gebhart/patrepeval huggingface dataset:
Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation (2015)

Bariatric surgery is currently the most effective procedure for the treatment of obesity. Given the role of the gut microbiota in regulating host metabolism and adiposity, we investigated the long-term effects of bariatric surgery on the microbiome of patients randomized to Roux-en-Y gastric bypass or vertical banded gastroplasty and matched for weight and fat mass loss. The two surgical procedures induced similar and durable changes on the gut microbiome that were not dependent on body mass index and resulted in altered levels of fecal and circulating metabolites compared with obese controls. By colonizing germ-free mice with stools from the patients, we demonstrated that the surgically altered microbiota promoted reduced fat deposition in recipient mice. These mice also had a lower respiratory quotient, indicating decreased utilization of carbohydrates as fuel. Our results suggest that the gut microbiota may play a direct role in the reduction of adiposity observed after bariatric surgery.
Apoptosis as a mechanism of keratinocyte death in toxic epidermal necrolysis (1996)

Toxic epidermal necrolysis (TEN) and Stevens-Johnson syndrome (SJS) are life-threatening diseases characterized by extensive epidermal destruction. The aim of our study was to investigate apoptosis in keratinocytes of patients with TEN and TEN/SJS overlap syndrome. Keratinocytes from TEN patients were found to undergo extensive apoptosis. These results suggest that cell destruction in TEN occurs as a result of apoptosis. Our findings suggest that apoptosis inhibitory agents may play an important part in the therapeutic strategy of TEN.
Enhancement of Dendritic Cells as Vaccines for Cancer (2010)

Dendritic cells are the most potent antigen-presenting cells known; owing to their ability to stimulate antigen-specific cytolytic and memory T-cell responses, their use as cancer vaccines is rapidly increasing. While clinical trials provide evidence that dendritic cells vaccines are safe and elicit immunological responses in most patients, few complete tumor remissions have been reported and further technological advances are required. An effective dendritic cell vaccine must possess and maintain several characteristics: it must migrate to lymph nodes, have a mature, Th1-polarizing phenotype expressed stably after infusion and present antigen for sufficient time to produce a T-cell response capable of eliminating a tumor. While dendritic cells are readily matured ex vivo, their phenotype and fate after infusion are rarely evaluable; therefore, strategies to ensure that dendritic cells access lymphoid tissues and retain an immunostimulatory phenotype are required. In order to best exploit dendritic cells as vaccines, they may require genetic modification and combination with other strategies including adoptive T-cell transfer, inhibition of regulatory T cells or modulation of inflammatory pathways.
Platelet-derived growth factor in vivo: levels, activity, and rate of clearance (1984)

Abstract Platelet-derived growth factor (PDGF) is a potent mitogen for many cultured connective tissue cells. It is present in concentrated form within the platelet alpha-granules and is believed to be released during platelet degranulation at sites of vascular injury. We have used a sensitive radioreceptor assay to measure PDGF levels in whole blood serum from normal humans [17.5 +/- 3.1 (SD) ng/mL] and baboons (2.7 +/- 1.2 ng/mL). PDGF was not detected in plasma from either species. In addition, plasma was found to substantially reduce the ability of added purified PDGF to bind to the cell surface PDGF receptor on cultured cells, suggesting that plasma may contain a PDGF-binding protein that would serve to inactivate PDGF released into plasma. Calculations of PDGF concentrations in serum have been corrected for the effects of the binding protein. 125I-PDGF injected intravenously into normal baboons was cleared rapidly from the plasma (t1/2 = two minutes). The rapid clearance of 125I-PDGF did not result from iodination damage, as purified unlabeled PDGF was cleared with comparable kinetics. The rapid clearance of purified and iodinated PDGF did not result from changes in PDGF structure during purification or from removal of PDGF-associated proteins during purification, as PDGF present in freeze-thaw lysates of fresh platelets was cleared equally rapidly. We conclude that release of PDGF at sites of vascular injury would greatly increase the local concentration of PDGF and that PDGF not localized to the site of injury would be rapidly cleared from the circulation.
Design optimization and stamper fabrication of light guiding plates using silicon based micro-features (2009)

This study applies a novel fabrication process of molding stamper that combines anisotropic wet etching of silicon-on-insulator (SOI) wafers with electroforming to produce precision stampers. Micron-size features, such as trapezoidal grooves and prisms, can be accurately fabricated and distributed. Because the feature geometry and the distribution can be accurately realized using the proposed scheme, the design optimization of light guide plate (LGP) become realistic. By observing the illumination characteristics of LED edge-lit LGP, the distribution pattern of the LGP is transformed into the parameter design of 7 anchor spacing and the spacing modulation amplitude. This study manipulates the distribution parameters using the fuzzy optimization to obtain a LGP design with high illumination uniformity. The design of a LGP of 3.5 inch using LED light source is used as an illustrated example. The optical software, TracePro is applied to simulate the luminance performance. The optimization converges quickly and provides the optimum design with an average brightness of 2266 (nit) and uniformity of 90% without any use of diffusive sheets. The application demonstrates the feasibility and effectiveness of the proposed scheme.
Motion-compensating long-term memory prediction (2002)

Motion-compensating long-term memory prediction extends the spatial displacement utilized in block-based hybrid video coding by a variable time delay permitting the use of more frames than the previously decoded one for motion compensation. The long-term memory covers the decoded frames of some seconds at encoder and decoder. We investigate the influence of memory size in our motion compensation scheme and analyze the trade-off between the bit-rates spent for motion compensated prediction and residual coding. Simulation results are obtained by integrating long-term memory prediction into an H.263 codec. PSNR improvements up to 2 dB for the Foreman sequence and 1.5 dB for the Mother-Daughter sequence are demonstrated in comparison to the TMN-2.0 H.263 coder.
Receptor for Advanced Glycation End Product (RAGE) Upregulation in Human Gingival Fibroblasts Incubated With Nornicotine (2005)

Nornicotine, AGE, and upregulation of RAGE may be involved in the pathogenesis of periodontal disease associated with smoking.
Mitochondrial Fission, Fusion, and Stress (2012)

Mitochondrial fission and fusion play critical roles in maintaining functional mitochondria when cells experience metabolic or environmental stresses. Fusion helps mitigate stress by mixing the contents of partially damaged mitochondria as a form of complementation. Fission is needed to create new mitochondria, but it also contributes to quality control by enabling the removal of damaged mitochondria and can facilitate apoptosis during high levels of cellular stress. Disruptions in these processes affect normal development, and they have been implicated in neurodegenerative diseases, such as Parkinson's.
Caffeine-assisted chemotherapy and minimized tumor excision for nonmetastatic osteosarcoma. (1998)

Osteosarcoma is usually treated with intensive preoperative and postoperative chemotherapy and wide tumor resection, resulting in a 60% to 70% 5-year survival rate. Caffeine has a DNA-repair inhibiting effect. We therefore investigated the impact of caffeine given in conjunction with chemotherapy and limb-sparing surgery on survival and local tumor control in patients with nonmetastatic, high-grade osteosarcoma. Twenty-two patients were given 3 to 5 preoperative courses of intra-arterial cisplatin (120 mg/m2, 1 to 2 hours) and caffeine (1.5 g/m2/day x 3 days) with or without doxorubicin (30 mg/m2/day x 2 days). Following this treatment, limb-sparing surgery was performed by means of intentional marginal excision aiming at preservation of important structures such as major neurovascular bundles, tendons, ligaments and the epiphysis. Three courses of cisplatin and doxorubicin combined with caffeine, and high-dose methotrexate with vincristine and citrovorum factor rescue were given intravenously as postoperative chemotherapy for 21 patients and three courses of high-dose methotrexate and combination of ifosfamide, etoposide and methotrexate for 1 patient. Following the preoperative chemotherapy, there were no viable tumor cells in 19 patients, only scattered foci of viable cells in 2 patients, and some areas of viable tumor cells in 1. The 21 patients with a good chemotherapeutic response on radiographs underwent minimized marginal excision. Functional evaluation of the affected limbs was excellent for 17 patients, good for 3, fair for 1, and poor for 1. No local tumor recurrence was seen in this series. Eighteen patients remain disease-free with a mean follow-up of 61 months. Two patients died of metastatic disease, 1 died of chemotherapy-related complications, and 1 died of unknown causes. The overall 5-year cumulative survival rate was 90%, and the 5-year event-free survival rate was 75%. Chemotherapeutic caffeine enhanced tumor necrosis and improved the success rate of limb-sparing surgery using marginal procedure without any adverse impact on survival. The results of our limited clinical trial appear to justify further prospective, multicenter randomized trials of the benefits of caffeine combined with chemotherapy for nonmetastatic osteosarcoma and other malignant neoplasms.
Gastrointestinal Microbiota–Mediated Control of Enteric Pathogens (2014)

The gastrointestinal (GI) microbiota is a complex community of microorganisms residing within the mammalian gastrointestinal tract. The GI microbiota is vital to the development of the host immune system and plays a crucial role in human health and disease. The composition of the GI microbiota differs immensely among individuals yet specific shifts in composition and diversity have been linked to inflammatory bowel disease, obesity, atopy, and susceptibility to infection. In this review, we describe the GI microbiota and its role in enteric diseases caused by pathogenic Escherichia coli, Salmonella enterica, and Clostridium difficile. We discuss the central role of the GI microbiota in protective immunity, resistance to enteric pathogens, and resolution of enteric colitis.
Nanotubes of the disulfides of groups 4 and 5 metals (2002)

Abstract Nanotubes of HfS 2 , ZrS 2 , NbS 2 , and TaS 2 have been obtained by the reduction of the corresponding metal trisulfides in a stream of H 2 (mixed with an inert gas in some cases) at elevated temperatures. The nanotubes have been characterized by transmission electron microscopy (TEM) and other techniques. These disulfide nanotubes make an important addition to the growing family of nanotubes of inorganic layered materials.
Expression of Cytokines in Placentas of Mice Undergoing Immunologically Mediated Spontaneous Fetal Resorptions1 (1993)

It is clear that the immune system and the reproductive system interact with and influence each other and that the immune system can have positive and negative regulatory effects on the outcome of pregnancy. The discovery of murine models of immunologically mediated spontaneous fetal resorptions has proved to be very useful for the study of immunological influences on pregnancy. In an attempt to elucidate the mechanisms underlying pregnancy impairment in one such "natural" model of pregnancy loss, we compared the expression of the cytokines tumor necrosis factor alpha, interferon tau, and interleukin-2 in placental tissue from a resorption-prone strain combination with the expression from a normal combination. We found significantly enhanced expression of these three cytokines in placentas from the resorption-prone combination using dot-blot hybridization and Northern hybridizations. Since these cytokines are abortifacients in vivo and have detrimental effects on the placenta, and hence on fetal development and survival, our demonstration of enhanced expression of these deleterious cytokines may give insight into the mechanisms involved in immunologically mediated spontaneous abortions.
Field-reversed configurations with a component of energetic particles (1982)

This review is concerned with the physics of field-reversed configurations created by energetic particles of large orbits, of which the earliest example is the Astron. The Astron concept has evolved into the Ion Ring Compressor in which a low-energy ring of ions is magnetically compressed to high energy for heating the confined plasma to thermonuclear ignition. A third version is the hybrid in which field reversal is created both by plasma currents as in a θ-pinch or a spheromak and a component of energetic large orbit ions to provide heating energy as well as improved stability. This paper treats first the injection, trapping, and formation of electron and ion rings from a theoretical standpoint as well as presenting the principal experimental results. The equilibria and the characteristics of the particle orbits are discussed in some detail including conditions under which the orbits cease to be integrable and pass to a stochastic description. The theory of magnetic compression of rings and the classical transport of heat and particles of the plasma confined in the closed-poloidal-field-line region is presented. The bulk of the review is concerned with low-frequency stability of such configurations by means of a generalized energy principle for treating the large-orbit particles in the Vlasov limit. The pathology of all possible unstable modes is discussed at some length. We conclude with an exhaustive survey of microinstabilities driven by the energetic particle current for a special model and conclude that most of them are stabilized by strong gradients in density and magnetic field. A brief discussion on drift modes follows. Our present theoretical understanding of these systems, although still incomplete in some respects, nevertheless leads to the view that the promise of the very favourable features of fusion reactors based on these concepts is a sufficient impetus for their continued experimental and theoretical study.
Mapping of Phosphorylation Sites by a Multi-Protease Approach with Specific Phosphopeptide Enrichment and NanoLC−MS/MS Analysis (2005)

We have developed a multi-protease approach that allows sensitive and comprehensive mapping of protein phosphorylation sites. The combined application of the low-specificity proteases elastase, proteinase K, and thermolysin in addition to trypsin results in high sequence coverage, a prerequisite for comprehensive phosphorylation site mapping. Phosphopeptide enrichment is performed with the recently introduced phosphopeptide affinity material titansphere. We have optimized the selectivity of the phosphopeptide enrichment with titansphere, without compromising the high recovery rate of approximately 90%. Phosphopeptide-enriched fractions are analyzed with a highly sensitive nanoLC-MS/MS system using a 25-microm-i.d. reversed-phase column, operated at a flow rate of 25 nL/min. The new approach was applied to the murine circadian protein period 2 (mPER2). A total of 21 phosphorylation sites of mPER2 have been detected by the multi-protease approach, whereas only 6 phosphorylation sites were identified using solely trypsin. Titansphere proved to be well suited for the enrichment of a large variety of phosphopeptides, including peptides carrying two, three, or four phosphorylated residues, as well as phosphopeptides containing more basic than acidic amino acids.
High-Resolution Dielectric Sensor Based on Injection-Locked Oscillators (2017)

The structure of a high-resolution microwave material sensor is presented based on the injection locking phenomenon. For a sample under test, the variation of center frequency and lock range of the oscillator with respect to a reference sample are measured to indicate the resonance frequency and quality factor of the resonator. A low power level and low phase noise injection locking can significantly reduce the lock range of the oscillator. Therefore, even small variations in the loop filter of the oscillator change the response and can be determined with a high sensitivity. The unknown sample is characterized based on the measured center frequency and quality factor of the resonator. An output power control (OPC) system increases the dynamic range of the sensor with respect to the dielectric constant of samples. Moreover, a method of material detection in the microwave frequency is proposed based on data from the OPC to eliminate the frequency analyzer from the system for Internet of Things (IoT) applications. As an example for validation, a 1-GHz sensor is fabricated and the measurement results are presented.
Effective in plane launching and focusing surface plasmons by a plasmonic lens (2009)

We implement in plane launching and focusing surface plasmons by fabricating Fresnel zone-plate like grating on a thin gold film. A subwavelength focal spot, with transverse FWHM=712nm, is observed at 830nm vacuum wavelength.
Left Atrial Appendage Closure Guided by Integrated Echocardiography and Fluoroscopy Imaging Reduces Radiation Exposure (2015)

ClinicalTrials.gov NCT01262508.
Complications of transluminal angioplasty. (1986)

Four hundred fifty-three percutaneous transluminal angioplasties in 352 patients were reviewed to determine the frequency, distribution, and cause of complications. The primary success rate was 89% (81%-82% for renal and distal runoff vessels, 91%-95% for the iliofemoral arteries). Fifty-nine complications occurred in 53 patients, including 20 puncture site complications, the most frequent being hematoma. The most important angioplasty complication was acute occlusion of the arterial lumen attributed to acute thrombosis (2%). Subintimal passage of the guide wire/catheter (2%) may also cause luminal compromise. Arterial dissection following balloon dilatation (1%) and distal emboli (1.5%) were less important clinically, and vessel wall rupture was rare (0.4%). Complications were two to four times more frequent for renal and distal popliteal/tibial compared with iliofemoral angioplasties; the lower success and higher complication rates are attributed to greater technical difficulty and the increased importance of spasm. Operator experience and technical refinements play an important role in reducing occurrence of serious complications. The frequency and severity of angioplasty complications compare favorably with the alternative surgical procedure.
Genome-Wide Analysis of Neuroblastomas using High-Density Single Nucleotide Polymorphism Arrays (2007)

This analysis demonstrates the power of SNP arrays for high-resolution determination of LOH and DNA copy number change in neuroblastoma, a tumor in which specific allelic changes drive clinical outcome and selection of therapy.
Hyperelastic pressure sensing with a liquid-embedded elastomer (2010)

A hyperelastic pressure transducer is fabricated by embedding silicone rubber with microchannels of conductive liquid eutectic gallium-indium. Pressing the surface of the elastomer with pressures in the range of 0-100 kPa will deform the cross-section of underlying channels and change their electric resistance by as much as 50%. Microchannels with dimensions as small as 25 mu m are obtained with a maskless, soft lithography process that utilizes direct laser exposure. Change in electrical resistance is measured as a function of the magnitude and area of the surface pressure as well as the cross-sectional geometry, depth and relative lateral position of the embedded channel. These experimentally measured values closely match closed-form theoretical predictions derived from plane strain elasticity and contact mechanics.
Morphometric evaluation of volume shifts between intra‐ and extra‐cellular space before and during global ischemia (1995)

Cellular and interstitial alterations seen at the onset and during the course of ischemia are dependent upon the method of cardiac arrest. Furthermore, a considerable mutual influence is exerted by the alterations in cellular and interstitial spaces.
In situ cyanogen bromide cleavage of N-terminally blocked proteins in a gas-phase sequencer. (1984)

Herein we describe a procedure for the in situ cyanogen bromide cleavage of N-terminally blocked proteins which have been immobilised onto the glass fiber sample disk of the gas-phase sequencer. In this manner, new amino terminii suitable for automated Edman degradation can be generated. Cytochrome C was cleaved using this method on the carboxyl side of methionine residues 65 and 80. This allowed sequence analysis to begin simultaneously at residues 66 and 81 (Table 1). This procedure offers an alternative sequencing tactic for methionine-containing proteins which are N-terminally blocked.
The Quaking I-5 Protein (QKI-5) Has a Novel Nuclear Localization Signal and Shuttles between the Nucleus and the Cytoplasm (1999)

The mouse quaking (qk) gene is essential in both myelination and early embryogenesis. Its product, QKI, is an RNA-binding protein belonging to a growing protein family called STAR (signal transduction and activator of RNA). All members have an approximately 200-amino acid STAR domain, which contains a single extended heteronuclear ribonucleoprotein K homologue domain flanked by two domains called QUA1 and QUA2. We found that QKI isoforms could associate with each other, while one of the lethal mutations qkI(kt4) with a single amino acid change in QUA1 domain, leads to a loss of QKI self-interaction. This suggests that the QUA1 domain is responsible for QKI dimerization. Three QKI isoforms have different carboxyl termini and different subcellular localization. Here, using GFP fusion protein, we identified a 7-amino acid novel nuclear localization sequence in the carboxyl terminus of QKI-5, which is conserved in a subclass of STAR proteins containing SAM68 and ETLE/T-STAR. Thus, we name this motif STAR-NLS. In addition, the effects of active transcription, RNA-binding and self-interaction on QKI-5 localization were analyzed. Furthermore, using an interspecies heterokaryon assay, we found that QKI-5, but not another STAR protein ETLE, shuttles between the nucleus and the cytoplasm, which suggests that QKI-5 functions in both cell compartments.