gebhart/patrepeval huggingface dataset:
T2 Magnetic Resonance: A Diagnostic Platform for Studying Integrated Hemostasis in Whole Blood—Proof of Concept (2014)

This proof-of-concept study demonstrates that T2MR has the potential to provide rapid and sensitive identification of patients at risk for thrombosis or bleeding and to identify new biomarkers and therapeutic targets with a single, simple-to-employ analytic approach that may be suitable for routine use in both research and diverse clinical settings.
Normal Bacterial Populations of the Intestine and Their Relation to Intestinal Function (1964)

IN the latter part of the nineteenth century discovery of the bacterial basis for many diseases, together with dramatic demonstrations of the potency of bacterial toxins, led to the concept of intestinal autointoxication. Vociferously championed by Metchnikoff,1 this theory held that noxious intestinal bacterial products were absorbed and were the cause of many of man's afflictions. Although widely accepted at first, the autointoxication concept received little or no support in the form of sound experimental data and was soon exploited by quacks and faddists. Indeed, scientific reaction against the theory may well have impeded subsequent objective investigation into the physiologic . . .
CD161 is a marker of all human IL‐17‐producing T‐cell subsets and is induced by RORC (2010)

We have previously shown that human Th17 lymphocytes are characterized by the selective expression of IL-23 receptor (IL-23R), CCR6, CD161, and the transcription factor retinoic acid-related orphan receptor C (RORC), and originate from a CD161(+)CD4(+) naïve T-cell precursor in response to the combined activity of IL-1β and IL-23. We show here that not only CD4(+)TCRαβ(+), but also CD8(+)TCRαβ(+), CD4(-)CD8(-) TCRαβ(+), and CD4(-)CD8(-) TCRγδ(+) circulating lymphocytes that produce IL-17 express the distinctive marker CD161 on their surface. In addition, we demonstrate that CD161 expression identifies CD8(+) and CD4(-)CD8(-) umbilical cord blood T cells that already express RORC and IL-23R mRNA and that can be induced to differentiate into IL-17-producing cells in the presence of IL-1β and IL-23. Finally, we provide evidence that umbilical cord blood naïve CD4(+)CD161(-) T cells, upon lentivirus-mediated transduction with RORC2 can acquire the ability to express IL-23R, IL-1RI, and CD161, as well as to produce IL-17. Taken together, these data allow to conclude that T-cell subsets able to produce IL-17, as well as precursors of IL-17-producing T cells, exhibit surface expression of CD161, and that this feature is at least in part RORC2-dependent.
(001) oriented FePt–Ag composite nanogranular films on amorphous substrate (2003)

By annealing the multilayer film with a stack structure of MgO 10 nm/Ag 20 nm/[FePt x nm/Ag 5 nm]5 at 550 °C for 1 h, (001)-oriented L10 FePt nanograins with high perpendicular magnetic anisotropy are obtained on an amorphous substrate. The 20-nm Ag underlayer plays an important role in improving (001) texture of FePt and decreasing the fct FePt ordering temperature. The switching volume and uniaxial magnetic anisotropy constant Ku of FePt–Ag composite films with a controllable FePt grain size are obtained by fitting the coercivity dependence on magnetic field sweeping rate employing coherent rotation model, taking into account the easy axis distribution.
Clinical research directions in pediatric cardiology (2009)

If the field of pediatric cardiology can adopt a comprehensive research agenda that identifies the most-needed studies, then research could be better coordinated, long-term and collaborative studies would be more readily organized and funded, and the overall financial and scientific efficiency of research in pediatric cardiology would be improved. Targeted research efforts are more likely to realize potential breakthroughs in areas such as genetic and epigenetic screening, biomarkers, cardioprotective strategies, life-course studies, long-term monitoring technologies, environmental influences on disease, evidence-based practice guidelines, and more rapid and safer development of drugs.
Abstract C74: Establishment and characterization of a HER2-positive, TDM1-resistant PDX breast model (2015)

Abstract Background: Ado-trastuzumab emtansine (T-DM1), a recently approved antibody-drug conjugate (ADC), is approved for treatment of high HER2 expressing (3+), trastuzumab resistant breast and gastric cancers. While this agent is effective, resistance often develops. To better understand the mechanisms for resistance to TDM1 in high HER2 expressing breast cancer we collected tissue from a patient following response and progression to TDM1 and established a xenograft model for preclinical drug screening. The resulting model ST1360B was genomically characterized and screened in vivo using high dose TDM1; anti-tumor activity was compared with two trastuzumab-resistant but TDM-1 sensitive HER2 (3+) breast PDX models designated ST225 and ST340. Methods: The high HER2 expressing (3+) TDM1 resistant breast PDX model ST1360B was established in athymic mice using pleural fluid collected from a thoracentesis. Establishment of the HER2 (3+) ST225 and ST340 models has been previously described. Clinical and PDX tissues were subjected to genomic analysis; for each model, DNA was extracted and subjected to comparative genomic hybridization and exon sequencing of known oncogenes; growth factor receptor and ligand densities was interrogated using immunohistochemistry. Drug sensitivity studies were performed evaluating sensitivity of models to single agent T-DM1, administered intravenously at 10 mg/kg on Day 0; weekly TDM1 dosing at 5 mg/kg was also evaluated in the ST1360B model Study endpoints included tumor volume and time from treatment initiation with tumor growth inhibition, delay and regression reported at study completion. Results: Genomic analysis of ST1360B identified amplified HER2 and TOP2A; interestingly CD44 was found highly amplified, suggesting a possible mechanism for TDM1 resistance in this model. Mutations were not identified in PIK3CA or other relevant genes. In efficacy studies TDM1 was confirmed active towards ST225 and ST340 model including tumor regressions and durable complete responses in both models (TGI&amp;gt;100%). However TDM1 was not effective in ST1360B, with only transient tumor growth inhibition even with weekly drug administration. Conclusion: We have established a model of TDM1 HER2 3+ resistant breast cancer and have characterized the model using comparative genomic hybridization and exon sequencing of known oncogenes, identifying amplified CD44 as a potential mechanism for drug resistance. This model can be utilized to better understand and to develop novel therapies to TDM1 resistance. Citation Format: Michael J. Wick, Teresa L. Vaught, Justin Meade, Monica Farley, Armando Diaz, Anthony W. Tolcher, Drew W. Rasco, Amita Patnaik, Murali Beeram, Kyriakos P. Papadopoulos. Establishment and characterization of a HER2-positive, TDM1-resistant PDX breast model. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C74.
Regulation of Dissimilatory Fe(III) Reduction Activity in Shewanella putrefaciens (1990)

Under anaerobic conditions, Shewanella putrefaciens is capable of respiratory-chain-linked, high-rate dissimilatory iron reduction via both a constitutive and inducible Fe(III)-reducing system. In the presence of low levels of dissolved oxygen, however, iron reduction by this microorganism is extremely slow. Fe(II)-trapping experiments in which Fe(III) and O(2) were presented simultaneously to batch cultures of S. putrefaciens indicated that autoxidation of Fe(II) was not responsible for the absence of Fe(III) reduction. Inhibition of cytochrome oxidase with CN resulted in a high rate of Fe(III) reduction in the presence of dissolved O(2), which suggested that respiratory control mechanisms did not involve inhibition of Fe(III) reductase activities or Fe(III) transport by molecular oxygen. Decreasing the intracellular ATP concentrations by using an uncoupler, 2,4-dinitrophenol, did not increase Fe(III) reduction, indicating that the reduction rate was not controlled by the energy status of the cell. Control of electron transport at branch points could account for the observed pattern of respiration in the presence of the competing electron acceptors Fe(III) and O(2).
5‐4: High Efficiency Top‐Emission Organic Light Emitting Diodes Realized Using Newly Developed Low Absorption Pure Ag cathode Configuration (2019)

We report, highly efficient red top emission organic light emitting diodes (TEOLEDs) having thin pristine Ag cathode unit with low absorption, uniform surface morphology and good electron injection property. TEOLEDs with Ag cathode unit exhibit almost 1.4 times improvement in current efficiency as well as low driving voltage compared with widely used Mg:Ag cathode and almost identical lifetime with Mg:Ag cathode.
Protonation of Histidine and Histidine−Tryptophan Interaction in the Activation of the M2 Ion Channel from Influenza A Virus (2001)

The M2 protein of influenza A virus forms a homotetramer ion channel in the lipid membrane. The channel is specific for proton conductance and is activated by low pH with a transition midpoint at pH 5.7. We have studied the structure of the transmembrane domain of the M2 ion channel by using UV resonance Raman spectroscopy, with special attention to the side chains of histidine (His37) and tryptophan (Trp41) residues. The Raman spectra provide direct evidence that the imidazole ring of His37 is protonated upon channel activation at low pH. Concomitantly, the UV resonance Raman scattering from Trp41 shows an unusual intensity change, which is ascribed to a cation-pi interaction between the protonated (cationic) imidazole ring of His37 and the indole ring of Trp41. The protonation of His37 and the Raman intensity change of Trp41 do not occur in the presence of amantadine that blocks the M2 ion channel. These observations clearly show that the protonation of His37 and concomitant cation-pi interaction with Trp41 is a key step in the activation of the M2 ion channel. The His37-Trp41 interaction associated with the channel activation is explained by assuming a conformational transition of His37 induced by electrostatic repulsion among the protonated imidazole rings of four His37 residues in the tetramer channel. Trp41 may play a role in stabilizing the channel open state through cation-pi interaction with His37. A molecular model for the activation of M2 ion channel is proposed on the basis of the gating mechanism.
A multispecialty approach to the diagnosis and management of pancreatic cancer (2000)

This article reviews recent developments in pancreatic cancer research and offers a multispecialty perspective on the diagnosis and management of this challenging disease. Current findings in the molecular biology of the disease and their implications for management are examined, as well as development in diagnostic techniques, including helical computed tomography (CT), magnetic resonance imaging (MRI), magnetic resonance cholangio-pancreatography (MRCP), and, particularly, endoscopic ultrasound-guided fine-needle aspiration. Surgical management, the role of adjuvant/neoadjuvant chemoradiation therapy, and the critical importance of accurate preoperative imaging are also addressed in this review. Palliative techniques, including endoscopic stenting for malignant obstructive jaundice and chemotherapy for locally advanced and metastatic disease, are discussed, and results of recent clinical trials in pancreatic cancer are summarized. Finally, future directions for research are identified.
Antibody phage display technologies with special reference to angiogenesis (2005)

The presence of blood vessels is a prerequisite for normal development, tissue growth, and tissue repair. However, its abnormal occurrence or absence can also potentiate disease processes. Angiogenic therapies have been used to stimulate blood vessel growth in ischemic conditions such as severe end-stage peripheral vascular disease, ischemic heart disease and stroke and for inhibition of angiogenesis in tumors. The targeting and identification of novel endothelial cell (EC) markers that can ultimately be used in angiogenic strategies is an expanding field but is limited by the availability of reagents. For instance repeated injection of mouse monoclonal antibodies (Mabs) against angiogenic EC, can result in the production of autoantibodies. Therefore, these mouse Mabs cannot be used for therapeutic purposes. Phage display technology was employed in this context to select antibodies, proteins, and peptides against known or novel EC antigens. Furthermore, technologies have been developed that enable the specific targeting of epitopes on cells including the endothelium with high-affinity/avidity antibodies. The focus for these antibody targeting strategies are markers that are unique or up-regulated on angiogenic EC including the vascular endothelial growth factor receptor (VEGFR) KDR, endoglin (CD105), and the extracellular domain B (ED-B) domain of fibronectin (FN). These markers are reviewed herein.
Trigonella foenum graecum (fenugreek) seed extract as an antineoplastic agent (2001)

The antineoplastic effect of Trigonella foenum graecum seed extract has been evaluated in the Ehrlich ascites carcinoma (EAC) model in Balb-C mice. Intra-peritoneal administration of the alcohol extract of the seed both before and after inoculation of EAC cell in mice produced more than 70% inhibition of tumour cell growth with respect to the control. Treatment with the extract was found to enhance both the peritoneal exudate cell and macrophage cell counts. The extract also produced a significant antiinflammatory effect. We report here the antiinflammatory and antineoplastic effects, of Trigonella foenum graecum seed extract.
Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases (2017)

The gut microbiota provides essential signals for the development and appropriate function of the immune system. Through this critical contribution to immune fitness, the gut microbiota has a key role in health and disease. Recent advances in the technological applications to study microbial communities and their functions have contributed to a rapid increase in host-microbiota research. Although it still remains difficult to define a so-called 'normal' or 'healthy' microbial composition, alterations in the gut microbiota have been shown to influence the susceptibility of the host to different diseases. Current translational research combined with recent technological and computational advances have enabled in-depth study of the link between microbial composition and immune function, addressing the interplay between the gut microbiota and immune responses. As such, beneficial modulation of the gut microbiota is a promising clinical target for many prevalent diseases including inflammatory bowel disease, metabolic abnormalities such as obesity, reduced insulin sensitivity and low-grade inflammation, allergy and protective immunity against infections.
Fast Solution of $\ell _{1}$-Norm Minimization Problems When the Solution May Be Sparse (2008)

The minimum lscr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -norm solution to an underdetermined system of linear equations <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</i> = <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ax</i> is often, remarkably, also the sparsest solution to that system. This sparsity-seeking property is of interest in signal processing and information transmission. However, general-purpose optimizers are much too slow for lscr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> minimization in many large-scale applications.In this paper, the Homotopy method, originally proposed by Osborne et al. and Efron et al., is applied to the underdetermined lscr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> -minimization problem min par <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</i> par <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> subject to <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</i> = <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ax</i> . Homotopy is shown to run much more rapidly than general-purpose LP solvers when sufficient sparsity is present. Indeed, the method often has the following <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> -step solution property: if the underlying solution has only <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> nonzeros, the Homotopy method reaches that solution in only <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> iterative steps. This <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> -step solution property is demonstrated for several ensembles of matrices, including incoherent matrices, uniform spherical matrices, and partial orthogonal matrices. These results imply that Homotopy may be used to rapidly decode error-correcting codes in a stylized communication system with a computational budget constraint. The approach also sheds light on the evident parallelism in results on lscr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sub> minimization and orthogonal matching pursuit (OMP), and aids in explaining the inherent relations between Homotopy, least angle regression (LARS), OMP, and polytope faces pursuit.
Push forward link-level scheduling for network-wide performance (1996)

A virtual circuit network with arbitrary topology is considered. The traffic streams follow prespecified routes, different in general for each stream, to reach their destination. A fluid traffic model is adopted and a processor sharing service discipline is considered. A policy is proposed for setting adaptively the fractions of the transmission capacity, which is allocated to the different traffic streams in the processor sharing discipline at each link. The amount of traffic arrived at the originating node of each link is measured for each stream. The fraction of the link capacity allocated to each stream is set to be proportional to the measured traffic. The traffic is measured continuously and the fractions are updated regularly based on the most recent traffic measurements. It is shown that eventually, the transmission capacity allocated to each stream converges to a quantity proportional to the average rate of the stream. Hence, if the capacity condition is satisfied, sufficient fractions of the capacity are allocated at each link for each stream. End-to-end performance guarantees are provided, if the traffic is regulated. The policy is distributed since each link adjusts the service fractions based on observations of the traffic arriving at its originating node only. Furthermore, it is adaptive since no information on the traffic characteristics is needed for the application of the policy.
Isolation and expression of human cytokine synthesis inhibitory factor cDNA clones: homology to Epstein-Barr virus open reading frame BCRFI. (1991)

We have demonstrated the existence of human cytokine synthesis inhibitory factor (CSIF) [interleukin 10 (IL-10)]. cDNA clones encoding human IL-10 (hIL-10) were isolated from a tetanus toxin-specific human T-cell clone. Like mouse IL-10, hIL-10 exhibits strong DNA and amino acid sequence homology to an open reading frame in the Epstein-Barr virus, BCRFI. hIL-10 and the BCRFI product inhibit cytokine synthesis by activated human peripheral blood mononuclear cells and by a mouse Th1 clone. Both hIL-10 and mouse IL-10 sustain the viability of a mouse mast cell line in culture, but BCRFI lacks comparable activity in this assay, suggesting that BCRFI may have conserved only a subset of hIL-10 activities.
Analysis of expression of cMOAT (MRP2), MRP3, MRP4, and MRP5, homologues of the multidrug resistance-associated protein gene (MRP1), in human cancer cell lines. (1997)

By screening databases of human expressed sequence tags, we have identified three new homologues of MRP1, the gene encoding the multidrug resistance-associated protein, and cMOAT (or MRP2), the canalicular multispecific organic anion transporter gene. We call these new genes MRP3, MRP4, and MRP5. MRP3, like cMOAT, is mainly expressed in the liver. MRP4 is expressed only at very low levels in a few tissues, and MRP5, like MRP1, is expressed in almost every tissue tested. To assess a possible role of these new MRP homologues in multidrug or cisplatin resistance, a large set of resistant cell lines was examined for the (over)expression of MRP1, cMOAT, MRP3, MRP4, and MRP5. We find that even in cells selected for a low level of resistance, several MRP-related genes can be up-regulated simultaneously. However, MRP4 is not overexpressed in any of the cell lines we analyzed; MRP3 and MRP5 are only overexpressed in a few cell lines, and the RNA levels do not seem to correlate with resistance to either doxorubicin or cisplatin. cMOAT is substantially overexpressed in several cell lines, and cMOAT RNA levels correlate with cisplatin but not doxorubicin resistance in a subset of resistant cell lines. Our results emphasize the need for gene-specific blocks in gene expression to define which transporter contributes to resistance in each resistant cell line.
Knowledge-based IMRT treatment planning for prostate cancer (2011)

The authors demonstrate a knowledge-based approach of using prior clinically approved treatment plans to generate clinically acceptable treatment plans of high quality. This semiautomated approach has the potential to improve the efficiency of the treatment planning process while ensuring that high quality plans are developed.
Effect of Ginseng Saponins on Cold Tolerance in Young and Elderly Rats (2000)

Acute systemic injection of ginseng saponin (GS) significantly elevated both the total and maximum heat production in young rats (3-6 months) and improved their cold tolerance under severe cold (-10 degrees C under helium-oxygen). However, pretreating the animal with the optimal dose (10 mg/kg) of GS devoid of Rg1 and Rb1 failed to elicit any beneficial effect in improving the cold tolerance. Pretreating the animal with Rb1, but not Rg1, increased thermogenesis as well as cold tolerance in young rats. A similar beneficial effect in improving cold tolerance was also observed when old rats (26-28 months) were pretreated with the same doses of Rb1 (2.5 and 5.0 mg/kg). Our results indicate that Rb1 is the key ingredient in GS-mediated enhancement in thermogenic capacity and that both young and old rats can benefit from this treatment for enhanced cold tolerance.
ChemInform Abstract: Bis(trifluoromethyl)sulfine, (CF3)2C=SO: Addition Reactions with Thiols, Amine N‐Oxides, Ethers, and 1,3‐Dipoles. (1988)

Abstract The sulfine (I) reacts with the thiols (II) via the sulfinic acid S‐esters (III) as intermediates to give the disulfanes (IV).