gebhart/patrepeval huggingface dataset:
Data from Checkpoint Inhibition of KIR2D with the Monoclonal Antibody IPH2101 Induces Contraction and Hyporesponsiveness of NK Cells in Patients with Myeloma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Immune checkpoint inhibitors have recently revolutionized cancer immunotherapy. On the basis of data showing KIR-ligand mismatched natural killer (NK) cells reduce the risk of leukemia and multiple myeloma relapse following allogeneic hematopoietic stem cell transplantation, investigators have developed a checkpoint inhibition antibody that blocks KIR on NK cells. Although &lt;i&gt;in vitro&lt;/i&gt; studies suggest the KIR2D-specific antibody IPH2101 induces KIR-ligand mismatched tumor killing by NK cells, our single-arm phase II clinical trial in patients with smoldering multiple myeloma was prematurely terminated due to lack of clinical efficacy. This study aimed at unveiling the underlying mechanisms behind the lack of clinical efficacy.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Treatment-naïve patients received an intravenous infusion of 1 mg/kg IPH2101 every other month for up to a year. Peripheral blood was collected at baseline and 24 hours after first infusion, followed by weekly samples for the first month and monthly samples thereafter. NK cell phenotype and function was analyzed using high-resolution flow cytometry.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Unexpectedly, infusion of IPH2101 resulted in rapid reduction in both NK cell responsiveness and KIR2D expression on the NK cell surface. &lt;i&gt;In vitro&lt;/i&gt; assays revealed KIR2D molecules are removed from the surface of IPH2101-treated NK cells by trogocytosis, with reductions in NK cell function directly correlating with loss of free KIR2D surface molecules. Although IPH2101 marginally augmented the antimyeloma cytotoxicity of remaining KIR2D&lt;sup&gt;dull&lt;/sup&gt; patient NK cells, the overall response was diminished by significant contraction and reduced function of KIR2D-expressing NK cells.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; These data raise concerns that the unexpected biological events reported in this study could compromise antibody-based strategies designed at augmenting NK cell tumor killing via checkpoint inhibition. &lt;i&gt;Clin Cancer Res; 22(21); 5211–22. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Felices and Miller, p. 5161&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
The effect of selective serotonin re‐uptake inhibitors on the risk of myocardial infarction in a cohort of patients with depression (2011)

Only longer term use of SSRIs was associated with reduced MI risk, suggesting that other mechanisms, besides an acute anti-platelet effect, may reduce MI risk.
Cycloidal Mass Spectrometer (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
The state-of-the-art 3D anisotropic intracranial hemorrhage segmentation on non-contrast head CT: The INSTANCE challenge (2023)

Automatic intracranial hemorrhage segmentation in 3D non-contrast head CT (NCCT) scans is significant in clinical practice. Existing hemorrhage segmentation methods usually ignores the anisotropic nature of the NCCT, and are evaluated on different in-house datasets with distinct metrics, making it highly challenging to improve segmentation performance and perform objective comparisons among different methods. The INSTANCE 2022 was a grand challenge held in conjunction with the 2022 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). It is intended to resolve the above-mentioned problems and promote the development of both intracranial hemorrhage segmentation and anisotropic data processing. The INSTANCE released a training set of 100 cases with ground-truth and a validation set with 30 cases without ground-truth labels that were available to the participants. A held-out testing set with 70 cases is utilized for the final evaluation and ranking. The methods from different participants are ranked based on four metrics, including Dice Similarity Coefficient (DSC), Hausdorff Distance (HD), Relative Volume Difference (RVD) and Normalized Surface Dice (NSD). A total of 13 teams submitted distinct solutions to resolve the challenges, making several baseline models, pre-processing strategies and anisotropic data processing techniques available to future researchers. The winner method achieved an average DSC of 0.6925, demonstrating a significant growth over our proposed baseline method. To the best of our knowledge, the proposed INSTANCE challenge releases the first intracranial hemorrhage segmentation benchmark, and is also the first challenge that intended to resolve the anisotropic problem in 3D medical image segmentation, which provides new alternatives in these research fields.
Welcome and Introduction to SPIE Conference 11700 (2021)

Introduction to SPIE Photonics West OPTO conference 11700: Optical and Quantum Sensing and Precision Metrology.
Transport of nicotinate by human organic anion transporters of SLC22 family (2006)

Nicotinate has been used as a lipid-lowering agent producing beneficial changes in serum lipids for atherosclerosis regression. The purpose of this study is to elucidate the molecular mechanisms underlying the transport of nicotinate by human organic anion transporters (OATs) of SLC22 family stably expressed in a mouse cell line derived from renal proximal tubule S2 segment. Among OATs tested (hOAT1-4), hOAT1 and hOAT2 mediated a time- and concentration-dependent uptake of nicotinate. We focused on the study of hOAT2 because it showed higher activity in nicotinate transport compared with hOAT1. hOAT2-mediated nicotinate uptake showed structural specificity, and was inhibited by some organic anions such as indocyanine green, glibenclamide, and probenecid and some NSAIDs (salicylic acid, diclofenac, ketoprofen, indomethacine, and ibuprofen). The identicication of nicotinate transporter will contribute to understanding the molecular basis of such a drug-drug interaction as salicylate-induced increase in serum nicotinate level.
Efficient optical interconnections for data-center computing systems (2013)

Within the past decade, the semiconductor computing industry has developed multicore and multithreaded core processors to overcome the challenges and shrinking benefits of traditional technology scaling. Multichip systems built using these components will require immense amount of off-chip bandwidth and low latency chip-to-chip links at the lowest energy cost possible. Wavelength-division multiplexed (WDM) silicon photonics have the potential to provide a solution for this immense interconnect problem. At Oracle, we are aggressively building a portfolio of active and passive nanophotonic devices, circuits, and multichip packaging with the aim to achieve sub-picojoule per bit communication links between computing elements in a large array “Macrochip”. To achieve ultralow energy consumption will certainly require integrating best-in-breed photonic devices with electronic circuits. While the juxtaposition of silicon photonic devices and VLSI circuits on the same silicon substrate represents the most intimate integration of electronic and photonic technologies, achieving this will require an immense amount of sophistication in design and process integration. Instead, hybrid integration of aggressive components, built on individually optimized technology platforms, is a pragmatic approach to achieving peak performance. Such “photonic bridge” chip components may be used as units in a larger transmitter or receiver array or as drop-in communication physical layer elements in a multi-chip computing node.
Storage Stability of Carotenoids in Orange Oil (1983)

ABSTRACT Citrus essential oils are used as flavoring agents in foods and beverages. Recently a premium price was paid for oils with a high carotenoid content because they were also used as natural coloring agents. Commercially manufactured samples of ‘Pineapple’ oils were concentrated 5, 10, and 25‐fold, stored for 12 moat –18, 4, 26, and 32°C and sampled periodically. The carotenoid content was measured spectrophotometrically with β‐carotene as a standard. From an initial value of 7.2 mg of β‐carotene/100g of oil, it decreased 6.6, 18.4, and 24.6% upon concentrating 5, 10, and 25‐fold, respectively. The 25‐fold sample lost 6% of its β‐carotene at –18°C and 90% at 32°C during 12 mo of storage. There was a highly significant fit of the time, temperature and concentration data to a second order model.
Doping Process for 3-D N-Type Trench Transistors-2-D Cross-Sectional Doping Profiling Study (2013)

Comparison study of doping a 3-D trench transistor structure is carried out by beam-line (BL) implant and plasma doping (PLAD) methods. Electron holography (EH) is used as a powerful characterization method to study 2-D cross-sectional doping profiles of arsenic-based doping processes. Quantitative definitions of junction depths x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">j</sub> in both vertical and lateral directions can be obtained. Good correlations of 2-D EH dopant profiles, 1-D secondary ion mass spectrometry/angle-resolved X-ray electron spectroscopy impurity profiles, and device electrical parameters are demonstrated. The results reveal an advantage of PLAD over BL implant: a much larger effective implant area for 3-D trench bottom. It leads to a deeper vertical junction depth x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">j</sub> (V) with a larger lateral junction depth x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">j</sub> (L). It is due to the PLAD technology with less angle variation issues and no line of sight shadowing effect. Enhancing the dopant lateral straggle by PLAD at the trench bottom is particularly useful for nonplanar device structures with low resistance buried dopant layers.
Design and Analysis of an Innovative Concept for Submerging Open-Sea Aquaculture System (2018)

This paper presents an innovative design of a system of cages for an open-sea aquaculture. The concept is based on an existing successful concept of a system, which is flexible, submersible, and has a single point mooring. The new design, besides being much larger, presents a new concept of stabilizing the system at the submerged state. This new system is preliminarily designed by a simplified method, and then analyzed by the AQUASIM finite elements software system. The results of the nonlinear hydroelastic analysis confirm that the preliminary design by simplified calculations is adequate to the design conditions. The new concept of stabilizing the system at the submerged state is studied by simulations of four configurations, where the optimal is selected. The simulations show that the cages always retain above 70% of the volume. The paper presents valuable information of a practical design, such as the method of the analysis, the environmental design criteria, the scantlings of the structure, and the obtained usage factors at extreme sea conditions. The system was recently being constructed, launched, and anchored at open-sea offshore Ashdod. It is now tested at the sea before cultivation of fishes.
Figure S1 from Genetic Alterations in the PI3K/AKT Pathway and Baseline AKT Activity Define AKT Inhibitor Sensitivity in Breast Cancer Patient-derived Xenografts (2023)

&lt;p&gt;Response to AZD5363 in PDX models recapitulates patients' response&lt;/p&gt;
Establishment and characterization of a new osteogenic cell line (MOS-J) from a spontaneous C57BL/6J mouse osteosarcoma. (2003)

In this paper we describe the establishment and characterization of a transplantable cell line derived from a spontaneously occurring chondroblastic osteosarcoma in a C57BL/6J mouse. The tumor line, MOS-J, forms solid tumors when injected intramuscularly into immunocompetent syngeneic hosts, mimicking endochondral bone development. These transplantable tumors have the capacity to destroy and invade existing bone and invade vessels in close proximity to the tumor. In culture, MOS-J cells form layers of pleomorphic cells with high mitotic activity. These cells have marked alkaline phosphatase activity and form calcified foci in vitro that stain with alizarin red. MOS-J cells also promote osteoclast development in vitro from normal bone marrow cells. These characteristics indicate the potential utility of the MOS-J osteosarcoma cell line as a model for studies of human osteosarcoma and bone biology.
ChemInform Abstract: 2‐Dibenzylaminobutane‐1,4‐diol: An Effective Chiral Building Block for the Synthesis of 1,2‐Amino Alcohols. (1995)

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.
Spectral Errors and Their Affect on Retrieval of Temperature and Water Vapor Profiles in the Presence of Clouds (2007)

The impact of spectral channel registration errors in an imaging grating spectrometer on the retrieval of temperature and water vapor profiles in the presence of opaque, low-level (~700 mb) clouds is investigated.
High Density of NRF2 Expression in Malignant Cells Is Associated with Increased Risk of CNS Metastasis in Early-Stage NSCLC (2021)

Nuclear factor erythroid 2-related factor 2 (NRF2) protein expression promotes cancer progression in non-small cell lung cancer (NSCLC). However, its role in the clinical setting has not been established. We retrospectively analyzed data from 304 patients with surgically removed NSCLC. Multiplex antibody staining of NRF2 and thioredoxin reductase 1 (TrxR1) was conducted and scored in cytokeratin-positive (CK+) cells within the whole-tissue core as well as the tumor and stromal compartments of each tissue microarray (TMA) core. A high density of NRF2+/CK+ cells in the whole-tissue core compartment was correlated with a higher risk of central nervous system (CNS) relapse OR = 7.36 (95% CI: 1.64-33.06). The multivariate analysis showed an OR = 8.00 (95% CI: 1.70-37.60) for CNS relapse in NRF2+/CK+ high-density cases. The density of TrxR1+/CK+ cells failed to show any statistically significant risk of relapse. The OS analyses for NRF2+/CK+ and TrxR1+/CK+ cell density failed to show any statistical significance. This is the first study to report a correlation between NRF2+/CK+ cell density and the risk of CNS relapse in early-stage NSCLC. The results of our study may impact the follow-up strategy for early-stage NSCLC patients and eventually improve their prognosis.
Specific inhibition of the Akt1 pleckstrin homology domain by D-3-deoxy-phosphatidyl-myo-inositol analogues. (2003)

Activation of Akt (protein kinase B), a Ser/Thr protein kinase that promotes cell survival, has been linked to tumorigenesis. Akt is activated by phosphorylation after binding of its pleckstrin homology (PH) domain to plasma membrane phosphatidyl-myo-inositol-3-phosphates, formed by phosphoinositide-3-kinase. We report a novel strategy to inhibit Akt activation based on the use of D-3-deoxy-phosphatidyl-myo-inositols (DPIs) that cannot be phosphorylated on the 3-position of the myo-inositol ring. We have studied the DPIs, DPI 1-[(R)-2,3-bis(hexadecanoyloxy)propyl hydrogen phosphate], its ether lipid derivative DPI 1-[(R)-2-methoxy-3-octadecyloxypropyl hydrogen phosphate] (DPIEL), and its carbonate derivative DPI 1-[(R)-2-methoxy-3-octadecyloxypropyl carbonate]. We demonstrate in platelet-derived growth factor-stimulated mouse NIH3T3 cells that the DPIs bind to the PH domain of Akt, trapping it in the cytoplasm and thus preventing Akt activation. DPIEL did not inhibit myristylated-Akt, a constitutively active membrane-bound Akt expressed in NIH3T3 cells, and cell growth was not inhibited, unlike in wild-type NIH3T3 cells. Molecular modeling and docking studies show that DPIEL binds with much higher affinity to Akt's PH domain as compared with DPI and DPI 1-[(R)-2-methoxy-3-octadecyloxypropyl carbonate]. This study shows that the DPIs are a novel class of growth inhibitory agents with a novel mechanism of action through binding to the PH domain of Akt and inhibition of Akt activation.
Coupling the folding of a β-hairpin with chelation-enhanced luminescence of Tb(iii) and Eu(iii) ions for specific sensing of a viral RNA (2016)

Rational modification of a natural RNA-binding peptide with a lanthanide EDTA chelator, and a phenanthroline ligand yields a highly selective luminescent sensor. The sensing mechanism relies on the RNA-triggered folding of the peptide into a β-hairpin, which promotes the coordination of the phenanthroline sensitizer, and the efficient sensitization of complexed lanthanide ions.
Clinical, Radiographic, and Ultrasonographic Comparison of Subscapularis Tenotomy and Lesser Tuberosity Osteotomy for Total Shoulder Arthroplasty (2010)

Both techniques resulted in improved clinical outcome scores. The lesser tuberosity osteotomy resulted in higher clinical outcome scores, a lower rate of subscapularis tendon tears, and universal healing of the osteotomy. This technique offers a means by which the rate of postoperative subscapularis tears may be reduced in patients undergoing total shoulder arthroplasty.
Panbinostat decreases cFLIP and enhances killing of cancer cells by immunotoxin LMB-100 by stimulating the extrinsic apoptotic pathway (2017)

LMB-100 (RG7787) is a recombinant immunotoxin, which kills mesothelin-expressing cancer cells and now being evaluated in phase 1 trials. To enhance the anti-tumor activity of LMB-100, we have searched for agents, already approved for cancer therapy, that can be combined with LMB-100 to increase its efficacy. Panbinostat is a pan-histone deacetylase inhibitor that is used to treat multiple myeloma. We incubated different types of cancer cells with panbinostat and LMB-100 and found that they interacted synergistically to cause cell death. We found that panbinostat and the combination increased levels of mRNAs encoding TNF/TNFR family members, as well as <i>BNIP3L</i> and <i>CASP-9</i>, and markedly decreased mRNA levels for <i>c-FLIP</i> and <i>BID</i>. Western blots confirmed a fall in levels of cFLIP protein and a rise in BNIP3L and caspase-9. The combination also increased levels of cleaved BID (t-BID), cleaved-capsase-3 and -8 and PARP. To assess the importance of the fall in cFLIP levels, we treated cells with the cFLIP inhibitor, Rocaglamide, and found it also enhanced killing of tumor cells by LMB-100. LMB-100, which activates the intrinsic pathway of apoptosis, and panbinostat, which activates the extrinsic pathway, work in a synergistic manner to kill cancer cell lines.
Profound accidental hypothermia in the deep South: clinical experience (1996)

Accidental hypothermia resulting from exposure is generally associated with frigid regions and not with the more temperate areas of the South. However, we present clinical experience from two cases in which the victims of motor vehicle accidents were exposed to the elements for prolonged periods and became profoundly hypothermic. The first patient was a 21-year-old male who was ejected from, and pinned under, his vehicle for approximately four hours in -15 degrees C ambient temperature. Upon admission to the Emergency Room, the patient was unresponsive with fixed and dilated pupils and his core temperature was 25 degrees C. After a prolonged period of cardiopulmonary resuscitation, percutaneous femoral to femoral cardiopulmonary bypass (CPB) was instituted for core rewarming. After reaching 37 degrees C, the patient was removed from bypass. The patient was discharged from the hospital on the fourth postoperative day. The second patient was a 40-year-old male who was ejected from his vehicle into a stream, where he was partially submerged for several hours. Although the ambient temperature was approximately 22 degrees C, his core temperature at admission was 27 degrees C. After a positive peritoneal lavage, the patient was taken to the Operating Room and placed on percutaneous femoral to femoral CPB for core rewarming. During rewarming, an exploratory laparotomy and a splenectomy were performed. The patient was discharged from the hospital on the seventh postoperative day. These cases are unique in that both were trauma patients with suspected internal injuries which required the avoidance of anticoagulation. Therefore, both cases utilized a Carmeda-bonded circuit without systemic anticoagulation.
Homogeneous and multiphase poly(methyl methacrylate) graft polymers via the macromonomer method (1990)

Abstract Anionic and group transfer polymerization processes were used to synthesize controlled molecular weight methacryloyloxy functionalized poly(dimethylsiloxane) and poly(methyl methacrylate) macromonomers having a narrow molecular weight distribution and high percent functionality. These macromonomers were anionically copolymerized with methyl methacrylate (MMA) to afford poly(methyl methacrylate)‐ graft ‐poly(methyl methacrylate) (PMMA‐g‐PMMA) and poly(methyl methacrylate)‐ graft ‐poly(dimethylsiloxane) (PMMA‐g‐PDMS) polymers having not only narrow molecular weight distribution graft parts but also backbone parts. The PMMA‐g‐PDMS system was fractionated using supercritical chlorodifluoromethane to determine its chemical composition distribution (CCD). The CCD for the PMMA‐g‐PDMS copolymerized in a living manner was substantially more narrow than the free radically copolymerized material. The PMMA‐g‐PMMA system was used to study the dilute solution properties of branched homopolymers. The appropriateness of the universal calibration gel permeation chromatography (GPC) method for branched systems exhibiting long chain branching was reaffirmed.
On the threshold of Maximum-Distance Separable codes (2010)

Starting from a practical use of Reed-Solomon codes in a cryptographic scheme published in Indocrypt'09, this paper deals with the threshold of linear q-ary error-correcting codes. The security of this scheme is based on the intractability of polynomial reconstruction when there is too much noise in the vector. Our approach switches from this paradigm to an Information Theoretical point of view: is there a class of elements that are so far away from the code that the list size is always superpolynomial? Or, dually speaking, is Maximum-Likelihood decoding almost surely impossible? We relate this issue to the decoding threshold of a code, and show that when the minimal distance of the code is high enough, the threshold effect is very sharp. In a second part, we explicit lower-bounds on the threshold of Maximum-Distance Separable codes such as Reed-Solomon codes, and compute the threshold for the toy example that motivates this study.