gebhart/patrepeval huggingface dataset:
Pharmacology of Pain (2010)

"This book provides a complete review of the pharmacology of pain, including mechanisms of drug actions, clinical aspects of drug use, and new developments. It describes the different systems involved in the perception, transmission, and modulation of pain and discusses the available options for pharmacological treatment of pain"--Provided by publisher.
High bit rate all-optical signal processing in a fiber photonic wire (2008)

We report the first demonstration of high bit rate signal processing by a fiber-based photonic wire. We achieve 160 Gb/s demultiplexing via four wave mixing in a 1.9 microm diameter photonic wire tapered from As(2)S(3) chalcogenide glass single mode fibre, with very low pump power requirements ( < 20 mW average power, 0.45 W peak power), enabled by a very high nonlinearity (gamma approximately 7850 W(-1) km (-1) ) and greatly reduced dispersion.
ChemInform Abstract: Rhodium/Chiral Diene‐Catalyzed Asymmetric 1,4‐Addition of Arylboronic Acids to Chromones: A Highly Enantioselective Pathway for Accessing Chiral Flavanones. (2015)

Abstract The challenging 1,4‐addition of a variety of aryl boronic acids (II) to chromones is realized employing a rhodium complex associated with a chiral diene ligand.
Long-term survival in non-human primates of stem cell-derived, MHC-unmatched corneal epithelial cell sheets (2022)

When corneal epithelial stem cells residing in the corneal limbus become dysfunctional, called a limbal stem cell deficiency (LSCD), corneal transparency is decreased, causing severe vision loss. Transplantation of corneal epithelial cell sheets (CEPS) derived from stem cells, including induced pluripotent stem cells, is a promising treatment for LSCD. However, the potential effect of human leukocyte antigen (HLA) concordance on CEPS transplantation has not been addressed. Here, we show that there is no difference in the immune response to CEPS between HLA-matched and -unmatched peripheral blood mononuclear cells in mixed lymphocyte reactions. CEPS transplantation in cynomolgus monkeys revealed that the immune response to major histocompatibility-unmatched CEPS was not strong and could be controlled by local steroid administration. Furthermore, programmed death ligand 1 was identified as an immunosuppressive molecule in CEPS under inflammatory conditions in vitro. Our results indicate that corneal epithelium has low immunogenicity and allogeneic CEPS transplantation requires mild immunosuppression.
Estimation of shear wave speed in the human uterine cervix (2013)

We propose that SWS estimation may be a valuable research and, ultimately, diagnostic tool for objective quantification of cervical stiffness/softness.
ChemInform Abstract: Intramolecular 1,3‐Dipolar Cyclization of Mesoionic Species Generated by Thermolysis of the Mixed Anhydrides of Acetic and N‐Alkynoyl‐1,2,3, 4‐tetrahydroisoquinoline‐3‐carboxylic Acids. (1993)

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.
Table S1 from Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma (2023)

&lt;p&gt;Supplementary Table 1&lt;/p&gt;
E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials (2022)

This work presents Neural Equivariant Interatomic Potentials (NequIP), an E(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular dynamics simulations. While most contemporary symmetry-aware models use invariant convolutions and only act on scalars, NequIP employs E(3)-equivariant convolutions for interactions of geometric tensors, resulting in a more information-rich and faithful representation of atomic environments. The method achieves state-of-the-art accuracy on a challenging and diverse set of molecules and materials while exhibiting remarkable data efficiency. NequIP outperforms existing models with up to three orders of magnitude fewer training data, challenging the widely held belief that deep neural networks require massive training sets. The high data efficiency of the method allows for the construction of accurate potentials using high-order quantum chemical level of theory as reference and enables high-fidelity molecular dynamics simulations over long time scales.
Front Matter: Volume 6842 (2008)

This PDF file contains the front matter associated with SPIE Proceedings Volume 6842, including the Title Page, Copyright information, Table of Contents, Introduction (if any), and the Conference Committee listing.© (2008) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Synthesis of KDO Using Indium-Mediated Allylation of 2,3:4,5-Di-O-isopropylidene-D-arabinose in Aqueous Media (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of KDO Using Indium-Mediated Allylation of 2,3:4,5-Di-O-isopropylidene-D-arabinose in Aqueous MediaJinming Gao, Ralph Haerter, Dana M. Gordon, and George M. WhitesidesCite this: J. Org. Chem. 1994, 59, 13, 3714–3715Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://pubs.acs.org/doi/10.1021/jo00092a040https://doi.org/10.1021/jo00092a040research-articleACS PublicationsRequest reuse permissionsArticle Views498Altmetric-Citations85LEARN 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 Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Unusual I/V characteristics of Nb/Al/AlOx/Al/AlOx/Nb SINIS tunnel junctions (2000)

Double-barrier Nb/Al-AlOx-Al-AlOx-(Al/)Nb devices with various thickness and purity of the middle Al layer were fabricated and investigated. It is found that the subgap structure that appears in the current voltage characteristics is very sensitive to the parameters of the middle film. In addition to the formerly reported gap-difference structure, we observed its half-voltage 'subharmonic' and a novel magnetic-field-sensitive structure that develops at a voltage V approximately equals (Delta) Nb/e ((Delta) Nb is the superconducting energy gap of Nb). In general, the devices with a cleaner Al electrode reveal better reproducibility of their characteristics, whereas the devices with 'impure' Al (deposited in presence of a small amount of oxygen added to the Ar) tend to have more complicated and difficult to reproduce subgap structure. In addition, an anomalously large Josephson critical current was observed for devices with a small thickness of the middle Al layer.© (2000) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.
Use of C-Reactive Protein After Spinal Surgery (2008)

CRP is more applicable, predictable, and responsive in the early postoperative period compared with ESR. The postoperative kinetics of CRP derived in this study seems to be conserved regardless of operation, magnitude, or region. Knowledge of the kinetics allows assessment of the degree of difference between actual and expected values. Using a second rise or failure to decrease as expected for CRP is sensitive for infection. A negative test is reassuring that infection is unlikely.
Single-conformation spectroscopy and population analysis of model γ-peptides: New tests of amide stacking (2011)

Single-conformation ultraviolet and infrared spectra of a series of model gamma-peptides are reported, with the goal of providing new tests of amide stacking as an amide-amide binding motif. The data also serve to illustrate the power and challenges of carrying out single-conformation spectroscopy of neutral molecules of this size in the gas phase under jet-cooled conditions. Building on recent work on Ac-γ2-hPhe-NHMe (James et al., J. Am. Chem. Soc., 2009, 131, 14243), the effects of derivatization and H2O complexation on amide stacking are studied. Ac-γ2-hPhe-N(Me)2 shows only amide stacked structures, blocking the competing position for formation of an amide-amide H-bond. The Ac-γ2-hPhe-NHMe-H2O complex includes structures in which the H2O molecule forms a bridge between the two stacked amide planes, retaining and enhancing amide stacking. IR population transfer methods are also employed to study the dynamics of photodissociation of the amide stacked-H2O complex. Finally, IR ion-gain spectroscopy is introduced as a means of recording infrared spectra containing contributions from all conformers present, based on IR-induced broadening of the UV absorptions. Its role in estimating fractional abundances is tested on Ac-γ2-hPhe-NHMe.
Efficient Exciton Transfer from In0.35Ga0.65As Template into InAs Quantum Dots Grown on GaAs （311）B Substrates (2006)

原子力量显微镜学(AFM ) 和力量依赖者微光致发光(mu-PL ) 光谱学被用来在在 GaAs (311 ) B 上在一个 In0.35Ga0.65As 模板上种的 InAs 量点(QD ) 学习结构和激子精力状态。In0.35Ga0.65As 模板，由仔细包装的连接房间的二在尺寸上的调制的层组成，有显著效果在 InAs QD 的光性质。由没有并且与 InAs，比较样品的排放系列， QD 和工作由铜锣等执行了。[J。Cryst。生长 251 (2003 ) 150；Appl。Phys.Lett。81 (2002 ) 3254 ] 我们断定 In0.35Ga0.65As 模板的存在提高 thephoto 吸收并且因此从 QD 的激子排放由于从进 QD 的模板的有效激子转移。而且，从 QD 的 PL 排放清楚地与增加刺激力量揭示四个分离精力层次， S， P， D，和 F。
Optimal Coalition Structures in Graph Games (2011)

Abstract. We consider the problem of finding the optimal coalition structure in Weighted Graph Games (WGGs), a simple restricted representation of coalitional games [12]. The agents in such games are vertices of the graph, and the value of a coalition is the sum of the weights of the edges present between coalition members. The optimal coalition structure is a partition of the agents to coalitions, that maximizes the sum of utilities obtained by the coalitions. We show that finding the optimal coalition structure is not only hard for general graphs, but is also intractable for restricted families such as planar graphs which are amenable for many other combinatorial problems. We then provide algorithms with constant factor approximations for planar, minor-free and bounded degree graphs. 1
Dual CRISPR interference and activation for targeted reactivation of X-linked endogenous FOXP3 in human breast cancer cells (2022)

The simultaneous activation and repression of the X-linked, endogenous FOXP3 and XIST from XCI offers a useful research tool and a potential therapeutic for female breast cancers.
Statistical Behavioral Models of Silicon Ring Resonators at a Commercial CMOS Foundry (2019)

We report on statistical behavioral models of silicon ring resonators in a commercial CMOS foundry. Process variability is inferred from optical tests and validated by inline metrology data. Significant reflection is observed on many designs, and the impact of reflection on system integration are discussed.
Big data analysis of cloud storage logs using spark (2017)

We use Apache Spark analytics to investigate the logs of an operational cloud object store service to understand how it is being used. This investigation involves going over very large amounts of historical data (PBs of records in some cases) collected over long periods of time retroactively. Existing tools, such as Elasticsearch-Logstash-Kibana (ELK), are mainly used for presenting short-term metrics and can-not perform advanced analytics such as machine learning. A possible solution is to save for long periods only certain aggregations or calculations produced from the raw log data, such as averages or histograms, however these must be decided in advance, and cannot be changed retroactively since the raw data has already been discarded. Spark allows us to gain insights going over historical data collected over long periods of time and to apply the historical models on online data in a simple and efficient way.
What Computer Algebra Systems Can and Cannot Do (2020)

For a family of related problems, the amount of time and memory required to complete a computation generally grows with the size of the example. Typical measures of size are the degrees or the number of digits, variables, factors, terms or matrix rows and columns in the inputs and outputs. This chapter contains estimates of the current upper boundaries for several fundamental classes of problems. Polynomial expansion is often necessary in order to enable critical cancellations. And expansion is sometimes necessary in order to explicitly exhibit certain coefficients of interest. Gaussian elimination is a common method for computing determinants or matrix inverses using approximate arithmetic on numeric entries. Computer algebra systems can be of help even when a closed-form solution is impossible or too bulky for use. Most systems provide functions that can compute a truncated series approximation to most expressions.
Guided cardiogenesis for safe stem cell-based therapy (2005)

Background/Aims Pluripotent embryonic stem cells are an emerging source for cardiotherapy, but harbor a risk for uncontrolled growth on transplantation to host tissue. This creates a need to identify a stem cell phenotype committed to the cardiac fate to achieve guided cardiogenesis for safe cell-based cardiac repair. Methods/Results Bolus delivery of uncommitted embryonic stem cells (>1000 cells/mg myocardium) into naïve hearts resulted into a teratogenic side effect. A tumor-free outcome was achieved with overexpression of the cytokine Tumor Necrosis Factor α (TNFα) which secured guided cardiogenesis of injected stem cells. Protein-based scans following TNFα stimulation demonstrated an increase in the secreted proteome, which included upregulation of downstream cardiogenic factors, such as Transforming Growth Factor β (TGFβ). With TNFα stimulation, the yield of stem cell-derived cardiomyocytes doubled, while the TGFβ antagonist, latency associated peptide, abolished the TNFα effect. The TNFα/TGFβ signaling recruited a proliferative cardiac precursor cell phenotype expressing master cardiac transcription factors, Csx/Nkx2.5 and MEF2C. Conclusions This study identifies a novel cell phenotype devoted to the cardiac fate that is recruited and amplified by TNFα initiated TGFβ signaling. With differentiation limited to cardiopotency, such cardiopoetic stem cells loose the teratenogenic capacity thereby enhancing the therapeutic index for cell-based cardiac repair. Clinical Pharmacology & Therapeutics (2005) 77, P3–P3; doi: 10.1016/j.clpt.2004.11.015
The Development of Sugar-Based Anti-Melanogenic Agents (2016)

The regulation of melanin production is important for managing skin darkness and hyperpigmentary disorders. Numerous anti-melanogenic agents that target tyrosinase activity/stability, melanosome maturation/transfer, or melanogenesis-related signaling pathways have been developed. As a rate-limiting enzyme in melanogenesis, tyrosinase has been the most attractive target, but tyrosinase-targeted treatments still pose serious potential risks, indicating the necessity of developing lower-risk anti-melanogenic agents. Sugars are ubiquitous natural compounds found in humans and other organisms. Here, we review the recent advances in research on the roles of sugars and sugar-related agents in melanogenesis and in the development of sugar-based anti-melanogenic agents. The proposed mechanisms of action of these agents include: (a) (natural sugars) disturbing proper melanosome maturation by inducing osmotic stress and inhibiting the PI3 kinase pathway and (b) (sugar derivatives) inhibiting tyrosinase maturation by blocking N-glycosylation. Finally, we propose an alternative strategy for developing anti-melanogenic sugars that theoretically reduce melanosomal pH by inhibiting a sucrose transporter and reduce tyrosinase activity by inhibiting copper incorporation into an active site. These studies provide evidence of the utility of sugar-based anti-melanogenic agents in managing skin darkness and curing pigmentary disorders and suggest a future direction for the development of physiologically favorable anti-melanogenic agents.
Human Homologs of Ubc6p Ubiquitin-conjugating Enzyme and Phosphorylation of HsUbc6e in Response to Endoplasmic Reticulum Stress (2006)

Ubiquitin-conjugating enzyme Ubc6p is a tail-anchored protein that is localized to the cytoplasmic face of the endoplasmic reticulum (ER) membrane and has been implicated in the degradation of many misfolded membrane proteins in yeast. We have undertaken characterization studies of two human homologs, hsUbc6 and hsUbc6e. Both possess tail-anchored protein motifs, display high conservation in their catalytic domains, and are functional ubiquitin-conjugating enzymes as determined by in vitro thiol-ester assay. Both also display induction by the unfolded protein response, a feature of many ER-associated degradation (ERAD) components. Post-translational modification involving phosphorylation of hsUbc6e was observed to be ER-stress-related and dependent on signaling of the PRK-like ER kinase (PERK). The phosphorylation site was mapped to Ser-184, which resides within the uncharacterized region linking the highly conserved catalytic core and the C-terminal transmembrane domain. Phosphorylation of hsUbc6e also did not alter stability, subcellular localization, or interaction with a partner ubiquitin-protein isopeptide ligase. Assays of hsUbc6e(S184D) and hsUbc6e(S184E), which mimic the phosphorylated state, suggest that phosphorylation may reduce capacity for forming ubiquitin-enzyme thiol-esters. The occurrence of two distinct Ubc6p homologs in vertebrates, including one with phosphorylation modification in response to ER stress, emphasizes diversity in function between these Ub-conjugating enzymes during ERAD processes.
Modeling the Self-assembly of the Cellulosome Enzyme (2011)

Most bacteria use free enzymes to degrade plant cell walls in nature. However, some bacteria have adopted a different strategy wherein enzymes can either be free or tethered on a protein scaffold forming a complex called a cellulosome. The study of the structure and mechanism of these large macromolecular complexes is an active and ongoing research topic, with the goal of finding ways to improve biomass conversion using cellulosomes. Several mechanisms involved in cellulosome formation remain unknown, including how cellulosomal enzymes assemble on the scaffoldin and what governs the population of cellulosomes created during self-assembly. Here, we present a coarse-grained model to study the self-assembly of cellulosomes. The model captures most of the physical characteristics of three cellulosomal enzymes (Cel5B, CelS, and CbhA) and the scaffoldin (CipA) from Clostridium thermocellum. The protein structures are represented by beads connected by restraints to mimic the flexibility and shapes of these proteins. From a large simulation set, the assembly of cellulosomal enzyme complexes is shown to be dominated by their shape and modularity. The multimodular enzyme, CbhA, binds statistically more frequently to the scaffoldin than CelS or Cel5B. The enhanced binding is attributed to the flexible nature and multimodularity of this enzyme, providing a longer residence time around the scaffoldin. The characterization of the factors influencing the cellulosome assembly process may enable new strategies to create designers cellulosomes.
Abstract 656: In Vivo Plaque Inflammation and Endothelial Permeability Independently Predict Atherosclerosis Progression: A Serial Multimodality Imaging Study (2016)

Background: Atheroma inflammation impairs plaque stability and promotes plaque progression and complications. However, it is unknown how measures of plaque biology relate to changes in plaque burden, and whether plaque biology can independently predict plaque progression in coronary-sized arteries. This study evaluated the ability of intravascular near-infrared fluorescence (NIRF) biological imaging to inform experimental atheroma progression in vivo. Methods: Atherosclerosis was induced by balloon-injury in the aorta of 14 cholesterol-fed rabbits. Serial intravascular ultrasound (IVUS) and dual-modality intravascular NIRF - optical coherence tomography (OCT) imaging was performed following injection of a NIRF molecular imaging agent of plaque inflammatory protease activity (ProSense VM110; n=7), or impaired plaque endothelial permeability (indocyanine green (ICG); n=7). Plaque progression was further assessed by IVUS change in plaque burden. Regression analysis was used to evaluate the association of NIRF with plaque progression. In vivo imaging results were corroborated by ex vivo fluorescence reflectance imaging, fluorescence microscopy, and histopathology. Results: Quantitative analysis of 1,811 axial images spanning individual plaques, the change in NIRF plaque biological signals from 8 to 12 weeks strongly correlated with IVUS plaque burden from 8 to 12 weeks (ProSense VM110: r=0.774; ICG: r=0.572; p&lt;0.0001). This finding remained significant on multivariate analysis adjusted for IVUS plaque burden, lumen area, and remodeling index (p&lt;0.001). In additional multivariate analyses, the baseline NIRF signal at 8 weeks further predicted the magnitude of plaque progression even after adjustment for baseline plaque burden (p&lt;0.001 for Prosense VM110; p=0.004 for ICG). Histology demonstrated NIRF agent uptake in inflamed, lipid-rich plaques. Conclusion: Plaque pathobiology and plaque burden progress in concert as assessed by translatable intravascular NIRF imaging technology. The baseline NIRF inflammation and impaired plaque permeability signals independently predict plaque progression. Integrated biological-microstructural imaging may enhance the ability to detect high-risk plaques at risk of progression.
Enhancing Crop Yield through Colonization of the Rhizosphere with Beneficial Microbes (2001)

At the start of this project, fungi in the genus Trichoderma were known to be potent biocontrol agents, and their primary mechanism was considered to via direct effects upon the target fungi. Due in large part to the efforts of the two PIs, we now know that this view is far too limited; while Trichoderma spp. do indeed have direct effects on pathogenic fungi, they have very far reaching effects directly upon plants. Indeed, these fungi must be considered as opportunistic plant symbionts; they provide a number of benefits to plants and themselves are favored by large numbers of healthy roots. Research under this BARD grant has demonstrated that These fungi induce resistance mechanisms in plants. They increase root development and depth of rooting; Bradyrhizobium enhances this effect in soybean. They enhance uptake of plant nutrients. They have abilities to solubilize nutrients, such as oxidized metals and insoluble phosphorus compounds by a variety of different mechanisms and biochemicals. This is a marked expansion of our knowledge of the abilities of these organisms. This knowledge has direct implications for understanding of basic plant responses and abilities, and already is being used to improve plant productivity and reduce pollution of the environment.