gebhart/patrepeval huggingface dataset:
Blocking CXCR4 alleviates desmoplasia, increases T-lymphocyte infiltration, and improves immunotherapy in metastatic breast cancer (2019)

Metastatic breast cancers (mBCs) are largely resistant to immune checkpoint blockade, but the mechanisms remain unclear. Primary breast cancers are characterized by a dense fibrotic stroma, which is considered immunosuppressive in multiple malignancies, but the stromal composition of breast cancer metastases and its role in immunosuppression are largely unknown. Here we show that liver and lung metastases of human breast cancers tend to be highly fibrotic, and unlike primary breast tumors, they exclude cytotoxic T lymphocytes (CTLs). Unbiased analysis of the The Cancer Genome Atlas database of human breast tumors revealed a set of genes that are associated with stromal T-lymphocyte exclusion. Among these, we focused on <i>CXCL12</i> as a relevant target based on its known roles in immunosuppression in other cancer types. We found that the CXCL12 receptor CXCR4 is highly expressed in both human primary tumors and metastases. To gain insight into the role of the CXCL12/CXCR4 axis, we inhibited CXCR4 signaling pharmacologically and found that plerixafor decreases fibrosis, alleviates solid stress, decompresses blood vessels, increases CTL infiltration, and decreases immunosuppression in murine mBC models. By deleting <i>CXCR4</i> in αSMA<sup>+</sup> cells, we confirmed that these immunosuppressive effects are dependent on CXCR4 signaling in αSMA<sup>+</sup> cells, which include cancer-associated fibroblasts as well as other cells such as pericytes. Accordingly, CXCR4 inhibition more than doubles the response to immune checkpoint blockers in mice bearing mBCs. These findings demonstrate that CXCL12/CXCR4-mediated desmoplasia in mBC promotes immunosuppression and is a potential target for overcoming therapeutic resistance to immune checkpoint blockade in mBC patients.
Significant Tumor Growth Inhibition from Naturally Occurring Lipid-Containing Polymer Prodrug Nanoparticles Obtained by the Drug-Initiated Method (2014)

International audience
Composition of Binary Self-Assembled Monolayers of Alkyltrichlorosilanes (1998)

Two binary self-assembled monolayer systems of alkyltrichlorosilane are examined for preferential deposition on a silicon oxide substrate. The surface compositions of these monolayers are monitored with contact angle, FTIR and X-ray photoelectron spectroscopy and compared to single component self-assembled monolayers. SAMs containing the small, relatively hydrophobic bromine end group show no detectable preferential deposition, but the more strongly hydrophilic methyl ester end group shows significant preferential deposition.
Stereoselective Single (Copper) or Double (Platinum) Boronation of Alkynes Catalyzed by Magnesia‐Supported Copper Oxide or Platinum Nanoparticles (2011)

Copper(II) oxide nanoparticles supported on magnesia have been prepared from Cu(II) supported on magnesia by hydrogen reduction at 400 °C followed by storage under ambient conditions. X-ray photoelectron spectroscopy of the material clearly shows that immediately after the reduction copper(0)-metal nanoparticles are present on the magnesia support, but they undergo fast oxidation to copper oxide upon contact with the ambient for a short time. TEM images show that the catalytically active CuO/MgO material is formed of well-dispersed copper oxide nanoparticles supported on fibrous MgO. CuO/MgO exhibits a remarkable catalytic activity for the monoborylation of aromatic, aliphatic, terminal, and internal alkynes, the products being formed with high regio- (borylation at the less substituted carbon) and stereoselectivity (trans-configured). CuO/MgO exhibits complete chemoselectivity towards the monoborylation of alkynes in the presence of alkenes. Other metal nanoparticles such as gold or palladium are inactive towards borylation, but undergo undesirable oligomerization or partial hydrogenation of the C≡C triple bond. In contrast, platinum, either supported on magnesia or on nanoparticulate ceria, efficiently promotes the stereoselective diborylation of alkynes to yield a cis-configured diboronate alkene. By using platinum as the catalyst we have developed a tandem diborylation/hydrogenation reaction that gives vic-diboronated alkanes from alkynes in one pot.
Paper 30: Functional Outcomes Following Anatomic Coracoclavicular Ligament Reconstruction (ACCR): A Prospective Study (2012)

Anatomic coracoclavicular ligament reconstruction (ACCR) has been shown to be an effective procedure from both an anatomic and biomechanical perspective. There has been no clinical outcome data on this procedure to date.
PNEUMATOSIS INTESTINALIS IN PATIENTS AFTER CADAVERIC KIDNEY TRANSPLANTATION POSSIBLE RELATIONSHIP WITH AN ACTIVE CYTOMEGALOVIRUS INFECTION (1984)

Four patients are described with pneumatosis intestinalis following cadaveric kidney transplantation, all with severe cytomegalovirus (CMV) infection. Two patients had a primary infection and 2 patients had a reactivation of CMV. One patient died because of disseminated CMV infection. Multiple inclusion bodies were found at postmortem examination in lungs and liver, and at the site of the ulcers in the gastrointestinal tract. Two patients had, concomitantly, an active, nonobstructive duodenal ulcer. In a control population of 17 patients who suffered from a duodenal ulcer post-transplant without any evidence of CMV-infection, we could not demonstrate pneumatosis intestinalis. We suggest a possible causal relationship between pneumatosis intestinalis and active CMV infection. The mechanisms that could be responsible for this relationship are discussed.
Mechanisms of the photoreactions of Cp2Fe2(CO)4 with phosphines and chlorocarbons (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanisms of the photoreactions of Cp2Fe2(CO)4 with phosphines and chlorocarbonsDavid R. Tyler, Maryke A. Schmidt, and Harry B. GrayCite this: J. Am. Chem. Soc. 1983, 105, 19, 6018–6021Publication Date (Print):September 1, 1983Publication History Published online1 May 2002Published inissue 1 September 1983https://pubs.acs.org/doi/10.1021/ja00357a010https://doi.org/10.1021/ja00357a010research-articleACS PublicationsRequest reuse permissionsArticle Views240Altmetric-Citations34LEARN 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
Silicon Biotechnology: Proteins, Genes and Molecular Mechanisms Controlling Biosilica Nanofabrication Offer New Routes to Polysiloxane Synthesis (2005)

Analysis of occluded proteins from the biosilica spicules produced by a sponge, and analysis of the cloned DNAs that code for these proteins, reveal that the proteins can act both catalytically and as macromolecular templates in vitro, directing the condensation of polysiloxanes from silicon alkoxides at neutral pH. These proteins (called “silicateins”) prove capable of directing the polymerization of silica and silsesquioxanes from the corresponding alkoxides under mild physiological conditions, whereas the anthropogenic synthesis of these materials typically requires acid or base catalysis. Homology between the silicateins and members of a well-characterized family of hydrolytic enzymes suggests a possible mechanism for protein-mediated catalysis of the rate-limiting step in polysiloxane synthesis. Genetic engineering and biotechnology offer the prospects of identifying the structural determinants of the polysiloxane synthesis-directing activities, developing new environmentally benign routes to synthesis of more ordered silsesquioxanes, and discovering the proteins, genes and molecular mechanisms controlling silicon metabolism in the sponge and other living systems.
A possible role for IVIg in the treatment of soft tissue sarcoma: A clinical case and an experimental model (2002)

A patient with a malignant peripheral nerve sheath tumor (MPNST) was treated with IVIg for multiple sclerosis. Her MPNST course was remarkably longer and more indolent than expected; she achieved a disease-free interval (DFI) of 30 months. Seven other patients, who were not treated by IVIg, had a relatively aggressive course (median DFI 3 months). These results led us to examine the effect of IVIg on the growth of sarcoma in vitro and in vivo in an experimental model of MCA-bearing mice. When added to MCA-105 sarcoma cell cultures, IVIg produced a dose-dependent inhibitory effect on [(3)H]-thymidine incorporation. The maximal inhibitory effect was at a concentration of 50 mg/ml IVIg. Cell cycle analysis revealed a hypodiploid peak at the lower fluorescence values which appeared in the samples treated with IVIg. These results demonstrate that the anti-proliferative activity results from an apoptotic effect of IVIg on the tumor cells. In a second set of experiments, we evaluated the capability of IVIg, when administered orally or subcutaneously, to inhibit the growth of MCA-105 sarcoma lung metastases. A decrease in the mean lung weight was observed in the mice that were treated by s.c. or oral administration, the latter being more effective. A possible role for IVIg in the treatment of MPNST and other soft tissue sarcomas is suggested.
Whither pharmacy informatics (2009)

Journal Article Whither pharmacy informatics Get access Dennis A. Tribble, Pharm.D., Dennis A. Tribble, Pharm.D. Chief Technology Officer ForHealth Technologies, Inc. 790 Fentress Boulevard Daytona Beach, FL 32114 (dtribble@fhtinc.com) Search for other works by this author on: Oxford Academic Google Scholar John Poikonen, Pharm.D., John Poikonen, Pharm.D. Director Clinical Informatics University of Massachusetts Memorial Medical Center Worchester, MA Search for other works by this author on: Oxford Academic Google Scholar Jerry Blair, B.S.Pharm., M.B.A., Jerry Blair, B.S.Pharm., M.B.A. Pharmacy Informatics Analyst Liberty Hospital Liberty, MO Search for other works by this author on: Oxford Academic Google Scholar Denny C. Briley, Pharm.D. Denny C. Briley, Pharm.D. Product Manager Medication Management Enterprise Solutions Product Strategy Pharmacy GE Healthcare IT Olathe, KS Search for other works by this author on: Oxford Academic Google Scholar American Journal of Health-System Pharmacy, Volume 66, Issue 9, 1 May 2009, Pages 813–815, https://doi.org/10.2146/ajhp090015 Published: 01 May 2009
Multimodal Imaging of Metals in a Retinal Degeneration Model to Inform on Ocular Disease (2023)

The metallome has been involved in the pathological investigation into ocular tissue for decades; however, as technologies advance, more information can be ascertained from individual tissue sections that were not previously possible. Herein, a demonstration of complementary techniques has been utilized to describe the distribution and concentrations of essential metals in both wildtype (WT) and rhodopsin (Rho−/−) ocular tissues. The multimodal approach described is an example of complementary datasets that can be produced when employing a multifaceted analytical approach. Heterogenous distributions of copper and zinc were observable within both WT and Rho−/− tissue by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), and the distributions of further trace elements notoriously problematic for ICP-MS analysis (phosphorous, Sulfur, chlorine, potassium, calcium, iron, and aluminum) were analysed by particle-induced X-ray emission (PIXE).
High temperature sensing with fiber Bragg gratings in sapphire-derived all-glass optical fibers (2014)

A structured sapphire-derived all-glass optical fiber with an aluminum content in the core of up to 50 mol% was used for fiber Bragg grating inscription. The fiber provided a parabolic refractive index profile. Fiber Bragg gratings were inscribed by means of femtosecond-laser pulses with a wavelength of 400 nm in combination with a two-beam phase mask interferometer. Heating experiments demonstrated the stability of the gratings for temperatures up to 950°C for more than 24 h without degradation in reflectivity.
Is Histological Investigation of Polyps Always Necessary? (2001)

A small right-sided polyp in a young patient is associated with a small risk (3.8 %) for advanced adenomatous tissue, indicating that histological investigation of such a polyp might not always be necessary. However, the recent recognition of flat adenomas and "mini" de novo colon carcinomas in the European population also may limit the usefulness of small polyp diameters in the exclusion of severe polyp histology.
Intelligent fusion of cup-to-disc ratio determination methods for glaucoma detection in ARGALI (2009)

Glaucoma is a leading cause of permanent blindness. ARGALI, an automated system for glaucoma detection, employs several methods for segmenting the optic cup and disc from retinal images, combined using a fusion network, to determine the cup to disc ratio (CDR), an important clinical indicator of glaucoma. This paper discusses the use of SVM as an alternative fusion strategy in ARGALI, and evaluates its performance against the component methods and neural network (NN) fusion in the CDR calculation. The results show SVM and NN provide similar improvements over the component methods, but with SVM having a greater consistency over the NN, suggesting potential for SVM as a viable option in ARGALI.
Improving Compound-Protein Interaction Prediction by Self-Training with Augmenting Negative Samples (2023)

Identifying compound-protein interactions (CPIs) is crucial for drug discovery. Because experimentally validating CPIs is often time-consuming and costly, computational approaches are expected to facilitate the process. Rapid growths of available CPI databases have accelerated the development of many machine learning methods for CPI predictions. However, their performance, particularly their generalizability against external data, often suffers from a data imbalance attributed to the lack of experimentally validated inactive (negative) samples. In this study, we developed a self-training method for augmenting both credible and informative negative samples to improve the performance of models impaired by data imbalances. The constructed model demonstrated a higher performance than those constructed with other conventional methods for solving data imbalances, and the improvement was prominent for external datasets. Moreover, examination of the prediction score thresholds for pseudo-labeling during self-training revealed that augmenting the samples with ambiguous prediction scores is beneficial for constructing a model with high generalizability. The present study provides guidelines for improving CPI predictions on real-world data, thus facilitating drug discovery.
Orthogonal transforms in sampling structure conversion (2003)

Alternative approaches for alias-free sampling structure conversion are considered. A formulation is given which can be utilized to perform decimation and interpolation filtering in the transform domain of an arbitrary orthogonal transform. The selection of transform and filtering specification, and the effects in image quality are also discussed. The multirate filtering problem is shown to consist of two phases: (1) selection of transform and (2) selection of linearly independent set of the subsampled basis functions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
O-Router (2009)

In this work, we present a new optical routing framework, O-Router for future low-power on-chip optical interconnect integration utilizing silicon compatible nano-photonic devices. We formulate the optical layer routing problem as the minimization of total on-chip optical modulator cost (laser power consumption) with Integer Linear Programming technique under various detection constraints. Key techniques for variable number reduction and routing speedup are also explored and utilized. O-Router is tested on optical netlist benchmarks modified from top global nets of ISPD98/08 routing benchmarks. O-Router experimental results are compared with conventional minimum spanning tree algorithm, demonstrating an average of over 50% improvement in terms of total on-chip optical layer power reduction.
Aristolochic acid I induces proximal tubule injury through ROS/HMGB1/mt DNA mediated activation of TLRs (2022)

Aristolochic acids (AAs) are extracted from certain plants as folk remedies for centuries until their nephrotoxicity and carcinogenicity were recognized. Aristolochic acid I (AAI) is one of the main pathogenic compounds, and it has nephrotoxic, carcinogenic and mutagenic effects. Previous studies have shown that AAI acts mainly on proximal renal tubular epithelial cells; however, the mechanisms of AAI-induced proximal tubule cell damage are still not fully characterized. We exposed human kidney proximal tubule cells (PTCs; HK2 cell line) to AAI in vitro at different time/dose conditions and assessed cell proliferation, reactive oxygen species (ROS) generation, nitric oxide (NO) production, m-RNA/ protein expressions and mitochondrial dysfunction. AAI exposure decreased proliferation and increased apoptosis, ROS generation / NO production in PTCs significantly at 24 h. Gene/ protein expression studies demonstrated activation of innate immunity (TLRs 2, 3, 4 and 9, HMGB1), inflammatory (IL6, TNFA, IL1B, IL18, TGFB and NLRP3) and kidney injury (LCN2) markers. AAI also induced epithelial-mesenchymal transition (EMT) and mitochondrial dysfunction in HK2 cells. TLR9 knock-down and ROS inhibition were able to ameliorate the toxic effect of AAI. In conclusion, AAI treatment caused injury to PTCs through ROS-HMGB1/mitochondrial DNA (mt DNA)-mediated activation of TLRs and inflammatory response.
Suppl video 4 from Neutrophil Conversion to a Tumor-Killing Phenotype Underpins Effective Microbial Therapy (2023)

&lt;p&gt;Neutrophil interactions with LLC cells lead to tumor cell blebbing.&lt;/p&gt;
THE ROLE OF OXYGEN IN YBa2Cu3O7−δ (1988)

Five observations concerning the role of oxygen in the high-T c superconductors YBa 2 Cu 3 O 7−δ are emphasized: (1) An internal electric field parallel to the c-axis constrains the redox reactions associated with the intercalation/disintercalation of oxygen primarily to the [ CuO 3−δ ] 3− layers located between Ba 2+ layers. (2) Intercalation of O 2− into the tetragonal YBa 2 Cu 3 O 6 phase results in an ordering onto one of the basal-plane axes of the Cu(1) layer, the b-axis of the orthorhombic phase. (3) Ordering between and within b-axis chains gives rise to discrete phases predicted to occur at O 6.875 , O 6.75 , O 6.5 , O 6.25 , and O 6.125 . (4) An equilibrium oxidation state for the intercalation layer depends not only on the oxygen partial pressure and temperature, but also on the cations of the structure. (5) At higher oxidation states of the intercalation layer, any oxygen atom on the a-axis interacts with a near-neighbor oxygen on the b-axis to trap out holes in a peroxide ion ( O 2 ) 2− .
Liquid Crystal System as Molecular Machinery: Investigation of Dynamic Impedance Matching between Molecular Core and Terminal Groups Using Rotor-Bearing Model (2000)

Liquid crystal phase stability is examined for liquid crystal terphenyls and their fluorinated derivatives, and some general rules are proposed that relate phase stability to molecular structures. A mechanical model is applied to explain the phase behaviours of these compounds. We postulate that liquid crystal phases are micromachine systems consisting of an ensemble of molecular rotors. The molecular core and terminals are the rotor and axes, respectively. The terminals also function as bearings for the subsequent layer's molecular rotors. Phenomena of the thermal stability of phase and polymorphism are interpreted in terms of basic mechanical and dynamical parameters: centre of gravity, eccentricity, moment of inertia and mass distribution. The importance of dynamic impedance matching between parts, rotors, axes and bearings, is emphasized. Fluorination effects on liquid crystallinity are explained in a unified manner on a mechanical and dynamical basis.
Mechanism of Alkane Transfer-Dehydrogenation Catalyzed by a Pincer-Ligated Iridium Complex (2003)

The mechanism of (PCP)Ir-catalyzed transfer-dehydrogenation has been elucidated for the prototypical substrate/acceptor couple, COA/TBE, at 55 degrees C (COA = cyclooctane; TBE = tert-butylethylene). The catalytic cycle may be viewed as the sum of two reactions: (i) hydrogenation of TBE by (PCP)IrH2 and C-H addition of a second mole of TBE to give (PCP)IrH(tert-butylvinyl), and (ii) dehydrogenation of COA by (PCP)IrH(tert-butylvinyl) to give (PCP)IrH2, COE, and TBE. These two stoichiometric reactions have been observed independently and their kinetics determined. The overall catalysis has also been monitored in situ, and (PCP)IrH2 and (PCP)IrH(tert-butylvinyl) have been observed as the resting states; the ratio of these two complexes is found to be proportional to [TBE]2. Based upon the proportionality constant thus obtained and the catalytic rate as a function of [TBE] (which reaches a maximum at ca. 0.3 M), the respective rate constants for the hydrogenation and dehydrogenation segments can be obtained. Good agreement is found between the rates independently obtained from stoichiometric and catalytic runs. Within the overall TBE-hydrogenation reaction, labeling experiments indicate that the rate-determining step is the reductive elimination of TBA (2,2-dimethylbutane) from (PCP)IrH(tert-butylethyl) (which is formed via insertion of TBE into an Ir-H bond of (PCP)IrH2). Based upon considerations of microscopic reversibility, it can be further inferred that the rate-determining step for the alkane dehydrogenations is C-H addition (and not beta-H elimination).
Impacts of dialysis adequacy and intradialytic hypotension on changes in dialysis recovery time (2020)

Incident patients who had higher spKt/V and less sessions with IDH episodes had a lower likelihood of changing to a longer DRT in first year of HD. Dose optimization strategies with cardiac stability in fluid removal should be tested.
The induction of interleukin-1 in humans and its metabolic effects (1986)

The Journal of Trauma: Injury, Infection, and Critical Care: May 1986 - Volume 26 - Issue 5 - p 491
Medial Kernels (2012)

Abstract We introduce the medial kernel, an association measure which provides for a robust construction of volume‐aware distances defined directly on point clouds. The medial kernel is a similarity measure defined as the likelihood of two points belonging to a common interior medial ball. We use the medial kernel to construct a random walk on the point cloud, where movement in the walk is restricted to regions containing similar medial balls. Our distances are defined as the diffusion distances of this random walk, assigning low distance to points belonging to similar medial regions. These distances allow for a robust means of processing incomplete point clouds, capable of distinguishing nearby yet separate undersampled components, while also associating points which are far in Euclidean distance yet mutually share an interior volume. We leverage these distances for several applications: volumetric part segmentation, the construction of function bases, and reconstruction‐by‐parts – a surface reconstruction method which adheres to the medial kernel.