gebhart/patrepeval huggingface dataset:
Localization and chemical synthesis of fibronectin peptides with melanoma adhesion and heparin binding activities (1988)

Tumor cell adhesion to the extracellular matrix is an important consideration in tumor metastasis. Recent results show that multiple adhesion-promoting domains for melanoma cells can be purified from proteolytic digests of fibronectin [McCarthy, J. B., Hagen, S. T., & Furcht, L. T. (1986) J. Cell Biol. 102, 179-188]. Monoclonal antibodies were generated against a tryptic/catheptic 33K heparin binding fragment of fibronectin derived from the carboxyl terminal of the A chain. This region contains a tumor cell adhesion-promoting domain(s). The amino-terminal sequence was determined for this fragment, as well as a tryptic 31K fragment which is located to the carboxyl-terminal side of the 33K heparin binding fragment in A chains of fibronectin. The partial sequence data demonstrate that arginyl-glycyl-aspartyl-serine (RGDS) or the related arginyl-glutamyl-aspartyl-valine (REDV) is not present in the 33K heparin binding fragment, confirming earlier results which demonstrated that cells adhere to this fragment by an RGDS-independent mechanism. Two monoclonal antibodies, termed AHB-1 and AHB-2, recognized epitopes common to heparin binding fragments derived from the carboxyl terminus of both the A and B chains of fibronectin. Monoclonal antibody AHB-2 inhibited melanoma adhesion to the 33K heparin binding fragment of fibronectin in a concentration-dependent manner, whereas monoclonal antibody AHB-1 had no effect on adhesion to this fragment. Neither monoclonal antibody inhibited adhesion to intact fibronectin. However, monoclonal AHB-2 potentiated the inhibitory effect of suboptimal levels of exogenous RGDS on cell adhesion to intact fibronectin. AHB-2 recognized an epitope common to both the A- and B-chain carboxyl-terminal heparin binding region of fibronectin.(ABSTRACT TRUNCATED AT 250 WORDS)
Monte Carlo Modeling of Light Transport in Multi-layered Tissues in Standard C (1992)

Abstract iii A Monte Carlo model of steady-state light transport in multi-layered tissue (mcml) and the corresponding convolution program (conv) have been coded in ANSI Standard C. The programs can therefore be executed on a variety of computers. Dynamic data allocation is used for mcml, hence the number of tissue layers and the number of grid elements of the grid system can be varied by users at run time as long as the total amount of memory does not exceed what the system allows. The principle and the implementation details of the model, and the instructions for using mcml and conv are presented here. We have verified some of the mcml and conv computation results with those of other theories or other investigators. iv Acknowledgement Acknowledgment We would like to thank a group of people who have helped us with this package directly or indirectly. Massoud Motamedi (University of Texas Medical Branch,
Review: Airway smooth muscle as a model for new investigative drugs in asthma (2008)

Bronchial asthma as such exists because airway smooth muscle (ASM) contracts excessively in response to various stimuli. After several decades during which research was mainly focused on airway inflammation, increasing attention is now being paid to a possible abnormal behaviour of ASM. Thus, ASM is regarded as a major target for anti-asthma treatments. This review first describes the mechanisms of ASM contraction and airway hyperresponsiveness, through cellular, animal and human models. The developments of new drugs targeting extra and/or intracellular pathway of ASM contraction are discussed.
Production of Sry knockout mouse using TALEN via oocyte injection (2013)

Recently developed transcription activator-like effector nuclease (TALEN) technology has enabled the creation of knockout mice, even for genes on the Y chromosome. In this study, we generated a knockout mouse for Sry, a sex-determining gene on the Y chromosome, using microinjection of TALEN RNA into pronuclear stage oocytes. As expected, the knockout mouse had female external and internal genitalia, a female level of blood testosterone and a female sexually dimorphic nucleus in the brain. The knockout mouse exhibited an estrous cycle and performed copulatory behavior as females, although it was infertile or had reduced fertility. A histological analysis showed that the ovary of the knockout mouse displayed a reduced number of oocytes and luteinized unruptured follicles, implying that a reduced number of ovulated oocytes is a possible reason for infertility and/or reduced fertility in the KO mouse.
EFFECTS OF THE TREM 1 PATHWAY MODULATION DURING HEMORRHAGIC SHOCK IN RATS (2009)

The triggering receptor expressed on myeloid cells (TREM) 1, a receptor expressed on the surface of neutrophils and monocytes/macrophages, synergizes with the Toll-like receptors in amplifying the inflammatory response mediated by microbial components. Because the pathogenesis of severe blood loss-induced excessive inflammation and multiple organ failure implies leukocyte activation and bacterial translocation, we hypothesized that the TREM-1 pathway modulation would prove beneficial in this setting. Wistar rats were subjected to a 1-h period of hemorrhagic shock and then reperfused with shed blood and ringer lactate for 1 h. At the time of reperfusion, animals were administered with LP17 (a synthetic soluble TREM-1 decoy receptor), a control peptide, or a vehicle (isotonic sodium chloride solution). Plasma concentration of TNF-alpha, IL-6, and soluble TREM-1 were measured by enzyme-linked immunosorbent assay. Lung permeability was assessed by the weight-dry ratio and fluorescein isothiocyanate-labeled albumin lung-blood ratio. Organ dysfunction was appreciated by measuring plasma aspartate aminotransferase and urea concentrations. Bacterial translocation was estimated by blood, mesenteric lymph nodes, and spleens culture. Hemorrhagic shock associated with cardiovascular collapse, lactic acidosis, systemic inflammatory response, and organ dysfunction that was partly prevented by LP17 administration. Hemorrhagic shock induced a marked increase in lung permeability that was also prevented by TREM-1 modulation. Finally, LP17 improved survival. Thus, the early modulation of the TREM-1 pathway by means of a synthetic peptide may be useful during severe hemorrhagic shock in rats in preventing organ dysfunction and improving survival.
Microdystrophin Gene Therapy of Cardiomyopathy Restores Dystrophin-Glycoprotein Complex and Improves Sarcolemma Integrity in the Mdx Mouse Heart (2003)

We established a simple gene transfer method for efficient and persistent transduction of the mdx mouse heart. AAV-mediated microdystrophin expression restored the critical dystrophin-glycoprotein complex and improved sarcolemma integrity of the mdx heart. Our results revealed the promise of AAV-microdystrophin gene therapy for cardiomyopathy in DMD.
Dual Macrolactonization/Pyran–Hemiketal Formation via Acylketenes: Applications to the Synthesis of (−)‐Callipeltoside A and a Lyngbyaloside B Model System (2008)

Two for one: Thermal generation of acylketenes in diol-containing substrates results in the title transformation. This transformation expands the scope of acylketene macrolactonizations and their application to the synthesis of complex macrolides. Triol and tetraol substrates have also been cyclized in highly regioselective fashion. Additionally, the challenging macrolactonization of a tertiary alcohol was achieved. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Reduction of menstrual blood loss in women suffering from idiopathic menorrhagia with a novel antifibrinolytic drug (Kabi 2161) (1995)

Kabi 2161 in a dosage of 2.4 g per day gave a statistically significant reduction in objectively measured menstrual blood loss in a two (41%) as well as in a four (33%) dosage regimen compared with placebo. Frequency of unwanted events did not differ from those during run-in or from those in the placebo group. The optimal daily dosage needs to be further evaluated in a dose titration study.
Activation of the endoplasmic reticulum stress response in autoimmune myositis: Potential role in muscle fiber damage and dysfunction (2005)

These results indicate that the ER stress response may be a major nonimmune mechanism responsible for skeletal muscle damage and dysfunction in autoimmune myositis. Strategies to interfere with this pathway may have therapeutic value in patients with this disease.
KenLM: Faster and Smaller Language Model Queries (2011)

We present KenLM, a library that implements two data structures for efficient language model queries, reducing both time and memory costs. The PROBING data structure uses linear probing hash tables and is designed for speed. Compared with the widelyused SRILM, our PROBING model is 2.4 times as fast while using 57 % of the memory. The TRIE data structure is a trie with bit-level packing, sorted records, interpolation search, and optional quantization aimed at lower memory consumption. TRIE simultaneously uses less memory than the smallest lossless baseline and less CPU than the fastest baseline. Our code is open-source1, thread-safe, and integrated into the Moses, cdec, and Joshua translation systems. This paper describes the several performance techniques used and presents benchmarks against alternative implementations. 1
Excipient Development for Pharmaceutical, Biotechnology, and Drug Delivery Systems (2006)

Excipient development for pharmaceutical, biotechnology, and drug delivery systems / , Excipient development for pharmaceutical, biotechnology, and drug delivery systems / , کتابخانه دیجیتال جندی شاپور اهواز
Sharp thermal emission and absorption from conformally coated metallic photonic crystal with triangular lattice (2008)

A metallic photonic crystal consisting of a triangular lattice of holes in a silicon layer coated with gold is fabricated at a lattice pitch of 3.75 μm using conventional lithographic methods. The photonic crystal exhibits a deep reflection minimum and sharp thermal emission peak near the lattice spacing. Scattering matrix simulations agree well with measurements. This simple structure with a single patterned metallic layer has no emission sidebands and can be scaled to other lattice spacings to tune the wavelength of the absorption and emission peak.
ATM and DNA-PK Function Redundantly to Phosphorylate H2AX after Exposure to Ionizing Radiation (2004)

H2AX phosphorylation is an early step in the response to DNA damage. It is widely accepted that ATM (ataxia telangiectasia mutated protein) phosphorylates H2AX in response to DNA double-strand breaks (DSBs). Whether DNA-dependent protein kinase (DNA-PK) plays any role in this response is unclear. Here, we show that H2AX phosphorylation after exposure to ionizing radiation (IR) occurs to similar extents in human fibroblasts and in mouse embryo fibroblasts lacking either DNA-PK or ATM but is ablated in ATM-deficient cells treated with LY294002, a drug that specifically inhibits DNA-PK. Additionally, we show that inactivation of both DNA-PK and ATM is required to ablate IR-induced H2AX phosphorylation in chicken cells. We confirm that H2AX phosphorylation induced by DSBs in nonreplicating cells is ATR (ataxia telangiectasia and Rad3-related protein) independent. Taken together, we conclude that under most normal growth conditions, IR-induced H2AX phosphorylation can be carried out by ATM and DNA-PK in a redundant, overlapping manner. In contrast, DNA-PK cannot phosphorylate other proteins involved in the checkpoint response, including chromatin-associated Rad17. However, by phosphorylating H2AX, DNA-PK can contribute to the presence of the damage response proteins MDC1 and 53BP1 at the site of the DSB.
Synthesis and Oxygen Reduction Activity of Shape-Controlled Pt3Ni Nanopolyhedra (2010)

Platinum-based alloys have been extensively shown to be effective catalysts for oxygen reduction reaction (ORR) in proton exchange membrane fuel cells (PEMFCs). Most of these catalysts are nanoparticles without shape control. Recently, extended Pt(3)Ni(111) surfaces prepared in ultrahigh vacuum were demonstrated to possess enhanced ORR catalytic activity as compared to the state-of-the-art carbon supported Pt (Pt/C) nanoparticle catalysts. How and whether this promising surface can be transformed into practical nanoscale electrocatalysts used in PEMFCs remain a challenge. We report a new wet-chemical approach of preparing monodisperse Pt(3)Ni nanoctahedra and nanocubes terminated with {111} and {100} facets, respectively. We further show that the ORR activity on the Pt(3)Ni nanoctahedra is approximately 5-fold higher than that of nanocubes with a similar size. Comparison of ORR activity between carbon-supported Pt(3)Ni nanoctahedra and commercial Pt/C reveals that the Pt(3)Ni nanoctahedra are highly active electrocatalysts. This synthetic strategy may be extended to the preparation of other shape-controlled fuel cell electrocatalysts.
A microenvironment-mediated c-Myc/miR-548m/HDAC6 amplification loop in non-Hodgkin B cell lymphomas (2013)

A dynamic interaction occurs between the lymphoma cell and its microenvironment, with each profoundly influencing the behavior of the other. Here, using a clonogenic coculture growth system and a xenograft mouse model, we demonstrated that adhesion of mantle cell lymphoma (MCL) and other non-Hodgkin lymphoma cells to lymphoma stromal cells confers drug resistance, clonogenicity, and induction of histone deacetylase 6 (HDAC6). Furthermore, stroma triggered a c-Myc/miR-548m feed-forward loop, linking sustained c-Myc activation, miR-548m downregulation, and subsequent HDAC6 upregulation and stroma-mediated cell survival and lymphoma progression in lymphoma cell lines, primary MCL and other B cell lymphoma cell lines. Treatment with an HDAC6-selective inhibitor alone or in synergy with a c-Myc inhibitor enhanced cell death, abolished cell adhesion–mediated drug resistance, and suppressed clonogenicity and lymphoma growth ex vivo and in vivo. Together, these data suggest that the lymphoma-stroma interaction in the lymphoma microenvironment directly impacts the biology of lymphoma through genetic and epigenetic regulation, with HDAC6 and c-Myc as potential therapeutic targets.
A game of surface codes: Large-scale quantum computing with lattice surgery (2019)

Given a quantum gate circuit, how does one execute it in a fault-tolerant architecture with as little overhead as possible? In this paper, we discuss strategies for surface-code quantum computing on small, intermediate and large scales. They are strategies for space-time trade-offs, going from slow computations using few qubits to fast computations using many qubits. Our schemes are based on surface-code patches, which not only feature a low space cost compared to other surface-code schemes, but are also conceptually simple~--~simple enough that they can be described as a tile-based game with a small set of rules. Therefore, no knowledge of quantum error correction is necessary to understand the schemes in this paper, but only the concepts of qubits and measurements.
Remote methane sensor using Tunable Diode Laser Spectroscopy (TDLS) via a 1W Raman Source (2009)

We report a long-range near-IR methane sensor for inspection of natural gas collection, storage sites and pipeline networks. The principle is that a laser carrier beam is directed at the target surface across a test path and the backscatter from the surface is collected via a large Fresnel lens onto the photoreceiver. A Raman amplifier has been designed to amplify the TDLS optical signal generated by a 1650.95nm DFB laser diode to over 1W CW. Combining the high power output of the Raman amplifier and the highly sensitive TDLS technique, we may report 100ppm.m sensitivity at more than 100m by extrapolation.
APPENDIX 5: The Large Ribosomal Subunit from H. marismortui at 9 Å Resolution (1999)

A surface rendering of a 9 A resolution X-ray map of the large ribosomal subunit shown in the crown view from the side that interacts with the 30S subunit. The projection on the left is ribosomal protein L1, and the RNA arm that supports it. The central protuberance, which includes 5S rRNA is in the top center of the image, and the projection on the right contains ribosomal proteins L7/L12. (Ban et al., Cell 93: 1105 [1998].) The RNA World, Second Edition. 1999 Cold Spring Harbor Laboratory Press 0-87969-561-7 For conditions see www.cshlpress.com/copyright.
RNA silencing is required for Arabidopsis defence against Verticillium wilt disease (2008)

RNA silencing is a conserved mechanism in eukaryotes that plays an important role in various biological processes including regulation of gene expression. RNA silencing also plays a role in genome stability and protects plants against invading nucleic acids such as transgenes and viruses. Recently, RNA silencing has been found to play a role in defence against bacterial plant pathogens in Arabidopsis through modulating host defence responses. In this study, it is shown that gene silencing plays a role in plant defence against multicellular microbial pathogens; vascular fungi belonging to the Verticillium genus. Several components of RNA silencing pathways were tested, of which many were found to affect Verticillium defence. Remarkably, no altered defence towards other fungal pathogens that include Alternaria brassicicola, Botrytis cinerea, and Plectosphaerella cucumerina, but also the vascular pathogen Fusarium oxysporum, was recorded. Since the observed differences in Verticillium susceptibility cannot be explained by notable differences in root architecture, it is speculated that the gene silencing mechanisms affect regulation of Verticillium-specific defence responses.
Reevaluation of the pathways for the biosynthesis of polyunsaturated fatty acids. (1995)

Recent studies refute the commonly accepted, but untested, hypothesis that 7,10,13,16-22:4 and 7,10,13,16,19-22:5 are desaturated at position 4 by a microsomal acyl-CoA-dependent desaturase. The synthesis of 4,7,10,13,16,19-22:6 occurs via the following reaction sequence: 7,10,13,16,19-22:5-->9,12,15,18,21-24:5-->6,9,12,15,18,21-24:6 4,7,10,13,16,19-22:6. The synthesis of 4,7,10,13,16-22:5 from 7,10,13,16-22:4 takes place via an analogous pathway. According to these pathways the 24-carbon acids that are made in the endoplasmic reticulum move to a site for partial beta-oxidation, which is most likely peroxisomes. The products of partial beta-oxidation, 4,7,10,13,16-22:5 and 4,7,10,13,16,19-22:6, then move back to the endoplasmic reticulum where they are used as substrates for membrane lipid biosynthesis. The ability of a fatty acid to serve as a substrate for continued peroxisomal beta-oxidation, versus its transfer out of peroxisomes for subsequent endoplasmic reticulum-associated esterification reactions, may be an important control for regulating membrane lipid fatty acid composition. Indeed, the revised pathways of polyunsaturated fatty acid biosynthesis imply that there is considerable intracellular movement and recycling of fatty acids between peroxisomes and the endoplasmic reticulum. In addition, these revised pathways require that two 18-carbon and two 24-carbon acids are substrates for desaturation at position 6. Also, as linoleate and linolenate are metabolized, respectively, to 6,9,12,15,18-24:5 and 6,9,12,15,18,21-24:6, three n-6 acids and three n-3 acids are substrates for malonyl-CoA dependent chain elongation. It remains to be determined how many microsomal enzymes are required to carry out these reactions and whether other ancillary enzymes are expressed in tissues whose membrane lipids accumulate very long-chain polyunsaturated acids with up to 36 carbon atoms.
Applications of microarray technology in breast cancer research (2001)

Microarrays provide a versatile platform for utilizing information from the Human Genome Project to benefit human health. This article reviews the ways in which microarray technology may be used in breast cancer research. Its diverse applications include monitoring chromosome gains and losses, tumour classification, drug discovery and development, DNA resequencing, mutation detection and investigating the mechanism of tumour development.
Validation of the 28-joint Disease Activity Score (DAS28) and European League Against Rheumatism response criteria based on C-reactive protein against disease progression in patients with rheumatoid arthritis, and comparison with the DAS28 based on erythrocyte sedimentation rate (2008)

The DAS28 (CRP) has been validated against radiographic progression and physical function. While the DAS28 (CRP) yielded a better EULAR response more often than the DAS28 (ESR), the validation profile was similar to the DAS28 (ESR), indicating that both measures are useful for assessing disease activity in patients with rheumatoid arthritis.
Disregulation of leukosialin (CD43, Ly48, sialophorin) expression in the B-cell lineage of transgenic mice increases splenic B-cell number and survival. (1995)

Leukosialin (also known as Ly48, CD43, and sialophorin) is a major cell surface sialoglycoprotein found on a variety of hematopoietically derived cells. The precise function of this molecule is poorly understood but it has been implicated in cell proliferation and intercellular adhesion. We developed a transgenic mouse model to assess leukosialin's function in vivo. Our approach was to alter mouse CD43 (mCD43) expression in the B-cell lineage where it is tightly regulated, by expressing it in peripheral B cells where it is normally absent. To drive expression of leukosialin in mature B cells, the immunoglobulin heavy chain enhancer was fused to the mCD43 gene. mCD43-immunoglobulin heavy chain enhancer transgenic mice display splenomegaly due to increased numbers of B cells. Transgenic B cells show a striking increase in their ability to survive in vitro compared to B cells from nontransgenic control mice. This prolonged survival is reflected in a decreased susceptibility to apoptosis. These observations suggest that mCD43 plays an important role in the regulation of B-cell survival. The alteration of the temporal expression, or "disregulation," of a gene in transgenic mice provides a general strategy for elucidating the in vivo role of other molecules involved in cell signaling and adhesion.
RtxA1‐Induced Expression of the Small GTPase Rac2 Plays a Key Role in the Pathogenicity ofVibrio vulnificus (2009)

Infection with the human pathogen Vibrio vulnificus leads to the generation of reactive oxygen species (ROS) via NAD(P)H oxidase (Nox) in host cells. In the present study, we employed mutant V. vulnificus strains to identify an essential virulence factor responsible for this ROS generation. We found that repeats-in-toxin A1 (RtxA1) expressed by V. vulnificus acts via Nox1 to induce significant ROS generation in the intestine epithelial cells, which ultimately results in cell death. Furthermore, RtxA1 modulates the small GTPase Rac2, which is known to play an important role in the activation of Nox. When mice were infected by the oral method, in contrast with the wild-type bacteria, an RtxA1-deficient V. vulnificus mutant was unable to induce ROS generation within the intestine and failed to cause death. These findings strongly suggest that RtxA1-induced Rac2 expression is a critical step underlying the pathogenicity of V. vulnificus.
Antibody-dependent infection of human macrophages by severe acute respiratory syndrome coronavirus (2014)

These results demonstrate that human macrophages can be infected by SARS-CoV as a result of IgG-mediated ADE and indicate that this infection route requires signaling pathways activated downstream of binding to FcγRII receptors.