gebhart/patrepeval huggingface dataset:
Structural basis for inactivation of PRC2 by G-quadruplex RNA (2023)

Cryo-EM structure of RNA-bound PRC2 dimer elucidates an unexpected mechanism of PRC2 inhibition by RNA.
Handbooks or Mentors? the Role of a Resident Physician Manual in Resident Education (2005)

Teaching hospitals with rotating residents face the challenge of training and orienting new personnel. We studied a pocket-sized resident manual used for meeting these challenges in a leading trauma center. This study examines motivations and barriers associated with adopting the resident manual through structured survey and semi-formal interview. Multiple factors shaped the use and effectiveness of the manual, including learning style, organizational culture, and specific usability issues. Findings suggest that organizational culture was the primary determinant of how the resident manual was used, as residents strongly favor attending physicians, fellows, and other residents as their first source of knowledge. Meanwhile, the small form factor of the resident manual afforded optimal accessibility as a quick reference source, but findings suggest enhanced searchability is necessary to realize the manual's full potential. Recommendations for future implementation strategies are made.
Interaction between complementary polymerization sites in the structural D and E domains of human fibrin. (1992)

Plasmic degradation products of human fibrin, fragments DD, D, and E, bind to fibrin. It has been inferred from this observation that the binding occurs by attraction of complementary sites located in the NH2- and COOH-terminal domains of the fibrin molecule. The interaction between fragments D1 and E1 has been investigated in this work since it represents the first step in the process of fibrin clot formation. Fragment D1, that was initially as active as fragment DD, lost most of its anticoagulant activity after purification by cation-exchange chromatography. The lability of fragment D1 function explained the previous unsuccessful attempts to form a complex between fragments D1 and E1. The loss of fragment D1 anticoagulant activity was not associated with the cleavage of the gamma 63-85 chain segment, since fragments D1A and D1 identically inhibited the fibrin monomer polymerization rate. In order to demonstrate the formation of a complex between fragments D1 and E1, three lines of experiments were advanced. First, the anticoagulant activity of fragment D1 was neutralized by fragment E1 in a dose-dependent manner, demonstrating that the association between these fragments involved polymerization sites. Second, two products, D1.E1 and D1.E1.D1, were stabilized in a reaction with bifunctional cross-linking reagents, proving the formation of D.E complexes in aqueous solution. Third, immobilized fragment D1 bound fragments E1 and E2, but not fragment E3, showing that fragments E1 and E2 attached via a polymerization site to the complementary one in fragment D1, since this association was disrupted by fibrin polymerization inhibitory peptide GPRP. These results provided direct evidence for specific binding between the structural D and E domains of fibrin mediated through complementary polymerization sites. Thus, the initial formation of fibrin clot fibers appears to be driven by specific association of these sites.
ChemInform Abstract: Overtone Line Narrowing and Intramolecular Vibrational Energy Redistribution in Substituted Toluenes (1991)

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.
LDMOS Drift Region With Field Oxides: Figure-of-Merit Derivation and Verification (2022)

We analytically and numerically investigate the performance of Laterally-Diffused Metal-Oxide-Semiconductor (LDMOS) transistors with Semi-circular Field OXide (S-FOX) focusing on mid-voltage (30 V – 100 V) power applications. We derive an analytical relation between breakdown voltage and on-resistance to realize the ideal behavior of the drift region for an LDMOS with S-FOX. Then, we find the optimized drift doping concentration minimizing the on-resistance at a given breakdown voltage. We introduce a new figure-of-merit for the drift region of a lateral device with S-FOX. We finally verify our ideal analytical findings with numerical results modeled and simulated in a commercial Technology Computer-Aided Design (TCAD).
Atropisomerism, Biphenyls, and Fluorine: A Comparison of Rotational Barriers and Twist Angles (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
PM soft magnetics knock on the door of commerciality (2007)

The net shape advantages of powder metallurgy can be applied to the manufacture of electric motors, offering the advantages of radical design alternatives…
Decoupled Control Scheme of Grid-Connected Split-Source Inverters (2017)

Grid-connected power conversion systems for renewable energy sources must fulfill several requirements, e.g., the high efficiency, the reduced cost and complexity, and, quite often, the boost capabilities that is usually achieved using a front-end dc-dc boost converter before the inversion stage, leading to a two-stage architecture. Meanwhile, single-stage power conversion systems, which perform the boosting operation within the inversion one, offer some potential advantages, in terms of reducing the complexity and the volume of the whole system. Among several proposed options, the split-source inverter (SSI) has been recently proposed by Abdelhakim et al. as an alternative option with some interesting features to the commonly used Z-source inverter. Taking into account that the SSI is controlled by a single parameter, i.e., its dc and ac sides are controlled by the modulation index, it is of paramount importance to investigate its control scheme in grid-connected mode, which has never been studied yet. Hence, this paper models the SSI dc side and proposes a modified modulation scheme combined with the commonly used synchronous reference frame control technique to achieve a decoupled control scheme of the SSI in grid-connected mode, i.e., the dc and the ac sides of the SSI can be controlled independently, which is convenient for many applications. The introduced control scheme is analyzed and simulated using a MATLAB/Simulink model, where a reduced scale 1-kVA grid-connected SSI is designed and simulated for the sake of experimental validation. Finally, the designed system is implemented experimentally to validate and verify the reported analysis and simulations.
Shared polygenic risk and causal inferences in amyotrophic lateral sclerosis (2019)

Here, we have developed a public resource (https://lng-nia.shinyapps.io/mrshiny) which we hope will become a valuable tool for the ALS community, and that will be expanded and updated as new data become available. Shared polygenic risk exists between ALS and educational attainment, physical activity, smoking, and tenseness/restlessness. We also found evidence that elevated low-desnity lipoprotein cholesterol is a causal risk factor for ALS. Future randomized controlled trials should be considered as a proof of causality. Ann Neurol 2019;85:470-481.
Time-Based Evaluation of Service-Based Business Process Elasticity in the Cloud (2013)

Cloud environments are being increasingly used for the deployment and execution of service-based business processes (SBPs). Among other properties, cloud provides elasticity in order to guarantee provisioning of necessary resources that ensure a smooth functioning of cloud services despite changes in solicitations. Provisioning of elastic infrastructures and platforms is not sufficient to provide elasticity of the deployed SBP. Therefore, SBPs should be provided with elasticity mechanisms to ensure their adaptation to the workload changes. In this paper, we propose a formal model, using timed Petri nets, for SBPs elasticity considering temporal constraints and an approach for time-based evaluation of SBPs elasticity strategies.
Sol‐Gel Synthesis of Supported Metals. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Numerical simulations used for a validity check on the laser induced photo-detachment diagnostic method in electronegative plasmas (2014)

Laser photo-detachment is used as a method to measure or determine the negative ion density and temperature in electronegative plasmas. In essence, the method consists of producing an electropositive channel (negative ion free region) via pulsed laser photo-detachment within an electronegative plasma bulk. Electrostatic probes placed in this channel measure the change in the electron density. A second pulse might be used to track the negative ion recovery. From this, the negative ion density and temperature can be determined. We study the formation and relaxation of the electropositive channel via a two-dimensional Particle-In-Cell/Mote Carlo collision model. The simulation is mainly carried out in a Hydrogen plasma with an electronegativity of α = 1, with a parametric study for α up to 20. The temporal and spatial evolution of the plasma potential and the electron densities shows the formation of a double layer (DL) confining the photo-detached electrons within the electropositive channel. This DL evolves into two fronts that move in the opposite directions inside and outside of the laser spot region. As a consequence, within the laser spot region, the background and photo-detached electron energy distribution function relaxes/thermalizes via collisionless effects such as Fermi acceleration and Landau damping. Moreover, the simulations show that collisional effects and the DL electric field strength might play a non-negligible role in the negative ion recovery within the laser spot region, leading to a two-temperature negative ion distribution. The latter result might have important effects in the determination of the negative ion density and temperature from laser photo detachment diagnostic.
Advances in the use of radiotherapy to reduce second breast cancers (2014)

David Brenner* speaks to Ruth Williamson, Commissioning Editor of Breast Cancer Management: David Brenner focuses on developing mechanistic models for the effects of ionizing radiation on living systems, dividing his research between the effects of high doses of ionizing radiation (relating to radiation therapy) and the effects of low doses of radiation (relating to medical, environmental and occupational exposures). In the field of medical imaging, he has focused on the risk–benefit balance of higher-dose imaging techniques; and in the field of radiotherapy, he has focused on optimizing fractionation schemes for different tumor types, to maximize tumor killing and minimize serious side effects. As well as being Director of the Center for Radiological Research (Columbia University, CO, USA), Brenner is the Director of the Radiological Research Accelerator Facility (Columbia University) and principal investigator of the Center for High-Throughput Minimally-Invasive Radiation Biodosimetry (Columbia University).
Tissue-type plasminogen activator variants with domain duplications and rearrangements (1989)

The interactions between tPA domains that are important for catalysis are poorly understood. We have probed the function of interdomain interactions by generating tPA variants in which domains are duplicated or rearranged. The proteins were expressed in a transient mammalian expression system and tested in vitro for their ability to activate plasminogen, induce fibrinolysis and bind to a forming fibrin clot. Duplication of the heavy chain domains of tPA produced enzymatically active tPA variants, many of which demonstrated similar in vitro amidolytic and fibrinolytic activity and similar fibrin affinity to the parent molecule. Zymographic analysis of the domain duplication tPA variants showed one major active species for each variant. Selection of the residues duplicated and the interdomain spacing were found to be critical considerations in the design of tPA variants with duplicated domains. We also rearranged the domains of tPA such that kringle 1 replaced the second kringle domain and vice versa. An analysis of these variants indicates that the first kringle domain can confer fibrin affinity to a tPA variant and function in place of kringle 2. Therefore, in wild-type tPA, the functions of kringle 1 and kringle 2 must be dependent partially on their orientation within the heavy chain of the protein. The functional autonomy of the heavy and light chains of tPA is demonstrated by the activity of a tPA variant in which the order of the heavy and light chains was reversed.
Salvage Treatment for Advanced Gastric Cancer Using FEP (5-FU, Etoposide, Cisplatin) Combination Chemotherapy (2002)

FEP combination chemotherapy seems to be an effective treatment regimen for gastric cancer as salvage chemotherapy. To confirm these results, large scale of clinical trials will be required.
Supplementary Methods from The Effect of Mouse Strain, Sex, and Carcinogen Dose on Toxicity and the Development of Lung Dysplasia and Squamous Cell Carcinomas in Mice (2023)

&lt;p&gt;Supplementary Methods&lt;/p&gt;
Draft genome sequence of Enterococcus faecium strain LMG 8148 (2016)

Enterococcus faecium, traditionally considered a harmless gut commensal, is emerging as an important nosocomial pathogen showing increasing rates of multidrug resistance. We report the draft genome sequence of E. faecium strain LMG 8148, isolated in 1968 from a human in Gothenburg, Sweden. The draft genome has a total length of 2,697,490 bp, a GC-content of 38.3 %, and 2,402 predicted protein-coding sequences. The isolation of this strain predates the emergence of E. faecium as a nosocomial pathogen. Consequently, its genome can be useful in comparative genomic studies investigating the evolution of E. faecium as a pathogen.
High-pressure structure and equation of state study of nitrosonium nitrate from synchrotron x-ray diffraction (2003)

Several nitrogen oxide compounds transform to nitrosonium nitrate (NO+NO3−) under high pressure. In this study, NO+NO3− was synthesized by laser heating of N2O in a diamond-anvil cell and characterized by x-ray diffraction as a function of pressure at room temperature and low temperature. The unit-cell parameters were refined up to 32.2 GPa at 300 K, resulting in a denser structure than reported previously. The pressure-volume relations for NO+NO3− at 300 K were fitted to both Birch-Murnaghan and Vinet equations of state. The analysis indicates that NO+NO3− is denser than other nitrogen-oxygen assemblages, consistent with the conclusion that formation of the ionic species is driven by density rather than entropic effects. The low-temperature x-ray-diffraction data represent the first in situ measurements for this material, revealing consistent structural information and evolutions under pressure. These observations provide additional information on the stability relations and reaction diagram of N2O and NO+NO3−.
Pericyte-Like Progenitors Show High Immaturity and Engraftment Potential as Compared with Mesenchymal Stem Cells (2012)

Mesenchymal stem cells (MSCs) and pericyte progenitors (PPs) are both perivascular cells with similar multipotential properties regardless of tissue of origin. We compared the phenotype and function of the 2 cell types derived from the same bone-marrow samples but expanded in their respective media - pericyte conditions (endothelial cell growth medium 2 [EGM-2]) for PPs and standard medium (mesenchymal stem cell medium [MSM]) for MSCs. After 3 weeks of culture, whatever the expansion medium, all cells showed similar characteristics (MSC markers and adipo-osteo-chondroblastic differentiation potential), although neuronal potential was greater in EGM-2- than MSM-cultured cells. As compared with MSM-cultured MSCs, EGM-2-cultured PPs showed higher expression of the pericyte-specific antigen 3G5 than α-smooth muscle actin. In addition, EGM-2-cultured PPs showed an immature phenotype, with upregulation of stemness OCT4 and SOX2 proteins and downregulation of markers of osteoblastic, chondroblastic, adipocytic and vascular smooth muscle lineages. Despite having less effective in vitro immunosuppression capacities than standard MSCs, EGM-2-cultured PPs had higher engraftment potentials when combined with biomaterials heterotopically-transplanted in Nude mice. Furthermore, these engrafted cells generated more collagen matrix and were preferentially perivascular or lined trabeculae as compared with MSM-cultured MSCs. In conclusion, EGM-2-cultured PPs are highly immature cells with increased plasticity and engraftment potential.
Regulators of G Protein Signaling 6 and 7 (1999)

Regulators of G protein signaling (RGS) proteins that contain DEP (disheveled, EGL-10, pleckstrin) and GGL (G protein gamma subunit-like) domains form a subfamily that includes the mammalian RGS proteins RGS6, RGS7, RGS9, and RGS11. We describe the cloning of RGS6 cDNA, the specificity of interaction of RGS6 and RGS7 with G protein beta subunits, and certain biochemical properties of RGS6/beta5 and RGS7/beta5 complexes. After expression in Sf9 cells, complexes of both RGS6 and RGS7 with the Gbeta5 subunit (but not Gbetas 1-4) are found in the cytosol. When purified, these complexes are similar to RGS11/beta5 in that they act as GTPase-activating proteins specifically toward Galpha(o). Unlike conventional G(betagamma) complexes, RGS6/beta5 and RGS7/beta5 do not form heterotrimeric complexes with either Galpha(o)-GDP or Galpha(q)-GDP. Neither RGS6/beta5 nor RGS7/beta5 altered the activity of adenylyl cyclases types I, II, or V, nor were they able to activate either phospholipase C-beta1 or -beta2. However, the RGS/beta5 complexes inhibited beta(1)gamma(2)-mediated activation of phospholipase C-beta2. RGS/beta5 complexes may contribute to the selectivity of signal transduction initiated by receptors coupled to G(i) and G(o) by binding to phospholipase C and stimulating the GTPase activity of Galpha(o).
Cellulose Nanocrystal Gels with Tunable Mechanical Properties from Hybrid Thermal Strategies (2023)

Gels are useful materials for drug delivery, wound dressings, tissue engineering, and 3D printing. These various applications require gels with different mechanical properties that can be easily tuned, also preferably excluding the use of chemical additives, which can be toxic or harmful to the body or environment. Here, we report a novel strategy to synthesize cellulose nanocrystal (CNC) gels with tunable mechanical properties. Sequential freeze-thaw cycling and hydrothermal treatments were applied to CNC suspensions in different orders to give a series of pristine CNC hydrogels. Freeze-drying of the hydrogels also afforded a series of lightweight CNC aerogels. The mechanical properties of the hydrogels and aerogels were studied by rheological measurements and compression strength tests, respectively. Specifically, the complex modulus of CNC hydrogels ranged from 160 to 32,000 Pa among eight different hydrogels, while Young's modulus of CNC aerogels was tuned from 0.114 to 3.98 MPa across five different aerogels. The microstructures of aerogels were also investigated by scanning electron microscopy and X-ray microtomography, which revealed remarkable differences between the materials. Solvent sorption-desorption tests showed that the reinforced networks have excellent stability over the basic CNC aerogels in ethanol, demonstrating a material enhancement from the preparation strategies we developed. Thermal conductivity and thermal stability for these materials were also investigated, and it was found that the lowest thermal conductivity was 0.030 W/m K, and all of the aerogels are generally stable below 280 °C. These characteristics also expand the potential applications of this family of CNC gels to lightweight supporting materials and thermal insulators.
Guanylyl Cyclase Activity Associated with Putative Bifunctional Integral Membrane Proteins in Plasmodium falciparum (2000)

We report here that guanylyl cyclase activity is associated with two large integral membrane proteins (PfGCalpha and PfGCbeta) in the human malaria parasite Plasmodium falciparum. Unusually, the proteins appear to be bifunctional; their amino-terminal regions have strong similarity with P-type ATPases, and the sequence and structure of the carboxyl-terminal regions conform to that of G protein-dependent adenylyl cyclases, with two sets of six transmembrane sequences, each followed by a catalytic domain (C1 and C2). However, amino acids that are enzymatically important and present in the C2 domain of mammalian adenylyl cyclases are located in the C1 domain of the P. falciparum proteins and vice versa. In addition, certain key residues in these domains are more characteristic of guanylyl cyclases. Consistent with this, guanylyl cyclase activity was obtained following expression of the catalytic domains of PfGCbeta in Escherichia coli. In P. falciparum, expression of both genes was detectable in the sexual but not the asexual blood stages of the life cycle, and PfGCalpha was localized to the parasite/parasitophorous vacuole membrane region of gametocytes. The profound structural differences identified between mammalian and parasite guanylyl cyclases suggest that aspects of this signaling pathway may be mechanistically distinct.
Salt nanoconfinement in zirconium-based metal–organic frameworks leads to pore-size and loading-dependent ionic conductivity enhancement (2020)

The effect of nanoscale confinement of a salt on its ionic conductivity was studied for [NEt4][TFSI] melt-loaded in three isoreticular zirconium-based MOFs: UiO-66, UiO-67, and PCN-56. Conductivity of the MOF-salt composites was up to a factor of 50 higher than the pure salt, and maximized with slightly less than full loading of the MOFs.
The natural history of locally confined prostate cancer: A review (1992)

The incidence of prostate cancer rises steeply in men over the age of 50 years. Mortality due to prostate cancer also increases, but not at the same rate as the incidence. In the U.S.A., a man has a lifetime risk of developing prostate cancer of about 1 in 11, but his risk of dying of the disease is about 1 in 22-33. Tumor DNA ploidy is one of the predictive features of the growth rate of prostate cancer. Patients with diploid tumors have a more favorable prognosis than those with aneuploid tumors, regardless of the stage or grade. Patients with stage A1 defined disease (less than 5% of the specimen being cancerous) have a relatively low risk of progression (about 12%) and death (about 3%). Evidence suggests that transurethral resection of the prostate (TURP) is effective in removing disease in about 62% of cases. Expectant management involves following a patient and giving hormonal therapy or TURP as necessary. Four studies with follow-up periods of 4-10 years have shown that the metastatic disease rate ranges from 9 to 37% and that deaths from prostate cancer range from 9 to 16%. Results from animal studies suggest that hormonal therapy only improves survival if it is given at the time of tumor implantation or shortly after, though it can be effective palliative treatment.
COMPACT BACKSCATTER FIBER OPTIC SYstems FOR SUBMICROSCOPIC PARTICLE SIZING (1994)

ABSTRACT A compact backscatter fiber optic system, comprising a semiconductor laser diode, a fiber optic probe and a self-contained photomultiplier, is described. Backscatter fiber optic probes provide easy access over a range of scattering angles between 95 and 175 degrees. Accuracy of the portable dynamic light scattering system is assessed through measurements made on a 39 nm polystyrene latex spheres suspension.
Supplementary Figure 3 from Integrative Radiogenomic Profiling of Squamous Cell Lung Cancer (2023)

&lt;p&gt;PDF file, 20K, High-throughput profiling of lung cancer cell lines.&lt;/p&gt;