gebhart/patrepeval huggingface dataset:
Low Temperature Plasma Etching Control through Ion Energy Angular Distribution and 3-Dimensional Profile Simulation. (2015)

Plasma etching has become a major part of semiconductor processing because it enables the production of smaller electronics with increased computational power. Plasma etching produces highly anisotropic features, which are needed to maintain feature size critical dimensions (CD) through directional ion wafer bombardment. As the semiconductor industry moves towards smaller feature sizes and higher aspect ratios, a better understanding of ion dynamics and control of the plasma etch processes becomes increasingly necessary. In prior technology nodes, 2-dimensional (2-d) feature profile models served very well to help optimize features and connect reactor scale properties to feature scale CDs. As CDs continue to shrink, the current technology nodes must utilize 3-dimensional (3-d) structures, whose optimization is considerably more difficult and not well represented by 2-d profile simulators. This dissertation investigated the plasma physics and plasma surface interactions in plasma etching chambers using a hybrid plasma equipment model to predict plasma properties and a Monte Carlo feature profile model to predict feature evolution. Algorithms for capturing ion sheath dynamics, controlling dual frequency powers on the same substrate and describing 3-d plasma surface kinetics have been developed and integrated into the models. With the addition of these new algorithms, three challenging areas have been investigated: ion multi-frequency sheath dynamics, control of ion energy angular distributions and 3-d plasma etching. The ion kinetics are found to be controlled through several critical parameters, such as shifting phases, tuning frequencies, and adjusting rf voltage ratios. The 3-d profile model addresses the complex feature pattern layout and aids in the physical understanding of ion 3-d bombardment on surfaces. With this improved capability, correlations of the variability of plasma tool performance with variability of feature dimensions are investigated.
An analysis of myeloma plasma cell phenotype using antibodies defined at the IIIrd International Workshop on Human Leucocyte Differentiation Antigens. (1988)

Fresh bone marrow from 43 cases of myeloma and three cases of plasma cell leukaemia has been phenotyped both by indirect immune-rosetting and, on fixed cytospin preparations, by indirect immunofluorescence. Both clustered and unclustered B cell associated antibodies from the IIIrd International Workshop on Human Leucocyte Differentiation Antigens were used. The results confirm the lack of many pan-B antigens on the surface of myeloma plasma cells, i.e. CD19-23, 37, 39, w40. Strong surface reactivity is seen with CD38 antibodies and with one CD24 antibody (HB8). Weak reactions are sometimes obtained with CD9, 10 and 45R. On cytospin preparations CD37, 39 and w40 are sometimes weakly positive, and anti-rough endoplasmic reticulum antibodies are always strongly positive. Specific and surface-reacting antiplasma cell antibodies are still lacking.
Purification and Biochemical Characterization of Alkaline Serine Protease from Caesalpinia bonducella (2010)

A high molecular weight serine protease has been purified to electrophoretic homogeneity from the seeds of Caesalpinia bonducella Flem. (Caesalpiniaceae) by the combination of size exclusion and ion exchange chromatography. About 524 fold purification was achieved with an overall recovery of 6.8%. The specific activity was found to be 86 U/mg/min at pH 8.0. The calculated K(m) and V(max) were 1.66 mg/mL and 496.68 units/min per mg of protein, respectively. The molecular mass was estimated to be about 63 kDa by sodium dodecyl sulfate PAGE. The enzyme showed optimum activity at pH 8.0 and exhibited its highest activity at 40 degrees C. The enzyme was strongly inhibited by 2mM phenylmethylsulfonyl fluoride (PMSF), suggesting the presence of a serine residue at the active site. PMSF showed a pure competitive type of inhibition with the serine protease enzyme. It was observed that enzyme activity was enhanced in the presence of dications and was active against a variety of modified substrates and natural proteins.
Molecular Basis of Transient Outward Potassium Current Downregulation in Human Heart Failure (1998)

These data provide further support for the hypothesis that Kv4.3 encodes all or part of the native cardiac Ito in humans and that part of the downregulation of this current in heart failure may be transcriptionally regulated.
Principles and applications of pencil tracing (1987)

Pencil tracing, a new approach to ray tracing, is introduced for faster image synthesis with more physical fidelity. The paraxial approximation theory for efficiently tracing a pencil of rays is described and analysis of its errors is conducted to insure the accuracy required for pencil tracing. The paraxial approimation is formulated from a 4x4 matrix (a system matrix) that provides the basis for pencil tracing and a variety of ray tracing techniques, such as beam tracing, ray tracing with cones, ray-object intersection tolerance, and a lighting model for reflection and refraction. In the error analysis, functions that estimate approximation errors and determine a constraint on the spread angle of a pencil are given.The theory results in the following fast ray tracing algorithms; ray tracing using a system matrix, ray interpolation, and extended 'beam tracing' using a 'generalized perspective transform'. Some experiments are described to show their advantages. A lighting model is also developed to calculate the illuminance for refracted and reflected light.
Life and Death of Neurons in the Aging Brain (1997)

Neurodegenerative disorders are characterized by extensive neuron death that leads to functional decline, but the neurobiological correlates of functional decline in normal aging are less well defined. For decades, it has been a commonly held notion that widespread neuron death in the neocortex and hippocampus is an inevitable concomitant of brain aging, but recent quantitative studies suggest that neuron death is restricted in normal aging and unlikely to account for age-related impairment of neocortical and hippocampal functions. In this article, the qualitative and quantitative differences between aging and Alzheimer's disease with respect to neuron loss are discussed, and age-related changes in functional and biochemical attributes of hippocampal circuits that might mediate functional decline in the absence of neuron death are explored. When these data are viewed comprehensively, it appears that the primary neurobiological substrates for functional impairment in aging differ in important ways from those in neurodegenerative disorders such as Alzheimer's disease.
Fiber Optic Shape Sensing For Flexible Structures (1990)

An optical-time-domain-reflectometry based shape sensor is presented. Fibers with air-gap splices at certain known positions are attached to the exterior of a flexible structure. The strain induced in each fiber section due to the bending of the structure is detected by the Optical Time Domain Reflectometer (OTDR) as shifts in the pulses reflected at the splices. The approximate shape of the structure is then determined using the strain information from each fiber section. Experimental results for simple shapes are given, and future directions for determining complex shapes are discussed.
Shuttles and Muscles: Linear Molecular Machines Based on Transition Metals (2001)

Transition-metal-containing rotaxanes can behave as linear motors at the molecular level. The molecules are set into motion either by an electrochemical reaction or using a chemical signal. In a first example, a simple rotaxane is described that consists of a ring threaded by a two-coordination-site axle. The ring contains a bidentate ligand, coordinated to a copper center. The axle incorporates both a bidentate and a terdentate ligand. By oxidizing or reducing the copper center to Cu(II) or Cu(I) respectively, the ring glides from a given position on the axle to another position and vice versa. By generalizing the concept to a rotaxane dimer, whose synthesis involves a quantitative double-threading reaction triggered by copper(I) complexation, a molecular assembly reminiscent of a muscle is constructed. By exchanging the two metal centers of the complex (copper(I)/zinc(II)), a large-amplitude movement is generated, which corresponds to a contraction/stretching process. The copper(I)-containing rotaxane dimer is in a stretched situation (overall length approximately 8 nm), whereas the zinc(II) complexed compound is contracted (length approximately 6.5 nm). The stretching/contraction process is reversible and it is hoped that, in the future, other types of signals can be used (electrochemical or light pulse) to trigger the motion.
X-ray crystallographic studies of IgG-Fcγ receptor interactions (2002)

Human Fc gamma receptors (Fc gamma Rs) for the Fc portion of IgG are major mediators of the adaptive immune response. Crystal structures of their extracellular domains were recently solved and shown to obey a common fold, resulting in a heart-shaped structure. Together with the multifunctional Fc fragment, whose structure was deciphered in the 1970s, the complex of an Fc gamma R with Fc was recently crystallized. Its crystal structure indicates that despite the dimeric character of the Fc fragment, only one Fc gamma R can bind to Fc, due to an introduced asymmetry within the homodimeric Fc, as well as by binding to symmetrically related residues of both Fc chains. Homology modelling suggested that the other Fc gamma Rs bind the Fc in a similar manner. The resolved complex structure can be regarded as a paradigm for Ig binding to Fc receptors and serves as a solid base for the design of compounds interfering with complex formation. Such molecules would be of invaluable benefit for the therapy of immunological disorders.
Gastrointestinal Tolerability Events in Relapsing–Remitting Multiple Sclerosis (RRMS) Patients Treated with Oral BG-12 (Dimethyl Fumarate) in DEFINE and CONFIRM (P01.164) (2013)

OBJECTIVE: To characterize gastrointestinal (GI) adverse events (AEs) in RRMS patients treated with BG-12 (dimethyl fumarate) twice daily (BID) in the DEFINE and CONFIRM studies.
Mono‐ and Di(dimethylamino)styryl‐Substituted Borondipyrromethene and Borondiindomethene Dyes with Intense Near‐Infrared Fluorescence (2006)

Four novel borondipyrromethene (BDP) and -diindomethene (BDI) dyes with one or two (dimethylamino)styryl extensions at the chromophore were synthesized and spectroscopically investigated. An X-ray crystal structure shows that the extended auxochrome is virtually planar. All dyes thus display intense red/near infrared (NIR) absorption and emission. The (dimethylamino)styryl group induces a charge-transfer character that entails bright solvatochromic fluorescence, which is only quenched with increasing solvent polarity according to the energy-gap law. The dye with an additional dimethylanilino group at the meso position of BDP shows a remarkable switching of lipophilicity by protonation. Two dyes with an 8-hydroxyquinoline ligand at the meso position display quenched emission in the presence of Hg2+ or Al3+ owing to electron transfer from the excited BDP to the complexed receptor. The BDI dye presents a pH indicator with bright fluorescence and extremely low fluorescence anisotropy.
Studies on 3,5-Dioxopiperidines: Novel and Facil Synthetic Routes to 3-Amino-5-hydroxypyridine Derivatives (1981)

Three novel synthetic routes to the title compounds were described.Modified Polonovski reaction of 3-acetarnido-l-benzyl-5-0~0- 3,4-dehydropiperidine (4) or Semmler-Nolff aromatization of l-benzyl-3-12 3.5-Dibromopyridine N-oxide (11) was prepared by the bromination of pyridine N-oxide in a considerable yield [M.
Globalisation, Qualifications and Livelihoods: Towards a research agenda (2000)

The economic, political and cultural manifestations of globalisation are distinguishable from its underlying causes. The definition of globalisation used in this paper focuses on 'the reduction of obstacles to trade'. A function of both economic policy and technological advance, trade barriers, financial regulations and cross-border communications have been liberalised. These are contributing to change in the composition, control and locus of livelihoods, the skill requirements of livelihoods, and life chances and social mobility of livelihood seekers more generally. Educational qualifications and assessments mediate livelihood creation and livelihood seeking, to different degrees in different contexts. The role of assessment in the certification and selection for jobs interacts with economic globalisation in two main ways. The first is through the impact of globalisation on the composition and volume of livelihoods and the demand of both livelihood creators and livelihood seekers for qualifications. The second is through the reduction of trade and communication barriers on the internationalisation and commercialisation of the assessment and qualification business. The paper concludes with a research agenda that explores these two strands and emphasises the interactions between global, national and local contexts and influences.
Convolutional-Code-Specific CRC Code Design (2015)

Cyclic redundancy check (CRC) codes check if a codeword is correctly received. This paper presents an algorithm to design CRC codes that are optimized for the code-specific error behavior of a specified feedforward convolutional code. The algorithm utilizes two distinct approaches to computing undetected error probability of a CRC code used with a specific convolutional code. The first approach enumerates the error patterns of the convolutional code and tests if each of them is detectable. The second approach reduces complexity significantly by exploiting the equivalence of the undetected error probability to the frame error rate of an equivalent catastrophic convolutional code. The error events of the equivalent convolutional code are exactly the undetectable errors for the original concatenation of CRC and convolutional codes. This simplifies the computation because error patterns do not need to be individually checked for detectability. As an example, we optimize CRC codes for a commonly used 64-state convolutional code for information length k=1024, demonstrating significant reduction in undetected error probability compared to the existing CRC codes with the same degrees. For a fixed target undetected error probability, the optimized CRC codes typically require 2 fewer bits.
Stable integrative transformation of Trypanosoma brucei that occurs exclusively by homologous recombination. (1991)

A calmodulin-neomycin-resistance fusion gene was introduced into Trypanosoma brucei by electroporation, and stably transformed cell lines were obtained. In all of the transformants, the fusion gene had integrated into the host genome at the cognate locus, evidently by homologous recombination within flanking calmodulin DNA. This unusual observation distinguishes trypanosomes as the only eukaryote other than yeast known to undergo gene targeting in essentially 100% of the stable transformants. It should now be possible to systematically manipulate the trypanosome genome, directing predetermined mutations to virtually any chromosomal locus.
Current application and future perspectives of molecular typing methods to study Clostridium difficile infections (2013)

Molecular typing is an essential tool to monitor Clostridium difficile infections and outbreaks within healthcare facilities. Molecular typing also plays a key role in defining the regional and global changes in circulating C. difficile types. The patterns of C. difficile types circulating within Europe (and globally) remain poorly understood, although international efforts are under way to understand the spatial and temporal patterns of C. difficile types. A complete picture is essential to properly investigate type-specific risk factors for C. difficile infections (CDI) and track long-range transmission. Currently, conventional agarose gel-based polymerase chain reaction (PCR) ribotyping is the most common typing method used in Europe to type C. difficile. Although this method has proved to be useful to study epidemiology on local, national and European level, efforts are made to replace it with capillary electrophoresis PCR ribotyping to increase pattern recognition, reproducibility and interpretation. However, this method lacks sufficient discriminatory power to study outbreaks and therefore multilocus variable-number tandem repeat analysis (MLVA) has been developed to study transmission between humans, animals and food. Sequence-based methods are increasingly being used for C. difficile fingerprinting/typing because of their ability to discriminate between highly related strains, the ease of data interpretation and transferability of data. The first studies using whole-genome single nucleotide polymorphism typing of healthcare-associated C. difficile within a clinically relevant timeframe are very promising and, although limited to select facilities because of complex data interpretation and high costs, these approaches will likely become commonly used over the coming years.
Differential Gene Expression Patterns and Interaction Networks in BCR-ABL–Positive and –Negative Adult Acute Lymphoblastic Leukemias (2007)

We identified prominent molecular features of BCR-ABL-positive adult ALL, which may be useful for developing novel therapeutic targets and prognostic markers in this disease.
Exploiting the Self-Assembly Strategy for the Design of Selective CuII Ion Chemosensors (1999)

Simply by mixing in water, a liphophilic dipeptide (L), a surfactant (S), and a fluorophore (F) self-assemble to give a sensor able to detect Cu(II) ions (see scheme). Despite the ease of construction, the sensor displays high selectivity and a low detection limit for the target ion. This new modular approach to sensing devices allows easy variations of the components, making optimization of the system very simple and fast.
Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products (2013)

Complex microbial ecosystems contain large reservoirs of unexplored biosynthetic diversity. Here we provide an experimental framework and data analysis tool to facilitate the targeted discovery of natural-product biosynthetic gene clusters from the environment. Multiplex sequencing of barcoded PCR amplicons is followed by sequence similarity directed data parsing to identify sequences bearing close resemblance to biosynthetically or biomedically interesting gene clusters. Amplicons are then mapped onto arrayed metagenomic libraries to guide the recovery of targeted gene clusters. When applied to adenylation- and ketosynthase-domain amplicons derived from saturating soil DNA libraries, our analysis pipeline led to the recovery of biosynthetic clusters predicted to encode for previously uncharacterized glycopeptide- and lipopeptide-like antibiotics; thiocoraline-, azinomycin-, and bleomycin-like antitumor agents; and a rapamycin-like immunosuppressant. The utility of the approach is demonstrated by using recovered eDNA sequences to generate glycopeptide derivatives. The experiments described here constitute a systematic interrogation of a soil metagenome for gene clusters capable of encoding naturally occurring derivatives of biomedically relevant natural products. Our results show that previously undetected biosynthetic gene clusters with potential biomedical relevance are very common in the environment. This general process should permit the routine screening of environmental samples for gene clusters capable of encoding the systematic expansion of the structural diversity seen in biomedically relevant families of natural products.
Different signal transduction properties of KDR and Flt1, two receptors for vascular endothelial growth factor. (1994)

Vascular endothelial growth factor (VEGF) is a homodimeric peptide growth factor which binds to two structurally related tyrosine kinase receptors denoted Flt1 and KDR. In order to compare the signal transduction via these two receptors, the human Flt1 and KDR proteins were stably expressed in porcine aortic endothelial cells. Binding analyses using 125I-VEGF revealed Kd values of 16 pM for Flt1 and 760 pM for KDR. Cultured human umbilical vein endothelial (HUVE) cells were found to express two distinct populations of binding sites with affinities similar to those for Flt1 and KDR, respectively. The KDR expressing cells showed striking changes in cell morphology, actin reorganization and membrane ruffling, chemotaxis and mitogenicity upon VEGF stimulation, whereas Flt1 expressing cells lacked such responses. KDR was found to undergo ligand-induced autophosphorylation in intact cells, and both Flt1 and KDR were phosphorylated in vitro in response to VEGF, however, KDR much more efficiently than Flt1. Neither the receptor-associated activity of phosphatidylinositol 3'-kinase nor tyrosine phosphorylation of phospholipase C-gamma were affected by stimulation of Flt1 or KDR expressing cells, and phosphorylation of GTPase activating protein was only slightly increased. Members of the Src family such as Fyn and Yes showed an increased level of phosphorylation upon VEGF stimulation of cells expressing Flt1 but not in cells expressing KDR. The maximal responses in KDR expressing porcine aortic endothelial cells were obtained at higher VEGF concentrations as compared to HUVE cells, i.e. in the presence of Flt1. This difference could possibly be explained by the formation of heterodimeric complexes between KDR and Flt1, or other molecules, in HUVE cells.
Efficient Transfer of Large-Area Graphene Films onto Rigid Substrates by Hot Pressing (2012)

Graphene films grown on metal substrates by chemical vapor deposition (CVD) method have to be safely transferred onto desired substrates for further applications. Recently, a roll-to-roll (R2R) method has been developed for large-area transfer, which is particularly efficient for flexible target substrates. However, in the case of rigid substrates such as glass or wafers, the roll-based method is found to induce considerable mechanical damages on graphene films during the transfer process, resulting in the degradation of electrical property. Here we introduce an improved dry transfer technique based on a hot-pressing method that can minimize damage on graphene by neutralizing mechanical stress. Thus, we enhanced the transfer efficiency of the large-area graphene films on a substrate with arbitrary thickness and rigidity, evidenced by scanning electron microscope (SEM) and atomic force microscope (AFM) images, Raman spectra, and various electrical characterizations. We also performed a theoretical multiscale simulation from continuum to atomic level to compare the mechanical stresses caused by the R2R and the hot-pressing methods, which also supports our conclusion. Consequently, we believe that the proposed hot-pressing method will be immediately useful for display and solar cell applications that currently require rigid and large substrates.