gebhart/patrepeval huggingface dataset:
New approaches in depth-scanning optical metrology (2004)

Depth-scanning is an established technique in macroscopic and microscopic 3-D metrology. Representative in this context are the confocal technique and the white-light interferometry. A new fast depth-scanning technique has been applied to a confocal point sensor to be used in a laser-welding application for in-process measurement. The depth measurement range can be extended to about +/-1 mm at about 1500 measurement cycles per second. The possibilities and the potential of these techniques are described. Another principle of depth-scanning is the chromatic confocal technique. In connection with a new approach, an innovative confocal setup enables the parallelization of the complete depth-scan for the complete measurement of a line cut of moved objects. In the macroscopic scale, the new measurement techniques of depth-scanning fringe projection (DSFP) was introduced recently. In the microscopic scale, it has been implemented successfully in a stereo microscope.
Structure–activity relationship of 3-methyl-1-phenyl-2-pyrazolin-5-one (edaravone) (2003)

This paper describes the discovery of a novel free radical scavenger, 3-methyl-1-phenyl-2-pyrazolin-5-one (edaravone, 1), as a potent antioxidant agent against lipid peroxidation. The structure-activity relationship of edaravone indicated that lipophilic substituents were essential to show its lipid peroxidation-inhibitory activity. In vivo studies revealed that edaravone showed brain-protective activity in a transient ischemia model.
High-performance organic thin-film transistors with metal oxide/metal bilayer electrode (2005)

We demonstrate bilayer source-drain (S-D) electrodes for organic thin film transistors (OTFT). The bilayer consists of a transition metal oxide (MoO3,WO3, or V2O5) layer and a metal layer. The metal oxide layer, directly contacting the organic semiconducting layer, serves as the charge-injection layer. The overcoated metal layer is responsible for the conduction of charge carriers. We found that the metal oxide layer coupled between pentacene and metal layers played an important role in improving the field-effect transistor characteristics of OTFTs. Devices with the bilayer S-D electrodes showed enhanced hole-injection compared to those with only metal electrode. High field-effect mobility of 0.4cm2∕Vs and on/off current ratios of 104 were obtained in the pentacene based TFTs using the bilayer S-D electrodes at a gate bias of −40V. The improvement is attributed to the reduction in the contact barrier and the prevention of metal diffusion into the organic layer and/or unfavorable chemical reaction between the organic layer and the metal electrode.
New Insights in HTLV-I Phylogeny by Sequencing and Analyzing the Entire Envelope Gene (2005)

The HTLV-I envelope plays a major role in the process of target cell infection. It is implied in the recognition of the viral receptor(s), penetration of the viral genetic material, and induction of host immunity to the virus. It is thus important to study the genetic variability of the viral env gene as well as its variation in terms of evolution. In a new approach to these features, we sequenced the entire env gene of 65 HTLV-I isolates originating from Gabon, French Guiana, West Indies, and Iran, such isolates representing all major HTLVI phylums but the Australo-Melanesian one. The sequences obtained and all PTLV-I (HTLV-I and STLV-I) env sequences available in the literature were analyzed. Phylogenetic studies using different algorithms (minimum evolution, neighbor joining, maximum parsimony, and maximum likelihood) gave the same clear-cut results. Newly sequenced HTLV-I isolates described in this report allocated in three well-defined subtypes: Cosmopolitan, Central African, and a new distinct one that we termed "Maroni" subtype (present in the Maroni Basin, French Guiana, and West Indies). Clearly, the most divergent PTLV-I strains present in Asia- Australo-Melanesia as well as African and Asian STLV-I derived from the same node in the phylogenetic tree as isolates of the Central African subtype. In addition, we showed that within each PTLV-I subtype, groups of isolates may be characterized by nonrandom and systematically associated mutations.
Respiration and Circulation. (1971)

Abstract : Sections on invertebrate respiration and circulation and plant respiration and fluid movement are covered in data book, but for the most part it is concerned with man and other vertebrates. Basic physical and chemical data, general principles governing behavior of gases and flow in vessels, and the exchange system at the cellular level are presented in tables, charts and equations. The data book contains contributions by 402 research scientists and is compiled in 232 tables, graphs, and two appendices. The contents are reported in eleven categories: (1) General principles; (2) Basic physical and chemical data; (3) Thorax and ventilation; (4) Airway and gas movement; (5) Blood gases; (6) Heart and pumping action; (7) Vascular system and blood distribution; (8) capillaries and the exchange system; (9) Invertebrate respiration; (10) invertebrate circulation; and (11) Plant respiration and fluid movement. (Author)
Glucocorticoids modulate macrophage surface oligosaccharides and their bone binding activity. (1984)

The circumstantial evidence that indicates that glucocorticoids (GC) may stimulate osteoclastic resorption in vivo has recently found support in observations that demonstrate that these compounds effectively increase the activity of isolated resorptive cells (osteoclasts, macrophage polykaryons, and elicited macrophages [MO] ) in vitro. Data are presented here that indicate that this stimulation by GC is due to an enhancement of the initial stage of the resorption process, the attachment of cells to bone, and that this is caused by alterations of cell surface oligosaccharides. Specifically, dexamethasone and cortisol enhance by 80% the attachment of MO to bone surfaces in a dose dependent manner but do not alter or reduce the binding of these cells to other surfaces (plastic, collagen, and hydroxyapatite crystals). The effect of GC on cell-bone attachment is blocked by the glycosylation inhibitor, tunicamycin, and the glycosylation modifier, swainsonine; this demonstrates that asparagine-linked oligosaccharides are involved in the stimulatory process. Flow cytometric analysis of GC-treated cells using a panel of fluoresceinated lectins confirms this by indicating a selective, enhanced exposure of plasma membrane-associated N-acetylglucosamine and N-acetylgalactosamine residues, sugars we have previously shown to be pivotal in MO-bone binding. Finally, progesterone, a known GC antagonist, blocks GC-stimulated resorption, macrophage-bone binding, and membrane oligosaccharide modification, presumably by competing for the GC receptor. Progesterone alone alters none of these processes. Thus, GC stimulates the resorptive activity of macrophages by enhancing the initial events in the degradative process (cell-bone binding) and does so, apparently, via receptor-mediator alteration of cell surface glycoproteins.
Impact of pore size on the vascularization and osseointegration of ceramic bone substitutes in vivo (2007)

The repair of bone defects with biomaterials depends on a sufficient vascularization of the implantation site. We analyzed the effect of pore size on the vascularization and osseointegration of biphasic calcium phosphate particles, which were implanted into critical-sized cranial defects in Balb/c mice. Dense particles and particles with pore sizes in the ranges 40-70, 70-140, 140-210, and 210-280 microm were tested (n = 6 animals per group). Angiogenesis, vascularization, and leukocyte-endothelium interactions were monitored for 28 days by intravital microscopy. The formation of new bone and the bone-interface contact (BIC) were determined histomorphometrically. Twenty-eight days after implantation, the functional capillary density was significantly higher with ceramic particles whose pore sizes exceeded 140 microm [140-210 microm: 6.6 (+/-0.8) mm/mm(2); 210-280 microm: 7.3 (+/-0.6) mm/mm(2)] than with those whose pore sizes were lesser than 140 microm [40-70 microm: 5.3 (+/-0.4) mm/mm(2); 70-140 microm: 5.6 (+/-0.3) mm/mm(2)] or with dense particles [5.7 (+/-0.8) mm/mm(2)]. The volume of newly-formed bone deposited within the implants increased as the pore size increased [40-70 microm: 0.07 (+/-0.02) mm(3); 70-140 microm: 0.10 (+/-0.06) mm(3); 140-210 microm: 0.13 (+/-0.05) mm(3); 210-280 microm: 0.15 (+/-0.06) mm(3)]. Similar results were observed for the BIC. The data demonstrates pore size to be a critical parameter governing the dynamic processes of vascularization and osseointegration of bone substitutes.
Advances in Metabolite Identification (2011)

One of the central challenges to metabolomics is metabolite identification. Regardless of whether one uses so-called 'targeted' or 'untargeted' metabolomics, eventually all paths lead to the requirement of identifying (and quantifying) certain key metabolites. Indeed, without metabolite identification, the results of any metabolomic analysis are biologically and chemically uninterpretable. Given the chemical diversity of most metabolomes and the character of most metabolomic data, metabolite identification is intrinsically difficult. Consequently a great deal of effort in metabolomics over the past decade has been focused on making metabolite identification better, faster and cheaper. This review describes some of the newly emerging techniques or technologies in metabolomics that are making metabolite identification easier and more robust. In particular, it focuses on advances in metabolite identification that have occurred over the past 2 to 3 years concerning the technologies, methodologies and software as applied to NMR, MS and separation science. The strengths and limitations of some of these approaches are discussed along with some of the important trends in metabolite identification.
Nanostructuring of alkanethiols with ultrasharp field emitters (1995)

We have investigated the electron beam exposure of self-assembled monolayers (SAM) of alkanethiols on gold. SAM resist systems are of growing interest for proximal probe lithography due to their high chemical selectivity though being as thin as a monolayer. For this purpose a custom built proximal probe lithography device was used. The electrons emanate from an ultrasharp tungsten tip, providing extraordinary field emission properties—small emission angle and low emission energy. In contrast to common scanning tunneling microscope (STM) lithography our system can be operated not only in tunneling mode, but also in true field emission mode, i.e., at much larger tip-to-sample distances (typically 10–100 nm). Therefore the latter mode allows much higher writing speeds, as the tip does not have to follow the sample topography as accurately as in the STM mode. The first results obtained by exposure in the field emission mode are presented.
Power scaling in passively mode-locked large-mode area fiber lasers (1998)

We report on a novel approach toward generating high peak powers in passively mode-locked fiber lasers. By appropriate design the fiber's mode area is increased by a factor of /spl sim/30 compared to standard fiber. This increased area effectively decreases the nonlinearity thus, increasing the power necessary to form stable soliton-like pulses.
Anticancer and Antiviral Sulfonamides (2003)

The sulfonamides constitute an important class of drugs, with several types of pharmacological agents possessing antibacterial, anti- carbonic anhydrase, diuretic, hypoglycemic and antithyroid activity among others. A large number of structurally novel sulfonamide derivatives have ultimately been reported to show substantial antitumor activity in vitro and in vivo. Although they have a common chemical motif of aromatic/heterocyclic or amino acid sulfonamide, there are a variety of mechanisms of their antitumor action, such as carbonic anhydrase inhibition, cell cycle perturbation in the G1 phase, disruption of microtubule assembly, functional suppression of the transcriptional activator NF-Y, and angiogenesis (matrix metalloproteinase, MMP) inhibition among others. Some of these compounds selected via elaborate preclinical screenings or obtained through computer-based drug design, are currently being evaluated in clinical trials. The review summarizes recent classes of sulfonamides and related sulfonyl derivatives disclosed as effective tumor cell growth inhibitors, or for the treatment of different types of cancer. Another research line that progressed much in the last time regards different sulfonamides with remarkable antiviral activity. Thus, at least two clinically used HIV protease inhibitors possess sulfonamide moieties in their molecules, whereas a very large number of other derivatives are constantly being synthesized and evaluated in order to obtain compounds with less toxicity or activity against drug-resistant viruses. Several non nucleoside HIV reverse transcriptase or HIV integrase inhibitors containing sulfonamido groups were also reported. Another approach to inhibit the growth of retroviruses, including HIV, targets the ejection of zinc ions from critical zinc finger viral proteins, which has as a consequence the inhibition of viral replication in the absence of mutations leading to drug resistance phenotypes. Most compounds with antiviral activity possessing this mechanism of action incorporate in their molecules primary sulfonamide groups. Some small molecule chemokine antagonists acting as HIV entry inhibitors also possess sulfonamide functionalities in their scaffold.
Design of sampled grating DBR lasers with integrated semiconductor optical amplifiers (2000)

High output powers and wide range quasicontinuous tuning have been achieved in a sampled-grating distributed Bragg reflector laser with an integrated semiconductor-optical-amplifier. Using an amplifier with a curved passive output waveguide to suppress back reflection, we have achieved a quasicontinuous tuning range of over 50 nm and peak output powers greater than +8 dBm. Optimizing the device structure and the sampled-grating mirror design has enabled tuning ranges of up to 72 nm in devices without amplifiers.
Histogram-based estimation techniques in database systems (1997)

Many commercial database management systems maintain histograms to summarize the contents of relations in order to perform efficient estimation of query result sizes and access plan costs. The accuracy of these estimates is often of critical importance. But, there has never been a systematic study of all histogram aspects and their effectiveness in providing accurate estimations. In this thesis, we identify (theoretically and experimentally) the most accurate classes of histograms for estimating the sizes and distributions of the results of several important query operators and provide efficient (sampling-based) techniques to construct these histograms. All of these histograms are novel and differ in fundamental ways from traditional histograms. We provide a systematic classification of all classes of histograms based on certain canonical aspects of histograms that determine their effectiveness in a given estimation problem. We also provide techniques to capture dependencies between attributes in a relation and show that these techniques are far more accurate than the traditional attribute independence assumption. Finally, we use histograms to effectively balance load during parallel joins, thus demonstrating their versatility. Our over all conclusion from the accuracy and efficiency of histogram-based techniques is that they can be used both for enhanced accuracy in traditional applications (e.g., query optimizers) as well as in novel applications that can benefit from estimates (e.g., approximate query processors and load balancers).
Identification of nuclear pre-replication centers poised for DNA synthesis in Xenopus egg extracts: immunolocalization study of replication protein A. (1992)

We demonstrate by immunofluorescence that a 70-kD protein (P70) purified from Xenopus egg extracts is associated with subnuclear foci (about 200) which we propose to be an assembly of DNA pre-replication centers (preRCs). A cDNA encoding this protein reveals that P70 is the Xenopus homologue of replication protein A (RPA also called RF-A). RPA is know to be a cellular, three-subunit single-stranded DNA binding protein, which assists T-antigen in the assembly of the pre-priming complex in the SV40 replication system. The punctated preRCs exist transiently; they form post-mitotically during the period of nuclear membrane breakdown and disappear during ongoing DNA replication. P70 is homogeneously associated with chromatin at the later stages of the S-phase and is displaced from chromatin post replication, so that P70 cannot be detected on mitotic chromosomes. Double-immunofluorescence studies using biotin-dUTP demonstrate that initiation of DNA synthesis is confined to preRCs, resulting in the punctated replication pattern observed previously by others. PreRCs form efficiently on decondensed chromatin in membrane-free egg extracts if ATP and divalent cations are present. Our results suggest that preRCs are composed of an assembly of a large number of pre-initiation replication complexes poised for initiation at discreet subnuclear regions prior to nuclear reconstruction and initiation of DNA synthesis.
Functional Characterization of Novel Human and Mouse Equilibrative Nucleoside Transporters (hENT3 and mENT3) Located in Intracellular Membranes (2005)

The first mammalian examples of the equilibrative nucleoside transporter family to be characterized, hENT1 and hENT2, were passive transporters located predominantly in the plasma membranes of human cells. We now report the functional characterization of members of a third subgroup of the family, from human and mouse, which differ profoundly in their properties from previously characterized mammalian nucleoside transporters. The 475-residue human and mouse proteins, designated hENT3 and mENT3, respectively, are 73% identical in amino acid sequence and possess long N-terminal hydrophilic domains that bear typical (DE)XXXL(LI) endosomal/lysosomal targeting motifs. ENT3 transcripts and proteins are widely distributed in human and rodent tissues, with a particular abundance in placenta. However, in contrast to ENT1 and ENT2, the endogenous and green fluorescent protein-tagged forms of the full-length hENT3 protein were found to be predominantly intracellular proteins that co-localized, in part, with lysosomal markers in cultured human cells. Truncation of the hydrophilic N-terminal region or mutation of its dileucine motif to alanine caused the protein to be relocated to the cell surface both in human cells and in Xenopus oocytes, allowing characterization of its transport activity in the latter. The protein proved to be a broad selectivity, low affinity nucleoside transporter that could also transport adenine. Transport activity was relatively insensitive to the classical nucleoside transport inhibitors nitrobenzylthioinosine, dipyridamole, and dilazep and was sodium ion-independent. However, it was strongly dependent upon pH, and the optimum pH value of 5.5 probably reflected the location of the transporter in acidic, intracellular compartments.
A Polycrystalline Oxide TFT Driven Active Matrix-OLED Display (2012)

We developed a high mobility polycrystalline oxide semiconductor, IGO (Indium Gallium Oxide), which is the crystalline In2O3 based random orientation polycrystalline material. The polycrystalline IGO has two unique characteristics. One is the high mobility with a wide window for fabrication process and the property is much stable. The other is the wet etching tolerance which enables the merged photolithography process. In spite of the low temperature process below 300°C, the mobility of polycrystalline IGO TFT was over 20cm2/Vs with the standard deviation smaller than 1cm2/Vs and the shift of the threshold voltage after positive bias temperature stress (Vg=Vd=15V, 10, 000s) was smaller than 0.3V. These results imply that the interruption of carrier conductivity at the grain boundaries of polycrystalline structure can be neglected with respect to the TFT characteristics and the reliability. From these properties, we concluded that the polycrystalline IGO is one of the promising channel materials for the backplane TFT of future OLED displays.
Establishing Best Practices and Guidance in Population Modeling: An Experience With an Internal Population Pharmacokinetic Analysis Guidance (2013)

This tutorial describes the development of a population pharmacokinetic (Pop PK) analysis guidance within Pfizer, which strives for improved consistency and efficiency, and a more systematic approach to model building. General recommendations from the Pfizer internal guidance and a suggested workflow for Pop PK model building are discussed. A description is also provided for mechanisms by which conflicting opinions were captured and resolved across the organization to arrive at the final guidance. CPT: Pharmacometrics &amp; Systems Pharmacology (2013) 2, e51; doi: 10.1038/psp.2013.26 ; advance online publication 3 July 2013
Mitochondrial DNA sequence variation in human evolution and disease. (1994)

Germ-line and somatic mtDNA mutations are hypothesized to act together to shape our history and our health. Germ-line mtDNA mutations, both ancient and recent, have been associated with a variety of degenerative diseases. Mildly to moderately deleterious germ-line mutations, like neutral polymorphisms, have become established in the distant past through genetic drift but now may predispose certain individuals to late-onset degenerative diseases. As an example, a homoplasmic, Caucasian, tRNA(Gln) mutation at nucleotide pair (np) 4336 has been observed in 5% of Alzheimer disease and Parkinson disease patients and may contribute to the multifactorial etiology of these diseases. Moderately to severely deleterious germ-line mutations, on the other hand, appear repeatedly but are eliminated by selection. Hence, all extant mutations of this class are recent and associated with more devastating diseases of young adults and children. Representative of these mutations is a heteroplasmic mutation in MTND6 at np 14459 whose clinical presentations range from adult-onset blindness to pediatric dystonia and basal ganglial degeneration. To the inherited mutations are added somatic mtDNA mutations which accumulate in random arrays within stable tissues. These mutations provide a molecular clock that measures our age and may cause a progressive decline in tissue energy output that could precipitate the onset of degenerative diseases in individuals harboring inherited deleterious mutations.
Quantitative and temporal correlation between circulating cell-free Epstein-Barr virus DNA and tumor recurrence in nasopharyngeal carcinoma. (1999)

Recently, cell-free EBV DNA has been detected in the plasma and serum of patients with nasopharyngeal carcinoma (NPC). We studied the relationship between plasma/serum EBV DNA and tumor recurrence. Using real-time quantitative PCR, the median plasma EBV DNA concentration in 10 patients with tumor recurrence was determined to be 32,350 copies/ml, whereas that in 15 patients in continuous remission for a mean period of 2 years was 0 copy/ml. Longitudinal follow-up of 17 NPC patients revealed 6 individuals with tumor recurrence and 11 patients who remained in remission. Significant elevations in serum EBV DNA, sometimes up to 6 months before detectable clinical deterioration, were observed in the patients who subsequently developed tumor recurrence. Continuously low or undetectable levels of serum EBV DNA were observed in the patients who remained in remission. These results suggest that plasma/serum cell-free EBV DNA may be a valuable tool for the monitoring of NPC patients for the early detection of tumor recurrence.