gebhart/patrepeval huggingface dataset:
Assessment of Executive Function in Patients with Mild Traumatic Brain Injury (1999)

The results suggest that tests of specific frontal lobe executive functions are valuable in diagnosing and monitoring recovery from mild TBI.
Application of immunosignatures to the assessment of Alzheimer's disease (2011)

We propose that "immunosignaturing" technology may have potential as a diagnostic tool in AD.
A Novel Mechanism of Cyclooxygenase-2 Inhibition Involving Interactions with Ser-530 and Tyr-385 (2003)

A variety of drugs inhibit the conversion of arachidonic acid to prostaglandin G2 by the cyclooxygenase (COX) activity of prostaglandin endoperoxide synthases. Several modes of inhibitor binding in the COX active site have been described including ion pairing of carboxylic acid containing inhibitors with Arg-120 of COX-1 and COX-2 and insertion of arylsulfonamides and sulfones into the COX-2 side pocket. Recent crystallographic evidence suggests that Tyr-385 and Ser-530 chelate polar or negatively charged groups in arachidonic acid and aspirin. We tested the generality of this binding mode by analyzing the action of a series of COX inhibitors against site-directed mutants of COX-2 bearing changes in Arg-120, Tyr-355, Tyr-348, and Ser-530. Interestingly, diclofenac inhibition was unaffected by the mutation of Arg-120 to alanine but was dramatically attenuated by the S530A mutation. Determination of the crystal structure of a complex of diclofenac with murine COX-2 demonstrates that diclofenac binds to COX-2 in an inverted conformation with its carboxylate group hydrogen-bonded to Tyr-385 and Ser-530. This finding represents the first experimental demonstration that the carboxylate group of an acidic non-steroidal anti-inflammatory drug can bind to a COX enzyme in an orientation that precludes the formation of a salt bridge with Arg-120. Mutagenesis experiments suggest Ser-530 is also important in time-dependent inhibition by nimesulide and piroxicam.
Extremely broadband tunable semiconductor lasers for optical communication (2001)

Summary form only given. Sumary form only given. Broadband characteristics are important for optical communication. This work reports the study on the design of MQWs for broadband semiconductor lasers/amplifiers. The study shows that, with properly designed sequence of nonidentical MQWs made of InGaAsP/InP materials, the emission bandwidth could be nearly 300 nm. Using the designed MQWs as the laser gain material, the external-cavity semiconductor laser exhibits an extremely broadband tuning range, covering from 1300 nm to 1540 nm.
Bend losses of higher-order modes in dispersion-flattened multiple-clad optical fibres (1987)

The bending losses and effective cutoff wavelengths of the disturbing LPX1 and LP02 modes in dispersion-flattened, multiple-clad, quasi-single-mode fibres have been evaluated numerically. Even when the theoretical cutoff wavelengths of the LPn and LP02 modes are within the usual interval of operating wavelengths (1·3 &lt; λ &lt; 1·7μm), because of the extremely large bending losses of these modes, the effective cutoff wavelength can be below 1·3μm. These fibres are thus effectively single-moded.
Evaluation of sgRNA Target Sites for CRISPR-Mediated Repression of TP53 (2014)

The CRISPR (clustered regularly interspaced short palindromic repeats) platform has been developed as a general method to direct proteins of interest to gene targets. While the native CRISPR system delivers a nuclease that cleaves and potentially mutates target genes, researchers have recently employed catalytically inactive CRISPR-associated 9 nuclease (dCas9) in order to target and repress genes without DNA cleavage or mutagenesis. With the intent of improving repression efficiency in mammalian cells, researchers have also fused dCas9 with a KRAB repressor domain. Here, we evaluated different genomic sgRNA targeting sites for repression of TP53. The sites spanned a 200-kb distance, which included the promoter, transcript sequence, and regions flanking the endogenous human TP53 gene. We showed that repression up to 86% can be achieved with dCas9 alone (i.e., without use of the KRAB domain) by targeting the complex to sites near the TP53 transcriptional start site. This work demonstrates that efficient transcriptional repression of endogenous human genes can be achieved by the targeted delivery of dCas9. Yet, the efficiency of repression strongly depends on the choice of the sgRNA target site.
Detection Efficiency of Bare and Moderated BF3-Gas-Filled Proportional Counters for Isotropic Neutron Fluxes (1966)

An elaborate calibration of BF3-gas-filled proportional counters with and without moderator was made for isotropic neutron fluxes. The effective sensitivity of a hare BF3 counter in a nondiffusing medium was determined by means of a calibrated indium foil. The flux-depression effect in a diffusing medium was experimentally evaluated. Details of the experimental techniques and results are described. For the measurement of fast neutrons, energy dependence of sensitivity of two differently moderated counters was determined in the energy region from 1 eV to 10 MeV. Angular dependence of sensitivity of the moderated counters and its dependence on neutron energy are also described.
Production of natural value-added compounds: an insight into the eugenol biotransformation pathway (2013)

During the past few years, the production of natural value-added compounds from microbial sources has gained tremendous importance. Due to an increase in consumer demand for natural products, various food and pharmaceutical industries are continuously in search of novel metabolites obtained from microbial biotransformation. The exploitation of microbial biosynthetic pathways is both feasible and cost effective in the production of natural compounds. The environmentally compatible nature of these products is one major reason for their increasing demand. Novel approaches for natural product biogeneration will take advantage of the current studies on biotechnology, biochemical pathways and microbiology. The interest of the scientific community has shifted toward the use of microbial bioconversion for the production of valuable compounds from natural substrates. The present review focuses on eugenol biotransformation by microorganisms resulting in the formation of various value-added products such as ferulic acid, coniferyl alcohol, vanillin and vanillic acid.
Expandable intraluminal vascular graft: a feasibility study. (1986)

An expandable intraluminal graft mounted coaxially over an angioplasty balloon catheter was used in dog arteries. The graft, a wire mesh tube that has the ability to retain its expanded shape, opposes elastic recoil of the arterial wall after maximum balloon inflation. Eighteen grafts were placed in the abdominal aorta and iliac femoral, renal, superior mesenteric, and carotid arteries of eight dogs through femoral or carotid arteriotomies. Two grafts were placed in areas of artificially induced stenosis, completely restoring the lumen. Overall patency rate at 35 weeks was 77%. Histopathologic examination of patent grafts showed complete endothelialization at 3 weeks. The smaller caliber grafts and those that had outflow obstruction showed significant degrees of intimal hyperplasia.
Who is WHO and what was REAL? (2002)

The principles of the new WHO classification of haematopoietic and lymphoid tumours are based on those defined in the Revised European American classification of Lymphoid neoplasms (REAL), published by the International Lymphoma Study Group (ILSG) in 1994. Thus, the new WHO classification may be considered an updated version of the REAL classification rather than of the old WHO classification published in 1976. Disease entities are defined on the basis of morphological, phenotypic, genotypic, and clinical data. The relative impact of these characteristics varies among different diseases and there is "no gold standard". Thus, the strict hierarchy among diagnostic criteria, headed by morphology and followed by immunohistochemistry and genetics, has been discontinued. The WHO classification not only encompasses lymphoid tumours but extends to myeloid, mast cell and histiocytic/dendritic cell malignancies. Neoplasms are primarily stratified according to their tumour cell lineage. For each neoplasm a cell of origin is postulated. The classification of lymphoid malignancies recognises three major categories, B-cell neoplasms, T-/NK-cell neoplasms, and Hodgkin lymphomas. B-cell and T-cell lymphomas are further divided into precursor neoplasms and mature neoplasms, the latter being subdivided according to their clinical manifestation into disseminated/leukaemic, extranodal and nodal malignancies. In contrast to previous classifications, the neoplasms are grouped neither according to their histological grade (Kiel classification) nor according to their clinical aggressiveness (International Working Formulation). However, the histological grade is considered a prognostic factor which enters into the description of each disease entity. Hodgkin's disease, now more appropriately termed Hodgkin lymphoma, comprises nodular lymphocyte-predominant Hodgkin lymphoma and classical Hodgkin lymphomas of nodular sclerosis, mixed cellularity, lymphocyte-depleted and lymphocyte-rich subtype. For practical purposes this minireview disregards the description of myeloid, macrophage/histiocytic, dendritic cell and mast cell disorders. Furthermore, the present paper is restricted to those lymphoid tumours that are not already identically described in the REAL classification, in order to focus on what is really new in the WHO classification.
Islet transplantation: Present clinical situation and future aspects (2001)

Beta-cell replacement either by pancreatic organ or islet cell transplantation is the only treatment to achieve an insulin-independent, normoglycemic state and to avoid hypoglycemic episodes in patients with type 1 diabetes mellitus. This article will review the state-of-the-art in clinical islet cell transplantation at the dawn of the new millennium and will provide an outlook on the basis of extended personal experience.
Spatial Sound Encoding Including Near Field Effect: Introducing Distance Coding Filters and a Viable, New Ambisonic Format (2003)

Higher Order Ambisonics have been increasingly investigated in the past years, and found promising as a rational, scalable and flexible way to encode, transmit and r ender 3D sound fields. Nevertheless, studies concer ning virtual source imaging or natural 3D sound encoding mainly focussed on the directional encoding of plane waves , and neglected the near field effect of finite distance sources though it's present in any ordinary sound f ield. This paper highlights that with near field, the inf inite bass-boost affecting ambisonic components makes the currently accepted format unviable. By introducing from the e ncoding stage a near field compensation of reproduc tion loudspeakers, a viable, modified ambisonic format i s defined, distance-coding filters are designed, an d higher order ambisonic recording and synthesis become practicable.
Association of a RING finger protein with the cytoplasmic domain of the human type-2 tumour necrosis factor receptor (1995)

A human gene encoding a protein that specifically binds to the intracellular domain of the 75 kDa type-2 tumour necrosis factor (TNF) receptor (TNFR-2IC) has been identified using the yeast-based two-hybrid system. The N-terminal half of the TNF receptor-associated protein (TRAP) contains RING finger and zinc finger motifs often found in DNA-binding proteins including transcription factors. The 2.4 kb TRAP mRNA was barely detectable, if present at all, in lung, and variably expressed in heart, liver, placenta, brain, skeletal muscle, kidney and the pancreas; interestingly, the TRAP was more highly expressed in transformed cell lines than in normal tissues. This observation may be consistent with a role for this TRAP in promoting or regulating cellular proliferation. After in vitro transcription/translation and 35S labelling the TRAP was precipitated using a fusion protein consisting of glutathione S-transferase and the intracellular domain of TNFR-2 (TNFR-2IC), which showed that the two proteins directly interact in a mammalian cell-free system and also that identification of the TRAP was not an artifact of the two-hybrid system. By using truncated TNFR-2ICs for in vitro precipitation of 35S-TRAP, it was shown that the C-terminal half of the TNFR-2IC contains the domain necessary for interaction with TRAP. The TRAP identified in the present study shares considerable homology with, and may be the human homologue of, a mouse protein, TNF receptor-associated factor 2 (TRAF2), that binds mouse TNFR-2.
Optimal and consistent protein glycosylation in mammalian cell culture (2009)

In the biopharmaceutical industry, mammalian cell culture systems, especially Chinese hamster ovary (CHO) cells, are predominantly used for the production of therapeutic glycoproteins. Glycosylation is a critical protein quality attribute that can modulate the efficacy of a commercial therapeutic glycoprotein. Obtaining a consistent glycoform profile in production is desired due to regulatory concerns because a molecule can be defined by its carbohydrate structures. An optimal profile may involve a spectrum of product glycans that confers a desired therapeutic efficacy, or a homogeneous glycoform profile that can be systemically screened for. Studies have shown some degree of protein glycosylation control in mammalian cell culture, through cellular, media, and process effects. Studies upon our own bioprocesses to produce fusion proteins and monoclonal antibodies have shown an intricate relationship between these variables and the resulting protein quality. Glycosylation optimization will improve therapeutic efficacy and is an ongoing goal for researchers in academia and industry alike. This review will focus on the advancements made in glycosylation control in a manufacturing process, as well as the next steps in understanding and controlling protein glycosylation.
The limited importance of factor Xa inhibition to the anticoagulant property of heparin in thromboplastin-activated plasma (1988)

The antifactor Xa activities of heparin fractions are widely used as an ex vivo index of their antithrombotic efficacy. Its clinical meaning, however, remains speculative. In the study reported, we measured the effects of standard heparin, a synthetic pentasaccharide heparin (antifactor Xa activity only), and a low molecular weight heparin (LMWH) on factor Xa, factor Va, and thrombin generation in thromboplastin-activated plasma. We clearly demonstrated that the antifactor Xa activity of heparin contributed little in its anticoagulant activity. The inhibition of factor Va generation, dependent on the heparin antithrombin activity only, is of prime importance to the inhibition of thrombin generation in plasma. The inhibition of thrombin generation by the LMWH was comparable with that of standard heparin on the basis of their respective antithrombin specific activities, but not on the basis of their antifactor Xa activities.
Toward Novel Flexible Display - Top-Emitting OLEDs on Al-Laminated PET Substrates (2005)

We developed a flexible organic LED (OLED) using a top-emitting OLED (TOLED) architecture. The concept of our flexible OLED design is based on integration of a TOLED structure on an aluminum-laminated polyethylene terephthalate (Al-PET) substrate. Microcavity TOLEDs were formed for color tuning and efficiency enhancement. For a flexible TOLED with a 110-nm-thick poly (p-phenylenevinylene) light-emitting layer, it exhibited a luminous efficiency of 4.6 cd/A at 10 V. The performance of a TOLED made on a plastic substrate is analyzed and compared with that of the identical device on a rigid glass substrate. It is demonstrated that the flexible TOLED on Al-PET foil can be bent to a substantial degree without breaking.
Pathway for Differentiation of Human Embryonic Stem Cells to Vascular Cell Components and Their Potential for Vascular Regeneration (2007)

We could identify the differentiation process from human ES cells to vascular cell components and demonstrate that expansion and transplantation of vascular cells at the appropriate differentiation stage may constitute a novel strategy for vascular regenerative medicine.
Random mutagenesis-PCR to introduce alterations into defined DNA sequences for validation of SNP and mutation detection methods (2001)

Sensitive and high throughput techniques are required for the detection of DNA sequence variants such as single nucleotide polymorphisms (SNPs) and mutations. One problem, common to all methods of SNP and mutation detection, is that experimental conditions required for detection of DNA sequence variants depend on the specific DNA sequence to be analyzed. Although algorithms and other calculations have been developed to predict the experimental conditions required to detect DNA sequence variation in a specific DNA sequence, these algorithms do not always provide reliable information and experimental conditions for SNP and mutation detection must be devised empirically. Determination of experimental conditions for detection of DNA sequence variation is difficult when samples containing only wild type sequence are available. When patient derived positive controls are used, increasingly there are valid concerns about commercial ownership and patient privacy. This report presents a rapid and efficient method, employing random mutagenesis-PCR (RM-PCR) using low fidelity DNA polymerase, to randomly introduce single and multiple base substitutions and deletions into DNA sequences of interest. Clones with sequence changes were used to validate denaturing HPLC (DHPLC) algorithm predictions, optimize conditions for mutation detection in exon 15 of the tyrosine kinase domain of the MET proto-oncogene, and to confirm the association between specific DNA sequence changes and unique DHPLC chromatographic profiles (signatures). Finally, DNA from 33 papillary renal carcinoma (PRC) patients was screened for mutations in exon 15 of MET using "validated" DHPLC conditions as a proof of principle application of RM-PCR. Use of RM-PCR for DHPLC and other SNP/mutation detection methods is discussed along with challenges associated with detecting sequence alterations in mixed tumor/normal tissue, pooled samples, and from regions of the genome that have been amplified during tumorigenesis or duplicated during evolution. Hum Mutat 17:210-219, 2001. Published 2001 Wiley-Liss, Inc.
Photolytic Release of Carboxylic Acids Using Linked Donor−Acceptor Molecules:  Direct versus Mediated Photoinduced Electron Transfer to N-Alkyl-4-picolinium Esters (2005)

[reaction: see text] Efficient photorelease (Phi = 0.7) of carboxylic acids is achieved with a covalently linked mediator (benzophenone) protecting group (N-alkyl-4-picolinium ester) molecule. The mechanism involves initial photoreduction of the mediator, followed by rapid electron transfer to the protecting group.
Stimulation of lipid peroxidation and hydroxyl-radical generation by the contents of human atherosclerotic lesions (1992)

Lipid peroxidation within human arterial lesions is thought to play an important role in the development of atherosclerosis. Peroxidation can be accelerated by the presence of 'catalytic' iron or copper ions. Gruel samples from advanced atherosclerotic lesions in the abdominal aortae of human cadavers were tested for pro-oxidant properties. All samples contained bleomycin-detectable iron and phenanthroline-detectable copper. Almost all gruel samples stimulated peroxidation of rat liver microsomes, and this was usually inhibited by the iron-ion chelator desferrioxamine. Some samples stimulated formation of hydroxyl radicals from H2O2 in the presence of ascorbate, a reaction again inhibited by desferrioxamine. We conclude that the interior of human advanced atherosclerotic lesions is a highly pro-oxidant environment, and that the use of copper or iron ions to promote peroxidation of low-density lipoproteins in vitro may be a valid model for events in the arterial wall.
Quantum pillar structures on n+ gallium arsenide fabricated using ‘‘natural’’ lithography (1993)

Random arrays of CsCl hemispherically shaped islands with average diameters as small as 500 Å have been made on n+GaAs substrates. The CsCl behaves as a resist of high selectivity when the GaAs is reactively ion etched in a BCl3 plasma. The resulting structure is a set of pillars all the same height, but with varying diameters, typically ±15% of the average value, 〈D〉. Typical pillar packing density, S, is 20%. Photoluminescence (PL) studies were made at 10 K on n+ and semi-insulating GaAs using 514.5 nm exciting radiation. PL spectra from n+GaAs structures of 〈D〉=520±78 Å, h=800 Å, S=20%; 〈D〉=610±97 Å, h=450 Å, S=12%; 〈D〉=1215±210 Å, h=600 Å, S=20%, as well as a plane surface, are reported. There is a shift in the peak value of the PL curves with respect to the planar structure of 26, 13, and 2.5 meV, respectively. It may be possible to understand these shifts in terms of quantum confinement effects if the effective pillar size is reduced by surface space charge effects.
MONITORING SECRETORY MEMBRANE WITH FM1-43 FLUORESCENCE (1999)

FM1-43 and similar styryl dyes have proven useful as probes for membrane trafficking because they reversibly stain membranes, are impermeable to membranes, and are more fluorescent when bound to membranes than when in solution. Because these dyes stain membranes in an activity-dependent manner, they are ideal for studies of neurotransmitter release mechanisms such as synaptic vesicle recycling, exocytosis, and endocytosis. FM dyes have been used in conjunction with other techniques such as fluorescent calcium indicator dyes and electrophysiological techniques to elucidate mechanisms of presynaptic calcium homeostasis and modulation of neurotransmitter release. Presynaptic membranes have been marked by FM dyes in studies of synaptogenesis and reinnervation. As a probe for endocytosed membranes, these dyes have been used to examine vacuole formation in yeast. These versatile membrane dyes are useful in a variety of applications.
Counting mitoses by image processing in Feulgen stained breast cancer sections: The influence of resolution (1997)

Counting of mitotic cells has been shown to be of prognostic value in breast cancer in different retrospective studies. Up to now the number of mitoses is assessed mainly manually according to a standardized but strict protocol. Although such a manual procedure is reasonably reproducible, automatic counting of mitotic cells offers the potential for greater objectivity and reproducibility. This paper describes the influence of resolution on automatic recognition by image processing of mitotic cells in Feulgen stained breast cancer sections. Using the image recording, correction and segmentation procedure described in a previous study, five specimens were analyzed: one was used to serve as a training set and four were put aside for later use as independent test set. For each slide, objects from a pre-selected area were recorded at increasing resolution. For each object, contour features and optical density measurements were computed and stored in a data file for statistical analysis. The results showed that increased resolution using a 40x objective lowered the number of misclassified mitoses compared with a 20x objective (overall mean percentage of misclassified mitoses over training and all test specimens: 20x, 24.57; 40x, 7.96). The number of misclassifications of non-mitoses was almost stable per specimen but varied between specimens (19-42%) due to differences among tissues. Given the improvement in classifying mitoses and the possibility to evaluate interactively the measurement result, the described semi-automated mitoses pre-screener of histological sections may be suitable for further testing in a clinical setting.