gebhart/patrepeval huggingface dataset:
HNF4α as a Marker for Invasive Mucinous Adenocarcinoma of the Lung (2012)

A new lung adenocarcinoma classification was recently proposed by IASLC/ATS/ERS. In this classification, invasive mucinous adenocarcinoma (IMC) is placed in a new category because of its unique radiologic, morphologic, and genetic characteristics. Minimal cytologic atypia characterizes this tumor; thus, it is occasionally difficult to make a diagnosis with a biopsy specimen. We used immunohistochemistry to examine HNF4α expression in a tissue microarray consisting of 278 lung adenocarcinoma specimens. In addition, we analyzed the clinicopathologic features, including EGFR, KRAS, and ALK mutation status. HNF4α expression was detected in 33 of the 37 surgically resected IMCs. The tumor cells were uniformly labeled with the molecule in all of the corresponding biopsy specimens, whereas the normal cells were not. Although HNF4α was also expressed in other lung adenocarcinoma subtypes, those with HNF4α expression shared IMC features, including negative TTF-1 expression (P<0.001), positive CDX2 expression (P<0.001), positive KRAS mutation status (P=0.001), and negative EGFR mutation status (P<0.001). Although some ALK-positive adenocarcinomas showed IMC morphology, the tumors were negative for HNF4α, suggesting that they belonged to a different group of tumors. We found that HNF4α labeled all of the IMC tumors except the ALK-positive adenocarcinomas. Thus, HNF4α positivity could serve as a useful marker for overcoming the diagnostic difficulties caused by minimal nuclear atypia and sparse tumor cells in small biopsy samples. Because other adenocarcinoma subtypes with HNF4α expression share clinicopathologic features with IMC, these adenocarcinomas, especially the columnar cell type of acinar-predominant adenocarcinoma, might constitute a biological spectrum of IMC.
Modeling Heat and Mass Transfer Limitation Processes of Gas Hydrate Formation Under Slug Flow (2019)

International audience
Hardware Trojan for security LSI (2013)

A hardware Trojan has become a serious problem of consumer electronics in recent years. The present study proposes a new hardware Trojan in a countermeasure circuit and evaluates the weakness of the countermeasure circuit through simulation experiments.
Role of microtubules in ischemic preconditioning against myocardial infarction (2004)

Microtubules play a crucial role in the development of anti-infarct tolerance by PC as a mechanism supporting translocation of activated PKC.
Nondestructive inspection using continuous ultrasonic wave generation (2023)

Methods and apparatus are disclosed for analyzing structures by applying a continuous ultrasonic excitation and measuring steady state response of the structures using laser Doppler vibrometery, or other techniques. In one example, a method comprises applying a continuous signal having one or more periodic tones to the structure, generating measurements of wave response to the signal at each of a plurality of inspection points of the structure, and, for each of the periodic tones, estimating wavenumbers for a number of the inspection points of the structure based on the wave response measurements and the frequency of the periodic tones. The estimated wavenumbers can be used to determine properties of the structure, including defects, damage, or variation in thickness.
Longitudinal spin fluctuations in bcc and liquid Fe at high temperature and pressure calculated with a supercell approach (2020)

Investigating magnetic materials at realistic conditions with first-principles methods is a challenging task due to the interplay of vibrational and magnetic degrees of freedom. The most difficult contribution to include in simulations is represented by the longitudinal magnetic degrees of freedom [longitudinal spin fluctuation (LSF)] due to their inherent many-body nature; nonetheless, schemes that enable to take into account this effect on a semiclassical level have been proposed and employed in the investigation of magnetic systems. However, assessment of the effect of vibrations on LSF is lacking in the literature. For this reason, in this work we develop a supercell approach within the framework of constrained density functional theory to calculate self-consistently the size of local-environment-dependent magnetic moments in the paramagnetic, high-temperature state in the presence of lattice vibrations and for liquid Fe in different conditions. First, we consider the case of bcc Fe at the Curie temperature and ambient pressure. Then, we perform a similar analysis on bcc Fe at Earth's inner-core conditions, and we find that LSFs stabilize nonzero moments which affect atomic forces and the electronic density of states of the system. Finally, we employ the present scheme on liquid Fe at the melting point at ambient pressure and at Earth's outer-core conditions ($p\ensuremath{\approx}200$ GPa, $T\ensuremath{\approx}6000$ K). In both cases, we obtain local magnetic moments of sizes comparable to the solid-state counterparts.
Modifications in the synthesis of membrane‐associated chondroitin sulfate proteoglycans in hemopoietic progenitor cells are accompanied by alterations in their adhesive properties (1994)

In vitro studies in our laboratory have indicated that murine hemopoietic progenitor cell (HPC) lines, irrespective of their differentiation stage, synthesize and accumulate in the cell membrane a unique species of chondroitin sulfate proteoglycan (CS-PG). It has been postulated that CS-PG participates in HPC adhesion to pericellular stromal fibronectin by interacting with its heparin-promoting binding region. To further support this contention, we first attempted to modify CS-PG synthesis in HPC by the use of chlorate and p-nitrophenyl beta-D-xyloside, which inhibit sulfation and glycosaminoglycan (GAG) addition in proteoglycans, respectively. We then studied the effect that these modifications may have in the adhesive capacity of HPC to interact with fibronectin and its cell- and heparin-promoting binding chymotryptic fragments. Treatment with chlorate which resulted in a decreased sulfation of membrane-associated 35 S-labeled CS-PG, as judged by ion exchange chromatography, did not affect HPC adhesion to fibronectin or its fragments. However, beta-xyloside treatment which reduces the abundance of membrane-associated CS-PG, as evidenced by molecular sieve chromatography, produced a major and specific decrease in HPC adhesion to the heparin-promoting binding fragment of fibronectin. These results indicate that CS-PG are involved in HPC interaction with fibronectin, in a mode that seems to be dependent on the differentiation stage of HPC.
Inhibition of CDP-DG:Inositol Transferase by Inostamycin1 (1992)

Inostamycin, a novel microbial secondary metabolite, inhibited [3H]inositol and 32P1 incorporation into phosphatidylinositol (PtdIns) induced by epidermal growth factor (EGF) in cultured A431 cells, the IC50 being 0.5 micrograms/ml, without inhibiting macromolecular synthesis. The drug inhibited cellular inositol phosphate formation only when it was added at the same time as labeled inositol. It was found to inhibit in vitro CDP-DG:inositol transferase activity of the A431 cell membrane, the IC50 being about 0.02 micrograms/ml. It did not inhibit tyrosine kinase, PtdIns phospholipase C, or PtdIns kinase. Therefore, inhibition of PtdIns turnover by inostamycin must be due to the inhibition of CDP-DG:inositol transferase. Thus, inostamycin is a novel inhibitor of CDP-DG:inositol transferase.
Preparation and characterization of high‐performance dehydrating pervaporation alginate membranes (1998)

In a previous work, sodium alginate dense membranes demonstrated a good combination of selectivity and permeation flux for dehydrating organic solvents by pervaporation. In this article, the pervaporation performances of alginate composite membranes has been investigated to find out the best condition of membrane formation and the optimum operating conditions. Some ultrafiltration membranes made of poly-(vinylidene fluoride), polyacrylonitrile, and hydrolyzed polyacrylonitrile—either commercially available or prepared in our laboratories—were used as supports for the composite membranes. Sodium alginate dense membranes, modified through ion exchange of sodium with multivalent metal ions (such as Al3+, Cr3+, Fe3+, and Mg2+) have also been prepared, and their permselectivities have been tested for the water–ethanol mixture. An interesting stability of the modified membranes in long-term operation is expected. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 68: 959–968, 1998
Data from Evaluation of Trends and Prognosis Over Time in Patients with AML Relapsing After Allogeneic Hematopoietic Cell Transplant Reveals Improved Survival for Young Patients in Recent Years (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Relapsed acute myeloid leukemia (AML) post allogeneic hematopoietic cell transplantation (allo-HCT) has a dismal prognosis.&lt;/p&gt;Experimental Design:&lt;p&gt;To assess prognosis of patients with recurrent AML post allo-HCT over time, we analyzed European Society for Blood and Marrow Transplantation registry data of 8,162 adult patients with AML who relapsed between 2000 and 2018 after allo-HCT performed in first complete remission from matched sibling, unrelated, or haploidentical donors.&lt;/p&gt;Results:&lt;p&gt;The 2-year overall survival (OS) rate from relapse was 17%. For 3,630 patients, &lt;50 years of age, the 2-year OS continuously increased from 16% between 2000 and 2004 to 18% for 2005–2009, to 21% for 2010–2014, and to 26% for 2015–2018 (&lt;i&gt;P&lt;/i&gt; = 0.001). Improvement over time was noted both after relapse within and beyond 6 months from allo-HCT. On multivariate analysis among patients &lt;50 years of age, OS was positively affected by a later year of relapse (baseline: 2000–2004; HR, 0.82; &lt;i&gt;P&lt;/i&gt; &lt; 0.02 for 2010–2014 and HR, 0.72; &lt;i&gt;P&lt;/i&gt; = 0.0002 for 2015–2018), good performance status, favorable cytogenetics, and longer time from transplant to relapse, but negatively affected by increasing age. In contrast, among 4,532 patients, &gt;50 years of age, the year of relapse had no influence on OS (16% for 2000–2004 and 14% for 2015–2018; &lt;i&gt;P&lt;/i&gt; = 0.56). Regarding treatment, encouraging results were observed after second allo-HCT, which was performed within 2 years after relapse in 17% of the entire cohort, resulting in a 2-year OS of 30.7%.&lt;/p&gt;Conclusions:&lt;p&gt;Outcome after posttransplant relapse among younger patients has improved significantly in recent years, likely reflecting, among other factors, the efficacy of posttransplant salvage including second allo-HCT.&lt;/p&gt;&lt;/div&gt;
Chenodeoxycholic Acid-mediated Activation of the Farnesoid X Receptor Negatively Regulates Hydroxysteroid Sulfotransferase (2006)

Hydroxysteroid sulfotransferase catalyzing bile acid sulfation plays an essential role in protection against lithocholic acid (LCA)-induced liver toxicity. Hepatic levels of Sult2a is up to 8-fold higher in farnesoid X receptor-null mice than in the wild-type mice. Thus, the influence of FXR ligand (chenodeoxycholic acid (CDCA) and LCA) feeding on hepatic Sult2a expression was examined in FXR-null and wild-type mice. Hepatic Sult2a protein content was elevated in FXR-null and wild-type mice fed a LCA (1% and 0.5%) diet. Treatment with 0.5% CDCA diet decreased hepatic Sult2a to 20% of the control in wild-type mice, but increased the content in FXR-null mice. Liver Sult2a1 (St2a4) mRNA levels were reduced to 26% in wild-type mice after feeding of a CDCA diet, while no decrease was observed on Sult2a1 mRNA levels in FXR-null mice after CDCA feeding. A significant inverse relationship (r(2)=0.523) was found between hepatic Sult2a protein content and small heterodimer partner (SHP) mRNA level. PCN-mediated increase in Sult2a protein levels were attenuated by CDCA feeding in wild-type mice, but not in FXR-null mice. Human SULT2A1 protein and mRNA levels were decreased in HepG2 cells treated with the FXR agonists, CDCA or GW4064 in dose-dependent manners, although SHP mRNA levels were increased. These results suggest that SULT2A is negatively regulated through CDCA-mediated FXR activation in mice and humans.
Transaction of heterologous promoters by HIV–1 tat (1991)

To determine whether HIV-1 tat can transactivate a heterologous promoter lacking HIV sequences other than the TAR element, TAR was placed downstream of the chicken beta-actin promoter. Tat increased expression directed by the actin-TAR promoter to a degree equal to tat induction of the HIV-1 LTR. Optimal transactivation was observed when TAR was positioned downstream of the actin promoter such that the expected cap site of transcripts from this promoter would be the same as in transcripts directed by the HIV-1 LTR. Tat was able to transactivate, though to a lesser extent, a promoter consisting solely of a TATA element fused to TAR. Thus, tat induction does not require HIV-1 LTR promoter sequences other than TAR. Tat, when fused to the DNA binding domain of BPV-1 E2, was able to transactivate a truncated SV40 promoter containing upstream E2 binding sites, indicating that tat may be capable of transactivation when directed by a DNA binding protein to an upstream site in a heterologous promoter lacking all HIV sequences. Substitution of Ala for Lys at position 41 of tat in the tat-E2 fusion, a mutation which dramatically decreases tat transactivation of the HIV-1 LTR, eliminated this transactivation.
A Decentralized Cooperative Control Scheme With Obstacle Avoidance for a Team of Mobile Robots (2013)

The problem of formation control of a team of mobile robots based on the virtual and behavioral structures is considered in this paper. In the virtual structure, each mobile robot is modeled by an electric charge. The mobile robots move toward a circle, and due to repulsive forces between the identical charges, regular polygon formations of the mobile robots will be realized. For swarm formation, a virtual mobile robot is located at the center of the circle, and other mobile robots follow it. In the introduced approach, each mobile robot finds its position in the formation autonomously, and the formation can change automatically in the case of change in the number of the mobile robots. This paper also proposes a technique for avoiding obstacles based on the behavioral structure. In this technique, when a mobile robot gets close to an obstacle, while moving toward its target, a rotational potential field is applied to lead the mobile robot to avoid the obstacle, without locating in local minimum positions.
Implant for Augmentation of Cerebral Blood Flow Trial 1: A Pilot Study Evaluating the Safety and Effectiveness of the Ischaemic Stroke System for Treatment of Acute Ischaemic Stroke (2009)

The implant for augmentation of cerebral blood flow trial-1 will determine the safety and tolerability of the ischaemic stroke system 500 in acute ischaemic stroke as reflected by the incidence of adverse events.
Genomic analysis distinguishes phases of early development of the mouse atrio-ventricular canal (2009)

Valve formation during embryonic heart development involves a complex interplay of regional specification, cell transformations, and remodeling events. While many studies have addressed the role of specific genes during this process, a global understanding of the genetic basis for the regional specification and development of the heart valves is incomplete. We have undertaken genome-wide transcriptional profiling of the developing heart valves in the mouse. Four Serial Analysis of Gene Expression libraries were generated and analyzed from the mouse atrio-ventricular canal (AVC) at embryonic days 9.5-12.5, covering the stages from initiation of endothelial to mesenchymal transition (EMT) through to the beginning of endocardial cushion remodeling. We identified 14 distinct temporal patterns of gene expression during AVC development. These were associated with specific functions and signaling pathway members. We defined the temporal distribution of mesenchyme genes during the EMT process and of specific Notch and transforming growth factor-beta targets. This work provides the first comprehensive temporal dataset during the formation of heart valves. These results identify molecular signatures that distinguish different phases of early heart valve formation allowing gene expression and function to be further investigated.
Micromechanics of rock friction 2: Quantitative modeling of initial friction with contact theory (1992)

A constitutive model is developed which predicts the mechanical properties of two rough surfaces in contact under shear load during the early stages of the development of frictional sliding. The model includes the development of slip at the contacts, a phenomenon which begins immediately upon shear loading. Upon initial application of the normal load, the model predicts that the joint consists of a finite number of contacts which are subject to a wide variety of local normal loads. As the shear load is increased, sliding of the contacts develops progressively, with the contacts under low local normal load sliding first. This gradual development of sliding is the cause of the experimentally observed nonlinear force‐displacement relation for deformation of the joint in shear. Two asperity scale strength laws are examined, one based on the adhesion theory of friction and the other based on observations of frictional strength for brittle elastic solids. The model is tested with experiments on lapped surfaces of Westerly Granite with a variety of surface roughnesses and under a range of normal loads from 10 to 35 MPa. Geometric parameters used in the model are constrained by direct measurement of surface profiles. For both strength laws, the model quantitatively predicts the shear compliance and development of slip for the first few microns of shear displacement, successfully describing the effect of surface roughness and normal load. This model helps explain the initial yield in the friction curve which corresponds to the gradual transition from the elastic deformation and partial slip of asperity contacts to a condition of fully sliding contacts. When a large population of contacts are fully sliding, the model under‐estimates the frictional strength, indicating that displacement strengthening mechanisms are important to the ultimate frictional strength of rocks.
Adverse Effects of Arsenic Exposure on Motor Function among Children in Bangladesh (2011)

Background and Aims: Several reports indicate that drinking water arsenic (WAs) and manganese (WMn) are associated with children’s intellectual function. Very little is known, however, about possible associations with other neurological outcomes such as motor function. Methods: We investigated the associations of WAs and WMn with motor function in 304 children in Bangladesh, aged 8-11 years. In addition to water, we measured arsenic and manganese concentrations in blood, urine and toenails. We assessed motor function with the Bruininks-Oseretsky Test (BOT-2), which can be summarized with a total score of overall motor proficiency (TMC) or in four subscales: fine manual control (FMC), manual coordination (MC), body coordination (BC) and strength and agility (SA). Results: Log transformed blood As (BAs) was associated with decreases in TMC (ß= -3.65, p&lt;0.01), FMC (ß= -1.70, p&lt;0.05) and BC (ß= -1.61, p&lt;0.01), with adjustment for gender, school attendance, head circumference, mother’s intelligence, plasma ferritin, blood Mn, Pb, and Se. Other measures of As exposure (water As, urinary As, and toenail As) demonstrated similar associations. We also have observed a strong positive association between square transformed blood selenium (BSe) and motor function, another novel finding. A significant association between BSe and TMC (ß=3.54, p&lt;0.005), FMC (ß=1.55, p&lt;0.005) and MC (ß=1.57, p&lt;0.005) was found in the unadjusted models; the relationship between BSe and MC remained significant in the full model. Mn exposure was not associated with motor function. Conclusion: Our research demonstrates an adverse association of As exposure and a protective association of Se on motor function in children.
Solid state bonding of spheroidal graphite cast irons. (Report 4). Impact characteristics of solid state bonded joints of ferritic spheroidal craphite cast iron. (1990)

Impact characteristics of diffusion bonded joints of ferritic shperoidal graphite cast iron and the cast iron to mild steel have been investigated using an instrumented Charpy impact test machine. The tests were performed at 0°C after ferritizing the joints. Main results obtained are as follows; (1) Absorbed energy of the cast iron joints bonded without an insert metal had about 5 J, which was much lower than that of the base metal. (2) Absorbed energy of the cast iron joints bonded with Ni foil as an insert metal became higher than that of the joint without Ni foil. The absorbed energy increased with the increas of the thickness of Ni feil and the absorbed energy was reached the base metal level when 50-μm thick Ni foil was used an insert metal. (3) Bond toughness of the cast iron to the mild steel joint bonded without the insert metal increased with the increase of the bonding temperature. When the bonding temperature was upper than 900°C, the absorbed energy was higher than that specified by Japanese Industrial Standard, which is 12.7 J. (4) Bond toughness of the cast iron to the mild steel joints bonded with Ni foil of 10 or 20μm in thickness at 820°C was almost the same as that of the cast iron base metal.
Fluid instabilities in turbocharger compression systems (2017)

Turbochargers increase the power density of internal combustion engines, which allows the displaced volume to be reduced and the fuel efficiency to be improved for the same level of performance. However, the demand for turbocharger centrifugal compressors to deliver increasingly elevated boost pressures, over a wide air flow range, results in unfavorable flow fields that generate narrow and broadband noises within the engine air induction system. The present study is a combined computational and experimental effort, focusing on identifying unsteady fluid-flow instabilities in a turbocharger compression system installed on a bench top stand. This work concentrates primarily on prediction of mild and deep surge instabilities, since they limit the low-flow operating range. Surge occurs near the Helmholtz resonance frequency of the compression system (including a compressor inlet duct, centrifugal compressor, compressor outlet duct, plenum, plenum outlet duct, and a valve) and results in low frequency pressure fluctuations throughout the compression system. Additionally, the compressor flow field adapts to operation at reduced flow rates by forming rotating instabilities in the impeller inducer and vaneless diffuser, which contribute to the occurrence of surge and produce noise as they interact with the rotating impeller and stationary volute.
STEM HAADF Image Simulation of the Orthorhombic M1 Phase in the Mo‐V‐Nb‐Te‐O Propane Oxidation Catalyst (2011)

Abstract A full frozen phonon multislice simulation of high angle annular dark field scanning transmission electron microscopy (HAADF STEM) images from the M1 phase of the Mo‐V‐Nb‐Te‐O propane oxidation catalyst has been performed by using the latest structural model obtained using the Rietveld method. Simulated contrast results are compared with experimental HAADF images. Good agreement is observed at ring sites, however significant thickness dependence is noticed at the linking sites. The remaining discrepancies between the model based on Rietveld refinement and image simulations indicate that the sampling of a small volume element in HAADF STEM and averaging elemental contributions of a disordered site in a crystal slab by using the virtual crystal approximation might be problematic, especially if there is preferential Mo/V ordering near the (001) surface.