gebhart/patrepeval huggingface dataset:
Fcγ receptor type IIIA polymorphisms influence treatment outcomes in patients with inflammatory arthritis treated with tumor necrosis factor α–blocking agents (2005)

These results suggest that FcgammaRIIIA-158 polymorphisms may affect the outcome of treatment with TNF blocking agents. Better understanding of the factors affecting responses to these agents could result in improved outcomes of treatment.
Use of platelet-rich fibrin over skin wounds: Modified secondary intention healing (2013)

The healing process after any surgical intervention has always posed a challenge for the surgeons. In spite of the advances in wound closure techniques and devices, there is a crucial need for newer methods of enhancing the healing process to achieve optimal outcomes. Fibrin adhesives and platelet concentrates have proven useful in various treatment modalities in the fields of microvascular and plastic surgery. This case report shows its unique use in the field of maxillofacial and cutaneous surgery. It shows an innovative technique of enhancement of skin wound healing by local application of platelet-rich fibrin.
Detection of Zika Virus in Urine (2014)

We describe the kinetics of Zika virus (ZIKV) detection in serum and urine samples of 6 patients. Urine samples were positive for ZIKV >10 days after onset of disease, which was a notably longer period than for serum samples. This finding supports the conclusion that urine samples are useful for diagnosis of ZIKV infections.
Intraocular Lens Power Calculation for Cataract Surgery after Photorefractive Keratectomy for High Myopia (1997)

Refraction-derived keratometric values provided the most accuracy in calculating IOL powers. Our results suggest the SRK/T formula was the most accurate for corneal plane calculations, while the SRK-II formula was the most accurate for spectacle plane calculations.
Helical twists of collagen model peptides (2006)

Average helical twists were calculated by the method of Sugeta and Miyazawa (Biopolymers 1967, 5, 673-679) for all of the collagen model peptides analyzed to date. Calculation of the helical twists of all triplets in each peptide strand provided novel insights for several model peptides. In the (Pro-Pro-Gly)n (n = 9 and 10), the helical twists showed cyclic fluctuations between 40 and 65 degrees with a 20 A period, suggesting that their molecular conformations were close enough to the ideal 7/2-helix to show the helical repeat of 20 A. Rather small helical twists in the guest regions of IBP in complex and T3-785 were attributed to the interaction with Integrin I domain and a relaxed conformation caused by three consecutive triplets lacking imino acid residues, respectively. Although most of the triplets used in this study were imino acid-rich triplets, helical twists were scattered in a wide range from 30 to 70 degrees with an overall average of 52.6 degrees . This distribution of helical twists indicated a strong preference for the 7/2-helical conformation (51.4 degrees ) rather than the 10/3-helical model (36 degrees ).
A decision tree method for finding and classifying names in Japanese texts (1998)

This paper describes a system whichusesadecision tree to ndandclassify names in Japanese texts. The decision tree uses part-of-speech, character type, and special dictionary information to determine the probability that aparticular type of name opens or closes at agiven position in the text. The output isgenerated from the consistent sequence of nameopens and name closes with the highest probability. This system does not require any human adjustment. Experiments indicate good accuracy with asmall amount of training data, and demonstrate the system&amp;apos;s portability. Theissues of training data size and domain dependency are discussed. 1
Morphological evolution and strain relaxation of Ge islands grown on chemically oxidized Si(100) by molecular-beam epitaxy (2005)

We have previously demonstrated that high-quality Ge can be grown on Si by the touchdown process, where chemically oxidized Si is exposed to a Ge molecular beam. The causes of strain relaxation in the Ge epilayer were also proposed and discussed. Herein, we present a detailed analysis on the morphological evolution and strain relaxation of nanoscale Ge islands on SiO2-covered Si in order to identify the mechanisms by which the high-quality epilayer forms. During the touchdown, the Ge seeds are anchored to the underlying Si. This immobility of Ge islands gives rise to a unique bimodal size distribution during coarsening. Three events are observed during coalescence: (1) merging of two small (&amp;lt;10nm) islands largely driven by surface diffusion, (2) merging of a small island and a big island (∼50nm), and (3) merging of two big islands. The coalescence of two small islands is characterized by the formation of twins or stacking faults at the two merging fronts. In contrast, no stacking fault or grain boundary results from the coalescence of large islands, indicating that their coalescence is favorable in achieving high-crystalline quality. For the Ge epilayer, the compressive strain exists mostly within 2nm from the heterojunction, resulting in a fully relaxed Ge epilayer. We attribute the relaxation to three mechanisms: (1) the strain at the junction pad decays below the critical limit within 2nm, a scale exactly comparable with the dimension of individual Ge–Si junction; (2) the remaining SiO2 serves as artificially introduced 60° dislocations; and (3) the intermixing between Ge and Si at the heterojunction reduces the effective lattice mismatch.
A Response to Critics of The Truly Disadvantaged (1989)

I appreciate the thoughtful comments by the authors of those papers that focused on my book, even though I disagree with many of the arguments. I was especially pleased with Edna Bonacich's accurate interpretation of my arguments in the first several pages of her article. And I was impressed with Andrew Billingsley's comprehensive discussion of what he takes to be the "three distinct, yet overlapping phases or central themes in" my work. I wish I were able on this occasion to discuss this broader coverage of my scholarship, but for sake of brevity, I shall only focus on the criticisms of The Truly Disadvantaged. My response will not include an attempt to "answer" each of the critical comments seriatim, rather it will focus on those points that allow me to highlight and clarify the most important arguments in the book. In the process I hope to correct several of the more serious misinterpretations and distortions of my thesis.
Retrovirus-mediated gene transduction into canine peripheral blood repopulating cells (1994)

Abstract Genetically marked peripheral blood progenitor cells were used to investigate their contribution to long-term hematopoietic reconstitution after autologous marrow and peripheral blood cell transplantation. After autologous marrow harvest and cryopreservation, canine peripheral blood progenitor cells were mobilized in three dogs by treatment with recombinant canine stem cell factor for 8 days. Peripheral blood mononuclear cells were collected and enriched for major histocompatibility complex (MHC) class II antigen-positive cells by avidin-biotin immunoadsorption, thereby enriching for repopulating cells. Subsequently, the cells were cocultivated for 24 hours on irradiated vector-producing packaging cells (PA317/LN), followed by an 11-day incubation in a vector containing long-term marrow culture system. On the day of transplantation, the animals were irradiated with 9.2 Gy total body irradiation (TBI), and transduced peripheral blood cells and untransduced cryopreserved marrow cells were infused within 2 hours of TBI. All three dogs engrafted. Two dogs are long-term survivors showing intermittently G418-resistant marrow-derived colony- forming unit granulocyte-macrophage colonies at a median of 1% and 2%, respectively (range, 1% to 10%), for now up to 48 weeks after transplantation. Neo-specific sequences were detected by polymerase chain reaction in peripheral blood granulocytes for now up to 65 weeks and in peripheral blood lymphocytes for up to 75 weeks after transplantation. Peripheral blood samples of the dogs were free of helper virus and no side effects from the transduction were observed. One of the three dogs died from chronic canine distemper sclerosing encephalitis on day 84, whereas the other two dogs are alive at 15 and 17 months. Our data show successful retroviral transduction of canine peripheral blood repopulating cells. Long-term persistence of marked myeloid and lymphoid cells after transplantation suggests that peripheral blood contains repopulating cells that contribute to long- term hematopoietic reconstitution after otherwise lethal TBI.
The Chirp z-Transform Algorithm and Its Application (1969)

We discuss a computational algorithm for numerically evaluating the z-transform of a sequence of N samples. This algorithm has been named the chirp z-transform algorithm. Using this algorithm one can efficiently evaluate the z-transform at M points in the z-plane which lie on circular or spiral contours beginning at any arbitrary point in the z-plane. The angular spacing of the points is an arbitrary constant; M and N are arbitrary integers. The algorithm is based on the fact that the values of the z-transform on a circular or spiral contour can be expressed as a discrete convolution. Thus one can use well-known high-speed convolution techniques to evaluate the transform efficiently. For M and N moderately large, the computation time is roughly proportional to (N + M) log <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> (N + M) as opposed to being proportional to N · M for direct evaluation of the z-transform at M points. Applications discussed include: enhancement of poles in spectral analysis, high resolution narrow-band frequency analysis, interpolation of band-limited waveforms, and the conversion of a base 2 fast Fourier transform program into an arbitrary radix fast Fourier transform program.
High speed determination of beta‐receptor blocking agents in human urine by liquid chromatography/tandem mass spectrometry (2001)

Beta-receptor blocking agents are present on the international market in a huge variety. The International Olympic Committee prohibits the use of these drugs in several sport sections and doping control laboratories analyse urine samples of high-performance athletes with different techniques. Therefore, fast and reliable methods are required to enable a sensitive detection of many drugs and a high throughput of samples. In the present study a screening procedure is described using high speed liquid chromatography and multiple reaction monitoring to identify 32 beta-receptor blocking agents extracted from human urine. Urine specimens (blank urine samples, spiked urine samples and specimens of excretion studies) were hydrolysed, extracted and analysed within 7 min. Quasi-molecular ions (M(+) + H) of the beta-blockers are generated by means of an atmospheric pressure chemical ionization interface followed by collision-induced dissociation in a triple quadrupole mass spectrometer and subsequent detection of daughter ions. Proposals for the origin of common and individual secondary ions are presented.
Repeated intravenous ketamine therapy in a patient with treatment-resistant major depression (2008)

In this patient with a co-occurring substance use disorder, repeated administrations of ketamine produced positive results. Since the second application has been less efficacious, doses and schedule of administrations need to be further investigated.
GENETIC AND MOLECULAR ANALYSIS OF CIRCADIAN RHYTHMS (1996)

The first part of this review summarizes the two best understood aspects of the two best understood circadian systems, the feedback oscillators of Neurospora and Drosophila, concentrating on what we know about the frequency (frq), period (per) and timeless (tim) genes. In the second part, the general circadian genetic and molecular literature is surveyed, with an eye to describing what is known from a variety of systems about input to the oscillator (entrainment), and how the oscillator might work and be temperature compensated, in emerging systems including Synechococcus, Gonyaulax, Arabidopsis, hamsters, and mice. Finally, the conversation of the molecular components of clocks is analyzed: both frq and per are widely conserved in their respective phylogenetic classes. Pharmacological data suggests that most other organisms use a day-phased oscillator of the type seen in Neurospora rather than a night-phased oscillator such as in Drosophila.
Microbial production of L-tyrosine: a review. (1997)

Microbial production of L-tyrosine by direct fermentation and by enzymatic methods has been reviewed. Achievements in this regard made through recombinant DNA techniques have also been included. The review also includes biosynthesis and regulation of tyrosine.
High quality depth map upsampling for 3D-TOF cameras (2011)

This paper describes an application framework to perform high quality upsampling on depth maps captured from a low-resolution and noisy 3D time-of-flight (3D-ToF) camera that has been coupled with a high-resolution RGB camera. Our framework is inspired by recent work that uses nonlocal means filtering to regularize depth maps in order to maintain fine detail and structure. Our framework extends this regularization with an additional edge weighting scheme based on several image features based on the additional high-resolution RGB input. Quantitative and qualitative results show that our method outperforms existing approaches for 3D-ToF upsampling. We describe the complete process for this system, including device calibration, scene warping for input alignment, and even how the results can be further processed using simple user markup.
Evolution of the Health Benefits of Soy Isoflavones (1998)

Soy is a unique dietary source of the isoflavones, genistein and daidzein. It has been part of the Southeast Asian diet for nearly five millenia, whereas consumption of soy in the United States and Western Europe has been limited to the 20th century. Heavy consumption of soy in Southeast Asian populations is associated with reduction in the rates of certain cancers and cardiovascular disease. Recent experimental evidence suggests that phytochemicals in soy are responsible for its beneficial effects, which may also include prevention of osteoporosis, a hereditary chronic nose bleed syndrome, and autoimmune diseases. Exposure of soy formula-fed infants to the potential estrogenizing effects of the isoflavones is limited by the first pass effect of the liver following the uptake of isoflavones from the gut. Several mechanisms of action of isoflavones have been proposed-both through estrogen-dependent and estrogen-independent pathways.
Distortion-free delivery of nanojoule femtosecond pulses from a Ti:sapphire laser through a hollow-core photonic crystal fiber (2004)

We demonstrate propagation of femtosecond pulses in the 800-nm range through a hollow-core photonic crystal fiber with preserved temporal and spectral profiles for pulse energies up to 4.6 nJ. Without the use of a prechirping unit, 170-fs pulses were transmitted essentially undistorted at 812 nm, near the zero-dispersion wavelength. Because of the air guidance of pulses, intensity-dependent nonlinear effects were minimal, with only 15% pulse broadening occurring at 350-mW average output power. This fiber thus is excellently suited for applications that require single-mode delivery of high-energy ultrashort pulses to the fiber output face such as, for example, miniaturized multiphoton microscopes.
Vascular endothelial growth factor C induces angiogenesis in vivo (1998)

Vascular endothelial growth factor C (VEGF-C) recently has been described to be a relatively specific growth factor for the lymphatic vascular system. Here we report that ectopic application of recombinant VEGF-C also has potent angiogenic effects in vivo. VEGF-C is sufficiently potent to stimulate neovascularization from limbal vessels in the mouse cornea. Similar to VEGF, the angiogenic response of corneas induced by VEGF-C is intensive, with a high density of new capillaries. However, the outgrowth of microvessels stimulated by VEGF-C was significantly longer than that induced by VEGF. In the developing embryo, VEGF-C was able to induce branch sprouts from the established blood vessels. VEGF-C also induced an elongated, spindle-like cell shape change and actin reorganization in both VEGF receptor (VEGFR)-2 and VEGFR-3-overexpressing endothelial cells, but not in VEGFR-1-expressing cells. Further, both VEGFR-2 and VEGFR-3 could mediate proliferative and chemotactic responses in endothelial cells on VEGF-C stimulation. Thus, VEGF-C may regulate physiological angiogenesis and participate in the development and progression of angiogenic diseases in addition to lymphangiogenesis.
Cooperative and Competitive Protein Interactions at the Hsp70 Promoter (1997)

Drosophila heat shock factor (HSF) binds to specific sequence elements of heat shock genes and can activate their transcription 200-fold. Though HSF has an acidic activation domain, the mechanistic details of heat shock gene activation remain undefined. Here we report that HSF interacts directly with the general transcription factor TBP (TATA-box binding protein), and these two factors bind cooperatively to heat shock promoters. A third factor that binds heat shock promoters, GAGA factor, also interacts with HSF and further stabilizes HSF binding to heat shock elements (HSEs). The interaction of HSF and TBP is explored in some detail here and is shown to be mediated by residues in both the amino- and carboxyl-terminal portions of HSF. This HSF/TBP interaction can be specifically disrupted by competition with the potent acidic transcriptional activator VP16. We further show that the acidic domain of the largest subunit of Drosophila RNA polymerase II (Pol II) associates with TBP in vitro and is specifically displaced from TBP upon addition of HSF. The region of TBP that mediates both HSF and Pol II acidic domain binding maps to the conserved carboxyl-terminal repeats and depends on at least one of the TBP residues known to be contacted by VP16 and to be critical for transcription activation. We discuss these findings in the context of a model in which HSF triggers hsp70 transcription by freeing the hsp70 promoter-paused Pol II from the constraints on elongation caused by the affinity of Pol II for general transcription factors.
Maximum power point tracking with temperature compensation of photovoltaic for air conditioning system with fuzzy controller (1996)

Fuzzy control has received a great deal of attention due to its excellent behavior when applied to complex and nonlinear system. As fuzzy theory is close to human reasoning, fuzzy controllers are easy to design and cheap to produce. In this paper, we investigate the possibilities of P/sub max/ control using the fuzzy controller, and we also examine the optimal power converter using a step-up chopper circuit to operate the solar cell at an optimal voltage of compensated voltage (i.e. of determined transducer by temperature (-40/spl deg/C/spl sim/+100/spl deg/C)). The proposed step-up maximum power point tracking (MPPT) system is studied by simulation and is implemented by using a microcomputer which controls the duty ratio of an IGBT boost converter.
In vitro mutagenesis of a full-length cDNA clone of Semliki Forest virus: the small 6,000-molecular-weight membrane protein modulates virus release (1991)

We report on the construction of a full-length cDNA clone of Semliki Forest virus (SFV). By placing the cDNA under the SP6 promoter, infectious RNA can be produced in vitro and used to transfect cells to initiate virus infection. To achieve efficient transfections, a new protocol for electroporation of RNA was developed. This method gave up to 500-fold improvement over the traditional DEAE-dextran transfection procedure. Since virtually 100% of the cells can be transfected by electroporation, this method is a useful tool for detailed biochemical studies of null mutations of SFV that abolish production of infections virus particles. We used the cDNA clone of SFV to study what effects a deletion of the 6,000-molecular-weight membrane protein (6K membrane protein) had on virus replication. The small 6K protein is part of the structural precursor molecule (C-p62-6K-E1) of the virus. Our results conclusively show that the 6K protein is not needed for the heterodimerization of the p62 and E1 spike membrane proteins in the endoplasmic reticulum, nor is it needed for their transport out to the cell surface. The absence of the 6K protein did, however, result in a dramatic reduction in virus release, suggesting that the protein exerts its function late in the assembly pathway, possibly during virus budding.
Changes in electrical activation modify the orientation of left ventricular flow momentum: novel observations using echocardiographic particle image velocimetry (2015)

Changes in electrical activation alter the orientation of blood flow momentum. The long-term CRT outcome correlates with the degree of re-alignment of haemodynamic forces. These preliminary results suggest that flow orientation could be used for optimizing the biventricular pacing setting. However, larger prospective studies are needed to confirm this hypothesis.
Mast cell tryptase is a mitogen for cultured fibroblasts. (1991)

Mast cells appear to promote fibroblast proliferation, presumably through secretion of growth factors, although the molecular mechanisms underlying this mitogenic potential have not been explained fully by known mast cell-derived mediators. We report here that tryptase, a trypsin-like serine proteinase of mast cell secretory granules, is a potent mitogen for fibroblasts in vitro. Nanomolar concentrations of dog tryptase strongly stimulate thymidine incorporation in Chinese hamster lung and Rat-1 fibroblasts and increase cell density in both subconfluent and confluent cultures of these cell lines. Tryptase-induced cell proliferation appears proteinase-specific, as this response is not mimicked by pancreatic trypsin or mast cell chymase. In addition, low levels of tryptase markedly potentiate DNA synthesis stimulated by epidermal growth factor, basic fibroblast growth factor, or insulin. Inhibitors of catalytic activity decrease the mitogenic capacity of tryptase, suggesting, though not proving, the participation of the catalytic site in cell activation by tryptase. Differences in Ca++ mobilization and sensitivity to pertussis toxin suggest that tryptase and thrombin activate distinct signal transduction pathways in fibroblasts. These data implicate mast cell tryptase as a potent, previously unrecognized fibroblast growth factor, and may provide a molecular link between mast cell activation and fibrosis.