gebhart/patrepeval huggingface dataset:
Measurement of inclusive jet cross sections in pp and PbPb collisions at sNN=2.76 TeV (2017)

Inclusive jet spectra from $pp$ and PbPb collisions at a nucleon-nucleon center-of-mass energy of $2.76\phantom{\rule{0.16em}{0ex}}\text{TeV}$, collected with the CMS detector at the CERN Large Hadron Collider, are presented. Jets are reconstructed with three different distance parameters ($R=0.2$, 0.3, and 0.4) for transverse momentum (${p}_{\mathrm{T}}$) greater than $70\phantom{\rule{0.16em}{0ex}}\mathrm{GeV}/\mathrm{c}$ and pseudorapidity $|\ensuremath{\eta}|&lt;2$. Next-to-leading-order quantum chromodynamic calculations with nonperturbative corrections are found to overpredict jet production cross sections in $pp$ for small distance parameters. The jet nuclear modification factors for PbPb compared to $pp$ collisions, show a steady decrease from peripheral to central events, along with a weak dependence on the jet ${p}_{\mathrm{T}}$. They are found to be independent of the distance parameter in the measured kinematic range.
Corepressor SMRT promotes oxidative phosphorylation in adipose tissue and protects against diet-induced obesity and insulin resistance (2011)

The ligand-dependent competing actions of nuclear receptor (NR)-associated transcriptional corepressor and coactivator complexes allow for the precise regulation of NR-dependent gene expression in response to both temporal and environmental cues. Here we report the mouse model termed silencing mediator of retinoid and thyroid hormone receptors (SMRT)(mRID1) in which targeted disruption of the first receptor interaction domain (RID) of the nuclear corepressor SMRT disrupts interactions with a subset of NRs and leads to diet-induced superobesity associated with a depressed respiratory exchange ratio, decreased ambulatory activity, and insulin resistance. Although apparently normal when chow fed, SMRT(mRID1) mice develop multiple metabolic dysfunctions when challenged by a high-fat diet, manifested by marked lipid accumulation in white and brown adipose tissue and the liver. The increased weight gain of SMRT(mRID1) mice on a high-fat diet occurs predominantly in fat with adipocyte hypertrophy evident in both visceral and s.c. depots. Importantly, increased inflammatory gene expression was detected only in the visceral depots. SMRT(mRID1) mice are both insulin-insensitive and refractory to the glucose-lowering effects of TZD and AICAR. Increased serum cholesterol and triglyceride levels were observed, accompanied by increased leptin and decreased adiponectin levels. Aberrant storage of lipids in the liver occurred as triglycerides and cholesterol significantly compromised hepatic function. Lipid accumulation in brown adipose tissue was associated with reduced thermogenic capacity and mitochondrial biogenesis. Collectively, these studies highlight the essential role of NR corepressors in maintaining metabolic homeostasis and describe an essential role for SMRT in regulating the progression, severity, and therapeutic outcome of metabolic diseases.
Sirolimus plus nintedanib treats vascular pathology in HHT mouse models (2019)

ABSTRACT Hereditary hemorrhagic telangiectasia (HHT), a genetic bleeding disorder leading to systemic arteriovenous malformations (AVMs), is caused by loss-of-function mutations in the ALK1-ENG-Smad1/5/8 pathway. Evidence suggests that HHT pathogenesis strongly relies on overactivated PI3K-Akt-mTOR and VEGFR2 pathways in endothelial cells (ECs). In the BMP9/10-immunoblocked (BMP9/10ib) neonatal mouse model of HHT, we report here that the mTOR inhibitor, sirolimus, and the receptor tyrosine-kinase inhibitor, nintedanib, could synergistically fully block, but also reversed, retinal AVMs to avert retinal bleeding and anemia. Sirolimus plus nintedanib prevented vascular pathology in the oral mucosa, lungs, and liver of the BMP9/10ib mice, as well as significantly reduced gastrointestinal bleeding and anemia in inducible ALK1-deficient adult mice. Mechanistically, in vivo in BMP9/10ib mouse ECs, sirolimus and nintedanib blocked the overactivation of mTOR and VEGFR2, respectively. Furthermore, we found that sirolimus activated ALK2-mediated Smad1/5/8 signaling in primary ECs—including in HHT patient blood outgrowth ECs—and partially rescued Smad1/5/8 activity in vivo in BMP9/10ib mouse ECs. These data demonstrate that the combined correction of endothelial Smad1/5/8, mTOR, and VEGFR2 pathways opposes HHT pathogenesis. Repurposing of sirolimus plus nintedanib might provide therapeutic benefit in HHT patients.
Synthesis and structural characterisation of novel bimetallic dipyrromethene complexes: rotational locking of the 5-aryl group (2004)

Complexation of 2,8-diethyl-1,3,7,9-tetramethyl-5-(2-pyridyl)-dipyrromethene with zinc(II) generated an unprecedented structural motif for a dipyrromethene ligand, of formula Zn2(dipyrromethene)2X2, where X represents a coordinated anion.
Experimental research on crossing shock wave boundary layer interactions (1994)

Abstract : An experimental research effort of the Penn State Gas Dynamics Laboratory on the subject of crossing shock wave boundary layer interactions is reported. This three year study was supported by AFOSR Grant 89-0315. A variety of experimental techniques were employed to study the above phenomena including planar laser scattering flowfield visualization, kerosene lampblack surface flow visualization, laser-interferometer skin friction surveys, wall static pressure measurements, and flowfield five-hole probe surveys. For a model configuration producing two intersecting shock waves, measurements were made for a range of oblique shock strengths at freestream Mach numbers of 3.0 and 3.85. Additionally, measurements were made at Mach 3.85 for a configuration producing three intersecting waves. The combined experimental dataset was used to formulate the first detailed flowfield models of the crossing-shock and triple-shock wave/boundary layer interactions. The structure of these interactions was found to be similar over a broad range of interaction strengths and is dominated by a large, separated, viscous flow region. (AN)
Preface: Special issue on “International Computational Mechanics Symposium, 2012 (ICMS2012), Kobe” (2013)

to celebrate the 25th anniversary of the Division of Computational Mechanics which was established in 1988.There were more than 170 participants from 12 countries and 12 minisymposia covering a diverse field of computational mechanics in mechanical engineering.We received more than 25 contributions to the special issue and rigorous review processes took place.It is truly our pleasure to announce today that a number of high quality papers are archived in the ICMS2012 special issue.At this opportunity, we would like to thank the authors for their contributions, all the editors and reviewers for carefully handling and reviewing the papers.
Coherent Full-Duplex Double-Sided Two-Way Ranging and Velocity Measurement Between Separate Incoherent Radio Units (2019)

This paper presents a novel coherent full-duplex (FD) double-sided two-way ranging (CFDDS-TWR) technique for wireless locating and velocity measurement between separate radio units. The idea presented here is a quantum leap in wireless locating since it enables coherent ranging, continuous phase tracking, and velocity measurement between wireless units that operate incoherently with separate low-cost crystal oscillator clock sources. Frequency modulated continuous wave chirp sequences are exchanged in a FD manner between two radio units. The signals transmitted from two radio units are received, respectively, by each of the two units and down-converted in a mixer with the receiver's own transmit signal to generate a beat signal in each unit. The two beat signals are then processed together, after one beat signal is transmitted to the partner unit. Phase coherent range and Doppler phase measurements can be conducted between incoherent radio units. The presented CFDDS-TWR technique also offers options for reducing noise-like distortions caused by mixing the products of uncorrelated phase noise. We show both analytically and experimentally that the described compensation method reduces the noise level and enhances the dynamic range of the ranging signals tremendously-as evidenced by an improvement of around 24 dB in our results. These unique signal and synchronization properties show that the CFDDS-TWR method is a highly accurate measurement approach. Results acquired with a 24-GHz test system in a 7- to 17-m range demonstrate a standard deviation in range and velocity of 0.25 mm and 0.05 mm/s, respectively.
The structure of the lantibiotic lacticin 481 produced by Lactococcus lactis: location of the thioether bridges (1996)

The lantibiotic lacticin 481 is a bacteriocin produced by Lactococcus lactis ssp. lactis. This polypeptide contains 27 amino acids, including the unusual residues dehydrobutyrine and the thioether-bridging lanthionine and 3-methyllanthionine. Lacticin 481 belongs to a structurally distinct group of lantibiotics, which also include streptococcin A-FF22, salivaricin A and variacin. Here we report the first complete structure of this type of lantibiotic. The exact location of the thioether bridges in lacticin 481 was determined by a combination of peptide chemistry, mass spectrometry and NMR spectroscopy, showing connections between residues 9 and 14, 11 and 25, and 18 and 26.
Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study (2018)

Human G-protein coupled receptors (GPCRs) are important targets for pharmaceutical intervention against neurological diseases. Here, we use molecular simulation to investigate the key step in ligand recognition governed by the extracellular domains in the neuronal adenosine receptor type 2A (hA<sub>2A</sub>R), a target for neuroprotective compounds. The ligand is the high-affinity antagonist (4-(2-(7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-ylamino)ethyl)phenol), embedded in a neuronal membrane mimic environment. Free energy calculations, based on well-tempered metadynamics, reproduce the experimentally measured binding affinity. The results are consistent with the available mutagenesis studies. The calculations identify a vestibular binding site, where lipids molecules can actively participate to stabilize ligand binding. Bioinformatic analyses suggest that such vestibular binding site and, in particular, the second extracellular loop, might drive the ligand toward the orthosteric binding pocket, possibly by allosteric modulation. Taken together, these findings point to a fundamental role of the interaction between extracellular loops and membrane lipids for ligands' molecular recognition and ligand design in hA<sub>2A</sub>R.
Sampling to make maps for site-specific weed management (2005)

Growers need affordable methods to sample weed populations to reduce herbicide use with site-specific weed management. Sampling programs and methods of developing sampling programs for integrated pest management are not sufficient for site-specific weed management because more and different information is needed to make treatment maps than simply estimate average pest density. Sampling plans for site-specific weed management must provide information to map the weeds in the field but should be developed for the objective of prescribing spatially variable management. Weed scientists will be most successful at designing plans for site-specific weed management if they focus on this objective throughout the process of designing a sampling plan. They must also learn more about the spatial distribution and dynamics of weed populations and use that knowledge to identify cost-effective plans, recommend methods to make maps as well as collect data, and find ways to evaluate maps that reflect management to be prescribed from the map. Foremost, sampling must be thought of as an ongoing process over time that uses many types of information rather than a single event of collecting one type of information. Specifically, scientists will need to identify common characteristics rather than just differences of the spatial distribution of weeds among fields and species, recognize that map accuracy may be a poor indicator of the value of a sampling plan, and develop methods to use growers' knowledge of the distribution of weeds and past spatially variable management within a field for both making a map and recommending a sampling plan. The value of proposed methods for sampling and mapping must also be demonstrated or adoption of site-specific weed management might be limited to growers who enjoy using sophisticated technology.
Phase-Space Function Recovery for Moving Target Imaging in SAR by Convex Optimization (2021)

In this paper, we present an approach for ground moving target imaging (GMTI) and velocity recovery using synthetic aperture radar. We formulate the GMTI problem as the recovery of a phase-space reflectivity (PSR) function which represents the strengths and velocities of the scatterers in a scene of interest. We show that the discretized PSR matrix can be decomposed into a rank-one, and a highly sparse component corresponding to the stationary and moving scatterers, respectively. We then recover the two distinct components by solving a constrained optimization problem that admits computationally efficient convex solvers within the proximal gradient descent and alternating direction method of multipliers frameworks. Using the structural properties of the PSR matrix, we alleviate the computationally expensive steps associated with rank-constraints, such as singular value thresholding. Our optimization-based approach has several advantages over state-of-the-art GMTI methods, including computational efficiency, applicability to dense target environments, and arbitrary imaging configurations. We present extensive simulations to assess the robustness of our approach to both additive noise and clutter, with increasing number of moving targets. We show that both solvers perform well in dense moving target environments, and low-signal-to-clutter ratios without the need for additional clutter suppression techniques.
Data from Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4–pRB Axis in Fibroblasts at the Invasive Tumor Edge (2023)

&lt;div&gt;Abstract&lt;p&gt;The invasive leading edge represents a potential gateway for tumor metastasis. The role of fibroblasts from the tumor edge in promoting cancer invasion and metastasis has not been comprehensively elucidated. We hypothesize that cross-talk between tumor and stromal cells within the tumor microenvironment results in activation of key biological pathways depending on their position in the tumor (edge vs. core). Here we highlight phenotypic differences between tumor-adjacent-fibroblasts (TAF) from the invasive edge and tumor core fibroblasts from the tumor core, established from human lung adenocarcinomas. A multiomics approach that includes genomics, proteomics, and O-glycoproteomics was used to characterize cross-talk between TAFs and cancer cells. These analyses showed that O-glycosylation, an essential posttranslational modification resulting from sugar metabolism, alters key biological pathways including the cyclin-dependent kinase 4 (CDK4) and phosphorylated retinoblastoma protein axis in the stroma and indirectly modulates proinvasive features of cancer cells. In summary, the O-glycoproteome represents a new consideration for important biological processes involved in tumor–stroma cross-talk and a potential avenue to improve the anticancer efficacy of CDK4 inhibitors.&lt;/p&gt;Significance:&lt;p&gt;A multiomics analysis of spatially distinct fibroblasts establishes the importance of the stromal O-glycoproteome in tumor–stroma interactions at the leading edge and provides potential strategies to improve cancer treatment.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by De Wever, p. 537&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Catastrophic-Optical-Damage-Free InGaN Laser Diodes With Epitaxially Formed Window Structure (2011)

High-power InGaN-based laser diodes (LDs) are expected as light-sources of various high-power applications. The catastrophic-optical-damage (COD) is a major failure mechanism to limit the output power, where optical absorption at a light-emitting facet causes an irreversible damage to the LDs. In this paper, a window structure in InGaN-based LDs to suppress the COD is demonstrated for the first time. The structure is formed by the metal organic chemical vapor deposition growth over a recess placed besides of the ridge-waveguide. The In composition in the quantum well which is corresponding to the bandgap energy is reduced by controlling the local tilt angle at the sidewall of the recess. Thus, the formed window structure eliminates undesired optical absorption at the cleaved facet so that extremely high light output power over 2 W in narrow-stripe ridge-waveguide InGaN-based blue-violet LDs is achieved without any CODs.
Research Guides: Edwin Markham Archive: Finding Aids and Shelf Lists (2012)

The Edwin Markham collection contains the correspondence, manuscripts, and personalia of American poet Charles Edwin Anson Markham.
Characterization and parameterized generation of synthetic combinational benchmark circuits (1998)

The development of new field-programmed, mask-programmed, and laser-programmed gate-array architectures is hampered by the lack of realistic test circuits that exercise both the architectures and their automatic placement and routing algorithms. In this paper, we present a method and a tool for generating parameterized and realistic synthetic circuits. To obtain the realism, we propose a set of graph-theoretic characteristics that describe a physical netlist, and have built a tool that can measure these characteristics on existing circuits. The generation tool uses the characteristics as constraints in the synthetic circuit generation. To validate the quality of the generated netlists, parameters that are not specified in the generation are compared with those of real circuits and with those of more "random" graphs.
Interventions Against West Nile Virus, Rift Valley Fever Virus, and Crimean-Congo Hemorrhagic Fever Virus: Where Are We? (2010)

ARBO-ZOONET is an international network financed by the European Commission's seventh framework program. The major goal of this initiative is capacity building for the control of emerging viral vector-borne zoonotic diseases, with a clear focus on West Nile virus, Rift Valley fever virus, and Crimean-Congo hemorrhagic fever virus. To evaluate the status quo of control measures against these viruses, an ARBO-ZOONET meeting was held in Istanbul, Turkey, from 19 to 20 November 2009. The symposium consisted of three themes: (1) vaccines: new and existing ones; (2) antivirals: existing and new developments; and (3) antivector vaccines. In addition, a satellite workshop was held on epidemiology and diagnosis. The meeting brought together foremost international experts on the subjects from both within and without the ARBO-ZOONET consortium. This report highlights selected results from these presentations and major conclusions that emanated from the discussions held.
Hematuria following stereotactic body radiation therapy (SBRT) for clinically localized prostate cancer (2015)

SBRT for prostate cancer was well tolerated with hematuria rates comparable to other radiation modalities. Patients factors associated with BPH, such as larger prostate volume, alpha antagonist usage, and prior history of procedures for BPH are at increased risk for the development of hematuria.
Building End-to-End IoT Applications with QoS Guarantees (2020)

Many industrial players are currently challenged in building distributed CPS and IoT applications with stringent end-to-end QoS requirements. Examples are Vehicle-to-X applications, Advanced Driver-Assistance Systems (ADAS) or functionalities in the Industrial Internet of Things (IIoT). Currently, there is no comprehensive solution allowing to efficiently program, deploy, and operate such distributed applications. This paper will focus on real-time concerns, in building distributed CPS and IoT systems. Thereby, the focus lies, on the one hand, on mechanisms required inside of the IoT (compute) nodes, and, on the other hand, on communication protocols such as TSN and 5G connecting them. In the authors' view, the required building blocks for a first end-to-end technology stack are available. However, their integration into a holistic framework is missing.
Computer assisted identification of metabolite mass spectra: How can machine learning and quantum mechanics help? (2016)

info:eu-repo/semantics/nonPublished
Investigation of a Premixed Reacting Jet in an Unstable Transverse Flow Field (2011)

Graduate Research Assistant, School of Aeronautics and Astronautics, AIAA Student Member 2 Formerly Post Doctoral Student at Purdue University Zucrow Laboratory; currently at Blue Origin, Kent, WA 3 Formerly Senior Engineer Purdue University Zucrow Laboratory; currently at Blue Origin, Kent, WA 4 Associate Professor of Aeronautics and Astronautics, Associate Fellow AIAA 5 Ph.D Candidate, Mechanical, Materials, and Aerospace Engineering, AIAA Student Member 6 Siemens Engineer 7 Siemens Engineer Investigation of a Premixed Reacting Jet in an Unstable Transverse Flow Field
Observations of Near‐Surface Current Shear Help Describe Oceanic Oil and Plastic Transport (2017)

Abstract Plastics and spilled oil pose a critical threat to marine life and human health. As a result of wind forcing and wave motions, theoretical and laboratory studies predict very strong velocity variation with depth over the upper few centimeters of the water column, an observational blind spot in the real ocean. Here we present the first‐ever ocean measurements of the current vector profile defined to within 1 cm of the free surface. In our illustrative example, the current magnitude averaged over the upper 1 cm of the ocean is shown to be nearly four times the average over the upper 10 m, even for mild forcing. Our findings indicate that this shear will rapidly separate pieces of marine debris which vary in size or buoyancy, making consideration of these dynamics essential to an improved understanding of the pathways along which marine plastics and oil are transported.
Metabolomics in Sepsis and Its Impact on Public Health (2017)

Sepsis, with its often devastating consequences for patients and their families, remains a major public health concern that poses an increasing financial burden. Early resuscitation together with the elucidation of the biological pathways and pathophysiological mechanisms with the use of "-omics" technologies have started changing the clinical and research landscape in sepsis. Metabolomics (i.e., the study of the metabolome), an "-omics" technology further down in the "-omics" cascade between the genome and the phenome, could be particularly fruitful in sepsis research with the potential to alter the clinical practice. Apart from its benefit for the individual patient, metabolomics has an impact on public health that extends beyond its applications in medicine. In this review, we present recent developments in metabolomics research in sepsis, with a focus on pneumonia, and we discuss the impact of metabolomics on public health, with a focus on free/libre open source software.