gebhart/patrepeval huggingface dataset:
Anisotropic flow of identified hadrons in Xe-Xe collisions at $$ \sqrt{s_{\mathrm{NN}}} $$ = 5.44 TeV (2021)

A bstract Measurements of elliptic ( v 2 ) and triangular ( v 3 ) flow coefficients of π ± , K ± , p+ $$ \overline{\mathrm{p}} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mover> <mml:mi>p</mml:mi> <mml:mo>¯</mml:mo> </mml:mover> </mml:math> , $$ {\mathrm{K}}_{\mathrm{S}}^0 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mi>K</mml:mi> <mml:mi>S</mml:mi> <mml:mn>0</mml:mn> </mml:msubsup> </mml:math> , and Λ+ $$ \overline{\Lambda} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mover> <mml:mi>Λ</mml:mi> <mml:mo>¯</mml:mo> </mml:mover> </mml:math> obtained with the scalar product method in Xe-Xe collisions at $$ \sqrt{s_{\mathrm{NN}}} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:msub> <mml:mi>s</mml:mi> <mml:mi>NN</mml:mi> </mml:msub> </mml:msqrt> </mml:math> = 5 . 44 TeV are presented. The results are obtained in the rapidity range | y | &lt; 0 . 5 and reported as a function of transverse momentum, p T , for several collision centrality classes. The flow coefficients exhibit a particle mass dependence for p T &lt; 3 GeV/ c , while a grouping according to particle type (i.e., meson and baryon) is found at intermediate transverse momenta (3 &lt; p T &lt; 8 GeV/ c ). The magnitude of the baryon v 2 is larger than that of mesons up to p T = 6 GeV/ c . The centrality dependence of the shape evolution of the p T -differential v 2 is studied for the various hadron species. The v 2 coefficients of π ± , K ± , and p+ $$ \overline{\mathrm{p}} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mover> <mml:mi>p</mml:mi> <mml:mo>¯</mml:mo> </mml:mover> </mml:math> are reproduced by MUSIC hydrodynamic calculations coupled to a hadronic cascade model (UrQMD) for p T &lt; 1 GeV/ c . A comparison with v n measurements in the corresponding centrality intervals in Pb-Pb collisions at $$ \sqrt{s_{\mathrm{NN}}} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:msub> <mml:mi>s</mml:mi> <mml:mi>NN</mml:mi> </mml:msub> </mml:msqrt> </mml:math> = 5 . 02 TeV yields an enhanced v 2 in central collisions and diminished value in semicentral collisions.
Mycobacterium tuberculosis Lsr2 Is a Global Transcriptional Regulator Required for Adaptation to Changing Oxygen Levels and Virulence (2014)

M. tuberculosis causes nearly two million deaths per year and infects nearly one-third of the world population. The success of this aerobic pathogen is due in part to its ability to successfully adapt to constantly changing oxygen availability throughout the infectious cycle, from the high oxygen tension during aerosol transmission to anaerobiosis within necrotic lesions. An understanding of how M. tuberculosis copes with these changes in oxygen tension is critical for its eventual eradication. Using a mutation in lsr2, we demonstrate that the Lsr2 protein present in all mycobacteria is a global transcriptional regulator in control of genes required for adaptation to changes in oxygen levels. M. tuberculosis lacking lsr2 was unable to adapt to both high and very low levels of oxygen and was defective in long-term anaerobic survival. Lsr2 was also required for disease pathology and for chronic infection in a mouse model of TB.
Labelling the origin of food products: towards sustainable territorial development? (2014)

The transition from domestic to market economy in rural areas of Europe is an ongoing process that affect and is affected by local and global dynamics. The outcome of this process is unique, but if we analyse and compare each case, it is possible to find patterns and common tendencies. This book highlights the unique and common elements of these transitions, and in order to do so, it takes as reference one case from the south of Europe, the attempt to achieve a PDO certification for local cured sheep cheese, and other from Western Europe, the design and unfold of a Regional Label for local lamb meat. The thesis of this book underline is the existence of a “quality turn” in Europe, and analyse how Origin Food Labels can instruments to institutionalise new forms of co-production and co-evolution that enhance sustainable territorial development. At the same time, the ethnographic nature of this research highlights that these are controversial and political processes, where local and non-local actors with different interests find each other and try to unfold their own projects. The use of a comparative strategy highlights how these transitions are influenced by local institutional frameworks and cultural patterns, but it also shows how collective action can change them.
Optical propagation across the Chesapeake Bay: comparison of experiment to theory (2021)

Optical propagation through deep turbulence is important to understand for applications such as free space optical communication The United States Naval Research Laboratory has maintained a 16 km range across the Chesapeake Bay for over a decade. A 1550 nm beam is transmitted from one end to the other where a variety of instruments measure optical parameters such as transmission, scintillation index, aperture averaging, and angle of arrival variation. In addition, meteorological parameters are collected using a weather station at CBD as well as NOAA buoys on the bay. In this work, we present comparisons of measurement optical scintillation index, distribution functions and aperture averaging to calculations using extended Rytov theory and and wave optics calculations.
Midfoot Arthrodesis following Multi-Joint Stabilization with a Novel Hybrid Plating System (2012)

The healing rate and time to arthrodesis compared favorably to similar published studies. Based on these results, hybrid plating was a reliable and consistent alternative for fixation in midfoot arthrodesis, especially in multi-joint disease.
Enhanced Heat Capacity of Salt Hydrate by In-Situ Formed Nanostructure (2017)

Silica nanoparticles and polyethylene-block-poly were doped in sodium acetate trihydrate to in-situ synthesize stelliform nanostructure to enhance the effective specific heat capacity of sodium acetate trihydrate. Sodium dodecyl sulfate and methanol were also used in the synthesis to help the dispersion. A modulated differential scanning calorimeter was employed to characterize the specific heat capacity of pure sodium acetate trihydrate and their nano samples. The measurement was repeated multiple times on different days to confirm the repeatability of the measurement. The result shows the specific heat capacity was enhanced by 11% in comparison with pure sodium acetate trihydrate. The conventional effective specific heat capacity model was compared with the experimental result.
Determination of Key Active Components in Different Edible Oils Affecting Lipid Accumulation and Reactive Oxygen Species Production in HepG2 Cells (2018)

Owing to the poor ability of cells to decompose triglycerides, most studies of edible oil have depended on animal or clinical trials. However, such trials are expensive and time-consuming, and the results are limited to considerable individual differences. This is the first study to comprehensively investigate the effect of different oils on the lipid accumulation and reactive oxygen species (ROS) production in HepG2 cells by hydrolyzing oil to fatty acids with integrated fat content. In addition, the key components of fatty acid composition, phytosterol, polyphenols, and tocopherol/tocotrienol in different oils, contributing to a decrease in content of lipid accumulation, cholesterol, ROS, and malondialdehyde (MDA), were analyzed using multivariate analysis. The results showed that the lipid accumulation content of coconut oil, Pu'er tea oil, olive oil, and flaxseed oil at a concentration of 200 μM decreased by 45.98 ± 0.75, 50.35 ± 1.37, 40.43 ± 2.44, and 42.76 ± 1.88%, respectively, compared with the lard. In addition, the ROS contents of Pu'er tea oil, olive oil, and flaxseed oil had no significant difference from that of control cells ( p < 0.05). In the results, (3β,5α)-stigmastan-3-yl, cholane-5,20(22)-diene-3b-ph, and β-sitosterol were determined to be the key components in edible oils associated with lipid accumulation and ROS production.
EMPFEHLUNGEN FUER DIE DURCHFUEHRUNG ZERSTOERUNGSFREIER UND ZERSTOERUNGSARMER PRUEFVERFAHREN IM RAHMEN DER BAUWERKSPRUEFUNG NACH DIN 1076 (1984)

AUF GRUND DER ERFAHRUNGEN DES BEI PRUEFUNGEN VON BRUECKEN UND ANDEREN BAUWERKEN EINGESETZTEN PERSONALS EINZELNER BUNDESLAENDER UND GEMEINDEN, SOWIE EINER SCHRIFTTUMSSTUDIE DES OESTERREICHISCHEN BUNDESMINISTERIUMS FUER BAUTEN UND TECHNIK, WIEN, WIRD UEBER PRUEFMETHODEN UND GERAETE BERICHTET. ES SIND AUCH VERFAHREN EINBEZOGEN, DIE IN DER PRAXIS KAUM ANWENDUNG FINDEN, UND WEITERER ENTWICKLUNG BEDUERFEN. DIE PRUEFVERFAHREN SIND NACH DREI WERTUNGSSTUFEN EINGETEILT: OERTLICHE VERFAHREN MIT EINFACHEN HILFSMITTELN, OERTLICHE VERFAHREN MIT GERAETEN, DIE IM PRUEFWAGEN MITGEFUEHRT WERDEN, ZUSAETZLICHE PRUEFVERFAHREN UND LABORUNTERSUCHUNGEN DURCH DRITTE. DIE PRUEFVERFAHREN DER DREI WERTUNGSSTUFEN WERDEN ERLAEUTERT UND BEURTEILT. BEHANDELT WERDEN AUCH CHEMISCHE UNTERSUCHUNGEN AN BAUWERKEN, U.A. DER NACHWEIS VON CHLORIDEN MITTELS DER AQUAQUANTMETHODE, DER AQUAMERCKMETHODE UND DER QUANTABMETHODE, DER ROSTGRAD NACH DIN 53 210, DIE BLASENBILDUNG IN SCHUTZSCHICHTEN NACH DIN 53 209, DIE GITTERSCHNITTPRUEFUNG NACH DIN 53 151.
Probing the role of C‐1 ester group in Naja naja phospholipase  A2–phospholipid interactions using butanetriol‐containing  phosphatidylcholine analogues (1999)

To understand the role of the ester moiety of the sn-1 acyl chain in phospholipase A2-glycerophospholipid interactions, we introduced an additional methylene residue between the glycerol C1 and C2 carbon atoms of phosphatidylcholines, and then studied the kinetics of hydrolysis and the binding of such butanetriol-containing phospholipids with Naja naja phospholipase A2. Hydrolysis was monitored by using phospholipids containing a NBD-labelled sn-2 acyl chain and binding was ascertained by measuring the protein tryptophan fluorescence. The hydrolysis of butanetriol-containing phospholipids was invariably slower than that of the glycerol-containing phospholipids. In addition, the enzyme binding with the substrate was markedly decreased upon replacing the glycerol residue with the 1,3,4-butanetriol moiety in phosphatidylcholines. These results have been interpreted to suggest that the sn-1 ester group in glycerophospholipids could play an important role in phospholipase A2-phospholipid interactions.
Preliminary Design Studies of a High Sensitivity Small Animal DOI-PET Scanner: jPET-RD (2005)

We present a preliminary study on the design of a high sensitivity small animal DOI-PET scanner: jPET-RD (for Rodents with DOI detectors), which is under development at the National Institute of Radiological Sciences in Japan. The scanner composed of two rings of six detector blocks arranged in a hexagonal shape with an inner radius of 88 mm. Each detector consists of a four-layer array of 32/spl times/32 scintillator crystals each measuring 1.44/spl times/1.44/spl times/4.5 mm/sup 3/ and a 256ch flat panel position sensitive photomultiplier tube (FP-PS-PMT). The FP-PS-PMT has a large effective area of 49/spl times/49 mm/sup 2/ and multi anodes of 16/spl times/16ch, which can be read out in parallel. We simulated the scanner for various parameters of the number of DOI channels and the length of crystal. Simulated data were reconstructed using the maximum likelihood expectation maximization with accurate system modeling. The trade-off results between background noise and spatial resolution shows that only shortening the length of crystal does not improve the trade-off at all, and that four-layer DOI information improves uniformity of spatial resolution in the whole FOV. Monte Carlo simulations were also performed using the EGS4 code to measure absolute sensitivity and count rate capability with a small cylindrical phantom. We also evaluated the impact of critical design parameters on the noise equivalent count rate (NECR) and LOR errors caused by inter-crystal Compton scatters. Simulation results show that this scanner can achieve high sensitivity and high NECR, which can be further improved by using an appropriate anode segmentation of the FP-PS-PMT.
Galiellalactone reduces the expression of pro-inflammatory marker genes in pro-atherosclerotic mice. (2015)

&lt;p&gt;RNA isolated from aortas of ApoE-deficient mice either fed for 18 weeks with normal chow diet (ND) or western-type diet (WD) (treated with Galiellalactone (Gal) or vehicle (PBS/EtOH) for 6 weeks) was analyzed for CTSS (&lt;b&gt;A&lt;/b&gt;), SPP1 (&lt;b&gt;B&lt;/b&gt;), TNFα (&lt;b&gt;C&lt;/b&gt;), S100A8 (&lt;b&gt;D&lt;/b&gt;), iNOS (&lt;b&gt;E&lt;/b&gt;), IL6 (&lt;b&gt;F&lt;/b&gt;), and IL17 (&lt;b&gt;G&lt;/b&gt;) mRNA expression in qPCR experiments. Data shown are mean + SEM of 4–10 mice (*** = p &lt; 0.001; ** = p &lt; 0.01; * = p &lt; 0.05; ns = not significant vs. WD + PBS/EtOH; one-way ANOVA).&lt;/p&gt;
Heterogeneity and renal mass biopsy: a review of its role and reliability. (2014)

Increased abdominal imaging has led to an increase in the detection of the incidental small renal mass (SRM). With increasing recognition that the malignant potential of SRMs is heterogeneous, ranging from benign (15%-20%) to aggressive (20%), enthusiasm for more conservative management strategies in the elderly and infirmed, such as active surveillance (AS), have grown considerably. As the management of the SRM evolves to incorporate ablative techniques and AS for low risk disease, the role of renal mass biopsy (RMB) to help guide individualized therapy is evolving. Historically, the role of RMB was limited to the evaluation of suspected metastatic disease, renal abscess, or lymphoma. However, in the contemporary era, the role of biopsy has grown, most notably to identify patients who harbor benign lesions and for whom treatment, particularly the elderly or frail, may be avoided. When performing a RMB to guide initial clinical decision making for small, localized tumors, the most relevant questions are often relegated to proof of malignancy and documentation (if possible) of grade. However, significant intratumoral heterogeneity has been identified in clear cell renal cell carcinoma (ccRCC) that may lead to an underestimation of the genetic complexity of a tumor when single-biopsy procedures are used. Heterogeneous genomic landscapes and branched parallel evolution of ccRCCs with spatially separated subclones creates an illusion of clonal dominance when assessed by single biopsies and raises important questions regarding how tumors can be optimally sampled and whether future evolutionary tumor branches might be predictable and ultimately targetable. This work raises profound questions concerning the genetic landscape of cancer and how tumor heterogeneity may affect, and possibly confound, targeted diagnostic and therapeutic interventions. In this review, we discuss the current role of RMB, the implications of tumor heterogeneity on diagnostic accuracy, and highlight promising future directions.
Reduced GFAP Expression in Bergmann Glial Cells in the Cerebellum of Sigma-1 Receptor Knockout Mice Determines the Neurobehavioral Outcomes after Traumatic Brain Injury (2021)

Neuroprotective effects of Sigma-1 receptor (S1R) ligands have been observed in multiple animal models of neurodegenerative diseases. Traumatic brain injury (TBI)-related neurodegeneration can induce long-lasting physical, cognitive, and behavioral disabilities. The aim of our study was to evaluate the role of S1R in the development of neurological deficits after TBI. Adult male wild-type CD-1 (WT) and S1R knockout (S1R-/-) mice were subjected to lateral fluid percussion injury, and behavioral and histological outcomes were assessed for up to 12 months postinjury. Neurological deficits and motor coordination impairment were less pronounced in S1R-/- mice with TBI than in WT mice with TBI 24 h after injury. TBI-induced short-term memory impairments were present in WT but not S1R-/- mice 7 months after injury. Compared to WT animals, S1R-/- mice exhibited better motor coordination and less pronounced despair behavior for up to 12 months postinjury. TBI induced astrocyte activation in the cortex of WT but not S1R-/- mice. S1R-/- mice presented a significantly reduced GFAP expression in Bergmann glial cells in the molecular layer of the cerebellum compared to WT mice. Our findings suggest that S1R deficiency reduces TBI-induced motor coordination impairments by reducing GFAP expression in Bergmann glial cells in the cerebellum.
Viscoelastic Response of Nafion. Effects of Temperature and Hydration on Tensile Creep (2008)

The tensile creep of the acid form of Nafion N1110 was examined under controlled environmental conditions of temperature, 25 ≤ T ≤ 110 °C, and water activity, 0 ≤ aw ≤ 0.95. Water plasticizes Nafion at 25 °C; creep strain after 1 h increases and the elastic modulus decreases with increasing water activity. At temperatures ≥40 °C the elastic modulus of Nafion goes through a maximum as a function of water activity; the elastic modulus of Nafion increases as aw increases from 0 to 0.01 and then decreases with increasing water activity for aw > 0.1. Under dry conditions (aw = 0), Nafion undergoes a transition between 60 and 80 °C where its creep rate increases rapidly and its elastic modulus decreases with increasing temperature. Above this transition temperature a small water activity, aw < 0.1, dramatically reduces the creep rate and increases the elastic modulus of Nafion—at elevated temperature water stiffens Nafion. At intermediate temperatures (40−80 °C) the elastic and viscous components of creep recovery show two local minima as functions of water activity at constant temperature. We attribute the transitions in the viscoelastic response of Nafion to microphase structural transitions driven by changes in temperature and water activity.
Blockage of methylcitrate cycle inhibits polyketide production in Aspergillus nidulans (2004)

Aspergillus nidulans produces the polyketide toxin sterigmatocystin (ST) of which the biosynthetic and pathway specific regulatory genes compose a stc gene cluster. A previous mutagenesis screen identified 23 mutants defective in production of ST. Five mutants constitute a single locus. Genetic complementation and sequencing analysis revealed the mutant locus to be mcsA encoding methylcitrate synthase that converts propionyl-CoA to methylcitrate. Feeding downstream products of methylcitrate synthase, methylcitrate and pyruvate, did not restore ST production in mcsA mutants, indicating that loss of methylcitrate cycle products is not the cause of the ST defect. However, propionate, a precursor for propionyl-CoA, inhibited ST production and induced transcription of mcsA in the wild type. Furthermore, propionate impaired formation of two polyketide spore pigments whereas overexpression of mcsA relieved inhibition of ST production by propionate. Transcription analyses revealed that disruption of mcsA did not affect expression of the specialized fatty acid synthase genes (stcJ and stcK) or polyketide synthase gene (stcA) required for formation of norsolorinic acid (NOR), the first stable intermediate in the ST biosynthetic pathway. Feeding studies showed that NOR but not hexanoic acid (the fatty acid produced by StcJ/StcK and primer unit of StcA) or malonate (source of the extender unit of StcA) restored ST production in the mcsA mutant. We hypothesize that excess buildup of propionyl-CoA in mcsA mutants interferes with polyketide synthase activity.
Solid-phase XRN1 reactions for RNA cleavage: application in single-molecule sequencing (2021)

Modifications in RNA are numerous (∼170) and in higher numbers compared to DNA (∼5) making the ability to sequence an RNA molecule to identify these modifications highly tenuous using next generation sequencing (NGS). The ability to immobilize an exoribonuclease enzyme, such as XRN1, to a solid support while maintaining its activity and capability to cleave both the canonical and modified ribonucleotides from an intact RNA molecule can be a viable approach for single-molecule RNA sequencing. In this study, we report an enzymatic reactor consisting of covalently attached XRN1 to a solid support as the groundwork for a novel RNA exosequencing technique. The covalent attachment of XRN1 to a plastic solid support was achieved using EDC/NHS coupling chemistry. Studies showed that the solid-phase digestion efficiency of model RNAs was 87.6 ± 2.8%, while the XRN1 solution-phase digestion for the same model was 78.3 ± 4.4%. The ability of immobilized XRN1 to digest methylated RNA containing m6A and m5C ribonucleotides was also demonstrated. The processivity and clipping rate of immobilized XRN1 secured using single-molecule fluorescence measurements of a single RNA transcript demonstrated a clipping rate of 26 ± 5 nt s-1 and a processivity of >10.5 kb at 25°C.
Phase II, two-stage, two-arm, PIK3CA mutation stratified trial of MK-2206 in recurrent endometrial cancer (EC). (2013)

5524 Background: EC has high rates of PI3K pathway alteration including PTEN mutation (50%) or IHC loss (&gt;50%), PIK3CA mutation (25-40%) and PIK3R1 (20%) mutation. MK-2206 is an allosteric inhibitor of AKT, an effector kinase of PI3K signals. We hypothesized that pts whose tumors harbored PIK3CA mutations would be more likely to benefit from MK-2206 than those without PIK3CA mutation. Methods: Pts had recurrent or advanced EC; all histologies except MMMT were eligible. Up to 2 prior chemo lines were permitted; excluding prior treatment with PI3K/MTOR inhibitors. The first 19 pts were treated with MK-2206 200mg QW; due to initial skin toxicity rates, the starting dose was amended to 135mg QW. Co-primary endpoints were objective response and 6 mo PFS. The first 37 pts were stratified retrospectively. PIK3CA MT included R88Q, K111N, E110K, E418K, C420R, E453K, E542K/V,E545K, Q546R, H701P, M1043V, H1047R/L/Y changes. Independent Simon 2-stage tests were planned within PIK3CA MT and WT stratum: for MT, n1=15 and n2=10 pts would allow discrimination of RR&lt;5% and 6moPFS&lt;10% versus RR&gt;25% or 6moPFS&gt;35%; for WT, n1=31 and n2=24 pts would discriminate RR&lt;5% and 6moPFS&lt;10% versus RR&gt;20% or 6moPFS&gt;25%. Results: 37 pts were enrolled (1 ineligible) before accrual was stopped as timely CLIA-compliant prospective mutation analysis was not feasible. By PIK3CA mutation analysis, 9 pts were MT: 1 pt had both PR and 6moPFS. 27 pts were WT: 1 pt had PR and 3 pts had 6moPFS. 2 pts with 6moPFS were treated at 200mg; 2 pts with 6moPFS were treated at 135mg. Each group had 1 PR. The most common toxicity was grade 3 rash (19%). Grade 3 and 4 toxicities occurred in 50% and 8% of pts. Exploratory analysis of histology found all pts with 6moPFS were classified as serous (4 of 8) as compared to all other histologies (0 of 28, p=.001). Targeted exome sequencing and copy number analysis of the PI3K pathway and PTEN IHC are underway. Associative studies will be reported. Conclusions: There is limited single agent activity of MK-2206 in both PIK3CA MT and PIK3CA WT EC populations. Activity was detected in pts with serous histology tumors and warrants further study. Clinical trial information: NCT01307631. [Table: see text]
A Single Phosphine Ligand Allows Palladium‐Catalyzed Intermolecular CO Bond Formation with Secondary and Primary Alcohols (2011)

Forging a bond: an efficient, general palladium catalyst for C-O bond-forming reactions of secondary and primary alcohols with a range of aryl halides has been developed using the ligand 1. Heteroaryl halides, and for the first time, electron-rich aryl halides can be coupled with secondary alcohols. A diverse set of substrate combinations are possible with just a single ligand, thus obviating the need to survey multiple ligands.