gebhart/patrepeval huggingface dataset:
Human immunodeficiency virus gp120 binding C'C" ridge of CD4 domain 1 is also involved in interaction with class II major histocompatibility complex molecules. (1992)

Using site-directed mutagenesis informed by high-resolution CD4 structural data, we have investigated the role of residues of the C'C'' ridge region of human CD4 on class II major histocompatibility complex (MHC) binding. This C'C'' ridge is homologous to the CDR2 loop of an immunoglobulin variable domain and is known to contain the binding site for human immunodeficiency virus (HIV) coat glycoprotein gp120. Here we report that this region is also involved in interaction with class II MHC. Exposed positively charged residues Lys-35, Lys-46, and Arg-59 and the exposed hydrophobic residue Phe-43 contribute significantly to class II MHC binding. Moreover, mutations in the buried residues Trp-62 and Ser-49, which support the top and bottom of the C'C'' ridge, respectively, disrupt class II MHC interaction. The HIV binding region appears to involve a restricted area of the larger class II MHC binding site on CD4. Strategies of drug design aimed at interrupting CD4-HIV interaction will need to consider the extensive overlap between class II MHC and HIV gp120 binding surfaces in this region of CD4.
Real-time natural scene analysis for a blind prosthesis (1981)

A real-time computer vision system designed for the limited environment of city sidewalks is presented. This system is part of a prototype mobility aid for the blind. The overall device endeavors to keep blind pedestrians on a safe path down the sidewalk, and also warn of upcoming obstacles. The scene analysis algorithm uses semantic models of the environment to interpret edges in the multi-frame image data as borders of various objects, as well as to assign distance estimates to these objects. The input is a 64 by 64 by 6 bit gray-scale image taken from the vantage point of the shoulder of a pedestrian once a second. Along with each image, the three dimensional transformation of the camera location since the previous frame is assumed to be provided by hardware. After an initial segmentation into edge lines represented as arcs of circles, predictions of edges (generated by analysis of previous frames) are used to identify edges in the current frame. Edges not identified by this process are incorporated into the portion of the three dimensional world model that they are the most consistent with. The induced three dimensional world model of objects can then be used to provide mobility information to the blind user. The emphasis throughout the system has been on efficiency. The design trade-offs and techniques used to obtain high processing rates are discussed. Most of the vision system is currently running in real-time on a 16 bit micro-processor. Field trials of the complete prototype device will begin soon. I
Formation and Spreading of Lipid Bilayers on Planar Glass Supports (1999)

The fusion and spreading of phospholipid bilayers on glass surfaces was investigated as a function of pH and ionic strength. Membrane fusion to the support was favorable at high ionic strength and low pH for vesicles containing a net negative charge; however, neutral and positively charged vesicles fused under all conditions attempted. This result suggests that van der Waals and electrostatic interactions govern the fusion process. Membrane spreading over a planar surface was favorable at low pH regardless of the net charge on the bilayer, and the process is driven by van der Waals forces. On the other hand membrane propagation is impeded at high pH or on highly curved surfaces. In this case a combination of hydration and bending interactions is primarily responsible for arresting the spreading process. These results provide a framework for understanding many of the factors that influence the effectiveness of scratches on planar supported bilayers as barriers to lateral diffusion and lead to a simple method to heal these scratches.
AROM: Processing big data with Data Flow Graphs and functional programming (2012)

The development in computational processing has driven towards distributed processing frameworks performing tasks in parallel setups. The recent advances in Cloud Computing have widely contributed to this tendency. The MapReduce model proposed by Google is one of the most popular despite the well-known limitations inherent to the model which constrain the types of jobs that can be expressed. On the other hand models based on Data Flow Graphs (DFG) for the processing and the definition of the jobs, while more complex to express, are more general and suitable for a wider range of tasks, including iterative and pipelined tasks. In this paper we present AROM, a framework for large scale distributed processing based on DFG to express the jobs and which uses paradigms from functional programming to define the operators. The former leads to more natural handling of pipelined tasks while the latter enhances genericity and reusability of the operators, as shown by our tests on a parallel and pipelined job performing the calculation of PageRank.
Structural transformations of Ge2Sb2Te5 films studied by electrical resistance measurements (2000)

Temperature dependent measurements of the electrical resistance have been employed to study structural changes in sputtered Ge2Sb2Te5 films. The pronounced changes of film resistance due to structural changes enable a precise determination of transition temperatures and activation energies. Furthermore the technique is sensitive enough to measure the influence of ultrathin capping layers on the transformation kinetics. With increasing temperature the Ge2Sb2Te5 films undergo a structural change from an amorphous to rock salt structure (Fm3m) around 140 °C and finally a hexagonal structure (p3̄m) around 310 °C. Both structural changes are accompanied by a major drop of resistance. Applying the Kissinger method [Anal. Chem. 29, 1702 (1957)] the activation energy for crystallization to the rock salt structure is determined to be 2.24±0.11 eV, and for the phase transformation to the hexagonal phase to be 3.64±0.19 eV, respectively. A thin capping layer of ZnS–SiO2 leads to an increase of the first transition temperature as well as of the corresponding activation energy (2.7±0.2 eV).
The Glycosylation Capacity of Insect Cells (2008)

It is generally accepted that insects primarily synthesise oligomannosidic and paucimannosidic N-glycan structures.Indeed, insects' capability to produce human-like complex type N-glycans has been a matter of controversy for a number of years.The relative or complete lack of these structures was primarily attributed to low (or undetectable) activities of the glycosyltransferases needed to drive the synthesis of hybrid and complex type N-glycans (i.e., b-1,2-N-acetylglucosaminyltransferases I and II, b-1,4-galactosyltransferase, a-2,3and a-2,6-sialyltransferases). Recent developments, fuelled by availability of genomic sequences and by advances in relevant methodologies, have shed some light on the subject, with a few unexpected twists.The identification of a transmembrane/Golgi hexosaminidase, an enzyme which removes a non-reducing N-acetylglucosamine residue during N-glycan biosynthesis, has demonstrated that the synthesis of complex-type N-glycans is actively and deliberately being prevented in insects.On the other hand, the characterisation of an active a-2,6-sialyltransferase in Drosophila, combined with the occurrence of sialylated N-glycan structures as detected in a detailed analysis of Drosophila embryos, has clearly shown that insects can, and need to, synthesise low levels of these structures.The current understanding of the insect N-glycan biosynthetic pathways taking place in Golgi apparatus and trans-Golgi network are elaborated and discussed.
Digital offset compensation of time-interleaved ADC using random chopper sampling (2002)

An ADC using several parallel cells suffers from offset differences between the cells, which causes non-harmonic distortion. A method for removing the offset in the digital domain is proposed. The method is based on a PRBS-controlled chopper at the ADC input, which transforms any input signal to noise. The randomization controls the batch size required for removing the offset by a mean value calculation. The measured results are SFDR=72 dB and SNDR=59.0 dB at 22 MS/s, an improvement of 19 dB and 10 dB respectively.
Pathogenesis of weight-related changes in blood pressure in dogs. (1989)

We have previously shown that weight gain in the dog results in an increase in blood pressure. To study the pathogenesis of the rise in blood pressure associated with weight gain, we compared the serial changes in blood pressure, body weight, sodium balance, plasma volume, and three hormones known to affect sodium balance (norepinephrine, insulin, and aldosterone) in seven dogs fed a high fat diet for 6 weeks and seven dogs fed a control diet. The sodium content of both diets was equal. During a 2-week control period, no differences were noted between the two groups. Weight gain was associated with a progressive increase in blood pressure (mean pressure increased by 18.5 +/- 2.1 mm Hg in the high fat group) and plasma volume (plasma volume increased from 1,426 +/- 202 to 2,053 +/- 250 ml in the high fat group). Sodium retention occurred after 1 week of the high fat diet and persisted. Over the 6-week period, the dogs on the high fat diet increased their cumulative sodium balance by 2,024 +/- 462 meq versus an increase of only 289 +/- 97 meq for the dogs on the control diet. In the high fat diet group of dogs, there was a significant relation between change in cumulative sodium balance and the change in blood pressure and plasma volume. After 1 week of the high fat diet, norepinephrine was the only hormone that significantly increased from baseline. Over the next 5 weeks norepinephrine increased no further, whereas fasting insulin and aldosterone progressively increased.(ABSTRACT TRUNCATED AT 250 WORDS)
A Major Histocompatibility Complex·Peptide-restricted Antibody and T Cell Receptor Molecules Recognize Their Target by Distinct Binding Modes (2004)

Antibodies with T cell receptor-like specificity possess a considerable diagnostic and therapeutic potential, but the structural basis of the interaction between an antibody and an histocompatibility antigen has so far not been determined. We present here the crystal structure (at 2.15 A resolution) of the recombinant, affinity-matured human antibody fragment Fab-Hyb3 bound to the tumor-associated human leukocyte antigen (HLA)/peptide complex HLA-A1.MAGE-A1. Fab-Hyb3 employs a diagonal docking mode resembling that of T cell receptors. However, other than these natural ligands, the antibody uses only four of its six complementarity-determining regions for direct interactions with the target. It recognizes the C-terminal half of the MAGE-A1 peptide, the HLA-A1 alpha1-helix, and N-terminal residues of the alpha2-helix, accompanied by a large tilting angle between the two types of molecules within the complex. Interestingly, only a single hydrogen bond between a peptide side chain and Fab-Hyb3 contributes to the interaction, but large buried surface areas with pronounced shape complementarity assure high affinity and specificity for MAGE-A1. The HLA-A1.MAGE-A1.antibody structure is discussed in comparison with those of natural ligands recognizing HLA.peptide complexes.
The 5′‐untranslated region of the human muscle acylphosphatase mRNA has an inhibitory effect on protein expression (1997)

The cDNA of the human muscle type acylphosphatase was isolated and characterized. The mRNA presents a very long 5'-untranslated region, covering the first half of the molecule: 175 bases of this part were cloned and prediction of the possible secondary structure showed that a very stable stem-loop structure could be formed in that region. Moreover, an additional AUG triplet was found upstream of the start codon of the protein, defining an open reading frame of 60 codons which overlapped that of acylphosphatase. The possible regulatory effect on translation of this part of the mRNA molecule was studied by means of transient transfection experiments: a 10-fold decrease in the expression of a reporter protein and a dramatic decrease in the corresponding mRNA was observed, due to the presence of the 5'-untranslated region of acylphosphatase mRNA. Mutagenesis of the upstream AUG triplet eliminated mRNA instability, leading to the hypothesis that the product of the upstream open reading frame could play a role in this mechanism.
Seizure onset detection based on one sEMG channel (2011)

We present a new method to detect seizure onsets of tonic-clonic epileptic seizures based on surface electromyography (sEMG) data. The proposed method is generic and based on a single channel making it ideal for a small detection or monitoring device. The sEMG signal is high-pass filtered with a Butterworth filter with a cut-off frequency of 150 Hz. The number of zero-crossings with a hysteresis of ± 50 μV is the only feature extracted. The number of counts in a window of 1 second and the number of windows to make a detection is tested with a leave-one-out method. On 6 patients the method performs with a sensitivity of 100%, a median latency of 7.6 seconds and a median false detection rate of 0.04/h.
Diabetes area participation analysis: a review of companies and targets described in the 2008 – 2010 patent literature (2010)

Type 2 diabetes is a complex disease with many potential points of intervention for pharmacotherapy. A majority of anti-diabetic patent applications claim chemical matter for just eight targets which include five enzymes, a GPCR, a family of nuclear hormone receptors and a class of sodium-dependent glucose co-transporters (11β-HSD1, DGAT1, DPP IV, glucokinase, GPR119, PPAR-α, -δ, -γ, SGLT1 and SGLT2, and stearoyl-CoA desaturase 1 (SCD1)). The major pharmaceutical companies are all pursuing some combination of these top eight targets. Several companies stand out for the breadth of new targets under investigation (e.g., F. Hoffmann-La Roche, Merck & Co., Pfizer, Takeda Pharmaceuticals, Sanofi-Aventis).
In silico prediction of tumor antigens derived from functional missense mutations of the cancer gene census (2012)

Antigen-specific immune responses against peptides derived from missense gene mutations have been identified in multiple cancers. The application of personalized peptide vaccines based on the tumor mutation repertoire of each cancer patient is a near-term clinical reality. These peptides can be identified for pre-validation by leveraging the results of massive gene sequencing efforts in cancer. In this study, we utilized NetMHC 3.2 to predict nanomolar peptide binding affinity to 57 human HLA-A and B alleles. All peptides were derived from 5,685 missense mutations in 312 genes annotated as functionally relevant in the Cancer Genome Project. Of the 26,672,189 potential 8-11 mer peptide-HLA pairs evaluated, 0.4% (127,800) display binding affinities < 50 nM, predicting high affinity interactions. These peptides can be segregated into two groups based on the binding affinity to HLA proteins relative to germline-encoded sequences: peptides for which both the mutant and wild-type forms are high affinity binders, and peptides for which only the mutant form is a high affinity binder. Current evidence directs the attention to mutations that increase HLA binding affinity, as compared with cognate wild-type peptide sequences, as these potentially are more relevant for vaccine development from a clinical perspective. Our analysis generated a database including all predicted HLA binding peptides and the corresponding change in binding affinity as a result of point mutations. Our study constitutes a broad foundation for the development of personalized peptide vaccines that hone-in on functionally relevant targets in multiple cancers in individuals with diverse HLA haplotypes.
Low dielectric constant materials for microelectronics (2003)

The ever increasing requirements for electrical performance of on-chip wiring has driven three major technological advances in recent years. First, copper has replaced Aluminum as the new interconnect metal of choice, forcing also the introduction of damascene processing. Second, alternatives for SiO2 with a lower dielectric constant are being developed and introduced in main stream processing. The many new resulting materials needs to be classified in terms of their materials characteristics, evaluated in terms of their properties, and tested for process compatibility. Third, in an attempt to lower the dielectric constant even more, porosity is being introduced into these new materials. The study of processes such as plasma interactions and swelling in liquid media now becomes critical. Furthermore, pore sealing and the deposition of a thin continuous copper diffusion barrier on a porous dielectric are of prime importance. This review is an attempt to give an overview of the classification, the characteristics and properties of low-k dielectrics. In addition it addresses some of the needs for improved metrology for determining pore sizes, size distributions, structure, and mechanical properties.
A link scheduling and ad hoc networking approach using directional antennas (2004)

There is strong interest within DoD to utilize high-gain, directional antennas at both the transmitting and receiving end of the link in a dynamic, ad hoc network environment. However, the application of directional antennas (e.g., phased-array or sectorized antennas) in a dynamic network of mobile nodes requires coordination of antenna steering at both the receiver and transmitter ends of the link. Our solution is to apply adaptive, link-state routing (be performed by the OLSR ad hoc routing protocol [T. Clausen et. al., September 1, 2001]) supported by a distributed, adaptive time division multiple access (TDMA) scheduler, which determines schedules based on cooperative decisions between each pair of neighbor nodes. The architecture that has been developed contains a high rate mission data channel with an adaptive TDMA link scheduling protocol designed to take advantage of high-gain directional antennas. Time slots on this channel are adaptively scheduled to meet dynamic traffic demand requirements and to avoid interference from adjacent transmitting nodes. In addition, the link scheduling protocol must adapt to changes in node neighborhood topology caused by node mobility and link obstructions. This architecture was tested and evaluated in two ways: by OPNET simulations and by field demonstrations.
Sequence specificity of adriamycin-DNA adducts in human tumor cells. (2003)

The anticancer anthracycline compound Adriamycin is a known topoisomerase II inhibitor but is also capable of exerting other cellular consequences. After intercalation, Adriamycin can form covalent adducts with DNA, and the magnitude of these adducts appears to be limited by the cellular availability of formaldehyde. Adducts produced by Adriamycin in the presence of formaldehyde have been well characterized in cell-free systems but not in cells. In this study, we show that when Adriamycin is used in conjunction with the formaldehyde-releasing prodrug AN-9 in IMR-32 tumor cells, this allows the formation of sufficiently high levels of adducts in genomic DNA to enable detection of their DNA sequence specificity for the first time. The 340-bp alpha-satellite EcoRI repeat sequence was isolated from drug-treated cells and digested with lambda-exonuclease to determine adduct sites at which exonuclease digestion was blocked. The Adriamycin adducts were formed predominantly at 5'-GC and GG sequences and unstable with respect to elevated temperatures and extended times at 37 degrees C. The use of three anthracycline derivatives lacking a 3'amino group demonstrated that this amino portion is critical for the formation of anthracycline adducts in cells. The structure of these drug-DNA adducts can therefore be considered to be identical to the Adriamycin adducts, which have been characterized rigorously in cell-free systems by X-ray crystallography, two-dimensional nuclear magnetic resonance, and mass spectrometry.
V. The epithelial sodium channel and its implication in human diseases (1999)

The epithelial Na+ channel (ENaC) controls the rate-limiting step in the process of transepithelial Na+ reabsorption in the distal nephron, the distal colon, and the airways. Hereditary salt-losing syndromes have been ascribed to loss of function mutations in the alpha-, beta-, or gamma-ENaC subunit genes, whereas gain of function mutations (located in the COOH terminus of the beta- or gamma-subunit) result in hypertension due to Na+ retention (Liddle's syndrome). In mice, gene-targeting experiments have shown that, in addition to the kidney salt-wasting phenotype, ENaC was essential for lung fluid clearance in newborn mice. Disruption of the alpha-subunit resulted in a complete abolition of ENaC-mediated Na+ transport, whereas knockout of the beta- or gamma-subunit had only minor effects on fluid clearance in lung. Disruption of each of the three subunits resulted in a salt-wasting syndrome similar to that observed in humans.
Reactive Oxygen Species in Proliferative Signaling (2000)

The traditional view of reactive oxygen species (ROS), such as H2O2 and superoxide (O2 −), as toxic byproducts of aerobic metabolism, and their use as antimicrobial agents by the immune system, might make the notion that ROS can act as positive regulators of cell proliferation somewhat counterintuitive. Nonetheless, evidence has accumulated over the past 10 years that strongly supports ROS regulation of a variety of cellular processes, including proliferation. The picture that has emerged indicates that ROS are previously unappreciated components of established regulatory pathways. More specifically, it appears that ROS act as messengers in signal transduction pathways (1).
CD38 deficiency in the tumor microenvironment attenuates glioma progression and modulates features of tumor-associated microglia/macrophages (2012)

Gliomas are the most frequent primary tumors of the brain, and for highly malignant gliomas there is no successful treatment. The tumor microenvironment contains large numbers of infiltrating microglia and macrophages (MM). There is increasing evidence that the tumor-associated MM support glioma expansion. CD38 is a multifunctional ectoenzyme that uses nicotinamide adenine dinucleotide as a substrate to generate second messengers. Previously we showed that CD38 deficiency modulates microglial "activation" and impaired recovery from head trauma by a microglia-associated mechanism. In view of the supportive role of MM in glioma progression and the role of CD38 in microglia activation, we hypothesize that deficiency of CD38 in the tumor microenvironment would inhibit glioma progression. Using the syngeneic GL261 model of glioma progression in wild-type and CD38 null mice, we show here that CD38 deficiency significantly attenuates glioma expansion and prolongs the life span of the glioma-bearing mice. The CD38 deficiency effect was associated with increased cell death and decreased metalloproteinase-12 expression in the tumor mass, as well as modulation of the tumor-induced MM properties, as indicated by a reduction in the expression of the MM marker F4/80 and matrix metalloproteinases. Our results thus suggest that CD38 participates in the tumor-supporting action of MM and that targeting CD38 might be a potential therapeutic approach for glioma treatment.
Skin and subcutaneous adipose layer thickness in adults with diabetes at sites used for insulin injections: implications for needle length recommendations (2010)

Injection site ST does not differ by clinically significant degrees in demographically diverse adults with diabetes; SCT has a wider range. Needles >or=8 mm, inserted perpendicularly, may frequently enter muscle in limbs of males and those with BMI <25 kg/m(2). With 90 degrees insertion, needles 4-5 mm enter the subcutaneous tissue with minimal risk of IM injection in virtually all adults. These data will assist recommending appropriate length needles for subcutaneous insulin injections in adults.