gebhart/patrepeval huggingface dataset:
Stabilized Optical Frequency Comb Source for Coherent Communication and Signal Processing (2007)

A semiconductor based, low noise mode-locked laser with 195 10.24 GHz spaced stabilized optical frequencies and a pulse timing jitter (1 Hz-100 MHz) of 11.4 fs for optical communication applications is demonstrated.
Molecular Details of a Coupled Binding and Folding Reaction between the Amyloid Precursor Protein and a Folded Domain (2021)

Intrinsically disordered regions in proteins often function as binding motifs in protein-protein interactions. The mechanistic aspects and molecular details of such coupled binding and folding reactions, which involve formation of multiple noncovalent bonds, have been broadly studied theoretically, but experimental data are scarce. Here, using a combination of protein semisynthesis to incorporate phosphorylated amino acids, backbone amide-to-ester modifications, side chain substitutions, and binding kinetics, we examined the interaction between the intrinsically disordered motif of amyloid precursor protein (APP) and the phosphotyrosine binding (PTB) domain of Mint2. We show that the interaction is regulated by a self-inhibitory segment of the PTB domain previously termed ARM. The helical ARM linker decreases the association rate constant 30-fold through a fast pre-equilibrium between an open and a closed state. Extensive side chain substitutions combined with kinetic experiments demonstrate that the rate-limiting transition state for the binding reaction is governed by native and non-native hydrophobic interactions and hydrogen bonds. Hydrophobic interactions were found to be particularly important during crossing of the transition state barrier. Furthermore, linear free energy relationships show that the overall coupled binding and folding reaction involves cooperative formation of interactions with roughly 30% native contacts formed at the transition state. Our data support an emerging picture of coupled binding and folding reactions following overall chemical principles similar to those of folding of globular protein domains but with greater malleability of ground and transition states.
Electronic Structure of Sr2Cu2ZnO2S2 Layered Oxysulfide with CuS Layers (2002)

The electronic structure of p-type semiconducting Sr2Cu2ZnO2S2 (SCZOS) was examined experimentally and theoretically. The band gap of SCZOS estimated by the optical absorption of its thin film was 2.7 eV, which is relatively large in chalcogenide semiconductors. Normal and inverse photoemission spectra were measured to observe the valence band or conduction band structure of this material. The observed band structure revealed that the Fermi level of SCZOS was located at the top of the valence band, and the bottom of the conduction band was approximately 2.5 eV above the Fermi level. These results demonstrate the wide-gap and p-type semiconducting nature of SCZOS. Comparison of the photoemission spectra with the density of states calculated by the tight-binding method led to the conclusion that the top of the valence band is mainly composed of a hybridized (Cu 3d)−(S 3p) band, and the bottom of the conduction band primarily consists of a dispersed Zn 4s band.
Abstract 5146: Phosphositeplus® and protein modifications in cancer, a case study: profiling tyrosine phosphorylated sites in AML and CML. (2013)

Abstract PhosphoSitePlus® (PSP) is an open, comprehensive, manually curated, and interactive resource for studying experimentally observed post-translational modifications, primarily of human and mouse proteins. It encompasses over 250,000 non-redundant modification sites, primarily phosphorylation, ubiquitinylation and acetylation. The results of thousands of mass spec experiments, many from various cancers, are aggregated and available for downloading from PSP. The cancers that are most widely represented in PSP include non-small cell lung cancer (NSCLC), chronic myelogenous leukemia (CML), acute myelogenous leukemia (AML), breast cancer (BRC), and gastric (GAC) cancer. In order to determine if the sort of binary data in PSP can be useful in identifying sites that are differentially tyrosine phosphorylated between various cancers, 284 CML and 160 AML datasets were downloaded from PSP and analyzed. Differences in the expression of tyrosine phosphorylation were observed: sites that were elevated in AML included PAG1 Tyr317/359/417, WASP Tyr291, SHP-1 Tyr536, and E-Syt1 Tyr822. Sites that were elevated in CML included Bcr and Abl sites as expected, as well as DYRK1A Tyr145, VASP Tyr39, CD2AP Tyr88, SHIP-2 Tyr986/1135/1162. These meta-analyses demonstrate that PSP provides a rich source of easily accessible data that enables proteomic profiling of multiple cancers. See www.phosposite.org Supported by NIH R44 CA126080, R43 GM65768, and R44 AA014848 Citation Format: Peter Hornbeck, Bin Zhang, Beth Murray, Elzbieta Skrzypek, Jon Kornhauser, Vaughan Latham. Phosphositeplus® and protein modifications in cancer, a case study: profiling tyrosine phosphorylated sites in AML and CML. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5146. doi:10.1158/1538-7445.AM2013-5146
Structure determination to calculate nonlinear optical coefficients in a class of organic material (1999)

A class of molecules with intramolecular two-dimensional charge transfer upon excitation has been synthesized. It is expected that these materials should be prospective candidates for nonlinear optical (NLO) applications such as second harmonic (SHG) generation. In order to optimize the macroscopic NLO properties of the compounds, it is necessary to relate their first hyperpolarizability tensors at a molecular level to those at a crystal bulk level. This requires a complete structure determination and refinement. However, the growth of sufficiently large single crystals, which are needed for structural analysis and refinement by x-ray methods, is a time-consuming and sometimes impossible task. Even larger crystals are required for NLO measurements. Single crystals of a considerably smaller size may be effectively used for complete structural analysis by electron diffraction combined with simulation methods. In addition the structure has been confirmed structure solution from electron diffraction intensities using maximum entropy and log likelihood methods. When the crystal structure of a given compound is known, its NLO properties may be estimated using quantum-mechanical methods for calculation of the molecular nonlinearity tensor and these may be related to the macroscopic coefficients of the crystalline nonlinearity tensor. In the present work, both ab initio and semiempirical quantum-mechanical calculations were employed.
Impact of the Ga flux incidence angle on the growth kinetics of\n self-assisted GaAs nanowires on Si(111) (2019)

In this work we show that the incidence angle of group-III elements fluxes\nplays a significant role on the diffusion-controlled growth of III-V nanowires\n(NWs) by molecular beam epitaxy (MBE). We present a thorough experimental study\non the self-assisted growth of GaAs NWs by using a MBE reactor equipped with\ntwo Ga cells located at different incidence angles with respect to the surface\nnormal of the substrate, so as to ascertain the impact of such a parameter on\nthe NW growth kinetics. The as-obtained results show a dramatic influence of\nthe Ga flux incidence angle on the NW length and diameter, as well as on the\nshape and size of the Ga droplets acting as catalysts. In order to interpret\nthe results we developed a semi-empirical analytic model inspired by those\nalready developed for MBE-grown Au-catalyzed GaAs NWs. Numerical simulations\nperformed with the model allow to reproduce thoroughly the experimental results\n(in terms of NW length and diameter and of droplet size and wetting angle),\nputting in evidence that under formally the same experimental conditions the\nincidence angle of the Ga flux is a key parameter which can drastically affect\nthe growth kinetics of the NWs grown by MBE.\n
Evaluation of sputtered Pd76Cu6Si18 metallic glass for MEMS application (2015)

S.240-247
Data from Semaphorin 3B Inhibits the Phosphatidylinositol 3-Kinase/Akt Pathway through Neuropilin-1 in Lung and Breast Cancer Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Semaphorin 3B (&lt;i&gt;SEMA3B&lt;/i&gt;), located at 3p21.3, is a secreted member of the semaphorin family important in axonal guidance. &lt;i&gt;SEMA3B&lt;/i&gt; undergoes allele and expression loss in lung and breast cancer and can function as a tumor suppressor. Previously, we found that SEMA3B induces apoptosis in tumor cells either by reexpression or when applied as a soluble ligand. SEMA3B-induced apoptosis was mediated, in part, by blocking vascular endothelial growth factor autocrine activity in tumor cells. In the current study, treatment of lung and breast cancer cells with picomolar concentrations of soluble SEMA3B inhibited their growth; induced apoptosis; and was associated with decreased Akt phosphorylation, increase in cytochrome &lt;i&gt;c&lt;/i&gt; release and caspase-3 cleavage, as well as increased phosphorylation of several proapoptotic proteins, including glycogen synthase kinase-3β, FKHR, and MDM-2. Lung and breast cancer lines resistant to SEMA3B did not show these signaling changes and a tumor-derived missense SEMA3B mutant was inactive in this regard, providing specificity. SEMA3B-mediated inhibition of proliferation and induction of apoptosis in cancer cells were blocked by expressing a constitutively active Akt mutant and are linked to tumor cell expression of neuropilin-1 (Np-1). SEMA3B-insensitive Np-1–negative tumor cells acquired sensitivity to SEMA3B after forced expression of Np-1, whereas SEMA3B-sensitive Np-1–positive tumor cells lost sensitivity to SEMA3B after knockdown of Np-1 by small interfering RNA. We conclude that SEMA3B is a potential tumor suppressor that induces apoptosis in SEMA3B-inactivated tumor cells through the Np-1 receptor by inactivating the Akt signaling pathway. [Cancer Res 2008;68(20):8295–303]&lt;/p&gt;&lt;/div&gt;
Creating a large angle coherent atomic beamsplitter without a magnetic field (1994)

Many atom interferometer applications would benefit from large angle atomic beamsplitters with narrow distributions. The interaction between a magnetic field and two standing wave laser fields can provide such a beamsplitter.1 Unfortunately, the required magnetic fields are undesirable in many interferometer applications, and few atomic systems have a suitable transition.
Neurotrauma: 2021 update (2021)

Despite the interruptions and restrictions to the progress of science that the COVID-19 pandemic has introduced, 2020 was marked by a number of important advances in the field of neurotrauma. Here, I will highlight what I believe are among the most important contributions. This year there were notable advances towards providing clinically useful information on neurotrauma outcome through the use of fluid biomarkers. I also introduce fascinating approaches to studying the role of microglia in nervous system repair and neuroinflammatory mechanisms leading to dysfunction through the use of colony-stimulating factor 1 receptor inhibitors, especially Plexxikon 5622 (PLX5622). Oral administration of this compound is able to deplete microglial elements and then, following withdrawal from the drug, a new population of microglia then repopulates the brain. Use of this approach in traumatic brain injury experimental models has produced important insights into the pathogenetic role of microglia in responding to this process. Important new data on the nature and distribution of tau involvement of neurons and astrocytes in cases of chronic traumatic encephalopathy (CTE) also appeared suggesting differences and similarities to Alzheimer s disease. Additionally, the use of tau-specific PET scan ligands in at-risk populations has suggested that this approach may be able to identify cases with CTE. Lastly, we note the death in the past year of a major contributor to the field of neurotrauma neuropathology, Professor J. Hume Adams.
Scaling the leading accuracy of deep equivariant models to biomolecular simulations of realistic size (2023)

This work brings the leading accuracy, sample efficiency, and robustness of deep equivariant neural networks to the extreme computational scale. This is achieved through a combination of innovative model architecture, massive parallelization, and models and implementations optimized for efficient GPU utilization. The resulting Allegro architecture bridges the accuracy-speed tradeoff of atomistic simulations and enables description of dynamics in structures of unprecedented complexity at quantum fidelity. To illustrate the scalability of Allegro, we perform nanoseconds-long stable simulations of protein dynamics and scale up to a 44-million atom structure of a complete, all-atom, explicitly solvated HIV capsid on the Perlmutter supercomputer. We demonstrate excellent strong scaling up to 100 million atoms and 70% weak scaling to 5120 A100 GPUs.
Microwave frequency beating between integrated quantum-dot ring lasers (2006)

We report on quantum-dot-based optoelectronic integrated circuit incorporating twin ring lasers, waveguides, directional couplers, Y-junction mixer, and photodetectors. Frequency beating between integrated quantum-dot ring lasers is demonstrated for the first time.
Data Supplement from Neuronal Pentraxin 2 Supports Clear Cell Renal Cell Carcinoma by Activating the AMPA-Selective Glutamate Receptor-4 (2023)

&lt;p&gt;Supplementary Figure 4. Measurement of intracellular calcium influx into (A) empty vector or (B) GluR4 transfected Caki1 cells treated with 1ng/µL R-NPTX2 and DMSO or CFM-2 (10µM) over time using the cell permeable fluorescently labeled calcium indicator Calcium GreenTM-1, AM. Results are calculated as change in fluorescence over time (min). (*) Denotes significant change in fluorescence as compared to DMSO control per time point, and (**) denotes a significant change between R-NPTX2 +/- CFM-2 treated cells. (C) Intracellular Ca2+ levels of NPTX2 and NPTX2-GluR4 transfected Caki1 cells pretreated for 1 hour with DMSO or specified doses of CFM-2. (*) Denotes a significant change in fluorescence of NPTX2 and NPTX2-GluR4 as compared to EV control, and (**) indicates significant changes in fluorescence between DMSO and CFM-2 treated groups&lt;/p&gt;
Glucose-Insulin Kinetics of the Extravascular Bioartificial Pancreas A Study Using Microencapsulated Rat Islets (1992)

The success of the extravascular bioartificial pancreas (BAP) is contingent on the rapid transfer of the glycemic signal across both an extravascular compartment and a semipermeable membrane and of insulin from the BAP to the recipient. To examine the possibility of microencapsulated islets such as the BAP to achieve satisfactory in vivo glucose-insulin kinetics, islets were isolated from Lewis rats, encapsulated in poly-L-lysine-alginate membranes, and isogenically transplanted into the peritoneal cavity of 14 streptozotocin induced diabetic rats. Fasting blood glucose (BG) was measured and intravenous glucose tolerance was tested at 8-10 weeks and compared with three control groups: 1) normal Lewis rats (n = 6); 2) untreated diabetic rats (n = 5); and 3) diabetic rats that received intraperitoneal implants of empty capsules (n = 4). Ten animals that received microencapsulated islets (5,271 +/- 431) promptly became normoglycemic, with a mean BG of 128 +/- 17 ng/dl 3 days after transplantation and maintained this level > 100 days. Intravenous glucose tolerance K-value for the group was 3.84 +/- 0.32 compared with 3.96 +/- 0.39 (p = 0.83) for the normal control group, and 0.60 +/- 0.12 (p < 0.01) and 0.40 +/- 0.15 (p < 0.01) for the diabetic control groups with and without empty capsules. The authors conclude from these results that, given sufficient beta-cell mass, a BAP without any vascular access can respond appropriately to an increase in blood glucose concentration, without overshoot hypoglycemia and within a lag lapse compatible with normal physiologic insulin delivery.(ABSTRACT TRUNCATED AT 250 WORDS)
Characterization and imaging of nanostructured materials using tabletop extreme ultraviolet light sources (2018)

Using a tabletop coherent extreme ultraviolet source, we extend current nanoscale metrology capabilities with applications spanning from new models of nanoscale transport and materials, to nanoscale device fabrication. We measure the ultrafast dynamics of acoustic waves in materials; by analyzing the material’s response, we can extract elastic properties of films as thin as 11nm. We extend this capability to a spatially resolved imaging modality by using coherent diffractive imaging to image the acoustic waves in nanostructures as they propagate. This will allow for spatially resolved characterization of the elastic properties of non-isotropic materials.
Fluorine- and Hydroxyl-Terminated Hyperbranched Poly(phenylquinoxalines) (PPQs) from Copolymerization of Self-Polymerizable AB and AB2, BA, and BA2 Monomers (2005)

The AB and AB2 quinoxaline monomers 2-(4-hydroxyphenyl)-3-phenyl-6-fluoroquinoxaline and 3-(4-hydroxyphenyl)-2-phenyl-6-fluoroquinoxaline (HPFQ) and 2,3-bis(4-hydroxyphenyl)-6-fluoroquinoxaline (BHFQ) were copolymerized to afford different degree of linear defects in hydroxyl-terminated hyperbranched poly(phenylquinoxalines) (HT-HPPQs). The other set of BA and BA2 monomers 2-(4-fluorophenyl)-3-phenyl-6-(4-hydroxyphenoxy)quinoxaline and 2-(4-fluorophenyl)-3-phenyl-6-(4-hydroxyphenoxy)quinoxaline (FPHPQ) and 2,3-bis(4-fluorophenyl)-6-(4-hydroxyphenoxy)quinoxaline (BFHPQ) were also copolymerized to prepared fluorine-terminated hyperbranched poly(phenylquinoxalines) (FT-HPPQs). On the basis of a MALDI−TOF study of the HT-HPPQ sample (AB2 20 mol %), random copolymerization indeed occurred. In the case of HT-HPPQ, the properties of polymer such as solubility, solution viscosity, Tg, and polymer degradation temperature were greatly influenced by the number of hydroxyl group on the surface. However, the properties of FT-HPPQ were much less influenced by the number of fluorine on the surface. The copolymers of AB and AB2 were soluble in most of aprotic solvents and phenolic solvents displaying intrinsic viscosities ranged from 0.27 to 1.11 dL/g in m-cresol at 30.0 ± 0.1 °C and glass transition temperatures (Tgs) ranged from 239 to 274 °C. Copolymers of BA and BA2 were also soluble in most of aprotic solvents and phenolic solvents displaying intrinsic viscosities ranged from 1.01 to 1.15 dL/g in m-cresol at 30.0 ± 0.1 °C. HT-HPPQs and FT-HPPQs underwent 5% weight losses when subjected to thermal gravimetric analysis ranged from 511 to 568 °C and from 556 to 588 °C in nitrogen atmosphere, respectively. The enhanced thermal stabilities of FT-HPPQs could be attributed to the fluorine terminal groups on the macromolecule surfaces. The melt viscosities of the HT-HPPQ sample (AB2 20 mol %) was greater than 107 Pa·s in the lower frequency range determined as a function of frequency sweep on a RMS-800 rheometer at 320 °C. The melt viscosity linearly decreased as the frequency increased. Thus, HT-HPPQ containing a 20 mol % AB2 monomer unit displayed a lower melt viscosity compared to its linear analogue at whole frequency range. However, the relative melt viscosity decrease of hyperbranched PPQ compared to its linear analogue was less than expected due to the formation of possible inter- and intramolecular hydrogen bonding.
Systematic Comparison of Two Axial Flux PM Machine Topologies: Yokeless and Segmented Armature versus Single Sided (2019)

This paper systematically compares two axial flux permanent magnet (AFPM) machines designed for a university student racing car application: a double-rotor single-stator yokeless and segmented armature (YASA) structure, and a single- stator single-rotor configuration. Both machines are optimized for minimum loss and active weight using 3D finite element analysis and the highest performing candidate designs are compared in more detail. The studies indicate that the benefits offered by the YASA configuration over the single-stator single-rotor machine are achieved only for specific designs that are heavier. For the design space with lower mass, albeit with increased losses, the Pareto front designs overlap which shows the performance of the two machines is very close to each other.
Targeting Dependency on the GPX4 Lipid Peroxide Repair Pathway for Cancer Therapy (2018)

ADVERTISEMENT RETURN TO ISSUEViewpointNEXTTargeting Dependency on the GPX4 Lipid Peroxide Repair Pathway for Cancer TherapyHengrui LiuHengrui LiuDepartment of Chemistry, Columbia University, New York, New York 10027, United StatesMore by Hengrui Liuhttp://orcid.org/0000-0002-5214-1572, Stuart L. Schreiber*Stuart L. SchreiberDepartment of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United StatesBroad Institute, Cambridge, Massachusetts 02142, United States*E-mail: [email protected]More by Stuart L. Schreiberhttp://orcid.org/0000-0003-1922-7558, and Brent R. Stockwell*Brent R. StockwellDepartment of Chemistry, Columbia University, New York, New York 10027, United StatesDepartment of Biological Sciences, Columbia University, 550 West 120th Street, MC 4846, New York, New York 10027, United States*E-mail: [email protected]More by Brent R. Stockwellhttp://orcid.org/0000-0002-3532-3868Cite this: Biochemistry 2018, 57, 14, 2059–2060Publication Date (Web):March 27, 2018Publication History Received13 March 2018Published online27 March 2018Published inissue 10 April 2018https://pubs.acs.org/doi/10.1021/acs.biochem.8b00307https://doi.org/10.1021/acs.biochem.8b00307editorialACS PublicationsCopyright © 2018 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views4974Altmetric-Citations63LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (381 KB) Get e-AlertscloseSUBJECTS:Cancer,Cancer therapy,Cells,Inhibitors,Lipids Get e-Alerts
Loss Control Measures on Capital Construction Projects (2009)

Construction is a very complex industry. Even after following many industry standards, safety rules, incidents/ accidents do happen. 95% of these incidents can be avoided with some care. Remaining 5% can be controlled with advance planning and controls. The contractor may want to increase its profit by using a bare minimum of the required safety standards. In order to be competitive during the bidding, the contractor budgets staffing, safety measures, safety submittals etc., based on the federal, state and local regulations and additional specific contract requirements. Ambiguous contract language and lack of specific requirement in the contract may lead to confusion, safety compromise and un-necessary claims.