gebhart/patrepeval huggingface dataset:
Abstract no.: 1 Statins and oxysterol‐induced vascular smooth muscle cell death (2006)

Objective The strength of the fibrous cap of an atherosclerotic plaque is maintained by smooth muscle cells (SMCs). 7‐Ketocholesterol (7‐KC), and other oxysterols formed inside plaques, are known to induce SMC death, thereby increasing the risk of rupture and myocardial infarction (MI). Statins are known to protect patients from MI, but paradoxically they induce apoptosis in vascular SMCs as well. The aim of this study was to investigate the cell death effects of statins in 7‐KC‐treated SMCs. Methods Rabbit aorta SMCs (50 000; passage 2–6) were seeded in 24 well plates in HAM F10 with 10% foetal bovine serum (FBS). The next day, they were exposed to 25 μ M 7‐KC and 10 −8 –10 −4 M of fluvastatin (fluva), simvastatin (simva) or pravastatin (prava) in the presence of 2% FBS. Uptake of neutral red (0.01%, added 16 h later) was measured for 2 h as viability index. Results SMC viability decreased from 100% to 55 ± 3% ( n = 28) upon 18 h exposure to 25 μ M 7‐KC. High concentrations of fluva (≥ 10 μ M ) or simva (≥ 1 μ M ) also induced a concentration‐dependent loss of SMC viability; prava was always without effect. Interestingly, fluva and simva partly reversed the viability loss evoked by 7‐KC. Similar effects were seen when mitochondrial function was assessed using the succinate dehydrogenase substrate MTT. Fluva and simva alone were without effect, but they attenuated the mitochondrial dysfunction induced by 7‐KC. In contrast, both statins and 7‐KC enhanced the conversion of the caspase substrate DEVD‐R110 by SMC monolayers. Conclusions The results confirm that 7‐KC and high concentrations of lipophilic statins induce SMC death and activate caspases. Yet, in 7‐KC treated SMCs statins paradoxically attenuated viability loss and mitochondrial dysfunction. This clearly illustrates that drug effects seen in normal SMCs are not necessarily predictive of their action in an atherosclerotic setting.
Validation of miR-31-3p Expression to Predict Cetuximab Efficacy When Used as First-Line Treatment in RAS Wild-Type Metastatic Colorectal Cancer (2018)

MiR-31-3p expression level was validated as a predictive biomarker of cetuximab therapy efficacy for patients with <i>RAS</i> WT mCRC.
Performance of a one-way ranging method for WBAN healthcare services (2009)

Localization is an important factor to enhance availability of healthcare monitoring systems for the patient and asset tracking. This paper provides an efficient ranging measurement technique of OWR method based on the impulse radio UWB for the WBAN healthcare services. When fixed reference nodes broadcast the ranging messages in a network, the mobile nodes measure the time of arrived messages and retrieve the time information written by the reference nodes. For the performance evaluation, the ranging and positioning error are investigated using the proposed method.
Submicron patterning of thin cobalt films for magnetic storage (1994)

We are investigating the feasibility of a recording medium in which each bit of information is stored in a single-domain magnetic particle. To this end we have developed a procedure for high-resolution patterning of magnetic recording films using direct write electron-beam lithography and a multistep sputter etching process. We have used this procedure to define small islands of polycrystalline magnetic thin film with feature sizes down to 0.1 μm. The patterning process is suitable for many different kinds of magnetic films, including single-crystal epitaxially grown films, and is designed to minimize physical and chemical damage to the magnetic material being patterned. Both atomic force microscopy and x-ray photoemission spectroscopy have been used to establish that the magnetic islands patterned using this process are physically isolated from each other.
<title>Target ranging using passive sensing approaches</title> (1995)

An integrated approach to extract depth, efficiently and accurately, from a sequence of images is presented in this paper. The method combines the ability of the stereo processing to acquire highly accurate depth measurements and the efficiency of the spatial and temporal gradient analysis. As a result of this integration, depth measurements of high quality are obtained at speed approximately ten-times higher than that of the stereo processing. Without any a priori information of the locations of the points in the scene, the correspondence problem in the stereo processing is computationally expensive. In our approach, we use the spatial and temporal gradient analysis, which has been shown to provide depth with high efficiency but limited accuracy, to guide the matching process of stereo. Extensive experiments on real- scenes have shown the ability to acquire depth with mean error of less than 3 percent.
Paternal physical and sedentary activities in relation to semen quality and reproductive outcomes among couples from a fertility center (2014)

The authors are supported by NIH grants R01-ES009718, ES000002, P30-DK046200, T32-DK007703-16 and ES022955 T32-HD060454. None of the authors has any conflicts of interest to declare.
Elimination of bottom-pinching effect in environmentally stable chemically amplified resists (1998)

Chemically amplified deep UV photoresist is well known with its sensitivity towards base contaminants either from track and stepper ambience or from substrate. The former gives 'T- top' formation whereas the latter leads to 'footing' in line pattern. This sensitivity originates from the chemically amplification nature that uses photoacid to catalyze the deprotection of resin. To overcome environmental unstability, a variety of chemically stable resists have been formulated. However, during evaluation of some of these new deep UV photoresist, 'bottom pinching' (BP) effect was observed for photoresist on top of organic bottom anti-reflection coating (BARC). BP effect is the slimming of photoresist line immediately above the substrate, which shows the photoresist actually dissolutes at a higher rate near the substrate. This might be caused by higher concentration of acid in the photoresist near the substrate. It is believed that the excess amount of acid diffuses out from the BARC layer. Thus, the softbake of BARC and photoresist, the post-exposure bake of photoresist are to be optimized for the 'bottom pinching' effect.
NKG2D Ligands in Tumor Immunity: Two Sides of a Coin (2015)

The activating/co-stimulatory receptor NKG2D (natural-killer group 2, member D) is expressed on the surface of all human NK, NKT, CD8(+) T, and subsets of γδ(+) T cells. The significance of NKG2D function in tumor immunity has been well demonstrated in experimental animal models. However, the role of human NKG2D ligands in regulating tumor immunity and cancer prognosis had been controversial in the literature. In this review, we summarize the latest advancement, discuss the controversies, and present evidence that membrane-bound and soluble NKG2D ligands oppositely regulate tumor immunity. We also discuss new perspectives of targeting NKG2D ligands for cancer immunotherapy.
Eukaryotic Regulatory Element Conservation Analysis and Identification Using Comparative Genomics (2004)

Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from evolutionary constraints. We systematically analyzed known human and Saccharomyces cerevisiae regulatory elements and discovered that human regulatory elements are more conserved between human and mouse than are background sequences. Although S. cerevisiae regulatory elements do not appear to be more conserved by comparison of S. cerevisiae to Schizosaccharomyces pombe, they are more conserved when compared with multiple other yeast genomes (Saccharomyces paradoxus, Saccharomyces mikatae, and Saccharomyces bayanus). Based on these analyses, we developed a sequence-motif-finding algorithm called CompareProspector, which extends Gibbs sampling by biasing the search in regions conserved across species. Using human-mouse comparison, CompareProspector identified known motifs for transcription factors Mef2, Myf, Srf, and Sp1 from a set of human-muscle-specific genes. It also discovered the NFAT motif from genes up-regulated by CD28 stimulation in T-cells, which implies the direct involvement of NFAT in mediating the CD28 stimulatory signal. Using Caenorhabditis elegans-Caenorhabditis briggsae comparison, CompareProspector found the PHA-4 motif and the UNC-86 motif. CompareProspector outperformed many other computational motif-finding programs, demonstrating the power of comparative genomics-based biased sampling in eukaryotic regulatory element identification.
Accelerated development of arthritis in mice lacking endothelial selectins (2005)

The selectins, along with very late antigen-4 and CD44, have been implicated in mediating leukocyte rolling interactions that lead to joint recruitment and inflammation during the pathogenesis of rheumatoid arthritis. Previously, we showed that P-selectin deficiency in mice resulted in accelerated onset of joint inflammation in the murine collagen-immunized arthritis model. Here, we report that mice deficient either in E-selectin or in E-selectin and P-selectin (E/P-selectin mutant) also exhibit accelerated development of arthritis compared with wild type mice in the CIA model, suggesting that these adhesion molecules perform overlapping functions in regulating joint disease. Analyses of cytokine and chemokine expression in joint tissue from E/P-selectin mutant mice before the onset of joint swelling revealed significantly higher joint levels of macrophage inflammatory protein-1alpha and IL-1beta compared to wild-type mice. IL-1beta remained significantly increased in E/P-selectin mutant joint tissue during the early and chronic phases of arthritis. Overall, these data illustrate the novel finding that E-selectin and P-selectin expression can significantly influence cytokine and chemokine production in joint tissue, and suggest that these adhesion molecules play important regulatory roles in the development of arthritis in E/P-selectin mutant mice.
Risk factors for SARS-CoV-2 seroprevalence following the first pandemic wave in UK healthcare workers in a large NHS Foundation Trust (2022)

<ns3:p> <ns3:bold>Background:</ns3:bold> We aimed to measure SARS-CoV-2 seroprevalence in a cohort of healthcare workers (HCWs) during the first UK wave of the COVID-19 pandemic, explore risk factors associated with infection, and investigate the impact of antibody titres on assay sensitivity. </ns3:p> <ns3:p/> <ns3:p> <ns3:bold>Methods:</ns3:bold> HCWs at Sheffield Teaching Hospitals NHS Foundation Trust were prospectively enrolled and sampled at two time points. We developed an in-house ELISA for testing participant serum for SARS-CoV-2 IgG and IgA reactivity against Spike and Nucleoprotein. Data were analysed using three statistical models: a seroprevalence model, an antibody kinetics model, and a heterogeneous sensitivity model. </ns3:p> <ns3:p/> <ns3:p> <ns3:bold>Results:</ns3:bold> Our in-house assay had a sensitivity of 99·47% and specificity of 99·56%. We found that 24·4% (n=311/1275) of HCWs were seropositive as of 12th June 2020. Of these, 39·2% (n=122/311) were asymptomatic. The highest adjusted seroprevalence was measured in HCWs on the Acute Medical Unit (41·1%, 95% CrI 30·0–52·9) and in Physiotherapists and Occupational Therapists (39·2%, 95% CrI 24·4–56·5). Older age groups showed overall higher median antibody titres. Further modelling suggests that, for a serological assay with an overall sensitivity of 80%, antibody titres may be markedly affected by differences in age, with sensitivity estimates of 89% in those over 60 years but 61% in those ≤30 years. </ns3:p> <ns3:p/> <ns3:p> <ns3:bold>Conclusions: </ns3:bold> HCWs in acute medical units and those working closely with COVID-19 patients were at highest risk of infection, though whether these are infections acquired from patients or other staff is unknown. Current serological assays may underestimate seroprevalence in younger age groups if validated using sera from older and/or more severe COVID-19 cases. </ns3:p>
DNA Damage-mediated Apoptosis Induced by Selenium Compounds (2003)

Selenium (Se) compounds, which are the most extensively studied cancer chemopreventive agents, induce apoptotic death of tumor cells. In the current study, we show that selenite-induced apoptosis involves DNA damage. We showed that selenite-induced apoptosis as evidenced by cleavage of poly(ADP-ribose) polymerase was reduced in NIH 3T3 cells treated with ATM small interfering RNA, suggesting the involvement of the DNA damage regulator ATM. Consistent with ATM/ATR involvement, selenite was also shown to stimulate Ser-139 phosphorylation of the ATM/ATR substrate H2AX. Selenite-induced apoptosis was shown to involve DNA topoisomerase II (Top II) as selenite-induced apoptosis was reduced in Top II-deficient HL-60/MX2 cells and in HL-60 cells co-treated with the Top II catalytic inhibitor ICRF-193. Using purified human recombinant Top II, selenite was shown to induce reversible Top II cleavage complexes in vitro. In the aggregate, these results suggest that selenite-induced apoptosis, which involves ATM/ATR and Top II, is likely to be because of DNA damage.
Endogenous N-terminal trimming of PrPSc occurs at a fairly variable level depending on the infected host cell (2008)

International audience
1C14 Development of an auto-positioning spreader for Mobile Harbor (2010)

The purpose of this study is to develop a spreader for loading and unloading a container in unstable environments of the open sea. In order to overcome the swing of a spreader due to waves and wind, an auto positioning spreader was proposed with three degrees of freedom (DOF). By constraining a spreader on the top of a container, DOFs for the auto positioning were reduced from six to three in three dimensional spaces and therefore the auto positioning spreader was easily implemented. Virtual force algorithm employing six proximity sensors was proposed to control the remaining three DOFs of the spreader system. A RecurDyn dynamic model and a one to twenty scale model were developed and the effectiveness of the new spreader system introduced in this paper was verified in both numerical simulation and downscale model test.
69-04: High resolution mapping with Rhythmia system for ventricular tachycardia ablation (2016)

The Rhtyhmia mapping system (Boston Scientific) allows multielectrode mapping through an minibasket catheter, containing 64 electrodes, by automatical acquisition of electrograms. Methods and results: 45 patients (43 male, 62.7 ± 13.8 years) underwent ventricular tachycardia (VT) ablation in 2 centers. 30 patients had Ischemic Cardiomyopathy (ICM), 12 were affected dy Idiopathic Dilated Cardiomyopathy (IDCM), 1 by Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC), 1 by Congenital Heart disease, 1 by Myocarditis. 34 patients had an already implanted ICD and 9 patients had a CRT-D. Left ventricular ejection fraction was 39.7 ± 13.1%. In 15 patients CT scanning was used before the procedure and 1 patients underwent both MRI and CT. In 30 (66.6%) patients the index ablation was the first VT ablation; the remaining patients had 1.7 ± 1.0 previous VT ablations. Hemodynamic support with ECMO was used during the procedure in 3 patients. Left ventricular endocardial mapping was performed acquiring 16439.4± 10406.7 (range 3127 – 36616) electrograms among 1894.8 ± 1234.1 beats analyzed; 173.4± 63.0 ml of left ventricular volume were mapped in 46.8 ± 20.8 minutes. Endocardial mapping was performed by transeptal approach in 44 (97.7%) patients and by transaortic approach in one patient. Eight (17.7%) patients underwent also epicardial mapping (4 IDCM, 3 ischemic, 1 ARVC). Left ventricular epicardial mapping was performed acquiring 19476.8± 1443.7 (range 12108 – 66374) electrograms among 1640.0 ± 1019.5 beats analyzed; 168.6± 72.8 ml of epicardial volume was mapped in 41.4 ± 21.3 minutes. More electrograms were acquired in the epicardium (17.3 ± 4.4) for each beat compared to the endocardial mapping (10.7 ± 5.9, p = 0.03); mapping was faster in the epicardium (582.0 ± 260.0 points acquired/minute of mapping) compared to the endocardium (203.4 ± 52.5, p = 0.03). After the ablation a VT was still inducible in 4 patients; 4 patients had at least 1 VT episode during 6.1 ± 2.3 months of follow-up. Conclusions: Rhythmia system allows and high density mapping of both the endocardial and the epicardial surfaces of the left ventricle. Mapping is faster in the epicardium than in the endocardium.
In situ analysis of perfluoro compounds in semiconductor process exhaust: Use of Li+ ion-attachment mass spectrometry (2001)

Ion-attachment mass spectrometry is capable of accurate and in situ analysis of multicomponent gases that may even include unknown components. We developed a compact apparatus that uses this method and examined its performance for perfluoro compounds, a class of greenhouse gases, using typical standard gases, and subsequently applied the method to the in situ analysis of exhaust gases from a dry-etching machine, where c-C4F8/O2/Ar plasma is generated. Perfluoro compounds of low concentration can be detected as quasimolecules without any fragmentation. In the exhaust gases, many components that are not considered in the current measurement protocol [J. Meyers, D. Green, P. Maroulis, and W. Reagen, Equipment Environmental Characterization Guidelines, Rev. 3.0 (INTEL, 1999)] are measured, as well as components already reported.
Orbital space stations with artificial gravity (1968)

Structural design and living-volume requirements of orbital space stations with artificial gravity
Tuning biphenyl dioxygenase for extended substrate specificity (1999)

Highly substituted polychlorinated biphenyls (PCBs) are known to be very resistant to aerobic biodegradation, particularly the initial attack by biphenyl dioxygenase. Functional evolution of the substrate specificity of biphenyl dioxygenase was demonstrated by DNA shuffling and staggered extension process (StEP) of the bphA gene coding for the large subunit of biphenyl dioxygenase. Several variants with an extended substrate range for PCBs were selected. In contrast to the parental biphenyl dioxygenases from Burkholderia cepacia LB400 and Pseudomonas pseudoalcaligenes KF707, which preferentially recognize either ortho- (LB400) or para- (KF707) substituted PCBs, several variants degraded both congeners to about the same extent. These variants also exhibited superior degradation capabilities toward several tetra- and pentachlorinated PCBs as well as commercial PCB mixtures, such as Aroclor 1242 or Aroclor 1254. Sequence analysis confirmed that most variants contained at least four to six template switches. All desired variants contained the Thr335Ala and Phe336Ile substitutions confirming the importance of this critical region in substrate specificity. These results suggest that the block-exchange nature of gene shuffling between a diverse class of dioxygenases may be the most useful approach for breeding novel dioxygenases for PCB degradation in the desired direction.
Circulating anti-filamin C autoantibody as a potential serum biomarker for low-grade gliomas (2014)

The present results suggest that serum anti-FLNC autoantibody can be a potential serum biomarker for early diagnosis of low-grade gliomas while it needs a large-scale clinical study.
Microscopic-Scale Examination of the Black and Orange–Yellow Colours of Architectural Glazes from Aššur, Khorsabad and Babylon in Ancient Mesopotamia (2022)

Three major corpora of architectural glazed bricks from Ancient Mesopotamia dating to the Neo-Assyrian (Aššur and Khorsabad sites) and the Neo-Babylonian (Babylon site) Periods have been submitted to an in-depth comparative study of the orange–yellow and black glazes. Distinct hues in the orange–yellow range were observed according to the archaeological site. They appear to have been well mastered by the glassmakers, consisting in the ex situ preparation of the antique lead antimonate pigment and its mixing with transparent soda-lime glass frit or with the glass-forming components. The intentional addition of hematite or of Cu2+ colouring ions in a controlled amount is suggested in two cases. SEM-EDX and Raman analysis of the lead antimonate pigments have pointed out different chemical substitutions in their pyrochlore structure, mainly Fe3+ in the Sb5+ site and Ca2+ in the Pb2+ site, the proportion of which being correlated to the pigment shade (from pale yellow to orange–red). Part of these substitutions arises from the chemical reaction of the pigment with the hematite and glass melt during firing. Regarding the black glazes, an unexpected colouring technique involving copper sulphide nanoparticles together with the chromophore Fe3+-S2− is highlighted for Khorsabad (8th century BC) and for Babylon (6th century BC). For Aššur blacks, the study reveals a change in their colouring technique between the 9th and 8th centuries BC, from a colouration with Mn oxides to an enigmatic one that could also have involved copper sulphide nanoparticles.
A novel optical biosensor for the early diagnosis of sepsis and severe Covid-19: the PROUD study (2020)

The studied OB seems valuable for the discrimination of infection severity.
PMCA4 inhibition does not affect cardiac remodelling following myocardial infarction, but may reduce susceptibility to arrhythmia (2021)

Ischaemic heart disease is the world's leading cause of mortality. Survival rates from acute myocardial infarction (MI) have improved in recent years; however, this has led to an increase in the prevalence of heart failure (HF) due to chronic remodelling of the infarcted myocardium, for which treatment options remain poor. We have previously shown that inhibition of isoform 4 of the plasma membrane calcium ATPase (PMCA4) prevents chronic remodelling and HF development during pressure overload, through fibroblast mediated Wnt signalling modulation. Given that Wnt signalling also plays a prominent role during remodelling of the infarcted heart, this study investigated the effect of genetic and functional loss of PMCA4 on cardiac outcomes following MI. Neither genetic deletion nor pharmacological inhibition of PMCA4 affected chronic remodelling of the post-MI myocardium. This was the case when PMCA4 was deleted globally, or specifically from cardiomyocytes or fibroblasts. PMCA4-ablated hearts were however less prone to acute arrhythmic events, which may offer a slight survival benefit. Overall, this study demonstrates that PMCA4 inhibition does not affect chronic outcomes following MI.
Phase Transitions of Hexadecane in Poly(alkyl methacrylate) Core−Shell Microcapsules (2010)

Microcapsules containing subfemtoliter volumes of n-hexadecane (HD) within a 4-40 nm thick shell of poly(alkyl methacrylates) were prepared. The size of the HD drop was varied between 50 and 140 nm. The alkyl substituents on the methacrylate monomer were varied to alter the surface tension between the HD and the polymer shell in order to investigate the effects of surface tension on the freezing point of the HD. The size dependence of the supercooling as predicted by the G-T equation was not observed in our systems. An effect on the magnitude of supercooling with variation in the side chains was observed, where freezing the HD in capsules with bulkier side chains requires a greater magnitude of supercooling. This is in agreement with the increased hydrophobic character of the polymers and also correlates with the decrease in glass transition temperature of the polymer. We also observed aging of the capsules, which could be accelerated by heating.