodes (2008)

Transparent metal electrodes fabricated by nanoimprint lithography show high optical transmittance as well as good electrical conductivity. Organic solar cells prepared using these transparent metal electrodes demonstrate an equal performance to those prepared with conventional ITO electrodes.
Enhanced 4D heart model based on high resolution dual source gated cardiac CT images (2007)

We have developed a new 4D heart model for use in the 4D NCAT phantom that, through modification of parameters that define it, is capable of modeling a wide variety of beating heart motions, normal and abnormal. High-resolution gated cardiac CT data of a healthy subject obtained from a dual source MSCT scanner was used to define the more detailed anatomy of the model. The study consisted of 100 gated time frames over a complete cardiac cycle. For each time frame, 3D NURBS and subdivision surfaces were created to model the four cardiac chambers as well as the coronary vessels, papillary muscles, valves, and other small details of the heart. The motion vector field of the chamber surfaces between adjacent gated time frames was set up by combining information from the CT data as well as the gated tagged MRI data upon which the original 4D NCAT heart model was based. The cardiac twisting motion of the heart cannot be ascertained from CT imaging data; therefore, the twisting motion in the original heart model was scaled to fit the new heart segmented from the CT data. Once the twisting motion was established, the radial and longitudinal contractions could be obtained by noting the epi- and endocardial borders in the gated MSCT images. The motion of the vessels and other cardiac structures was determined by tracking landmark points located on or within them for each subsequent time frame. Time curves were defined for the control points defining each surface creating a time changing 3D surface or 4D model for each heart structure. The resulting heart model was parameterized (including variables to alter the volume change and time duration of different portions of the cardiac cycle as well as the global and regional motion) so as to simulate normal and abnormal variations in the cardiac motion. The model will provide a useful simulation tool for evaluating and improving existing and emerging high resolution 4D imaging techniques used in the diagnosis of cardiac disease.
Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins (2004)

Molecular characterizations of bacteria often employ ribosomal DNA (rDNA) to establish the identity and relationships among organisms, but the use of rRNA sequences can be problematic as the result of alignment ambiguities caused by indels, the lack of informative characters, and varying functional constraints over the molecule. Although protein-coding regions have been used as an alternative to rRNA, there is neither consensus among the genes examined nor ways to rapidly obtain sequence information for such genes from uncharacterized bacterial species. To standardize the set of protein-coding loci assayed in bacterial genomes, we examined over 100 widely distributed genes to identify sets of universal primers for use in the PCR amplification of protein coding regions that are common to virtually all bacteria. From this set, we developed primer sets that each target of 10 genes spanning an array of genomic locations and functional categories. Although many of the primers contain sequence degeneracies that aid in targeting genes across diverse taxa, most are adequate for direct sequencing of amplification products, thereby eliminating intermediate cloning before sequence determination. We foresee the analysis of these protein-coding regions as being complementary to ribosomal DNA for answering questions pertaining to bacterial identification, classification, phylogenetics and evolution.
Nucleic acid vaccination strategies against infectious diseases (2015)

Taken together, this approach will have a major impact on future strategies for the prevention of infectious diseases. Better-designed nucleic acid constructs, novel delivery technologies, as well as the clarification of the mechanisms for antigen presentation will improve the potential applications of this vaccination strategy against microbial pathogens.
Cutting Edge: Suppressor of Cytokine Signaling 3 Inhibits Activation of NFATp (2002)

Recent studies have suggested that signaling initiated by the activation of Ag receptors and signaling activated through cytokine receptors may be regulated by a common set of inhibitory proteins. Suppressor of cytokine signaling 3 (SOCS-3), which has previously been demonstrated to inhibit cytokine signaling, is induced on TCR ligation. Overexpression of SOCS-3 can inhibit transcription driven by the IL-2 promoter in response to T cell activation. This inhibitory activity correlates with the suppression of calcineurin-dependent dephosphorylation and activation of the IL-2 promoter binding transcription factor, NFATp. Infection of primary murine T cells with a retrovirus encoding SOCS-3 blocks their IL-2 production in response to activation. Interestingly, SOCS-3 was found to coimmunoprecipitate with the catalytic subunit of calcineurin. These studies suggest that SOCS-3 may regulate T cell function as part of a negative feedback loop.
Implosion Property of Cannonball Target at 10.6 µm Laser Wavelength (1986)

Compressed core density of a Cannonball target of inner pellet irradiation type at 10.6 µm laser wavelength was measured using spectrally resolved neon X-ray emission. The implosion simulations by HIMICO code agreed well with the experimental results and showed that the dominant force of implosion is hot electron driven ablation pressure. Comparison of the simulation and experimental results clarified that the core density was compressed to 200 mg/cc due to the truncation of high energy electrons. We show that the hot electron driven Cannonball target is a feasible scheme for high density compression at 10.6 µm CO 2 laser.
Immunoglobulin fold characteristics of B7–1 (CD80) and B7–2 (CD86) (1994)

B7-1 and B7-2 are expressed on antigen-presenting cells and bind to the CD28 and CTLA-4 receptors on T cells. These interactions trigger a costimulatory pathway that is essential for T-cell activation. B7-1 and B7-2 are members of the immunoglobulin superfamily (IgSF) and, despite sharing common function, have only limited sequence similarity. The B7-1 extracellular region was previously subdivided into 2 IgSF domains, an N-terminal V(ariable)-like domain, followed by a C(onstant)-like domain. We recently reported that the V-like domains of B7-1 and B7-2 share some significant sequence similarities with 3 major histocompatibility complex (MHC)-encoded members of the IgSF. We have now applied inverse folding methodology to assess the compatibility of the B7-1 and B7-2 extracellular region sequences with currently available 3-dimensional structures. In these calculations, the sequences of the N-terminal (V-like) domains in B7-1 and B7-2 were not compatible with known structures, including the IgSF V-set. In contrast, the sequences of the C-like domains were compatible with IgSF C-set structures and were best recognized by the beta 2-microglobulin (beta 2m) domain of MHC Class I. A sequence comparison of the C-like domains in the B7 molecules showed that 11 of 17 rigorously conserved residues in B7-1 and B7-2 are not IgSF C-1 set consensus residues. When mapped onto the corresponding positions of the beta 2m structure, the conserved residues in B7 cluster on the surface, where they may interact with the B7 V-like domain or other molecules.
Research of Semantic Role Labeling and Application in Patent Knowledge Extraction. (2014)

Semantic Role Labeling (SRL) is a leading task of identifying arguments for a predicate and assigning semantically meaningful labels to them. SRL is crucial to information extraction, question answering, and machine translation. When applied to patent text, existing tools for SRL have unsatisfying performance because of long sentences. To improve performance in patent SRL systems, this study separates each sentence in patent abstracts into a simpler structure, and then labels semantic roles for the simplified sentence. At last, semantic information and semantic framework for frequently used words are used to extract patent knowledge. Our work demonstrates that the method used in this article can improve the performance in SRL system and obtain beneficial knowledge from patents.
Boom in the development of non‐peptidic β‐secretase (BACE1) inhibitors for the treatment of Alzheimer's disease (2008)

Abstract β‐Amyloid cleaving enzyme‐1 (BACE1) has become a significant target for the therapy of Alzheimer's disease. After the discovery of the first non‐peptidomimetic β‐secretase inhibitors by Takeda Chemicals in 2001, several research teams focused on SAR development of these agents. The non‐peptidic BACE1 inhibitors may potentially overcome the classical problems associated with the peptide structure of first generation, such as blood–brain barrier crossing, poor oral bioavailability and susceptibility to P‐glycoprotein transport. In the past 6 years a boom in research of non‐peptidic BACE1 inhibitors has disseminated findings over hundreds of publications and patents. The rapidly growing literature has been reviewed with particular emphasis on literature of pharmaceutical companies. © 2008 Wiley Periodicals, Inc. Med Res Rev, 29, No. 2, 295–338, 2009
Metagenomic Pyrosequencing and Microbial Identification (2009)

Both the approach of 16S rDNA amplicon sequencing and the whole-genome sequencing approach may be useful for human metagenomics, and numerous bioinformatics tools are being deployed to tackle such vast amounts of microbiological sequence diversity. Metagenomics, or genetic studies of microbial communities, may ultimately contribute to a more comprehensive understanding of human health, disease susceptibilities, and the pathophysiology of infectious and immune-mediated diseases.
High-speed noninterferometric nanotopographic characterization of Si wafer surfaces (2002)

We present a high-speed silicon wafer metrology tool capable of resolving surface features in the nanometer height range. This tool uses a high performance Shack-Hartman sensor to analyze the wavefront of a beam of light reflected from a silicon wafer surface. By translating the wafer to analyze small portions of the wafer in each camera frame and then continuously piecing the frames together, we can retain sub-millimeter spatial resolution while rapidly analyzing large apertures. This tool is particularly effective for resolving features near the wafer edge. We will describe the measures required to obtain this level of resolution. We also compare data taken with this device to that taken with the National Institute of Standards and Technology X-ray optics Calibration Interferometer (XCALIBIR). Finally, we show measurements of a variety of typical and atypical 200 mm diameter wafer samples.
Therapeutic vaccines: Realities of today and hopes for tomorrow (2004)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Electrical characterization of germanium p-channel MOSFETs (2003)

In this letter, we report germanium (Ge) p-channel MOSFETs with a thin gate stack of Ge oxynitride and low-temperature oxide (LTO) on bulk Ge substrate without a silicon (Si) cap layer. The fabricated devices show 2 /spl times/ higher transconductance and /spl sim/ 40% hole mobility enhancement over the Si control with a thermal SiO/sub 2/ gate dielectric, as well as the excellent subthreshold characteristics. For the first time, we demonstrate Ge MOSFETs with less than 100-mV/dec subthreshold slope.