gebhart/patrepeval huggingface dataset:
Recipient Toll-like receptors contribute to chronic graft dysfunction by both MyD88- and TRIF-dependent signaling (2009)

Toll-like receptors (TLRs) recognize specific molecular patterns derived from microbial components (exogenous ligands) or stressed cells (endogenous ligands). Stimulation of these receptors leads to a pronounced inflammatory response in a variety of acute animal models. Chronic allograft dysfunction (CAD) was regarded as a candidate disease to test whether TLRs influence chronic fibrosing inflammation. Potential endogenous renal TLR ligands, specifically for TLR2 and TLR4, have now been detected by a significant upregulation of glucose regulated protein (GRP)-94, fibrinogen, heat shock protein (HSP)-60, HSP-70, biglycan (Bgn) and high-mobility group box chromosomal protein 1 (HMGB1) in the acute and chronic transplant setting. In a genetic approach to define the contribution of TLR2 and TLR4, and their adaptor proteins MyD88 and TRIF [Toll/interleukin (IL)-1 receptor domain-containing adaptor-protein inducing interferon beta], to CAD, kidney transplantation of TLR wild-type grafts to recipients who were deficient in TLR2, TLR4, TLR2/4, MyD88 and TRIF was performed. TLR and adaptor protein deficiencies significantly improved the excretory function of chronic kidney grafts by between 65% and 290%, and histopathologic signs of chronic allograft damage were significantly ameliorated. T cells, dendritic cells (DCs) and foremost macrophages were reduced in grafts by up to 4.5-fold. The intragraft concentrations of IL-6, IL-10, monocyte chemotactic protein-1 (MCP-1) and IL-12p70 were significantly lower. TLR-, MyD88- and TRIF-deficient recipients showed a significant reduction in fibrosis. alpha-smooth muscle actin (alpha-SMA)-positive cells were decreased by up to ninefold, and collagen I and III were reduced by up to twofold. These findings highlight the functional relevance of TLRs and their two major signaling pathways in graft-infiltrating mononuclear cells in the pathophysiology of CAD. A TLR signaling blockade may be a therapeutic option for the prevention of CAD.
Use of differentiated pluripotent stem cells in replacement therapy for treating disease (2014)

Pluripotent stem cells (PSCs) directed to various cell fates holds promise as source material for treating numerous disorders. The availability of precisely differentiated PSC-derived cells will dramatically affect blood component and hematopoietic stem cell therapies and should facilitate treatment of diabetes, some forms of liver disease and neurologic disorders, retinal diseases, and possibly heart disease. Although an unlimited supply of specific cell types is needed, other barriers must be overcome. This review of the state of cell therapies highlights important challenges. Successful cell transplantation will require optimizing the best cell type and site for engraftment, overcoming limitations to cell migration and tissue integration, and occasionally needing to control immunologic reactivity, as well as a number of other challenges. Collaboration among scientists, clinicians, and industry is critical for generating new stem cell-based therapies.
Modulation of red cell glycolysis: interactions between vertebrate hemoglobins and cytoplasmic domains of band 3 red cell membrane proteins (2004)

Several vital functions/physical characteristics of erythrocytes (including glycolysis, the pentose phosphate pathway, ion fluxes, and cellular deformability) display dependence on the state of hemoglobin oxygenation. The molecular mechanism proposed involves an interaction between deoxyhemoglobin and the cytoplasmic domain of the anion-exchange protein, band 3 (cdB3). Given that band 3 also binds to membrane proteins 4.1 and 4.2, several kinases, hemichromes, and integral membrane proteins, and at least three glycolytic enzymes, it has been suggested that the cdB3-deoxyhemoglobin interaction might modulate the pathways mediated by these associated proteins in an O(2)-dependent manner. We have investigated this mechanism by synthesizing 10-mer peptides corresponding to the NH(2)-terminal fragments of various vertebrate cdB3s, determining their effects on the oxygenation reactions of hemoglobins from the same and different species and examining binding of the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase to the erythrocytic membrane of mouse erythrocytes. The cdB3 interaction is strongly dependent on pH and the number of negative and positive charges of the peptide and at the effector binding site, respectively. It lowers the O(2) association equilibrium constant of the deoxygenated (Tense) state of the hemoglobin and is inhibited by magnesium ions, which neutralize cdB3's charge and by 2,3-diphosphoglycerate, which competes for the cdB3-binding site. The interaction is stronger in humans (whose erythrocytes derive energy predominantly from glycolysis and exhibit higher buffering capacity) than in birds and ectothermic vertebrates (whose erythrocytes metabolize aerobically and are poorly buffered) and is insignificant in fish, suggesting that its role in the regulation of red cell glycolysis increased with phylogenetic development in vertebrates.
An analog VLSI cochlea with new transconductance amplifiers and nonlinear gain control (2002)

We show data from a working 45-stage analog VLSI cochlea, built on a 2.2 mm/spl times/2.2 mm tiny chip. The novel architectural features in this cochlea are: (1) The use of a wide-linear-range low-noise subthreshold transconductance amplifier. (2) The use of "fuse-like" nonlinear positive-feedback amplification in the second-order cochlear filter. Several new circuit techniques used in the design are described here. The fuse nonlinearity shuts off the positive-feedback amplification at large signal levels instead of merely saturating it, like in prior designs, and leads to increased adaptation and improved large-signal stability in the filter. The fuse filter implements a functional model of gain control due to outer hair cells in the biological cochlea. We present data for travelling-wave patterns in our silicon cochlea that reproduce linear and nonlinear effects in the biological cochlea.
Anisotropic Thermal Transport in Thermoelectric Composites of Conjugated Polyelectrolytes/Single-Walled Carbon Nanotubes (2016)

We report a method to determine the thermal conductivities of polymer composites with single-walled carbon nanotubes (SWNTs) using time-domain thermoreflectance. Both through-plane and in-plane thermal conductivities were determined. Two types of CPEs used in these studies are of the same conjugated backbone but with either cationic (CPE-PyrBIm4) or anionic (CPE-Na) pendant functionalities. The CPE-Na/SWNT composites are p-type conductors, whereas the CPE-PyrBIm4/SWNT counterparts exhibit n-type charge transport. The CPE/SWNT films were prepared through a filtration method that preferentially aligns the SWNTs in the in-plane direction. Attaching the composites onto glass substrates with a precoated heat transducer allows one to measure the through-plane thermal conductivity of materials with rough surfaces. The in-plane thermal conductivity can be measured by embedding thick samples into epoxy followed by microtoming to expose the relatively smooth cross sections. The thermal conductivity along the in-plane direction is found to be higher than that along the through-plane direction. Indeed, the anisotropy factor of thermal conductivity in these composites is approximately an order of magnitude, favoring in-plane direction.
Synthetic and enzyme inhibition studies of pepstatin analogs containing hydroxyethylene and ketomethylene dipeptide isosteres (1987)

Synthetic details for the preparation of a series of hydroxyethylene and ketomethylene dipeptide isosteres with control of stereochemistry at C(2) are described. Incorporation of the isosteres into peptide sequences derived from pepstatin afforded potent inhibitors of the aspartic protease porcine pepsin. When Leu-OH-Ala or Leu-OH-Phe was substituted for statine [3S,4S)-4-amino-3-hydroxy-6-methylheptanoic acid), inhibitors equipotent to the parent compound were obtained, whereas Leu-OH-Gly was a much less effective replacement for statine. A similar trend was evident in the corresponding ketones. The finding that structural features for good substrates do not closely parallel those for good inhibitors is discussed.
Listening to Brain Microcircuits for Interfacing With External World—Progress in Wireless Implantable Microelectronic Neuroengineering Devices (2010)

Acquiring neural signals at high spatial and temporal resolution directly from brain microcircuits and decoding their activity to interpret commands and/or prior planning activity, such as motion of an arm or a leg, is a prime goal of modern neurotechnology. Its practical aims include assistive devices for subjects whose normal neural information pathways are not functioning due to physical damage or disease. On the fundamental side, researchers are striving to decipher the code of multiple neural microcircuits which collectively make up nature's amazing computing machine, the brain. By implanting biocompatible neural sensor probes directly into the brain, in the form of microelectrode arrays, it is now possible to extract information from interacting populations of neural cells with spatial and temporal resolution at the single cell level. With parallel advances in application of statistical and mathematical techniques tools for deciphering the neural code, extracted populations or correlated neurons, significant understanding has been achieved of those brain commands that control, e.g., the motion of an arm in a primate (monkey or a human subject). These developments are accelerating the work on neural prosthetics where brain derived signals may be employed to bypass, e.g., an injured spinal cord. One key element in achieving the goals for practical and versatile neural prostheses is the development of fully implantable wireless microelectronic "brain-interfaces" within the body, a point of special emphasis of this paper.
Efficiently Encodable Irregular QC-LDPC Codes Constructed from Self-Reciprocal Generator Polynomials of MDS Codes (2010)

This letter presents a class of quasi-cyclic (QC) low-density parity-check (LDPC) codes which are efficiently encodable and have better memory efficiency than other randomly constructed QC-LDPC codes. The parity-check matrix of the codes is obtained from a block circulant matrix that is generated from a self-reciprocal generator polynomial of a maximum distance separable (MDS) code by replacing some of its block entries by all zero matrices. We show by simulations that the codes can achieve excellent error performance.
Effects of disulfide bond reducing agents on sperm chromatin structural integrity and developmental competence of in vitro matured oocytes after intracytoplasmic sperm injection in pigs (2009)

We recently reported that electrical activation followed by secondary chemical activation greatly enhanced the developmental competence of in vitro matured porcine oocytes fertilized by intracytoplasmic sperm injection (ICSI). We hypothesized that sperm treatment with disulfide bond reducing agents will enhance the development competence of porcine embryos produced by this ICSI procedure. We examined the effects of glutathione (GSH), dithiothreitol (DTT), GSH or DTT in combination with heparin on sperm DNA structure, paternal chromosomal integrity, pronuclear formation, and developmental competence of in vitro matured porcine oocytes after ICSI. Acridine orange staining and flow cytometry based sperm chromatin structure assay were used to determine sperm DNA integrity by calculating the cells outside the main population (COMP alphaT). No differences were observed in COMP alphaT values among GSH-treated and control groups. COMP alphaT values in GSH-treated groups were significantly lower than that in DTT-treated groups. Following ICSI, GSH treatments did not significantly alter paternal chromosomal integrity. Paternal chromosomal integrity in sperm treated with DTT plus or minus heparin was also the lowest among all groups. GSH-treated sperm yielded the highest rates of normal fertilization and blastocyst formation, which were significantly higher than that of control and DTT-treated groups. The majority of blastocysts derived from control and GSH-treated spermatozoa were diploid, whereas blastocysts derived from DTT-treated spermatozoa were haploid. In conclusion, sperm treatment with GSH enhanced the developmental capacity of porcine embryos produced by our optimized ICSI procedure.
The Roles of E6-AP and MDM2 in p53 Regulation in Human Papillomavirus-Positive Cervical Cancer Cells (2000)

The p53 tumor suppressor is regulated by the MDM2 oncoprotein through a negative feedback mechanism. MDM2 promotes the ubiquitination and proteasome-dependent degradation of p53, possibly by acting as a ubiquitin ligase. In cervical cancer cells containing high-risk human papillomaviruses (HPV), p53 is also targeted for degradation by the HPV E6 oncoprotein in combination with the cellular E6-AP ubiquitin ligase. In this report, we describe the identification of efficient antisense oligonucleotides against human E6-AP. The roles of MDM2 and E6-AP in p53 regulation were investigated using a novel E6-AP antisense oligonucleotide and a previously characterized MDM2 antisense oligonucleotide. In HPV16-positive and HPV-18 positive cervical cancer cells, inhibition of E6-AP, but not MDM2, expression results in significant induction of p53. In HPV-negative tumor cells, p53 is activated by inhibition of MDM2 but not E6-AP. Furthermore, treatment with both E6-AP and MDM2 antisense oligonucleotides in HPV-positive cells does not lead to further induction of p53 over inhibition of E6-AP alone. Therefore, E6-AP-mediated degradation is dominant over MDM2 in cervical cancer cells but does not have a significant role in HPV-negative cells.
Bivalent Ligand UDCA-LPE Inhibits Pro-Fibrogenic Integrin Signalling by Inducing Lipid Raft-Mediated Internalization (2018)

Ursodeoxycholyl lysophosphatidylethanolamide (UDCA-LPE) is a synthetic bile acid-phospholipid conjugate with profound hepatoprotective and anti-fibrogenic functions in vitro and in vivo. Herein, we aimed to demonstrate the inhibitory effects of UDCA-LPE on pro-fibrogenic integrin signalling. UDCA-LPE treatment of human embryonic liver cell line CL48 and primary human hepatic stellate cells induced a non-classical internalization of integrin β1 resulting in dephosphorylation and inhibition of SRC and focal adhesion kinase (FAK). Signalling analyses suggested that UDCA-LPE may act as a heterobivalent ligand for integrins and lysophospholipid receptor1 (LPAR1) and co-immunoprecipitation demonstrated the bridging effect of UDCA-LPE on integrin β1 and LPAR1. The disruption of either the UDCA-moiety binding to integrins by RGD-containing peptide GRGDSP or the LPE-moiety binding to LPAR1 by LPAR1 antagonist Ki16425 reversed inhibitory functions of UDCA-LPE. The lack of inhibitory functions of UDCA-PE and UDCA-LPE derivatives (14:0 and 12:0, LPE-moiety containing shorter fatty acid chain) as well as the consistency of the translocation of UDCA-LPE and integrins, which co-fractionated with LPE but not UDCA, suggested that the observed UDCA-LPE-induced translocation of integrins was mediated by LPE endocytic transport pathway.
MPEG-2 to H.264/AVC Transcoding for Efficient Storage of Broadcast Video Bitstreams (2006)

This paper introduces an HDD recording system that employs MPEG-2 to H.264/AVC transcoding to achieve efficient storage of broadcast streams. Novel transcoding techniques are presented and several system design issues are addressed. Experimental results show that high quality video could be maintained with the proposed system.
Robotic nurse duties in the urology operative room: 11 years of experience (2017)

The robotic nurse plays an essential role in a successful robotic surgery. As part of the robotic surgical team, the robotic nurse must demonstrate a high level of professional knowledge, and be an expert in robotic technology and dealing with robotic malfunctions. Each one of the robotic nursing team "nurse coordinator, scrub-nurse and circulating-nurse" has a certain job description to ensure maximum patient's safety and robotic surgical efficiency. Well-structured training programs should be offered to the robotic nurse to be well prepared, feel confident, and maintain high-quality of care.
Artifact of "To Pack or Not to Pack: A Generalized Packing Analysis and Transformation" (2023)

Artifact of the paper "To Pack or Not to Pack: A Generalized Packing Analysis and Transformation".- docker-packing-artifact.tar.gz: docker image for the execution of experiments- llvm-packing-v0.5.zip: LLVM source code with packing implementation (binary in docker image) - updated source code link - logs-and-graphs.zip: Log files and graphs that were used in the paper- packing-scripts.zip: scripts used to run experiments and Dockerfile source (also provided in docker image)- polybench-c-4.2.1-plus-contract-3d.zip: Polybench 4.2 and running example of paper (also provided in docker image)
Automated calibration of a camera sensor network (2005)

In this paper we present a new approach for the online calibration of a camera sensor network. This is the first step towards fully exploiting the potential for collaboration between mobile robots and static sensors sharing the same network. In particular we propose an approach for extracting the 3D pose of each camera in a common reference frame, with the help of a mobile robot. The camera poses can then be used to further refine the robot pose or to perform other tracking tasks. The analytical formulation of the problem of pose recovery is presented together with experimental results of a six node sensor network in different configurations.
生活科における「気付き」の概念についての基礎的研究 : 学習指導要領と指導要録の分析を通して (2004)

「気付き」は生活科のキーワードであるが, その使われ方や概念は一様ではない。本小論では, 学習指導要領と指導要録の分析を通して, 生活科における「気付き」に関する諸問題を考察し, 「気付き」の検討に必要な視点, 枠組みを得た。それをもとに, 「気付き」の概念を規定するとともに, 「気付き」の特質について考察した。ここでは, 「気付く」を, 「子どもが具体的な活動や体験, 思考や話し合いなどの学習活動によって対象に出会い, 自らの内面に, 何らかの事実, 関係, 疑問, 感情, 感覚などを生起させ, 子ども自身がそれを意識し自覚すること」と規定し, そのようにして意識され自覚された事実, 関係, 疑問, 感情, 感覚などを「気付き」とした。ここで示した生活科における「気付き」の概念や特質は, 暫定的なものであり, 今後, 生活科授業における子どもたちの具体的な「気付き」を通して吟味, 検討を進めていく必要がある。
Stereoselective Heteroatom-Assisted Allylic Alkylation of Cyclic Ethers with Grignard Reagents. A Convenient Route to Enantiomerically Pure Carbocycles (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTStereoselective Heteroatom-Assisted Allylic Alkylation of Cyclic Ethers with Grignard Reagents. A Convenient Route to Enantiomerically Pure CarbocyclesNicola M. Heron, Jeffrey A. Adams, and Amir H. HoveydaView Author Information Department of Chemistry, Merkert Chemistry Center Boston College, Chestnut Hill, Massachusetts 02167 Cite this: J. Am. Chem. Soc. 1997, 119, 26, 6205–6206Publication Date (Web):July 2, 1997Publication History Received20 March 1997Published online2 July 1997Published inissue 1 July 1997https://pubs.acs.org/doi/10.1021/ja970885nhttps://doi.org/10.1021/ja970885nrapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views1083Altmetric-Citations46LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Chemical reactions,Halogens,Inorganic compounds,Reagents,Substitution reactions Get e-Alerts
A Convenient Photocatalytic Fluorination of Unactivated CH Bonds (2014)

Abstract Fluorination reactions are essential to modern medicinal chemistry, thus providing a means to block site‐selective metabolic degradation of drugs and access radiotracers for positron emission tomography imaging. Despite current sophistication in fluorination reagents and processes, the fluorination of unactivated CH bonds remains a significant challenge. Reported herein is a convenient and economic process for direct fluorination of unactivated CH bonds that exploits the hydrogen abstracting ability of a decatungstate photocatalyst in combination with the mild fluorine atom transfer reagent N ‐fluorobenzenesulfonimide. This operationally straightforward reaction provides direct access to a wide range of fluorinated organic molecules, including structurally complex natural products, acyl fluorides, and fluorinated amino acid derivatives.
The effects of feedback and lateral connections on perceptual processing: A study using oscillatory networks (2011)

We model neural dynamical behavior during object perception using the principle of sparse coding in multilayer oscillatory networks. The network model consists of units with amplitude and phase variables, and allows the propagation of higher-level information to lower levels via feedback connections. We show that this model can replicate findings in the neuroscience literature, where measurements have shown that neurons in lower level visual areas respond in a delayed fashion to missing contours of whole objects. We contrast the behavior of feedback connections with that of lateral connections by selectively disabling these in our model to examine their contributions to object perception. This paper successfully extends the previously reported capabilities of oscillatory networks by applying them to model perceptual tasks.
A six-vertex model as a diffusion problem: derivation of correlation functions (1990)

A cellular automaton which describes diffusion of particles with exclusion in one dimension is shown to be equivalent to a six-vertex model on a critical line. The arrow-arrow correlation function of the six-vertex model is calculated exactly on this line using a transfer matrix method.