gebhart/patrepeval huggingface dataset:
Activation of [CrCl3{R-SN(H)S-R}] Catalysts for Selective Trimerization of Ethene: A Freeze-Quench Cr K-Edge XAFS Study (2014)

Homogeneous chromium catalysts for the selective conversion of ethene to hex-1-ene are formed from Cr(III) reagents, aminothioether ligands of the type HN(CH2CH2SR)2, and aluminum reagents. In this study, the early activation steps are investigated by EPR, UV–visible, and Cr K-edge XAFS spectroscopy; rapid stopped-flow mixing and a freeze-quench allows good quality EXAFS analysis of a species formed in ∼1 s of reaction. This is shown to involve reduction to Cr(II) and deprotonation of a NH group of the auxiliary ligand. This 4-coordinate metal center may act as precursor for the coordination of ethene and subsequent selective oligomerization.
PATH-07. INFRATENTORIAL HIGH-GRADE GLIOMAS: NEUROSURGICAL CASE SERIES WITH MOLECULAR ANALYSIS (2021)

Abstract INTRODUCTION Most high grade gliomas (HGG) are located supratentorially, while less than 1% arise infratentorially. Growing evidence suggests that infratentorial HGGs (iHGG) represent a collection of distinct molecular entities and that further elucidation of their molecular features can help guide management. We perform here a clinical and molecular analysis of our institutional iHGG case series. METHODS We retrospectively reviewed iHGG patients treated surgically at Brigham and Women’s Hospital (1992-2020), and evaluated their history of prior malignancies, tumor location, treatment, molecular profile, tumor recurrence, and survival. iHGG were identified by review of pathology records, using WHO Histologic Grading Criteria as grade III-IV gliomas located infratentorially. Molecular analysis data was obtained from pathology records. RESULTS Among 37 iHGGs, 16 (43%) were glioblastomas, 11 (30%) were anaplastic astrocytomas, 2 (5%) were diffuse midline gliomas, 2 (5%) were infiltrating gliomas, 2 (5%) were anaplastic ependymomas, 1 (3%) was an anaplastic oligodendroglioma, and 3 (8%) were HGG not otherwise specific. Sixteen (43%) patients were female, median age was 49 years. Fifteen patients had history prior malignancy, 11 of which received radiation and 8 chemotherapy. Surgical resection of iHGG included gross total resection in 4 (11%) and subtotal in 33 (89%). Twenty-one patients (57%) received adjuvant radiation and 19 (51%) chemotherapy. At follow-up, 13 (35%) patients demonstrated symptomatic deterioration, 15 (41%) were stable, and 7 (19%) were improved. Seven patients (19%) experienced recurrence at a mean time of 19 months, and one-year survival was 35%. Molecular analysis revealed 7/15 (47%) tumors were MGMT promoter methylated, IDH was mutated in 3/24 (13%), EGFR was amplified in 3/10 (30%), CDKN2A/B homozygous deletion in 4/7 (57%), TP53 was mutated in 14/15 (93%), and H3K27M was present in 4/10 (40%). CONCLUSIONS iHGGs demonstrate substantial distinction from their supratentorial counterparts. Herein we examined their clinical course, molecular features, management, and outcomes.
Survival ability of clinical isolates of methicillin-resistant Staphylococcus aureus. (1993)

The survival abilities of methicillin-resistant strains of Staphylococcus aureus were compared with those of sensitive strains. Absorbent cotton was inoculated with 10(8) cells of each strain tested and stored at 30% humidity at 25 degrees C. The numbers of cells of sensitive strains decreased significantly to well below those of resistant strains after 4 weeks, while cells of resistant strains remained above 10(3) after 14 weeks.
Aware of Scene Vehicles—Probabilistic Modeling of Car-Following Behaviors in Real-World Traffic (2018)

Heterogeneity exists in car following behaviors due to the driver's habit, fatigue, distraction, or surrounding traffic. This research proposes a method of modeling and reasoning heterogeneous car-following behaviors based on a stochastic system, where scene vehicles are involved explicitly in addition to the traditional leader-follower pair in characterizing driving situations, a hidden variable (driver state) is introduced to conjugate driving situations to heterogeneous models in predicting a driver's acceleration control, and the dynamic procedure is described using a dynamic Bayesian network. Experiments are conducted using a large set of naturalistic driving data that were collected by driving an instrumented vehicle on the multi-lane motorways in Beijing, where four distinctive driver states are learnt from data, characterizing the car-following procedure with normal, slow responsive, strong and prompt responsive, and unresponsive behavioral styles. By using the proposed scene-aware multi-state model for acceleration prediction, the error is reduced to 0.19 m/s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in average compared with 0.29 m/s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> of a single-state model. Influence of scene vehicles on a driver state and subsequently on velocity control is verified based on the data. To the best of our knowledge, this is the first work that explicitly incorporates scene vehicles as influential factors in a probabilistic approach for modeling and reasoning heterogeneous car-following behaviors, and the performance is demonstrated on a large set of naturalistic driving data.
The cellular pathology of lysosomal diseases (2011)

With a constitutive recycling function and the capacity to digest exogenous material as well as endogenous organelles in the process of autophagy, lysosomes are at the heart of the living cell. Dynamic interactions with other cellular components ensure that the lysosomal compartment is a central point of convergence in countless diverse diseases. Inborn lysosomal (storage) diseases represent about 70 genetically distinct conditions, with a combined birth frequency of about 1 in 7500. Many are associated with macromolecular storage, causing physical disruption of the organelle and cognate structures; in neurons, ectopic dendritogenesis and axonal swelling due to distension with membraneous tubules and autophagic vacuoles are observed. Disordered autophagy is almost universal in lysosomal diseases but biochemical injury due to toxic metabolites such as lysosphingolipid molecules, abnormal calcium homeostasis and endoplasmic reticulum stress responses and immune-inflammatory processes occur. However, in no case have the mechanistic links between individual clinico-pathological manifestations and the underlying molecular defect been precisely defined. With access to the external fluid-phase and intracellular trafficking pathways, the lysosome and its diseases are a focus of pioneering investment in biotechnology; this has generated innovative orphan drugs and, in the case of Gaucher's disease, effective treatment for the haematological and visceral manifestations. Given that two-thirds of lysosomal diseases have potentially devastating consequences in the nervous system, future therapeutic research will require an integrative understanding of the unitary steps in their neuro pathogenesis. Informative genetic variants illustrated by patients with primary defects in this organelle offer unique insights into the central role of lysosomes in human health and disease. We provide a conspectus of inborn lysosomal diseases and their pathobiology; the cryptic evolution of events leading to irreversible changes may be dissociated from the cellular storage phenotype, as revealed by the outcome of therapeutic gene transfer undertaken at different stages of disease.
Reciprocity and optical chirality (2017)

In this text we describe the role of optical chirality in the context of plasmonics. We clearly distinguish between 2D an 3D optical chirality and connect the problem with reciprocity and time symmetry. We compare our analysis with recent experimental results in nano-plasmonics and photonics.
Photochemical reaction at 3500 A. of nitric oxide with cyclohexane and toluene (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemical reaction at 3500 A. of nitric oxide with cyclohexane and tolueneJohn F. W. Keana and Carroll C. WrightCite this: J. Org. Chem. 1969, 34, 3, 729–730Publication Date (Print):March 1, 1969Publication History Published online1 May 2002Published inissue 1 March 1969https://pubs.acs.org/doi/10.1021/jo01255a053https://doi.org/10.1021/jo01255a053research-articleACS PublicationsRequest reuse permissionsArticle Views57Altmetric-Citations2LEARN 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-Alertsclose Get e-Alerts
Supplemental Figures 1-9 from Combined Targeting of the BRD4–NUT–p300 Axis in NUT Midline Carcinoma by Dual Selective Bromodomain Inhibitor, NEO2734 (2023)

&lt;p&gt;Supplemental Figure S1: NEO2734 induces differentiation in 10-15 cells. Supplemental Figure S2: Caspase-mediated apoptosis plays a minimal role in the activity of GNE-781, OTX015, or NEO2734. Supplemental Figure S3: BRD4-NUT protein levels decrease slightly upon exposure to NEO2734. Supplemental Figure S4: Global H3K27Ac levels do not change upon exposure to NEO2734. Supplemental Fig. S5. BRD4-NUT foci diminish over time course in TC-797 cells. Images were taken at identical magnification (1000x) with identical exposure settings per stain. Supplemental Figure S6. Dot plots of fold change of gene expression in samples treated with the indicated compound versus that in DMSO-treated samples. Supplemental Figure S7: Proportion of differentially expressed genes overlapping BRD4-NUT megadomains is greater in genes whose expression is downregulated in the presence of p300/CBP and/or BET bromodomain inhibition. Supplemental Figure S8: Tolerability in the full 10-15 mouse xenograft study. Supplemental Figure S9: Cleaved PARP is unchanged, but BRD4-NUT is somewhat depleted in mouse xenograft tumors exposed to NEO2734.&lt;/p&gt;
Studies of Some Strained-Ring Systems: Tricyclo-Octanes (1979)

&lt;p&gt;The present study has been directed towards the synthesis and base promoted rearrangements of some saturated and unsaturated halogenotricyclo-octanes. The preparation of a number of previously unknown 4,4,8- and 4,4,8,8-tetra-halogeno-anti-tricyclo[5,1,0,03,5]- octanes and the corresponding 3,3,8-tri- and 3,3,8,8-tetra-halogeno-anti-tricyclo[5,1,0,02,4] octanes has been accomplished and the stereo-chemistries of their ring systems established. The former tricyclo-octanes are base sensitive and on treatment with potassium t-butoxide give rise to mixtures of (E) - and (Z) -Beta-t-butoxystyrenes. However, the anti-tricyclo[5,1,0,02,4] octanes give no characterisable products on treatment with base. The mechanistic implications of the tricycle-octane - styrene conversion have been studied in some detail and halogenocyclo-octatetraenes and phenylacetylenes have been eliminated as intermediates. The behaviour of several methoxy-substituted 4,4,8,8-tetrahalogeno-anti-tricyclo[5,1,0,03,5] octanes with the same base has been studied, and it has been found that homotropilidenes are formed regiospecifically by 1,4-elimination. These conversions constitute the first known examples of such elimination experienced by ring-fused halogenocyclopropanes. From these studies, evidence is presented which implicates homotropilidenes and bicyclo[4,2,0]octa-2,4-dienes as intermediates in the production of styrenes, and a mechanism for the tricyclo-octane - styrene rearrangement has been proposed. A new and potentially versatile synthesis of 3,3-dihalogeno-anti tricyclo[5,1,0,02,4] oct-5-enes (anti-bishomobenzenes) has been developed. The new route employs readily available starting materials, involves sequential introduction of the cyclopropyl, gem-dihalogenocyclopropyl, and olefinic moieties and proceeds in an overall yield of about 14%. This represents a five-fold increase over the previously reported yields.&lt;/p&gt;
Energy-Shunting Hip Padding System Attenuates Femoral Impact Force in a Simulated Fall (1995)

Recent studies suggest that hip padding systems reduce the incidence of hip fractures during falls. However, no data exist on the force attenuating capacity of hip pads under realistic fall impact conditions, and thus it is difficult to compare the protective merit of various pad designs. Our goal is to design a comfortable hip padding system which reduces femoral impact force in a fall below the mean force required to fracture the elderly cadaveric femur. In pursuit of this objective, we designed and constructed a hip pad testing system consisting of an impact pendulum and surrogate human pelvis. We then developed a hip pad containing a shear-thickening material which allows for shunting of the impact energy away from the femur and into the surrounding soft tissue. Finally, we conducted experiments to assess whether the surrogate pelvis accurately represents the impact behavior of the human female pelvis in a fall, and to determine whether our energy-shunting pad attenuates femoral impact force in a fall more effectively than seven available padding systems. We found the surrogate pelvis accurately represented the human female pelvis in regional variation in soft tissue stiffness, total effective stiffness and damping, and impact force attenuation provided by trochanteric soft tissues. We also found that our padding system attenuated femoral impact force by 65 percent, thereby providing two times the force attenuation of the next best system. Moreover, the energy-shunting pad was the only system capable of lowering femoral impact force well below the mean force required to fracture the elderly femur in a fall loading configuration. These results suggest that the force attenuating potential of hip pads which focus on shunting energy away from the femur is superior to those which rely on absorbing energy in the pad material. While these in-vitro results are encouraging, carefully designed prospective clinical trials will be necessary to determine the efficacy of these approaches to hip fracture prevention.
Named Entity Recognition and Relation Extraction with Graph Neural Networks in Semi Structured Documents (2021)

The use of administrative documents to communicate and leave record of business information requires of methods able to automatically extract and understand the content from such documents in a robust and efficient way. In addition, the semi-structured nature of these reports is specially suited for the use of graph-based representations which are flexible enough to adapt to the deformations from the different document templates. Moreover, Graph Neural Networks provide the proper methodology to learn relations among the data elements in these documents. In this work we study the use of Graph Neural Network architectures to tackle the problem of entity recognition and relation extraction in semi-structured documents. Our approach achieves state of the art results in the three tasks involved in the process. Additionally, the experimentation with two datasets of different nature demonstrates the good generalization ability of our approach.
Surface roughness index, a novel approach to compare protein surfaces (2005)

In course of evolution similar sequences may diverge to change topology of the structure but active sites that are essential to protein function have a possibility to be maintained. Moreover, protein molecules of overall different structures could converge to similar functions by evolutionary development of similar active sites. In such cases, mere sequence based structure comparisons are likely to be inadequate in describing or identifying protein functions and evolutionary relationships among them. In this paper we show the importance of studying the surface roughness of protein to get the holistic information about protein structural similarity profile. Using an invariant coordinate system designed and referred by us as molecular coordinate system we have introduced a new parameter surface roughness index (SRI) to study the protein surface. The possible utility of SRI to explore protein structure is discussed.
The Multifaceted Mechanism of Leptin Signaling within Tumor Microenvironment in Driving Breast Cancer Growth and Progression (2014)

Adipokines represent likely candidates to mediate the increased breast cancer risk and the enhanced progression associated with obesity. Other contributors to obesity-related cancer progression are insulin/IGF-1 pathways and hormones. Among these, the adipokine leptin is the most intensively studied in both metabolism in general and in cancer due to the fact that leptin levels increase in proportion of fat mass. Leptin is primarily synthesized from adipocytes but it is also produced by other cells including fibroblasts. In this latter case, it has been well demonstrated how cancer-associated fibroblasts express leptin receptor and secrete leptin, which sustains a short autocrine loop and is able to target tumor epithelial cells enhancing breast cancer cell motility and invasiveness. In addition, it has been reported that leptin may induce breast cancer to undergo a transition from epithelial to spindle-like mesenchymal morphology, activating the signaling pathways devoted to the EMT. Thus, it emerges how leptin may play a crucial role in mediating malignant cell and tumor microenvironment interactions. Here, we present an overview of the role of leptin in breast cancer, covering the following topics: (1) leptin as an amplifier of estrogen signaling in tumor epithelial cells contributing to the promotion of carcinogenesis; (2) leptin as a crucial player in mediating tumor-stroma interaction and influencing EMT-linked mechanisms, that may sustain breast cancer growth and progression; (3) leptin and leptin receptor targeting as novel therapeutic strategies for breast cancer treatment.
Tip asymptotic of a hydraulic fracture driven by a power law fluid accounting for the presence of a fluid lag (2017)

We investigate the tip region of a hydraulic fracture driven by a power law fluid propagating at a constant velocity in an impermeable linear elastic isotropic medium. We account for the presence of a fluid lag of a priori unknown length at the tip of the fracture. The fluid pressurized fracture propagates perpendicular to the far-field compressive minimum stress in pure opening mode. The solution of this semi-infinite hydraulic fracture problem combines elastic deformation, lubrication flow in the filled region of the fracture and the quasi-static equilibrium fracture propagation condition. It exhibits a multiscale structure related to the strong fluid solid coupling at play near the fracture tip. For a Newtonian fluid, the solution derived by Garagash &amp; Detournay (2000) transition from the classical linear elastic fracture mechanics asymptote near the fracture tip to the viscous asymptote (Desroches et al., 1994) away from the tip. The fluid lag was shown to vanish for large values of a dimensionless fracture toughness encapsulating all the problem parameters (viscosity, fracture velocity, plane- strain elastic modulus).
From future states to images of identity (2007)

Abstract Purpose – The aim of this paper is to review the use of scenario‐building at the central government level in New Zealand and to consider an alternative technique – national imaging – for stimulating public discussion of the future. Design/methodology/approach – The paper briefly surveys New Zealand's history of prospective government before examining scenario construction during the Foresight Project convened by the Ministry of Research, Science and Technology during the late 1990s. Both the official scenarios produced and the guidance given to sector participants to produce their own scenarios are discussed. Findings – Scenario‐building in a national government context has pitfalls and limitations, namely that the technique is too ambitious, too socially unitary, and too implicitly long‐term to be really useful as a primary focus. Consideration of the shortcomings gives rise to an alternative procedure which focuses on developing images of national identity or conduct rather than envisioning or predicting future states. Practical implications – Scenario building need not be dispensed with, but should be subordinated to democratic discussion of ways of collectively orienting to the future. Originality/value – The paper introduces a new technique of "national imaging" as one that may better serve as an initial (not exclusive) tool of democratic envisioning of the future at the national level.
Policy Iteration for Multiplicative Noise Output Feedback Control (2022)

We propose a policy iteration algorithm for solving the multiplicative noise linear quadratic output feedback design problem. The algorithm solves a set of coupled Riccati equations for estimation and control arising from a partially observable Markov decision process (POMDP) under a class of linear dynamic control policies. We show in numerical experiments far faster convergence than a value iteration algorithm, formerly the only known algorithm for solving this class of problem. The results suggest promising future research directions for policy optimization algorithms in more general POMDPs, including the potential to develop novel approximate data-driven approaches when model parameters are not available.
Upregulated expression of complement inhibitory proteins on bladder cancer cells and anti‐MUC1 antibody immune selection (2008)

Membrane complement inhibitors (CD46, CD55 and CD59) are upregulated in some human cancers indicating that they play a role in immune evasion. We investigated complement inhibitor expression in bladder cancer and examined the hypothesis that selective pressure of an antibody response (anti-MUC1) results in the upregulated expression of complement inhibitors on tumor cells. Paired samples of tumor and normal tissue from 22 bladder cancer patients were analyzed for expression of MUC1, CD46, CD55 and CD59, and matched serum samples analyzed for anti-MUC1 IgM and IgG levels. Relationships between anti-MUC1 antibody levels and complement inhibitor expression were investigated. MUC1 mRNA was upregulated in 86% of tumor samples. CD46 was upregulated in 77%, CD55 in 55% and CD59 in 59% of tumors. Low titer anti-MUC1 IgM was detected in normal human sera, but was elevated in 41% of the bladder cancer patients. Anti-MUC1 IgG was virtually absent from normal sera, but present in 32% of the cancer patients. There was a direct relationship between anti-MUC1 antibody titer and expression level of complement inhibitors. Analysis of the correlation of each antibody with the expression of each complement inhibitor by Spearman's rank test revealed a strong correlation between both anti-MUC1 IgM and IgG levels and increased expression of CD46 and CD55, and combined anti-MUC1 IgM/IgG levels correlated with increased expression of all 3 complement inhibitors. In conclusion, the data demonstrate upregulated complement inhibitor expression and the presence of an anti-MUC1 antibody response in bladder cancer patients and support the hypothesis of antibody-mediated immune selection.