gebhart/patrepeval huggingface dataset:
PanDA for ATLAS distributed computing in the next decade (2017)

The Production and Distributed Analysis (PanDA) system has been developed to meet ATLAS production and analysis requirements for a data-driven workload management system capable of operating at the Large Hadron Collider (LHC) data processing scale. Heterogeneous resources used by the ATLAS experiment are distributed worldwide at hundreds of sites, thousands of physicists analyse the data remotely, the volume of processed data is beyond the exabyte scale, dozens of scientific applications are supported, while data processing requires more than a few billion hours of computing usage per year. PanDA performed very well over the last decade including the LHC Run 1 data taking period. However, it was decided to upgrade the whole system concurrently with the LHC’s first long shutdown in order to cope with rapidly changing computing infrastructure. After two years of reengineering efforts, PanDA has embedded capabilities for fully dynamic and flexible workload management. The static batch job paradigm was discarded in favor of a more automated and scalable model. Workloads are dynamically tailored for optimal usage of resources, with the brokerage taking network traffic and forecasts into account. Computing resources are partitioned based on dynamic knowledge of their status and characteristics. The pilot has been re-factored around a plugin structure for easier development and deployment. Bookkeeping is handled with both coarse and fine granularities for efficient utilization of pledged or opportunistic resources. An in-house security mechanism authenticates the pilot and data management services in off-grid environments such as volunteer computing and private local clusters. The PanDA monitor has been extensively optimized for performance and extended with analytics to provide aggregated summaries of the system as well as drill-down to operational details. There are as well many other challenges planned or recently implemented, and adoption by non-LHC experiments such as bioinformatics groups successfully running Paleomix (microbial genome and metagenomes) payload on supercomputers. In this paper we will focus on the new and planned features that are most important to the next decade of distributed computing workload management.
ChemInform Abstract: Regioselective Nucleophilic Ring Opening of Epoxides and Aziridines Derived from Homoallylic Alcohols. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
One‐Pot Tandem 1,4–1,2‐Addition of Phosphites to α,β‐Unsaturated Imines for the Synthesis of Glutamic Acid Analogues (2005)

Evidently so: New mechanistic findings indicate that addition of dialkyl trimethylsilyl phosphites to α,β-unsaturated imines has been incorrectly reported as an exclusive 1,2-addition. When α,β-unsaturated imines are used as substrates, 1-alkylamino 3-phosphonyl phosphonates are formed in high yields in the presence of a suitable proton source through a sequential 1,4- and 1,2-addition. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501830_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Cellular and Molecular Factors in Flexor Tendon Repair and Adhesions: A Histological and Gene Expression Analysis (2013)

Flexor tendon healing is mediated by cell proliferation, migration, and extracellular matrix synthesis that contribute to the formation of scar tissue and adhesion. The biological mechanisms of flexor tendon adhesion formation have been linked to transforming growth factor β (TGF-β). To elucidate the cellular and molecular events in this pathology, we implanted live flexor digitorum longus grafts from the reporter mouse Rosa26(LacZ/+) in wild-type recipients, and used histological β-galactosidase (β-gal) staining to evaluate the intrinsic versus extrinsic cellular origins of scar, and reverse transcription-polymerase chain reaction to measure gene expression of TGF-β and its receptors, extracellular matrix proteins, and matrix metalloproteinases (MMPs) and their regulators. Over the course of healing, graft cellularity and β-gal activity progressively increased, and β-gal-positive cells migrated out of the Rosa26(LacZ/+) graft. In addition, there was an evidence of influx of host cells (β-gal-negative) into the gliding space and the graft, suggesting that both graft and host cells contribute to adhesions. Interestingly, we observed a biphasic pattern in which Tgfb1 expression was the highest in the early phases of healing and gradually decreased thereafter, whereas Tgfb3 increased and remained upregulated later. The expression of TGF-β receptors was also upregulated throughout the healing phases. In addition, type III collagen and fibronectin were upregulated during the proliferative phase of healing, confirming that murine flexor tendon heals by scar tissue. Furthermore, gene expression of MMPs showed a differential pattern in which inflammatory MMPs were the highest early and matrix MMPs increased over time. These findings offer important insights into the complex cellular and molecular factors during flexor tendon healing.
Cysteine-scanning Mutagenesis of Transmembrane Segment 7 of the GLUT1 Glucose Transporter (1999)

The human erythrocyte facilitative glucose transporter (Glut1) is predicted to contain 12 transmembrane spanning alpha-helices based upon hydropathy plot analysis of the primary sequence. Five of these helices (3, 5, 7, 8, and 11) are capable of forming amphipathic structures. A model of GLUT1 tertiary structure has therefore been proposed in which the hydrophilic faces of several amphipathic helices are arranged to form a central aqueous channel through which glucose traverses the hydrophobic lipid bilayer. In order to test this model, we individually mutated each of the amino acid residues in transmembrane segment 7 to cysteine in an engineered GLUT1 molecule devoid of all native cysteines (C-less). Measurement of 2-deoxyglucose uptake in a Xenopus oocyte expression system revealed that nearly all of these mutants retain measurable transport activity. Over one-half of the cysteine mutants had significantly reduced specific activity relative to the C-less protein. The solvent accessibility and relative orientation of the residues within the helix was investigated by determining the sensitivity of the mutant transporters to inhibition by the sulfhydryl directed reagent p-chloromercuribenzene sulfonate (pCMBS). Cysteine replacement at six positions (Gln(282), Gln(283), Ile(287), Ala(289), Val(290), and Phe(291)), all near the exofacial side of the cell membrane, produced transporters that were inhibited by incubation with extracellular pCMBS. Residues predicted to be near the cytoplasmic side of the cell membrane were minimally affected by pCMBS. These data demonstrate that the exofacial portion of transmembrane segment 7 is accessible to the external solvent and provide evidence for the positioning of this alpha-helix within the glucose permeation pathway.
Controlling quantum interference in phase space with amplitude (2017)

We experimentally show a quantum interference in phase space by interrogating photon number probabilities (n = 2, 3, and 4) of a displaced squeezed state, which is generated by an optical parametric amplifier and whose displacement is controlled by amplitude of injected coherent light. It is found that the probabilities exhibit oscillations of interference effect depending upon the amplitude of the controlling light field. This phenomenon is attributed to quantum interference in phase space and indicates the capability of controlling quantum interference using amplitude. This remarkably contrasts with the oscillations of interference effects being usually controlled by relative phase in classical optics.
Full ($V_{\mathrm{g}},\ V_{\mathrm{d}}$) Bias Space Modeling of Hot-Carrier Degradation in Nanowire FETs (2019)

Simulations of hot-carrier degradation of nanowire field-effect transistors are reported. The simulations rely on the carrier energy distribution function, obtained by solving the Boltzmann transport equation. To model the contribution of impact ionization, the hydrodynamic scheme is employed. A range of pertinent physical mechanisms is invoked and discussed to adequately reproduce HCD measurements in the full ( V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> , V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> ) bias space. Impact ionization is discussed as an important ingredient of HCD at low gate, high drain voltages.
ChemInform Abstract: DECARYIOL, A NEW CEMBRANE DITERPENE FROM THE MARINE SOFT CORAL SARCOPHYTON DECARYI (1982)

Abstract Aus der im Titel genannten Korallenart werden als weitere Inhaltsstoffe die Cembran‐Diterpene Thunbergol (I), Decaryiol (II) und 3,4‐Epoxy‐nephthenol (III) isoliert.
Human trials of AIDS vaccines (1989)

From the Division of AIDS and the Office of the Director, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA. Wayne C. Koff, Vaccine Research and Development Branch, Basic Research and Development Program, Division of AIDS, NIAID, 6003 Executive Blvd. 234P, Rockville, Maryland 20892, USA.
Vitamin C and epigenetic regulation (2014)

Vitamin C (ascorbic acid) is an essential human nutrient. In addition to its role as an important antioxidant, vitamin C participates in collagen, catecholamine and carnitine in vivo synthesis. One important physiological function of vitamin C is serving as a co-factor of Fe2+/α-ketoglutaric-acid dependent dioxygenases, which contain many epigenetic enzymes. Vitamin C is thus critical for epigenetic regulation. We recently determined that vitamin C can enhance the induction efficiency of induced pluripotent stem cells (iPSCs) through its epigenetic regulatory role. In this review, we discuss the effect of vitamin C on epigenetic enzymes and somatic reprogramming, thereby expanding our understanding of vitamin C functionality in the areas of life sciences and human health.
Single photon emission from an InGaAs quantum dot precisely positioned on a nanoplane (2007)

This work demonstrates single photon emissions from a site-controlled quantum dot (QD) grown on a self-constructed nanoplane. The size of the nanoplane on the micron-sized multifacet structure is accurately controlled by a low surface reducing rate (∼16nm∕min). Single QD spectral lines were resolved and identified. The antibunching behavior reveals that single photons are emitted from the positioned QD.
Effective Area Formulation for Thermal Detector Characterization (2014)

We have derived an expression for the effective absorbing area for thermal infrared detectors having non-zero absorption in the support legs, which is different from the geometric areas of the constituent detector elements. This technique is particularly applicable to devices where sensitivity is more important than fill-factor, as opposed to standard imaging arrays. The effective area can simply be substituted in standard equations to obtain a good estimate of the detector performance under uniform flood illumination conditions. The formalism can also be used for estimating the contributions of the individual signal generating elements to the total measured signal. This approximation has been tested for MEMS infrared detectors with thermoelectric readout operating under vacuum. The responsivity of the same device calculated using the effective area approximation and measured using a tightly constrained absorbing area are found to match very closely, within 5% over the most wavelengths and within 15% at the shortest thermal infrared wavelengths.
Properties of Pd/Au thin film layered structures (1983)

We have synthesized, by rf sputtering, Pd/Au layered structures with periodicities (Pd+Au layers) that vary from 15–95 Å. The films have been characterized by x-ray diffraction. The individual metal layers have (111) orientation perpendicular to the plane of the film. We accurately model the positions and intensities of x-ray lines by a one-dimensional diffraction grating of Pd and Au layers and relate the observed x-ray line widths to loss of long-range layer coherence induced by dislocations at Pd–Au interfaces. We also find that the in-plane electrical resistivity of the films varies inversely, and the temperature coefficient of resistance directly with the layer period. We account for both of these trends by considering scattering of electrons from the metal interfaces, using a modified Fuchs theory.
Electron and Proton Flux for Carbon Dioxide Reduction in Methanosarcina barkeri During Direct Interspecies Electron Transfer (2018)

Direct interspecies electron transfer (DIET) is important in diverse methanogenic environments, but how methanogens participate in DIET is poorly understood. Therefore, the transcriptome of <i>Methanosarcina barkeri</i> grown via DIET in co-culture with <i>Geobacter metallireducens</i> was compared with its transcriptome when grown via H<sub>2</sub> interspecies transfer (HIT) with <i>Pelobacter carbinolicus</i>. Notably, transcripts for the F<sub>420</sub>H<sub>2</sub> dehydrogenase, Fpo, and the heterodisulfide reductase, HdrABC, were more abundant during growth on DIET. A model for CO<sub>2</sub> reduction was developed from these results in which electrons delivered to methanophenazine in the cell membrane are transferred to Fpo. The external proton gradient necessary to drive the otherwise thermodynamically unfavorable reverse electron transport for Fpo-catalyzed F<sub>420</sub> reduction is derived from protons released from <i>G. metallireducens</i> metabolism. Reduced F<sub>420</sub> is a direct electron donor in the carbon dioxide reduction pathway and also serves as the electron donor for the proposed HdrABC-catalyzed electron bifurcation reaction in which reduced ferredoxin (also required for carbon dioxide reduction) is generated with simultaneous reduction of CoM-S-S-CoB. Expression of genes for putative redox-active proteins predicted to be localized on the outer cell surface was higher during growth on DIET, but further analysis will be required to identify the electron transfer route to methanophenazine. The results indicate that the pathways for electron and proton flux for CO<sub>2</sub> reduction during DIET are substantially different than for HIT and suggest that gene expression patterns may also be useful for determining whether <i>Methanosarcina</i> are directly accepting electrons from other extracellular electron donors, such as corroding metals or electrodes.
Ginseng gintonin alleviates neurological symptoms in the G93A-SOD1 transgenic mouse model of amyotrophic lateral sclerosis through lysophosphatidic acid 1 receptor (2020)

Gintonin-mediated symptomatic improvements of ALS might be associated with the attenuations of neuronal loss and oxidative stress via the spinal LPA1 receptor regulations. The present results suggest that the spinal LPA1 receptor is engaged in ALS, and gintonin may be useful for relieving ALS symptoms.
AN ORDERED MAGNETIC FIELD IN THE PROTOPLANETARY DISK OF AB Aur REVEALED BY MID-INFRARED POLARIMETRY (2016)

ABSTRACT Magnetic fields ( B -fields) play a key role in the formation and evolution of protoplanetary disks, but their properties are poorly understood due to the lack of observational constraints. Using CanariCam at the 10.4 m Gran Telescopio Canarias, we have mapped out the mid-infrared polarization of the protoplanetary disk around the Herbig Ae star AB Aur. We detect ∼0.44% polarization at 10.3 μ m from AB Aur's inner disk ( r &lt; 80 au), rising to ∼1.4% at larger radii. Our simulations imply that the mid-infrared polarization of the inner disk arises from dichroic emission of elongated particles aligned in a disk B -field. The field is well ordered on a spatial scale, commensurate with our resolution (∼50 au), and we infer a poloidal shape tilted from the rotational axis of the disk. The disk of AB Aur is optically thick at 10.3 μ m, so polarimetry at this wavelength is probing the B -field near the disk surface. Our observations therefore confirm that this layer, favored by some theoretical studies for developing magneto-rotational instability and its resultant viscosity, is indeed very likely to be magnetized. At radii beyond ∼80 au, the mid-infrared polarization results primarily from scattering by dust grains with sizes up to ∼1 μ m, a size indicating both grain growth and, probably, turbulent lofting of the particles from the disk mid-plane.
Pore-scale processes in tertiary low salinity waterflooding in a carbonate rock: Micro-dispersions, water film growth, and wettability change (2022)

Development of water micro-droplets within the oil phase and detachment of oil layers from the rock surface were observed after low salinity waterflooding. During high salinity waterflooding, contact angles showed insignificant changes from the initial value of 115°, while the mean curvature and local capillary pressure values remained negative, consistent with oil-wet conditions. However, with low salinity, the decrease in contact angle to 102° and the shift in the mean curvature and capillary pressure to positive values indicate a wettability change. Overall, our analysis captured the in situ mechanisms and processes associated with the low salinity effect and ultimate increase in oil recovery.
Supplementary Figure S4 from PLEKHA5 as a Biomarker and Potential Mediator of Melanoma Brain Metastasis (2023)

&lt;p&gt;Effect of astrocytes on PLEKHA5 silencing and cell viability in A375Br cells. Cells were transfected with 40 nmol/L of PLEKHA5 siRNA in conditional medium of astrocytes for 96 h. Cell viability of A375Br cells cultured in the absence or presence astrocytes was similarly inhibited by PLEKHA5 siRNA.&lt;/p&gt;
Autophagy Declines with Premature Skin Aging resulting in Dynamic Alterations in Skin Pigmentation and Epidermal Differentiation (2020)

Autophagy is a membrane traffic system that provides sustainable degradation of cellular components for homeostasis, and is thus considered to promote health and longevity, though its activity declines with aging. The present findings show deterioration of autophagy in association with premature skin aging. Autophagy flux was successfully determined in skin tissues, which demonstrated significantly decreased autophagy in hyperpigmented skin such as that seen in senile lentigo. Furthermore, an exacerbated decline in autophagy was confirmed in xerotic hyperpigmentation areas, accompanied by severe dehydration and a barrier defect, which showed correlations with skin physiological conditions. The enhancement of autophagy in skin ex vivo ameliorated skin integrity, including pigmentation and epidermal differentiation. The present results indicate that the restoration of autophagy can contribute to improving premature skin aging by various intrinsic and extrinsic factors via the normalization of protein homeostasis.
T cell changes after combined nucleoside analogue therapy in HIV primary infection (1999)

These results show that early therapy with nucleoside analogues can correct the immunological abnormalities observed in CD4 and CD8 T cell subsets at the time of PHI. This early kinetics in T cell recovery appears to be faster than in established disease.
Identifying Most Predictive Items (2004)

Frequent itemsets and association rules are generally accepted concepts in analyzing item-based databases. The Apriori-framework was developed for analyzing categorical data. However, many data include numerical values. Therefore, most existing techniques transform numerical values to categorical values. The transformation is done such that the rules are optimal with respect to support or confidence.
Soloution conformation of an olionucleotide containing a G.G mismatch determined by nuclear manetic resonance and molecular mechanics (1991)

We have determined by two-dimensional nuclear magnetic resonance studies and molecular mechanics calculations the three dimensional solution structure of the non-selfcomplementary oligonucleotide, d(GAGGAGGCACG). d(CGTGCGTCCTC) in which the central base pair is G.G. This is the first structural determination of a G.G mismatch in a oligonucleotide. Two dimensional nuclear magnetic resonance spectra show that the bases of the mismatched pair are stacked into the helix and that the helix adopts a classical B-DNA form. Spectra of the exchangeable protons show that the two guanosines are base paired via their imino protons. For the non-exchangeable protons and for some of the exchangeable protons nuclear Overhauser enhancement build up curves at short mixing times have been measured. These give 84 proton-proton distances which are sensitive to the helix conformation. One of the guanosines adopts a normal anti conformation while the other is syn or close to syn. All non-terminal sugars are C2' endo. These data sets were incorporated into the refinement of the oligonucleotide structure by molecular mechanics calculations. The G.G mismatch shows a symmetrical base pairing structure. Although the mismatch is very bulky many of its features are close to that of normal B-DNA. The mismatch induces a small lateral shift in the helix axis and the sum of the helical twist above and below the mismatch is close to that of B-DNA.
Clinical outcome with enalapril in symptomatic chronic heart failure; a dose comparison (1998)

NETWORK did not demonstrate a relationship between dose of enalapril and clinical outcome in patients with heart failure selected from both primary care and hospital practice.
Quantifying a Biocatalytic Product from a Few Living Microbial Cells Using Microfluidic Cultivation Coupled to FT-ICR-MS (2019)

The in vivo quantification of metabolic products from microbial single cells is one of the last grand challenges in (bio)analytical chemistry. To date, no label-free analytical concept exists that is powerful enough to detect or even quantify the minute amounts of secreted low molecular weight compounds produced by living and isolated single bacteria or yeast cells. Coupling microfluidic cultivation systems with ultrahigh resolution electrospray-ionization mass spectrometry with its exquisite sensitivity and specificity offers the prospect of single-cell product analysis and quantification, but has not been successfully implemented yet. We report an analytical framework that interfaces noninvasive microfluidic trapping and cultivation of a few bacterial single cells with the analysis of their catalytic products by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Cell trapping was performed with the microfluidic Envirostat platform for cultivating bacterial cells under continuous perfusion via negative dielectrophoresis (nDEP). A total of 1.5 μL of product-containing cell supernatant was sampled into microcapillaries using a dead volume-reduced world-to-chip interface. The samples were analyzed with a nanoESI ion source coupled to a FT-ICR-MS (limit of detection for lysine: 0.5 pg). As a biocatalytic model system, we analyzed few Corynebacterium glutamicum DM 1919 pSenLys cells that synthesized l-lysine from d-glucose. Secreted lysine was quantified from a few cells (down to 19). Single-cell specific lysine productivities were 2 and 10 fmol/cell/h. This demonstrates that coupling microfluidics and mass spectrometry (SIC-MS) now enables the quantification of catalytic products and extracellular metabolites from only a few living microbial cells.