gebhart/patrepeval huggingface dataset:
Identifying Novel Targets for Treatment of Liver Fibrosis: What Can We Learn from Injured Tissues which Heal Without a Scar? (2015)

The liver is unique in that it is able to regenerate. This regeneration occurs without formation of a scar in the case of non-iterative hepatic injury. However, when the liver is exposed to chronic liver injury, the purely regenerative process fails and excessive extracellular matrix proteins are deposited in place of normal liver parenchyma. While much has been discovered in the past three decades, insights into fibrotic mechanisms have not yet lead to effective therapies; liver transplant remains the only cure for advanced liver disease. In an effort to broaden the collection of possible therapeutic targets, this review will compare and contrast the liver wound healing response to that found in two types of wound healing: scarless wound healing of fetal skin and oral mucosa and scar-forming wound healing found in adult skin. This review will examine wound healing in the liver and the skin in relation to the role of humoral and cellular factors, as well as the extracellular matrix, in this process. While several therapeutic targets are similar between fibrotic liver and adult skin wound healing, others are unique and represent novel areas for hepatic anti-fibrotic research. In particular, investigations into the role of hyaluronan in liver fibrosis and fibrosis resolution are warranted.
Broadband source sliced by cascaded interleavers (2009)

A new structure of spectrum-sliced broadband source consisting of an ASE source and two cascaded interleavers is presented. The proposed structure allows the engineer to optimize channel bandwidth and crosstalk easily.
Speeding Up String Pattern Matching by Text Compression: The Dawn of a New Era (2001)

††,☆ † † † †† †† † This paper describes our recent studies on string pattern matching in compressed texts mainly from practical viewpoints. The aim is to speed up the string pattern matching task, in comparison with an ordinary search over the original texts. We have successfully developed (1) an AC type algorithm for searching in Huffman encoded files, and (2) a KMP type algorithm and (3) a BM type algorithm for searching in files compressed by the so-called byte pair encoding (BPE). Each of the algorithms reduces the search time at nearly the same rate as the compression ratio. Surprisingly, the BM type algorithm runs over BPE compressed files about 1.2–3.0 times faster than the exact match routines of the software package agrep, which is known as the fastest pattern matching tool.
Anti-inflammatory Effects of Mi-saponin (1979)

The anti-inflammatory actions of Mi-saponin, which was isolated from the seeds of Madhuca longifolia L. and whose structures are closely related to those of the saponins of Senega and Polygala, were compared with those of two standard drugs, phenylbutazone and β-escin which is the saponin mixture present in the seeds of Aesculus hippocastanum L. (1) Mi-saponin was found to have anti-edematous action on carrageenin edema and inhibitory actions against increased vascular permeability, cotton pellet granulation and peritonitis-induced inflammatory exudate. (2) The anti-inflammatory actions of Mi-saponin were nearly equal to those of β-escin, whereas the actions of Mi-saponin were weaker than those of phenylbutazone in general. (3) In some cases the concurrent use of Mi-saponin with phenylbutazone exerted anti-granulation action stronger than that of the individual compounds.
Expression of a Truncated Cystic Fibrosis Transmembrane Conductance Regulator with an AAV5-pseudotyped Vector in Primates (2007)

Gene therapy using recombinant adeno-associated virus (rAAV2) vectors for cystic fibrosis has shown gene transfer and remarkable safety, yet indeterminate expression. A new construct has been characterized with a powerful exogenous promoter, the cytomegalovirus enhancer/chicken beta-actin promoter, driving a truncated CF transmembrane conductance regulator (CFTR), pseudotyped in an AAV5 viral coat. Our goal is to demonstrate that airway delivery of a pseudotyped rAAV5 vector results in gene transfer as well as expression in non-human primates. Aerosolized pseudotyped rAAV5-DeltaCFTR or rAAV5-GFP (green fluorescent protein) genes were delivered to four and six lungs, respectively. The pseudotyped rAAV5 vector did result in GFP gene transfer (1.005x10(6) copies/mug DNA on average) and quantifiable gene expression. Microscopy confirmed protein expression in airway epithelium. Similarly, the vector also resulted in vector-specific CFTR DNA (1.24x10(5) copies/microg) and mRNA expression. Immunoprecipitation and (32)P phosphoimaging were used to demonstrate CFTR protein expression, as qualitatively enhanced beyond the barely detectable endogenous expression in untreated animals. Based on these promising studies, this CFTR minigene construct is a therapeutic candidate.
TSCH and 6TiSCH for Contiki: Challenges, Design and Evaluation (2017)

Synchronized communication has recently emerged as a prime option for low-power critical applications. Solutions such as Glossy or Time Slotted Channel Hopping (TSCH) have demonstrated end-to-end reliability upwards of 99.99%. In this context, the IETF Working Group 6TiSCH is currently standardizing the mechanisms to use TSCH in low-power IPv6 scenarios. This paper identifies a number of challenges when it comes to implementing the 6TiSCH stack. It shows how these challenges can be addressed with practical solutions for locking, queuing, scheduling and other aspects. With this implementation as an enabler, we present an experimental validation and comparison with state-of-the-art MAC protocols. We conduct fine-grained energy profiling, showing the impact of link-layer security on packet transmission. We evaluate distributed time synchronization in a 340-node testbed, and demonstrate that tight synchronization (hundreds of microseconds) can be achieved at very low cost (0.3% duty cycle, 0.008% channel utilization). We finally compare TSCH against traditional MAC layers: low-power listening (LPL) and CSMA, in terms of reliability, latency and energy. We show that with proper scheduling, TSCH achieves by far the highest reliability, and outperforms LPL in both energy and latency.
High-performance HEMT amplifiers with a simple low-loss matching network (1991)

A report is presented on the design and performance of a K-band high electron mobility transistor (HEMT) amplifier whose passive circuit consists of low-loss suspended stripline elements. Single-stage amplifiers were built at 4 GHz and 22 GHz by using readily available commercial HEMT devices. In the desired frequency range from 21 to 23 GHz for the high-frequency design, the best spot noise temperatures were 150 K and 65 K at 21.5 GHz for room and liquid nitrogen temperatures, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fast atom bombardment and tandem mass spectrometry of synthetic peptides and byproducts. (1992)

Mass spectrometry is a very powerful technique in the rapid determination of the structure of peptides. Synthetic peptides may be analyzed fully protected and partially or completely deprotected. Often, the molecular weight alone, readily obtained by fast atom bombardment mass spectrometry, is sufficient to establish the nature of the product and whether it is the expected one. Tandem mass spectrometry can be used to identify unexpected reaction products which sometimes form during removal of protecting groups, the incomplete removal of such groups, as well as to distinguish between structural isomers.
Bioorthogonal Copper Free Click Chemistry for Labeling and Tracking of Chondrocytes <i>In Vivo</i> (2016)

Establishment of an appropriate cell labeling and tracking method is essential for the development of cell-based therapeutic strategies. Here, we are introducing a new method for cell labeling and tracking by combining metabolic gylcoengineering and bioorthogonal copper-free Click chemistry. First, chondrocytes were treated with tetraacetylated N-azidoacetyl-D-mannosamine (Ac4ManNAz) to generate unnatural azide groups (-N3) on the surface of the cells. Subsequently, the unnatural azide groups on the cell surface were specifically conjugated with near-infrared fluorescent (NIRF) dye-tagged dibenzyl cyclooctyne (DBCO-650) through bioorthogonal copper-free Click chemistry. Importantly, DBCO-650-labeled chondrocytes presented strong NIRF signals with relatively low cytotoxicity and the amounts of azide groups and DBCO-650 could be easily controlled by feeding different amounts of Ac4ManNAz and DBCO-650 to the cell culture system. For the in vivo cell tracking, DBCO-650-labeled chondrocytes (1 × 10(6) cells) seeded on the 3D scaffold were subcutaneously implanted into mice and the transplanted DBCO-650-labeled chondrocytes could be effectively tracked in the prolonged time period of 4 weeks using NIRF imaging technology. Furthermore, this new cell labeling and tracking technology had minimal effect on cartilage formation in vivo.
Property Specification and Static Verification of UML Models (2008)

We present a static verification tool (SVT), a system that performs static verification on UML models composed of UML class and state machine diagrams. Additionally, the SVT allows the user to add extra behavior specification in the form of guards and effects by defining a small action language. UML models are checked against properties written in a special-purpose property language that allows the user to specify linear temporal logic formulas that explicitly reason about UML components. Thus, the SVT provides a strong foundation for the design of reliable systems and a step towards model-driven security.
Characterization of the calmodulin-binding sites of muscle phosphofructokinase and comparison with known calmodulin-binding domains. (1987)

Calmodulin has been shown to interact with high affinity with muscle phosphofructokinase (Mayr, G. W. (1984) Eur. J. Biochem. 143, 513-520, 521-529). In this study, direct binding measurements indicated that each of the two subunits of dimeric phosphofructokinase bound two calmodulins with Kd values of about 3 nM and 1 microM, respectively, in a strictly Ca2+-dependent way. To get more detailed information about this interaction, calmodulin-binding fragments were isolated from a CNBr digest of phosphofructokinase using affinity chromatography on calmodulin-agarose. Two fragments, M11 (Mr 3080) and M22 (Mr 8060), formed a 1:1 stoichiometric complex with Ca2+-calmodulin. The amino acid sequences of these fragments were determined, and their positions in the three-dimensional structure-model of phosphofructokinase are proposed. Fragment M11, which binds to calmodulin with the higher affinity (Kd 11.4 nM), is located in a region of the subunit where two dimers have been proposed to make contacts if associating to active tetrameric enzyme. A stabilization of the dimeric form of the enzyme by binding of calmodulin supports this location of M11. The weaker binding fragment M22 (Kd 198 nM) corresponds to the C-terminal part of the polypeptide and contains the site which is phosphorylated by cAMP-dependent protein kinase. Both fragments have structural properties in common with the isolated calmodulin-binding domains of myosin light chain kinase: two cationic segments rich in hydrophobic residues, one constantly possessing a tryptophan, and the other exhibiting an amino acid sequence resembling sites phosphorylated by cAMP-dependent protein kinase.
Mn<sub>3</sub>O<sub>4</sub> Supported on Glassy Carbon: An Active Non-Precious Metal Catalyst for the Oxygen Reduction Reaction (2012)

In this work, we explore the interplay between manganese oxide (MnOx) nanomaterials and a glassy carbon (GC) support in catalyzing the oxygen reduction reaction (ORR) in an alkaline environment. Initially, we characterize the ORR activity of bare GC electrodes as a function of heat treatments in air, and find that ORR activity increases with increasing temperature up to 500 °C. Modification of GC with size-selected 1 nm MnOx nanoparticles prior to the 500 °C heat treatment yields a highly porous GC (pGC) structure, devoid of MnOx. This pGC sample exhibits the highest ORR performance of the bare carbon electrodes reaching an onset potential of 0.75 V vs the reversible hydrogen electrode (RHE) and a complete 2-electron reduction of oxygen to peroxide. Having established ORR activity of bare GC electrodes, we deposit size-selected 14 nm MnO nanoparticles onto the GC and pGC electrodes and then incite phase changes in MnO through heat treatments in air. Electrochemical characterization of the resulting electrodes reveals that MnO nanoparticles offer no improvement in the ORR onset potential over bare GC or pGC and only slightly increase the number of electrons transferred. By contrast, thermal oxidation of MnO nanoparticles to Mn3O4 at 500 °C, confirmed by Mn L-edge X-ray absorption spectroscopy, results in an improved ORR onset potential of 0.80 V and a 4-electron reduction of oxygen. Thus at low overpotentials, where GC and pGC were inactive for the ORR, MnOx sites must contribute to all steps of the reaction. The catalyst’s estimated specific activity of 3700 μA·cm–2cat at 0.75 V compares favorably with specific activities of Pt/C as well as the best nonprecious metal catalysts. This establishes Mn3O4 as another MnOx phase with high activity for the ORR.
A monoclonal anti-HEBFPP antibody with specificity for lymphocyte surface molecules mediating adhesion to Peyer's patch high endothelium of the rat. (1986)

Cell surface molecules involved in lymphocyte adhesion to high endothelial cell venules (HEV) of Peyer's patches (PP) have been studied in the rat by using a mouse monoclonal anti-HEBFPP (1B.2) antibody. We previously showed that rat thoracic duct lymph contains a high endothelial cell binding factor termed HEBFPP, which in vitro blocks lymphocyte binding sites of HEVPP but not HEVLN. Monoclonal 1B.2 antibody was produced by fusing P3U1 myeloma cells with spleen cells of a mouse immunized with this material. Immunoprecipitation studies with 125I surface-labeled rat thoracic duct lymphocytes (TDL) showed that the antibody recognized an 80-kilodalton protein. This antigen was present in the majority of TDL, spleen, LN, and PP cells but was found on few (5 to 10%) thymus and bone marrow cells (indirect immunofluorescence). Treatment of TDL with 1B.2 antibody blocked their ability to bind in vitro to HEVPP; antibody treatment did not interfere with TDL adhesion to HEVLN. Analysis of 1B.2 antigen isolated from lymph and detergent lysates of TDL by antibody-affinity chromatography showed that this material had the capacity to block lymphocyte binding sites of HEVPP but not HEVLN. In contrast, material with such blocking activity was not isolated from detergent lysates of thymocyte, a population deficient in HEV-binding cells. The results indicate that the 1B.2 antigen is a component of the lymphocyte surface recognition structure mediating adhesion to HEVPP and provide further evidence that distinct adhesion molecules of rat TDL mediate interaction with high endothelium of LN and PP.
Prior sleep with zolpidem enhances the effect of caffeine or modafinil during 18 hours continuous work. (2006)

MOD and CAF may be of value in promoting performance and wakefulness during shiftwork or military operations while zolpidem improves prophylactic sleep quality without any deleterious effect after waking. We concluded that a zolpidem/ caffeine or modafinil combination could be useful in a context of environmental conditions not conducive to sleep.
Ubiquitylation by Trim32 causes coupled loss of desmin, Z-bands, and thin filaments in muscle atrophy (2012)

During muscle atrophy, myofibrillar proteins are degraded in an ordered process in which MuRF1 catalyzes ubiquitylation of thick filament components (Cohen et al. 2009. J. Cell Biol. http://dx.doi.org/10.1083/jcb.200901052). Here, we show that another ubiquitin ligase, Trim32, ubiquitylates thin filament (actin, tropomyosin, troponins) and Z-band (α-actinin) components and promotes their degradation. Down-regulation of Trim32 during fasting reduced fiber atrophy and the rapid loss of thin filaments. Desmin filaments were proposed to maintain the integrity of thin filaments. Accordingly, we find that the rapid destruction of thin filament proteins upon fasting was accompanied by increased phosphorylation of desmin filaments, which promoted desmin ubiquitylation by Trim32 and degradation. Reducing Trim32 levels prevented the loss of both desmin and thin filament proteins. Furthermore, overexpression of an inhibitor of desmin polymerization induced disassembly of desmin filaments and destruction of thin filament components. Thus, during fasting, desmin phosphorylation increases and enhances Trim32-mediated degradation of the desmin cytoskeleton, which appears to facilitate the breakdown of Z-bands and thin filaments.
A 2-dB noise figure 900-MHz differential CMOS LNA (2001)

This paper proposes a new circuit topology for RF CMOS low noise amplifier (LNA). Since pMOS devices are approaching the performances of nMOS devices in scaled technologies, the idea is to realize the input stage shunting an inductively degenerated nMOS stage with a pMOS one. In this way, due to the inherent current reuse, the performances can be improved using the same power consumption. Since the devices of an inductively degenerated input stage are working in moderate inversion (at least at moderate power dissipation), prior to the stage optimization an appropriate moderate inversion model is introduced. A fully differential 900-MHz 0.35-/spl mu/m CMOS LNA (plus output buffer) prototype achieves the following performances: 2-dB noise figure (NF), 17.5-dB power gain, -6-dBm IIP3 with 8-mA current consumption from a 2.7-V voltage supply. To the author's knowledge, this is the lowest reported NF for a fully differential CMOS LNA operating at this power consumption level. As an additional feature, this LNA has a programmable gain.
Exploiting Temporal Correlation of Speech for Error Robust and Bandwidth Flexible Distributed Speech Recognition (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, the temporal correlation of speech is exploited in front-end feature extraction, client-based error recovery, and server-based error concealment (EC) for distributed speech recognition. First, the paper investigates a half frame rate (HFR) front-end that uses double frame shifting at the client side. At the server side, each HFR feature vector is duplicated to construct a full frame rate (FFR) feature sequence. This HFR front-end gives comparable performance to the FFR front-end but contains only half the FFR features. Second, different arrangements of the other half of the FFR features creates a set of error recovery techniques encompassing multiple description coding and interleaving schemes where interleaving has the advantage of not introducing a delay when there are no transmission errors. Third, a subvector-based EC technique is presented where error detection and concealment is conducted at the subvector level as opposed to conventional techniques where an entire vector is replaced even though only a single bit error occurs. The subvector EC is further combined with weighted Viterbi decoding. Encouraging recognition results are observed for the proposed techniques. Lastly, to understand the effects of applying various EC techniques, this paper introduces three approaches consisting of speech feature, dynamic programming distance, and hidden Markov model state duration comparison. </para>
Electronic structure calculations of hexagonal and cubic phases of Co3Pt (2003)

Using first principles electronic structure calculations we investigated structural and magnetic properties of three distinct phases of Co3Pt. Relaxed lattice constants, total energies, magnetocrystalline anisotropies, and density of states were calculated for each phase at their equilibrium lattice constants, as well as under expansion and contraction stresses. These computations may help clarify the results of some recent but ambiguous experiments on Co3Pt.
An Interpolation and Compaction Technique for Gridded Data. (1983)

An interpolation technique is implemented which is applicable to terrain data defined on a rectangular grid. The technique also allows for data compaction, i.e., effectively representing the given data using less space than required by the raw data. The technique involves finding bicubic polynomials which represent the terrain surface over small subgrids. These surfaces are then pieced together to form a global surface which is both continuous and smooth over the entire region. (Author)
Rectal Organoids Enable Personalized Treatment of Cystic Fibrosis (2019)

In vitro drug tests using patient-derived stem cell cultures offer opportunities to individually select efficacious treatments. Here, we provide a study that demonstrates that in vitro drug responses in rectal organoids from individual patients with cystic fibrosis (CF) correlate with changes in two in vivo therapeutic endpoints. We measured individual in vitro efficaciousness using a functional assay in rectum-derived organoids based on forskolin-induced swelling and studied the correlation with in vivo effects. The in vitro organoid responses correlated with both change in pulmonary response and change in sweat chloride concentration. Receiver operating characteristic curves indicated good-to-excellent accuracy of the organoid-based test for defining clinical responses. This study indicates that an in vitro assay using stem cell cultures can prospectively select efficacious treatments for patients and suggests that biobanked stem cell resources can be used to tailor individual treatments in a cost-effective and patient-friendly manner.
User interface design assistance for large-scale software development (2002)

The User Interface Design Assistant (UIDA) addresses the specific design problems of style and integration consistency throughout the user interface development process and aids in the automated feedback and evaluation of a system's graphical user interface according to knowledge-based rules and project-specific design examples. The UIDA system is able to quickly identify inconsistent style guide interpretations and UI design decisions resulting from distributed development of multiple UI sub-systems. This case arises when each sub-system conforms to the general style guide rules, but when integrated together, may appear inconsistent.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>