gebhart/patrepeval huggingface dataset:
12B-4 Real-Time Multi-Component Hemodynamic Measurement in Vascular Aneurysms Using Echo Particle Image Velocimetry: Comparison of In Vitro and Computational Results (2007)

Abdominal aortic aneurysms (AAAs) are localized balloon-shaped expansions commonly found in the infrarenal segment of the abdominal aorta, between the renal arteries and the iliac bifurcation. From a biomechanical standpoint, AAA rupture risk is related to mechanical and hemodynamic factors such as localized flow fields and velocity patterns, and flow- induced stresses within the fluid and in the aneurysm structure. Thus, localized hemodynamics proximal, within and distal to AAA formations play an important role in modulating the disease process, and non-invasive and easy-to-implement methods to characterize and quantify these complex hemodynamics would be tremendously useful. Based on the synthesis of two existing technologies, particle image velocimetry (PIV) and brightness-mode (B-mode) contrast ultrasound echo imaging, we have recently developed an ultrasound based velocimetry technique, termed echo particle image velocimetry (Echo PIV), to perform accurate non-invasive measurement of velocity profiles, multiple velocity vectors and local shear rate in arteries and hearts by identifying and tracking flow tracers (ultrasound contrast microbubbles) within the flow fields. Here, we examine the utility of Echo PIV for quantifying the complex hemodynamics found within aneurysms. Three-dimensional computational fluid dynamics (CFD) simulations were used for comparison. The Echo PIV system was used to measure velocity vectors within in vitro fusiform AAA models. Ultrasound contrast microbubbles (Optisonreg, Amersham, UK) were seeded into the flows. To verify Echo PIV results, 3D computational fluid dynamics (CFD) was used on an identical aneurysm model. The computational solid model was imported into ICEM-CFD (ANSYS Inc., PA) and meshed using 35,000 hexahedral elements. The same flow conditions were used for both in vitro and CFD studies. Comparison results show that Echo PIV measures the flow field accurately and provides clear delineation of the complex flow patterns within the AAA model. To verify the performance of the Echo PIV system on a point-by-point basis, we compared velocity profiles at the bulge center from both CFD and Echo PIV results. Difference in velocity magnitudes was < 5 %, verifying the accuracy of Echo PIV in this model. Echo PIV was also able to resolve the multiple velocity scales seen within the vascular aneurysm (< 2 cm/sec to > 20 cm/sec). These results show that our custom-designed Echo PIV system is capable of accurately providing detailed multi-component, angle- independent velocity vectors within vascular aneurysms.
The nucleophilic ring‐opening of N‐benzylquinuclidinium bromide (1997)

Abstract N ‐Benzylquinuclidinium bromide was ring opened by a series of heteronucleophiles, in the presence of cesium carbonate, to yield the corresponding N ‐benzyl‐4‐(2‐hetero‐ethyl)piperidines. The best yields were found with thiophenol (56%), phenol (55%), and benzimidazole (38%) as nucleophiles.
Surface roughness formation in Si during Cs+ ion bombardment (1994)

The dependence of the formation of surface roughness in Si on the incident angle of the Cs+ primary ion in secondary ion mass spectrometry is reported. No ripples formed in the analytical crater bottom when the primary ion incident angle was from 0° to 30° for sputtered depths of less than 4 μm, but ripples were observed when the incident angle was from 45° to 75°. The depth of ripple formation became shallower with the incident angle increasing. Cross sections of ripples observed by a scanning electron microscope and a transmission electron microscope suggest that ripples grow by forming facets from those plane faces with the largest sputtering rates so that the shapes of the facets remain constant during sputtering.
OPCML Is a Broad Tumor Suppressor for Multiple Carcinomas and Lymphomas with Frequently Epigenetic Inactivation (2008)

Thus, through functional epigenetics, we identified OPCML as a broad tumor suppressor, which is frequently inactivated by methylation in multiple malignancies.
SERUM LIPID PROFILE CHANGES WITH WEIGHT LOSS COMBINED WITH LIFESTYLE ACTIVITY OR VIGOROUS AEROBIC EXERCISE (1999)

1886 Physical inactivity and obesity are both risk factors for heart disease. The purpose of this study was to assess changes in serum lipids that accompany a 13-week weight loss program combined with either: 1) lifestyle activity or 2) vigorous aerobic exercise. The lifestyle group accumulated 30 min of moderate intensity activity throughout each day, while the aerobic group completed three bouts of vigorous exercise each week. All participants were prescribed a low fat diet of 12-1500 kcal/d. Patients were 42 obese adults with a mean baseline BMI of 30.9 ± 2.8 kg/m2. No differences in weight loss were seen between groups, which averaged 8.7 ± 3.7 kg over 13 weeks. Changes in serum lipids (* = P<0.5, † = P < 0.01) are presented below: (Table)TableThese data demonstrate that similar and significant improvements in lipid profiles can be achieved by combining weight loss with a program of either lifestyle activity or vigorous aerobic exercise. Supported by American Heart Association (MD Affiliate)
Direct Bandgap Material Based on Thin Film of Te97Ga3Nanoparticles (2012)

Thin ﬁlm of Te97Ga3 nanoparticles has been synthesized using the E-beam evaporation method. The sample was characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), Photoluminescence (PL) and Raman spectroscopy. XRD result of the deposited film suggests a polycrystalline structure, whereas, the SEM images display uniform morphology with nanoparticles of size around 15 nm. A direct bandgap (Eg) has been observed in the as-synthesized thin film, which is different to that of the microstructure counterpart. Photoluminescence and Raman spectra for this thin film were also studied. The obtained results on this Te97Ga3 nanomaterial especially its direct bandgap might be useful for development of optical disks and other semiconducting devices.
Clover V3 Assembly (2017)

We present an assembly of the genome of subterranean clover, <em>Trifolium subterraneum</em>, an important pasture legume. Specifically, <em>in situ</em> Hi-C data (48X) was used to correct misjoins and anchor, order, and orient scaffolds in a previously published genome assembly (TSUd_r1.1; scaffold N50: 287kb). This resulted in an improved genome assembly (TrSub3; scaffold N50: 56Mb) containing eight chromosome-length scaffolds that span 95% of the sequenced bases in the input assembly.
Simulations of Air-assisted Primary Atomization at Different Air-to-Liquid Injection Angles for Entrained Flow Gasification (2021)

Highly-resolved numerical simulations have been performed for a coaxial, twin-fluid nozzle, which is designed for fundamental research of the atomization process in entrained flow gasification (EFG). Objective of the work is to reveal specifically the influence of the relative injection angle $\alpha$ between the central liquid jet and the annular airflow (external-mixing) on the primary atomization. A glycerol/water mixture with a dynamic viscosity of 200 mPa·s is atomized at atmospheric condition and with a gas-toliquid ratio of 0.6. The angle of attack between liquid and airflow has been varied from $\alpha$ = 0° to 60°. The computational grid consists of approx. 10 million cells, using a smallest resolution of 25 µm. In agreement with the corresponding experiment, the calculated breakup morphology is characterized by a pulsating mode destabilization, accompanied by disintegration of membrane-type ligaments. The breakup of the liquid jet is found to be enhanced from $\alpha$ = 0° to 30°, which leads to a decrease of the liquid core length $L_C$. This is attributable to a reinforced aerodynamic interaction or an enhanced multiphase momentum transfer from the gas to the liquid phase, respectively. The gas flow velocity close to the liquid jet is increased in this case, which is in accordance with results obtained from the PIV measurement. The reason for the increase of local flow velocity is shown to be caused by an increased local static pressure at the base of the liquid jet with increased $\alpha$, which results in a favorable pressure gradient in main flow direction. However, further increase of $\alpha$ from 30° to 60° leads to a decreased flow velocity around the liquid jet, so that $L_C$ increases and the atomization performance decreases with $\alpha$. The behavior is further elucidated by means of the multiphase momentum exchange or the liquid phase kinetic energy, which increase from $\alpha$ = 0° to 30° and decreases with further increased $\alpha$. The result reveals the essential impact of the nozzle design parameters on the atomization process in addition to the general operating parameters. In summary, there exists an optimal relative injection angle between the liquid and air streams in the range of 30°
Heat and Mass Transfer Study to Understand Thermal-Cycling Absorption Process (TCAP) Scale-Up Issues (2019)

TCAP was invented by SRNL and is a world-leading technology in hydrogen isotope separation, a critical process for fusion energy development and scientific research. External interests inquiries have been received for as high as a 1000-fold throughput increase over the currently available TCAP system. This study determined a major factor impacting TCAP column scale-up. A model derived by J. Calvin Giddings indicates that the combination of a coiled packed column and an increase in the column tube radius results in reduction of column separative performance. Reevaluation of data from SRNL TCAP column testing performed in 2004 indicates that the results are consistent with the Giddings model. Work with the Auburn University Center for Microfibrous Materials Manufacturing indicates that microfibrous entrapped sorbents (MFES) made from copper microfibers and Pd K could resolve issues with channeling and improve heat transfer and cycle time in TCAP columns.
OP38 Tofacitinib for the treatment of Ulcerative Colitis: An integrated summary of safety data from the global OCTAVE and RIVETING clinical trials (2022)

Abstract Background Tofacitinib is an oral, small molecule JAK inhibitor for the treatment of ulcerative colitis (UC). Efficacy and safety of tofacitinib were evaluated in randomised, placebo-controlled Phase (P)2 (NCT00787202) and P3 (NCT01465763; NCT01458951; NCT01458574) studies, an open-label, long-term extension (OLE) study (NCT01470612) and an ongoing P3b/4 study (NCT03281304). We report updated tofacitinib safety analyses from the tofacitinib UC clinical programme, with inclusion of a 6-month interim analysis of data from the P3b/4 study, up to 7.8 years of tofacitinib exposure. Methods This analysis included 1157 patients (pts) receiving tofacitinib 5 or 10 mg BID from completed P2/P3/OLE studies, and the ongoing P3b/4 study (as of 20 Feb 2020; Overall+P3b/4 Cohort). Proportions and incidence rates (IRs; unique pts with events/100 pt-years [PY] of exposure) were evaluated for deaths and adverse events (AEs) of special interest. Opportunistic infections (OIs), malignancies, major adverse cardiovascular events (MACE) and gastrointestinal perforations were adjudicated. Results Table 1 shows demographics and clinical characteristics. In the Overall+P3b/4 Cohort, 1157 pts received ≥1 dose of tofacitinib 5 or 10 mg BID; 955 (83%) received a predominant dose of 10 mg BID; 397/1157 (34.3%) pts had received tofacitinib for &amp;gt;4.1 years. Median treatment duration was 623 (range, 1–2850) days (2999.7 PY of exposure). Table 2 shows safety data for AEs of special interest in the Overall+P3b/4 Cohort. IRs (95% confidence intervals) for all tofacitinib doses: deaths, 0.23 (0.09, 0.46); serious infections, 1.69 (1.26, 2.21); herpes zoster (non-serious and serious), 3.30 (2.67, 4.04); OIs, 1.03 (0.70, 1.46); malignancies (excluding non-melanoma skin cancer [NMSC]), 0.84 (0.55, 1.24); NMSC, 0.73 (0.45, 1.10); MACE, 0.29 (0.13, 0.55); deep vein thrombosis, 0.03 (0.00, 0.18); pulmonary embolism, 0.19 (0.07, 0.42); and gastrointestinal perforations, 0.10 (0.02, 0.28). IRs for AEs of special interest were similar to prior Overall Cohort analyses.1 Conclusion The safety profile of tofacitinib in pts with UC from the tofacitinib UC clinical programme was generally consistent with that of other UC therapies, including biologics, with the exception of herpes zoster.2 IRs for AEs of special interest have remained stable over an extended period of time (up to 7.8 years) with inclusion of final data from the OLE study and an interim analysis of data from the P3b/4 study.1,3 References 1. Sandborn WJ et al. United European Gastroenterol J 2021; 9 (Suppl 8): Abstract OP152. 2. Curtis JR et al. Inflamm Bowel Dis 2021; 27: 1394–1408. 3. Sandborn WJ et al. United European Gastroenterol J 2020; 8 (Suppl 8): Abstract OP494.
Pancreatic cancer (2014)

Pancreatic cancer remains largely an incurable disease necessitating the development of novel therapeutic approaches. Adoptive immunotherapy using chimeric antigen receptor (CAR)-transduced T cells represents an alternative treatment with curative potential. We present an overview of the engineering of novel CARs targeting prostate stem cell antigen (PSCA), implications for the development of immunotherapies, and potential strategies to circumvent on-target/off-tumor toxicities.
Holistic Valorization of Hemp through Reductive Catalytic\nFractionation (2021)

Despite the increased\nuse of hemp fiber, negligible attention has\nbeen given to upgrade the hemp hurd, which constitutes up to 70 wt\n% of the hemp stalk and is currently considered a low-value byproduct.\nIn this work, valorization of hemp hurd was performed by reductive\ncatalytic fractionation (RCF) in the presence of a metal catalyst.\nWe found an unexpectedly high yield of monophenolic compounds (38.3\nwt %) corresponding to above 95% of the theoretical maximum yield.\nThe high yield is explained by both a thin cell wall and high S-lignin\ncontent. In addition, organosolv pulping was performed to generate\na pulp that was bleached to produce dissolving-grade pulp suitable\nfor textile fiber production (viscosity, 898 mL/g; ISO-brightness,\n90.2%) and nanocellulose. Thus, we have demonstrated a novel value\nchain from a low-value side stream of hemp fiber manufacture that\nhas the potential to increase textile fiber production with 100% yield\nand also give bio-oil for green chemicals.
Control of the phase of light beams by optical feedback (1989)

It is shown that the wavefront of a relatively weak light beam can be controlled by a wavefront corrector in a feedback loop and this leads to phase modulation of the original optical field and to a considerable reduction in the optical load on the corrector.
Benchmarking energy consumption and latency for neuromorphic computing in condensed matter and particle physics (2022)

The massive use of artificial neural networks (ANNs), increasingly popular in many areas of scientific computing, rapidly increases the energy consumption of modern high-performance computing systems. An appealing and possibly more sustainable alternative is provided by novel neuromorphic paradigms, which directly implement ANNs in hardware. However, little is known about the actual benefits of running ANNs on neuromorphic hardware for use cases in scientific computing. Here we present a methodology for measuring the energy cost and compute time for inference tasks with ANNs on conventional hardware. In addition, we have designed an architecture for these tasks and estimate the same metrics based on a state-of-the-art analog in-memory computing (AIMC) platform, one of the key paradigms in neuromorphic computing. Both methodologies are compared for a use case in quantum many-body physics in two dimensional condensed matter systems and for anomaly detection at 40 MHz rates at the Large Hadron Collider in particle physics. We find that AIMC can achieve up to one order of magnitude shorter computation times than conventional hardware, at an energy cost that is up to three orders of magnitude smaller. This suggests great potential for faster and more sustainable scientific computing with neuromorphic hardware.
Is there something wrong in paradise? Christian beliefs and the safety of novel BCR/ABL1 inhibitors (2011)

We take the liberty and opportunity to discuss adverse events and event reporting in patients with chronic myeloid leukemia (CML) treated with second generation BCR/ABL1-targeting drugs. The study of Ahmet Emre Eskazan[1][1] suggests that CML patients treated with low-dose dasatinib (100 mg daily)
A Single Amino Acid Determines the Selectivity and Efficacy of Selective Negative Allosteric Modulators of CaV1.3 L-Type Calcium Channels (2020)

Ca<sup>2+</sup> channels with a Ca<sub>V</sub>1.3 pore-forming α<sub>1</sub> subunit have been implicated in both neurodegenerative and neuropsychiatric disorders, motivating the development of selective and potent inhibitors of Ca<sub>V</sub>1.3 versus Ca<sub>V</sub>1.2 channels, the calcium channels implicated in hypertensive disorders. We have previously identified pyrimidine-2,4,6-triones (PYTs) that preferentially inhibit Ca<sub>V</sub>1.3 channels, but the structural determinants of their interaction with the channel have not been identified, impeding their development into drugs. By a combination of biochemical, computational, and molecular biological approaches, it was found that PYTs bind to the dihydropyridine (DHP) binding pocket of the Ca<sub>V</sub>1.3 subunit, establishing them as negative allosteric modulators of channel gating. Site-directed mutagenesis, based on homology models of Ca<sub>V</sub>1.3 and Ca<sub>V</sub>1.2 channels, revealed that a single amino acid residue within the DHP binding pocket (M1078) is responsible for the selectivity of PYTs for Ca<sub>V</sub>1.3 over Ca<sub>V</sub>1.2. In addition to providing direction for chemical optimization, these results suggest that, like dihydropyridines, PYTs have pharmacological features that could make them of broad clinical utility.
Orca (2014)

The performance of analytical query processing in data management systems depends primarily on the capabilities of the system's query optimizer. Increased data volumes and heightened interest in processing complex analytical queries have prompted Pivotal to build a new query optimizer.
Structural Basis of the Promiscuous Inhibitor Susceptibility of Escherichia coli LpxC (2013)

The LpxC enzyme in the lipid A biosynthetic pathway is one of the most promising and clinically unexploited antibiotic targets for treatment of multidrug-resistant Gram-negative infections. Progress in medicinal chemistry has led to the discovery of potent LpxC inhibitors with a variety of chemical scaffolds and distinct antibiotic profiles. The vast majority of these compounds, including the nanomolar inhibitors L-161,240 and BB-78485, are highly effective in suppressing the activity of Escherichia coli LpxC (EcLpxC) but not divergent orthologs such as Pseudomonas aeruginosa LpxC (PaLpxC) in vitro. The molecular basis for such promiscuous inhibition of EcLpxC has remained poorly understood. Here, we report the crystal structure of EcLpxC bound to L-161,240, providing the first molecular insight into L-161,240 inhibition. Additionally, structural analysis of the EcLpxC/L-161,240 complex together with the EcLpxC/BB-78485 complex reveals an unexpected backbone flipping of the Insert I βa-βb loop in EcLpxC in comparison with previously reported crystal structures of EcLpxC complexes with l-threonyl-hydroxamate-based broad-spectrum inhibitors. Such a conformational switch, which has only been observed in EcLpxC but not in divergent orthologs such as PaLpxC, results in expansion of the active site of EcLpxC, enabling it to accommodate LpxC inhibitors with a variety of head groups, including compounds containing single (R- or S-enantiomers) or double substitutions at the neighboring Cα atom of the hydroxamate warhead group. These results highlight the importance of understanding inherent conformational plasticity of target proteins in lead optimization.
Influence of bioreactor scale and complex medium on probing control of glucose feeding in cultivations of recombinant strains of Escherichia coli (2006)

The objective of this work was to evaluate the performance of a feedback glucose control strategy (the probing strategy) in production relevant bioreactors with complex and mineral media. Experimental results from fed-batch cultivations with two recombinant Escherichia coli constructs expressing two different human therapeutic proteins were used to assess the performance and limitations of the glucose probing technique. Even though the performance of the probing strategy was affected by scale and complex media, this methodology rapidly identified a glucose feed protocol similar to an experimentally derived feed regime. This methodology may serve as a powerful tool for industrial process development and in optimization of glucose feed regimes when transferring process technology from one bioreactor system to another.
Analysis of Bone Mineral Density and Biochemical Markers in Hip Fractures Injured by Low-energy Trauma (2004)

Purpose: This study was conducted to compare bone mineral den sity (BMD) and biochemical markers of bone metabolism of an osteoporotic hip fracture group with those of a control group. Materials and Methods: The fracture group included 76 patients with hip fractures who were injured by low energy trauma from November, 1999 to August, 2003. The control group consisted of 83 patients recruited over the same period. There were 22 men and 54 women in the fracture group, with an average age of 67.2 years for men and 71.1 years for women. In the control group, there were 22 men and 61 women, of average age 67.9 years for men and 70.1 years for women. There were no siginificant differences in age, height, weight, or body mass index. We analyzed BMD by a dual energy X-ray absorptiometry (DEXA). Bone specific alkaline phosphatase (B-ALP) and osteocalcin were used as markers of bone formation and urine-deoxypyridinoline (DPD) as a maker of bone resorption. Results: B-ALP showed a significant decrease in the fracture group (p