gebhart/patrepeval huggingface dataset:
Transcriptional Profiling Identifies the Signaling Axes of IGF and Transforming Growth Factor-β as Involved in the Pathogenesis of Osteosarcoma (2015)

Based on these transcriptional profiles, a coordinated theme of clustered gene deregulation in osteosarcoma has emerged. Cell proliferation driven by the IGF axes during bone growth is unrestrained owing to downregulation of IGFBPs and cell cycle regulators. Tumor cells may be maintained in an undifferentiated state secondary to impaired TGF-b/BMP signaling. This wellpreserved pattern suggests that the alterations in the signaling axes of IGF-1 and TGF-b, in concert with cell cycle regulators, may be an important pathogenic basis of osteosarcoma. CLINIC RELEVANCE: This study provides a possible molecular basis of pathogenesis of osteosarcoma. This may help to develop new therapeutic targets and strategy for this disease. Preclinical and subsequently clinical testing of inhibitors of the IGF-1 and TGF pathways would be warranted.
Macrophage-specific expression of class A scavenger receptors enhances granuloma formation in the absence of increased lipid deposition (2001)

Class A scavenger receptors (SR-A) have several proposed functions that could impact atherosclerosis and inflammatory processes. To define the function of SR-A in vivo, we created C57BL/6 transgenic mice that expressed bovine SR-A under the control of the restricted macrophage promoter, lysozyme (lyso-bSR-A). bSR-A mRNA was present in cultured peritoneal macrophages of transgenic mice and tissues that contain significant macrophages including spleen, lung, and ileum. Functional overexpression of SR-A was demonstrated in peritoneal macrophages both by augmented cholesterol ester deposition in response to AcLDL and enhanced adhesion in transgenic mice compared with nontransgenic littermates. To determine whether macrophage-specific expression of bSR-A regulated inflammatory responses, granulomas were generated by subcutaneous injection of carrageenan. Granuloma size was significantly increased in lyso-bSR-A transgenic mice compared with wild-type littermates [421 ± 51 mg (n = 11) vs. 127 ± 22 mg (n = 10), P < 0.001]. However, the larger granulomas in lyso-bSR-A transgenic mice were only associated with an increase in unesterified cholesterol, and not cholesterol esters. Furthermore, granulomas from transgenic mice had an increase in the number of macrophages within the tissue.Therefore, macrophage expression of bSR-A increased presence of this cell type in granulomas without enhancing the deposition of cholesterol esters, consistent with a role of the adhesive property of the protein.—Daugherty, A., N. Kosswig, J. A. Cornicelli, S. C. Whitman, S. Wolle, and D. L. Rateri. Macrophage-specific expression of class A scavenger receptors enhances granuloma formation in the absence of increased lipid deposition. J. Lipid Res. 2001. 42: 1049–1055.
Genetic relatedness of ceftriaxone-resistant and high-level azithromycin resistant Neisseria gonorrhoeae cases, United Kingdom and Australia, February to April 2018 (2019)

Between February and April 2018, three ceftriaxone-resistant and high-level azithromycin-resistant <i>Neisseria gonorrhoeae</i> cases were identified; one in the United Kingdom and two in Australia. Whole genome sequencing was used to show that the isolates from these cases belong to a single gonococcal clone, which we name the A2543 clone.
Quality-Aware Retrieval of DataObjects from AutonomousSources forWeb-B ased Repositories (2008)

I.INTRODUCTION AstheWebbecomes thedominant mediumforinformation delivery andcommerce, anincreasing numberofapplications havetheir services heavily rely ondata repositories inutilizing information collected fromvarious Websources. Forexample, comparison shopping service providers suchasMySimon.com search andindex products fromalarge numberofmerchant Websites, andallow users tocompare prices fromcompeting stores bycollecting asubstantial amountofinformation from manyautonomous sources ontheWeb. Building ahigh-quality repository ischallenging especially whenremoteWeb sources aredynamic: newdataobjects areadded, andexisting dataobjects aredeleted orupdated frequently. Inaddition, theseWeb sources mightnotbe collaborative inthesense that applications will notbenotified foranychanges. Therefore, applications havetoquery remote sources periodically toretrieve thelatest information. Asa consequence, thelocal repository cannotmirror theremote sources completely. Hence, weneedquality metrics toquantify thegoodness ofthelocal repository withrespective tothe remote sources. Thegoalofthispaperistodevelop a framework for designing gooddatarepositories forWebapplications. The central themeofourapproach istoemploy statistical methods topredict quality metrics. Theseprediction quantities canbe usedtoanswerimportant questions suchas:Howsoonshould thelocal repository besynchronized tohaveaquality ofat
Assisting versus repelling force-feedback for human learning of a line following task (2012)

Previous work has shown that training with `assist-as-needed' method using force-feedback joystick can improve driving performance of children and adults. This work is the first study to evaluate training with a repelling force versus an assisting force for learning of a line following task. We designed a robotic training wheelchair that can accurately localize itself in the training environment, and implemented assisting and repelling force fields on the force-feedback joystick. The training protocol included three groups. The control (CT) group received no force feedback. The assisting force (AF) group was trained using the `assist-as-needed' paradigm. The repelling force (RF) group was trained with the repelling force field. We observed that both the AF and RF group improved their driving skills, however, the RF group had the greatest trajectory error reduction. We believe that this pilot study could provide a promising foundation regarding robotic wheelchair algorithm effects on adult learning.
Simple and Complex Centromeric Satellites in <i>Drosophila</i> Sibling Species (2018)

Centromeres are the chromosomal sites of assembly for kinetochores, the protein complexes that attach to spindle fibers and mediate separation of chromosomes to daughter cells in mitosis and meiosis. In most multicellular organisms, centromeres comprise a single specific family of tandem repeats-often 100-400 bp in length-found on every chromosome, typically in one location within heterochromatin. <i>Drosophila melanogaster</i> is unusual in that the heterochromatin contains many families of mostly short (5-12 bp) tandem repeats, none of which appear to be present at all centromeres, and none of which are found only at centromeres. Although centromere sequences from a minichromosome have been identified and candidate centromere sequences have been proposed, the DNA sequences at native <i>Drosophila</i> centromeres remain unknown. Here we use native chromatin immunoprecipitation to identify the centromeric sequences bound by the foundational kinetochore protein cenH3, known in vertebrates as CENP-A. In <i>D. melanogaster</i>, these sequences include a few families of 5- and 10-bp repeats; but in closely related <i>D. simulans</i>, the centromeres comprise more complex repeats. The results suggest that a recent expansion of short repeats has replaced more complex centromeric repeats in <i>D</i><i>. melanogaster</i>.
Surface Diffusion of Palladium and Its Prevention over Supported Palladium Catalyst (1969)

著者らの既往の研究によれば担体付き金属触媒はつぎの2通りの機構で, シンタリングによる活性低下をきたす。すなわち一つは担持金属結晶の成長による粒子径増大に基づく量的シンタリングであり, 他の一つは結晶の格子不整減少による活性強度低下に基づく質的シンタリングである。カチオン交換法でつくったシリカ・アルミナ担持パラジウム触媒を試料に選び, 量的シンタリングが起こるさい金属が担体表面を二次元拡散する様子をX線回折, 電子顕微鏡などの研究手段により検討した。またパラジウムの担体表面の二次元拡散を防ぐような助触媒を探索して, 量的シンタリング防止策を検討し, つぎの結果が得られた。(1) 担体表面拡散過程におけるパラジウムはパラジウムカチオン, たとえば Pd2+ の状態になっていると考えられ, 逓送現象によるパラジウム結晶の成長は酸素の化学吸着にもとづき, PdO の生成すなわち Pd2+ の生成により促進されると推定された。(2) Al3+ や Th4+ などの 3～4 価の金属カチナンを担体付きパラジウム触媒に添加すると上記のパラジウムの二次元拡散にもとづく量的シンタリングが防止された。しかし, 1価の Li+ や2価の Ba2+ などを触媒に添加してもシンタリングは防止されなかった。
Fourier Transform Infrared Absorption Spectroscopy for Quantitative Analysis of Gas Mixtures for Homeland Security Applications (2015)

Abstract Chemical detectors are crucial tools for first responders during emergency-response scenarios and for continuous monitoring of public spaces for general safety. For those who depend upon chemical detectors for safety and security, ensuring that detectors alarm at specified levels is critical. During detector performance evaluation, the accurate delivery of known concentrations of the chemical target to the detector is a key aspect of the test. Referee methods enable the analyte test concentration and associated uncertainties in the analyte test concentration to be validated by independent analysis, which is especially important for reactive analytes. This work demonstrates a method to use Fourier transform infrared (FT-IR) absorption spectroscopy for quantitatively evaluating the composition of vapor streams containing hazardous materials at acute exposure guideline levels (AEGL) under test conditions defined in recently published standard specifications for chemical vapor detectors. The described method covers the use of primary reference spectra to establish analyte concentrations, the generation of secondary reference spectra suitable for measuring analyte concentrations under specified testing environments, and the use of referee feedback to compensate for depletion of the test analyte. Important benefits of this approach included verification of the test analyte concentration with characterized uncertainties by in situ measurements co-located with the detector under test, near-real-time feedback, and broad applicability to toxic industrial chemicals.
NEW FILTERING METHODS WITH “VIBROSEIS”* (1966)

ABSTRACT In order to obtain high resolution correlograms, it is of importance amongst other things to get reflection signals with large bandwidth. An advantage of the VIBROSEIS *** method is that the frequencies radiated by the vibrators can be matched to the transmission response of the subsurface involved. By choosing the right frequency range, the highest possible amplitude and most favourable form may be given to the reflection signals. In a reflection correlogram, individual signals cannot be considered in isolation. Signals of different origin are interfering with one another. They very often have different amplitudes, so that it may be desirable in many cases to filter out events of certain apparent velocity. With the VIBROSEIS method this may be achieved quite simply. All frequencies of the noise signal are uniformly suppressed. The advantage is that noise signals, e.g. refraction signals, which cannot be sufficiently attenuated by wavelength filtering, may be completely eliminated by this velocity filtering without affecting the bandwith of the desired signal. The total dynamic range of the tape recording can be used for the registration of wanted events. To perform this kind of filtering several vibrators are necessary in the field; each of them is controlled by an individual signal. There is an unavoidable error of static and dynamic corrections which causes the results of reflection measurements to deteriorate when using multiple coverage. High frequency components especially are seriously affected by destructive interference. This difficulty can be avoided by using a VIBROSEIS signal with high frequency component amplitudes supported. For the probability of error of corrections a normal distribution is assumed. A smoothed amplitude characteristic may be achieved after stacking. The amplitude characteristic of seismic devices is commonly reduced to about 100 cps bandwidth. For further improvement of resolution of VIBROSEIS correlograms it is necessary to apply special filtering methods. This is of particular interest when any kind of gain control is used to display weak events more clearly. With increasing amplification the sidelobes of the strong signals may reach the size of the weak events. In order to eliminate this effect, the amplitude characteristic of the VIBROSEIS signal is adjusted for optimum suppression of side‐lobes.
Pilot study of p62 DNA vaccine in dogs with mammary tumors (2014)

Our previous data demonstrated profound anti-tumor and anti-metastatic effects of p62 (sqstm1) DNA vaccine in rodents with various types of transplantable tumors. Testing anti-cancer medicine in dogs as an intermediary step of translational research program provides two major benefits. First, clinical data collected in target animals is required for FDA/USDA approval as a veterinary anti-cancer drug or vaccine. It is noteworthy that the veterinary community is in need of novel medicine for the prevention and treatment of canine and feline cancers. The second more important benefit of testing anti-cancer vaccines in dogs is that spontaneous tumors in dogs may provide invaluable information for human trials. Here, we evaluated the effect(s) of p62 DNA vaccine on mammary tumors of dogs. We found that p62 DNA vaccine administered i.m. decreased or stabilized growth of locally advanced lesions in absence of its overall toxic effects. The observed antitumor activity was associated with lymphocyte infiltration and tumor encapsulation via fibrotic reaction. This data justifies both human clinical trials and veterinary application of p62 DNA vaccine.
Interfacial aspects of the stability of polyglycerol ester covered bubbles against coalescence (2012)

Most liquid foams are not stable, with one destabilization process being coalescence. The current study aims at better understanding the coalescence of bubbles covered by the non-ionic surfactant polyglycerol ester (PGE) in dilute solutions. Large deformations of bubble surfaces are of importance in understanding coalescence as they can induce coalescence events. Furthermore, during coalescence and the subsequent shape relaxation large deformations are imposed on the surfaces. These large deformation experiments were carried out using interfacial shear and dilatational rheology. Furthermore isolated coalescence events of bubbles were observed. The largest fraction of the interfacial shear modulus was recovered within 1 minute of halting the large deformations, with the overall recovery happening on a timescale of hours. When mimicking coalescence by reducing the surface area, a short-term increase in the elastic modulus was observed in dilatational rheology. The remarkably slow, two-mode exponential shape relaxation recorded for sufficiently covered bubbles following their coalescence hints at important interfacial structuring phenomena. As a result of the low solubility of PGE, coalescence appears to help in achieving a certain stability level at short timescales via an increase in surface coverage and the growth of multi-layer domains. Finally, coalescence patterns in two-dimensional foams were investigated, which suggested that in the absence of prior coalescence, very long adsorption times (>12 hours) are required to reach significant stability. These experiments also revealed a remarkable stability of polyglycerol ester foams against Ostwald ripening.
Role of endogenous CYP450 metabolites of arachidonic acid in maintaining the glomerular protein permeability barrier (2007)

This study examined the metabolism of arachidonic acid (AA) by cytochrome P-450 enzymes in isolated glomeruli and the effects of selective inhibitors of the synthesis of 20-hydroxyeicosatetraenoic acid (20-HETE) and epoxyeicosatetraenoic acids (EETs) on glomerular permeability to albumin (P(alb)). Glomeruli avidly produced 20-HETE, EETs, dihydroxyeicosatetraenoic acids (diHETEs), and HETEs when incubated with exogenous AA. N-hydroxy-N'-(4-butyl-2-methylphenyl)formamidine (HET0016; 10 microM) selectively inhibited the formation of 20-HETE by 95% and increased P(alb) from 0.00 +/- 0.08 to 0.73 +/- 0.10 (n = 43 glomeruli, 4 rats). Addition of a 20-HETE mimetic, 20-hydroxyeicosa-5(Z),14(Z)-dienoic acid (20-5,14-HEDE; 1 microM) opposed the effects of HET0016 (10 microM) to increase P(alb) (0.21 +/- 0.10, n = 36 glomeruli, 4 rats). Preincubation of glomeruli with exogenous AA to increase basal production of 20-HETE had a similar effect. We also examined the effect of an epoxygenase inhibitor, N-methylsulfonyl-6-(2-propargyloxyphenyl)hexanamide (MSPPOH; 5 microM), on P(alb). MSPPOH (5 microM) significantly increased P(alb) but had no effect on the synthesis of EETs in glomeruli incubated with AA. However, MSPPOH (5 microM) selectively reduced epoxygenase activity by 50% in glomeruli incubated without added AA. Pretreatment with 8,9-EET (100 nM) attenuated the effects of MSPPOH (5 microM) on P(alb). These results indicate that glomeruli produce 20-HETE, EETs, diHETEs, and HETEs and that endogenously formed 20-HETE and EETs play an essential role in the maintenance of the glomerular permeability barrier to albumin.
Bone marrow transplantation for chronic myeloid leukemia: the use of histocompatible unrelated volunteer donors. (1990)

We treated 17 patients with chronic myeloid leukemia (CML) by bone marrow transplantation using marrow from human leukocyte antigen (HLA)-matched unrelated donors. Patients were conditioned with a combination of in vivo monoclonal antibodies, chemotherapy with daunorubicin (n = 7) or busulfan (n = 10) and cyclophosphamide, and both total body and total lymphoid irradiation. Donor marrow was depleted of T cells by incubation with monoclonal antibodies of the Campath series. Fourteen (88%) of 16 evaluable patients had sustained engraftment. Four (27%) of the 15 evaluable patients developed acute graft-versus-host disease (GVHD) of grade II or greater, and 4 of 12 evaluable patients developed chronic GVHD. Three patients developed hematological and two developed cytogenetic evidence of relapse. Eight patients (47%) survive at a median follow-up of 32 months (range 10-51 months), giving an actuarial survival of 44%. Five patients remain alive without evidence of hematological or cytogenetic relapse, giving an actuarial disease-free survival of 27%. Pneumonitis caused or contributed to death in six of the nine patients who died. We conclude that T-cell depletion can prevent the severest forms of GVHD but also increases the risk of relapse after transplant with unrelated donors, as it does with HLA-identical siblings. Nevertheless the use of matched unrelated donors should be considered for CML patients who lack HLA-identical siblings.
Unanswered Questions in the Management of Stage I-III Merkel Cell Carcinoma (2014)

Many unanswered questions remain about what constitutes appropriate guidelines for treatment of Merkel cell carcinoma (MCC). In this review, we address current uncertainty surrounding optimal management of MCC. These areas of uncertainty include early recognition features; clinical and histopathologic prognostic factors; optimum margins of excision of the primary tumor; indications for and value of surgical staging of the clinically negative regional nodes; optimum management of the patient with pathologically positive regional nodes; and indications for and value of radiation to the primary and regional nodes. Through identifying and elaborating on these areas of uncertainty, the authors hope to foster additional research and ultimately improve the evidence base for future iterations of the NCCN Clinical Practice Guidelines in Oncology in this rare but increasingly encountered cutaneous malignancy. The intent, however, is not to exhaustively identify all areas of controversy, but rather to highlight clinically relevant questions that further studies could address to improve the standard of care for MCC.
PROTEIN EXPRESSION DURING HEAT STRESS IN THERMO‐INTOLERANT AND THERMO‐TOLERANT DIATOMS (2000)

To better understand how diatoms are capable of responding to environmental stress, protein expression during heat treatment of a thermo‐intolerant ( Phaeodactylum tricornutum ) and thermo‐tolerant ( Chaetoceros muelleri ) diatom (Chrysophyta) was investigated. The stress response is a universal and conserved mechanism of cell survival to unfavorable conditions. Typically, a 10 to 15° C temperature elevation above cell growth optimal causes constitutively expressed proteins to decrease and heat shock proteins (HSPs) to increase. HSPs are categorized by molecular weight among five classes with each apparently specialized for a particular function that enhances cell survival. One‐dimensional SDS‐PAGE of diatoms subjected to heat treatment revealed that P. tricornutum exhibited a typical stress response, but C. muelleri did not exhibit a characteristic response even at a greatly elevated temperature (50° C). This result was confirmed by total soluble protein assays. Chaetoceros muelleri may contain higher basal levels of HSPs than P. tricornutum allowing C. muelleri to better tolerate elevated temperatures. Western blot analysis using pea HSP70 (70 kDa) antisera of heat‐treated P. tricornutum and C. muelleri validated the hypothesis that thermo‐tolerant cells contain higher levels of constitutively expressed HSPs. Two‐dimensional gel electrophoresis of heat‐treated cells indicate that the small HSPs (17–30 kDa) played a role in the stress response similar to that found in vascular plants. Ongoing work is focused on the manipulation of the stress response through over‐expression of key hsp genes.
Subtask 3.3 - Feasibility of Direct Coal Liquefaction in the Modern Economic Climate (2009)

Coal liquefaction provides an alternative to petroleum for the production of liquid hydrocarbon-based fuels. There are two main processes to liquefy coal: direct coal liquefaction (DCL) and indirect coal liquefaction (ICL). Because ICL has been demonstrated to a greater extent than DCL, ICL may be viewed as the lower-risk option when it comes to building a coal liquefaction facility. However, a closer look, based on conversion efficiencies and economics, is necessary to determine the optimal technology. This report summarizes historical DCL efforts in the United States, describes the technical challenges facing DCL, overviews Shenhua's current DCL project in China, provides a DCL conceptual cost estimate based on a literature review, and compares the carbon dioxide emissions from a DCL facility to those from an ICL facility.
A Complete Characterization of Torque - Maximization for Permanent Magnet Non-Salient (2001)

This paper considers the problem of maximizing the torque of permanent magnet non-salient synchronous motors in the presence of voltage and current constraints. Formulas are given that enable a drive to extract the maxi- mum torque available'from a motor in real-time. Both the motoring and braking modes are considered, and it is shown that the well-known field-weakening formula cannot be used with some motors. An example is discussed to illustrate the contributions of the paper.
Cell death or survival: The complex choice of the Retinoblastoma tumor suppressor protein (2010)

Comment on: Milet C, et al. Cell Cycle 2010; 9(1): In press