gebhart/patrepeval huggingface dataset:
Exercise-induced satellite cell activation in growing and mature skeletal muscle (1987)

The time course and extent of satellite cell activation were studied in the soleus (m-SOL) and extensor digitorum longus (m-EDL) muscles of untrained growing and mature rats after a single bout of prolonged eccentric treadmill running. At 24, 48, 72, and 120 h postexercise, satellite cell mitotic activity was quantitated in autoradiographs of whole-fiber segments after injection of [3H]thymidine. Fiber damage and localization of labeled cells were also examined in muscle cross sections. Labeling in growing muscles progressively increased to peak levels (approximately 250% of control) at 72 h postexercise, whereas mature muscles exhibited an earlier peak (approximately 250% of control) at 24 (m-SOL) and 48 (m-EDL) h, followed by a more rapid decline to control levels by 120 h postexercise. In all exercised muscles the calculated satellite cell activation was far greater than required to repair the small number (less than 3.0%) of necrotic fibers identified at the light-microscopic level. These results suggest that satellite cells were activated not only on fibers exhibiting overt necrosis but also on those with lesions not discernible with light microscopy.
Assessing and improving TCP rate shaping over edge gateways (2004)

Computers installed with commercial/open-source software have been widely employed as organizational edge gateways to provide policy-based network management. Such gateways include firewalls for access control, and bandwidth managers for managing the narrow Internet access links. When managing the TCP traffic, pass-through TCP flows can introduce large buffer requirements, large latency, frequent buffer overflows, and unfairness among flows competing for the same queue. So, how to allocate the bandwidth for a TCP flow without the above drawbacks becomes an important issue. This study assesses and improves TCP rate shaping algorithms to solve the above problems through self-developed implementations in Linux, testbed emulations, live Internet measurements, computer simulations, modeling, and analysis. The widely deployed TCP rate control (TCR) approach is found to be more vulnerable to Internet packet losses and less compatible to some TCP sending operating systems. The proposed PostACK approach can preserve TCR's advantages while avoiding TCR's drawbacks. PostACK emulates per-flow queuing, but relocates the queuing of data to the queuing of ACKs in the reverse direction, hence minimizing the buffer requirement up to 96 percent. PostACK also has 10 percent goodput improvement against TCR under lossy WAN environments. A further scalable design of PostACK can scale up to 750Mbps while seamlessly cooperating with the link-sharing architecture. Experimental results can be reproduced through our open sources: 1) tcp-masq: a modified Linux kernel, 2) wan-emu: a testbed for conducting switched LAN-to-WAN or WAN-to-LAN experiments with RTT/loss/jitter emulations.
Protective Efficacy of Serially Up-Ranked Subdominant CD8+ T Cell Epitopes against Virus Challenges (2011)

Immunodominance in T cell responses to complex antigens like viruses is still incompletely understood. Some data indicate that the dominant responses to viruses are not necessarily the most protective, while other data imply that dominant responses are the most important. The issue is of considerable importance to the rational design of vaccines, particularly against variable escaping viruses like human immunodeficiency virus type 1 and hepatitis C virus. Here, we showed that sequential inactivation of dominant epitopes up-ranks the remaining subdominant determinants. Importantly, we demonstrated that subdominant epitopes can induce robust responses and protect against whole viruses if they are allowed at least once in the vaccination regimen to locally or temporally dominate T cell induction. Therefore, refocusing T cell immune responses away from highly variable determinants recognized during natural virus infection towards subdominant, but conserved regions is possible and merits evaluation in humans.
The evaluation of metabolic parameters and insulin sensitivity for a more robust diagnosis of the polycystic ovary syndrome (2008)

Our study highlights the fact that regardless of the diagnostic criteria used, evaluation of the metabolic parameters and insulin sensitivity is important for a correct diagnosis of PCOS and a therapeutic approach.
Self-Assembled Three-Dimensional Graphene Macrostructures: Synthesis and Applications in Supercapacitors (2015)

Graphene and its derivatives are versatile building blocks for bottom-up assembly of advanced functional materials. In particular, with exceptionally large specific surface area, excellent electrical conductivity, and superior chemical/electrochemical stability, graphene represents the ideal material for various electrochemical energy storage devices including supercapacitors. However, due to the strong π-π interaction between graphene sheets, the graphene flakes tend to restack to form graphite-like powders when they are processed into practical electrode materials, which can greatly reduce the specific surface area and lead to inefficient utilization of the graphene layers for electrochemical energy storage. The self-assembly of two-dimensional graphene sheets into three-dimensional (3D) framework structures can largely retain the unique properties of individual graphene sheets and has recently garnered intense interest for fundamental investigations and potential applications in diverse technologies. In this Account, we review the recent advances in preparing 3D graphene macrostructures and exploring them as a unique platform for supercapacitor applications. We first describe the synthetic strategies, in which reduction of a graphene oxide dispersion above a certain critical concentration can induce the reduced graphene oxide sheets to cross-link with each other via partial π-π stacking interactions to form a 3D interconnected porous macrostructure. Multiple reduction strategies, including hydrothermal/solvothermal reduction, chemical reduction, and electrochemical reduction, have been developed for the preparation of 3D graphene macrostructures. The versatile synthetic strategies allow for easy incorporation of heteroatoms, carbon nanomaterials, functional polymers, and inorganic nanostructures into the macrostructures to yield diverse composites with tailored structures and properties. We then summarize the applications of the 3D graphene macrostructures for high-performance supercapacitors. With a unique framework structure in which the graphene sheets are interlocked in 3D space to prevent their restacking, the graphene macrostructures feature very high specific surface areas, rapid electron and ion transport, and superior mechanical strength. They can thus be directly used as supercapacitor electrodes with excellent specific capacitances, rate capabilities, and cycling stabilities. We finally discuss the current challenges and future opportunities in this research field. By regarding the graphene as both a single-atom-thick carbon sheet and a conjugated macromolecule, our work opens a new avenue to bottom-up self-assembly of graphene macromolecule sheets into functional 3D graphene macrostructures with remarkable electrochemical performances. We hope that this Account will promote further efforts toward fundamental investigation of graphene self-assembly and the development of advanced 3D graphene materials for their real-world applications in electrochemical energy storage devices and beyond.
Cultured human endothelial cells stimulated with cytokines or endotoxin produce an inhibitor of leukocyte adhesion. (1988)

Activation of cultured human endothelial cells (HEC) by inflammatory stimuli, such as interleukin 1 (IL-1), tumor necrosis factor (TNF), and bacterial endotoxin (lipopolysaccharide, LPS), increases their surface adhesiveness for blood leukocytes and related cell lines. We now report that activated HEC also generate a soluble leukocyte adhesion inhibitor (LAI), which accumulates in conditioned media from IL-1-, TNF-, or LPS-treated, but not sham-treated, HEC cultures. LAI significantly inhibits the adhesion of PMN and monocytes to activated, but not unactivated, HEC. In contrast, LAI has no effect on the adhesion of lymphocytes, the promyelocytic cell line HL-60 or the monocyte-like cell line U937 to HEC monolayers. LAI appears to act directly on the leukocyte, but does not inhibit either agonist-induced responses in PMN (membrane depolarization, changes in cytosolic calcium concentration, superoxide production) or PMN attachment to serum-coated plastic surfaces. Endothelial generation of LAI is blocked by actinomycin D but not by aspirin or indomethacin. Preliminary biochemical characterization indicates that LAI is a soluble, protein-containing molecule that is heat- and acid-stable. Fractionation by HPLC gel filtration yields a single peak of LAI activity (14,000 less than Mr greater than 24,000). Thus, in addition to proadhesive cell surface changes, the endothelium may also actively contribute to the regulation of endothelial-leukocyte interactions at sites of inflammation in vivo through the production of soluble adhesion inhibitors such as LAI.
THE ECOLOGICAL FUNCTIONS OF THE PHYTOCHROME FAMILY. CLUES TO A TRANSGENIC PROGRAMME OF CROP IMPROVEMENT (1992)

Abstract— Phytochrome‐mediated proximity perception and induction of shade avoidance responses provide clues towards a novel genetic engineering approach for the improvement of crop plants. In this Commentary Article, I argue that the elimination, or disablement, of proximity perception and the associated shade avoidance syndrome by transgenic manipulation of phytochrome genes should provide a strategy for the creation of new crop plants in which a greater proportion of assimilates is incorporated into harvestable material. Such a programme would enable increases in agricultural productivity without a requirement for the increased application of agrochemicals. Some potential approaches towards realizing these goals are proposed.
Inhibited Spontaneous Emission in Solid-State Physics and Electronics (1987)

It has been recognized for some time that the spontaneous emission by atoms is not necessarily a fixed and immutable property of the coupling between matter and space, but that it can be controlled by modification of the properties of the radiation field. This is equally true in the solid state, where spontaneous emission plays a fundamental role in limiting the performance of semiconductor lasers, heterojunction bipolar transistors, and solar cells. If a three-dimensionally periodic dielectric structure has an electromagnetic band gap which overlaps the electronic band edge, then spontaneous emission can be rigorously forbidden.
Accelerating the Nonuniform Fast Fourier Transform (2004)

The nonequispaced Fourier transform arises in a variety of application areas, from medical imaging to radio astronomy to the numerical solution of partial differential equations. In a typical problem, one is given an irregular sampling of N data in the frequency domain and one is interested in reconstructing the corresponding function in the physical domain. When the sampling is uniform, the fast Fourier transform (FFT) allows this calculation to be computed in $O(N \log N)$ operations rather than $O(N^2)$ operations. Unfortunately, when the sampling is nonuniform, the FFT does not apply. Over the last few years, a number of algorithms have been developed to overcome this limitation and are often referred to as {\em nonuniform FFTs} (NUFFTs). These rely on a mixture of interpolation and the judicious use of the FFT on an oversampled grid [A. Dutt and V. Rokhlin, {\em SIAM J.\ Sci.\ Comput.}, 14 (1993), pp. 1368--1383].\\ \indent% In this paper, we observe that one of the standard interpolation or ``gridding" schemes, based on Gaussians, can be accelerated by a significant factor without precomputation and storage of the interpolation weights. This is of particular value in two- and three-dimensional settings, saving either $10^d N$ in storage in d dimensions or a factor of about 5--10 in CPU time (independent of dimension).
Receiving antenna design for miniature receivers (1977)

A design procedure is described which determines the minimum required volume and the optimum dimensions for a ferrite loaded loop receiving antenna. The frequency of operation, bandwidth, transmitted signal strength, desired signal-to-noise ratio, receiver sensitivity, and the relative permeability of the ferrite are required to determine the design. Useful approximations for flux averaging, demagnetization factor, atmospheric noise, and chassis loaded <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</tex> are given.
A cell line with characteristics of the periodontal ligament fibroblasts is negatively regulated for mineralization and Runx2/Cbfa1/Osf2 activity, part of which can be overcome by bone morphogenetic protein-2 (2002)

The periodontal ligament (PDL) is a connective tissue located between the cementum of teeth and the alveolar bone of the mandibula. It plays an integral role in the maintenance and regeneration of periodontal tissue. The cells responsible for maintaining this tissue are thought to be fibroblasts, which can be either multipotent or composed of heterogenous cell populations. However, as no established cell lines from the PDL are available, it is difficult to assess what type of cell promotes all of these functions. As a first step to circumvent this problem, we have cloned and characterized cell lines from the PDL from mice harboring a temperature-sensitive SV 40 large T-antigen gene. RT-PCR and in situ hybridization studies demonstrated that a cell line, designated PDL-L2, mimics the gene expression of the PDL in vivo: it expresses genes such as alkaline phosphatase, type I collagen, periostin, runt-related transcription factor-2 (Runx2) and EGF receptor, but does not express genes such as bone sialoprotein and osteocalcin. Unlike osteoblastic cells and a mixed cell population from the PDL, PDL-L2 cells do not produce mineralized nodules in the mineralization medium. When PDL-L2 cells were incubated in the presence of recombinant human bone morphogenetic protein-2 alkaline phosphatase activity increased and mineralized nodules were eventually produced, although the extent of mineralization is much less than that in osteoblastic MC3T3-E1 cells. Furthermore, PDL-L2 cells appeared to have a regulatory mechanism by which the function of Runx2 is normally suppressed.
Structure-Function Studies of Interleukin 15 using Site-specific Mutagenesis, Polyethylene Glycol Conjugation, and Homology Modeling (1997)

Interleukin (IL)-15 is a multifunctional cytokine that shares many biological activities with IL-2. This functional overlap, as well as receptor binding subunits shared by IL-15 and IL-2, suggests tertiary structural similarities between these two cytokines. In this study, recombinant human IL-15 was PEGylated via lysine-specific conjugation chemistry in order to extend the circulation half-life of this cytokine. Although PEGylation did extend the beta-elimination circulation half-life of IL-15 by greater than 50-fold, the biological activity of polyethylene glycol (PEG)-IL-15 was significantly altered. Specifically, PEG-IL-15 lost its ability to stimulate the proliferation of CTLL but took on the properties of a specific IL-15 antagonist in vitro. In comparing sequence alignments and molecular models for IL-2 and IL-15, it was noted that lysine residues resided in regions of IL-15 that may have selectively disrupted receptor subunit binding. We hypothesized that PEGylation of IL-15 interferes with beta but not alpha receptor subunit binding, resulting in the IL-15 antagonist activity observed in vitro. The validity of this hypothesis was tested by engineering site-specific mutants of human IL-15 as suggested by the IL-15 model (IL-15D8S and IL-15Q108S block beta and gamma receptor subunit binding, respectively). As with PEG-IL-15, these mutants were unable to stimulate CTLL proliferation but were able to specifically inhibit the proliferation of CTLL in response to unmodified IL-15. These results supported our model of IL-15 and confirmed that interference of beta receptor subunit binding by adjacent PEGylation could be responsible for the altered biological activity observed for PEG-IL-15.
THE CHARACTERIZATION OF FOUR NEW METABOLITES OF ADRENOCORTICAL HORMONES (1955)

SUMMARY 1. Four new metabolites of adrenal hormones have been isolated from human urine after ACTH administration and identified by isotopic dilution after a tracer dose of hydrocortisone-4-C14. The compounds obtained were (1) pregnane3ar,llp, 17o(,20a,21-pentol; (2) 3a, 1701,20a,21-tetra- hydroxypregnane-11-one; (3) pregnane-3a!, lip ,17a ,208,21-pentol; (4) 3ar, 17~~) 2Op ,21-tetrahydroxypregnane-1 l-one. Trivial names were sug- gested for these products. 2. On the basis of the isotopic dilution studies it was estimated that these compounds represent a minimum of 30 per cent of the metabolites of hydrocortisone found in the neutral ether-soluble extract of human urine after hydrolysis of their conjugates by means of beef liver @-glu- curonidase. 3. 3a, 17ar ,2Oa!, 21-Tetrahydroxypregnane-11-one was isolated from human urine after administration of 100 mg. of cortisone-t by vein. It was estimated that the metabolite represented about 6 per cent of radio- activity in the neutral ether-soluble fraction after hydrolysis by means of beef liver p-glucuronidase. 4. A novel and efficient synthesis for 3a, 17a,20a,21-tetrahydroxy- pregnane-11-one was described. The procedure is based upon the solvoly- sis of 3~r, 17a( ,21-triacetoxy-20P-p-toluenesulfonoxypregnane-ll-one with aqueous acetic acid in the presence of potassium acetate. The reaction is an example of “neighboring group effect ” in an acetyl migration with inversion of configuration. 5. The preparation of the related compounds, 3a,21-diacetoxy-17a-hy- droxy-20P-p-toluenesulfonoxypregnane-11-one, 3a,21-diacetoxy-17~u, ~OLU- epoxypregnane-11-one, and pregnane-3oL, llfl ,17ar ,2Oa! ,21 -pentol has been described. The authors express their gratitude to their colleagues Dr. Leon Hellman and Dr. Olaf Pearson for their cooperation in the studies with patients. We are especially indebted to Evelyn Meyer for technical assistance and to Friederike Herling for her valuable contributions to the interpretation of the infra-red spectra.
A Novel Juxtamembrane Domain Isoform of HER4/ErbB4 (1997)

Human epidermal growth factor receptor 4 (HER4) is a member of the epidermal growth factor (EGF) receptor subfamily of receptor tyrosine kinases that is activated by neuregulins (NRG), betacellulin (BTC), and heparin-binding EGF-like growth factor. Sequencing of full-length human HER4 cDNAs revealed the existence of two HER4 isoforms that differed by insertion of either 23 or 13 alternative amino acids in the extracellular juxtamembrane (JM) region. The 23-amino acid form (HER4 JM-a) and the 13-amino acid form (HER4 JM-b) were expressed in a tissue-specific manner, as demonstrated by reverse transcriptase-polymerase chain reaction analysis of mouse and human tissues. Both isoforms were expressed in neural tissues such as cerebellum, whereas kidney expressed HER4 JM-a only and heart HER4 JM-b only. In situ hybridization using specific oligonucleotides demonstrated transcription of both JM-a and JM-b isoforms in the mouse cerebellum. Tyrosine phosphorylation analysis indicated that both receptor isoforms were activated to the same extent by NRG-beta1 and BTC, and to a lesser extent by NRG-alpha1 and heparin-binding EGF-like growth factor. A functional difference was found, however, in response to phorbol ester treatment. Stimulation of cells with phorbol ester resulted in a loss of 125I-NRG-beta1 binding and in a reduction of total cell-associated HER4 protein in HER4 JM-a transfectants but not in HER4 JM-b transfectants. It was concluded that novel alternatively spliced isoforms of HER4 exist, that they are distributed differentially in vivo in mouse and human tissues, that they are both activated by HER4 ligands, and that they may represent cleavable and noncleavable forms of HER4.
Phase I Study in Advanced Cancer Patients of a Diversified Prime-and-Boost Vaccination Protocol Using Recombinant Vaccinia Virus and Recombinant Nonreplicating Avipox Virus to Elicit Anti–Carcinoembryonic Antigen Immune Responses (2000)

rV-CEA was more effective in its role as a primer of the immune system; avipox-CEA could be given up to eight times with continued increases in CEA T-cell precursors. Future trials should use rV-CEA first followed by avipox-CEA. Vaccines specific to CEA are able to generate CEA-specific T-cell responses in patients without significant toxicity. T-cell responses using vaccines alone may be inadequate to generate significant anticancer objective responses in patients with advanced disease. Cytokines such as GM-CSF and IL-2 may play a key role in generating such responses.
Selective incorporation of 5-hydroxytryptophan into proteins in mammalian cells (2004)

An orthogonal tryptophanyl-transfer RNA (tRNA) synthetase (TrpRS)-mutant opal suppressor tRNA(Trp) (mutRNA(UCA)(Trp)) pair was generated for use in mammalian cells. The anticodon loop of the Bacillus subtilis tRNA(Trp) was mutated to UCA, three positions in the D arm were mutated to generate an internal promoter sequence, and the mutRNA(UCA)(Trp) gene was inserted between the 5' and 3' flanking sequences of the tRNA(Trp-1) gene from Arabidopsis to enhance its expression in mammalian cells. In vitro aminoacylation assays and in vivo opal suppression assays showed that B. subtilis TrpRS (BsTrpRS) charges only the cognate mutRNA(UCA)(Trp) and no endogenous mammalian tRNAs. Similarly, the mutRNA(UCA)(Trp) is specifically charged by B. subtilis TrpRS and not by endogenous synthetases in mammalian cells. Site-directed mutagenesis was then used to alter the specificity of BsTrpRS to uniquely charge 5-hydoxy-l-tryptophan. The resulting mutant BsTrpRS-mutRNA(UCA)(Trp) pair allows the efficient and selective incorporation of 5-hydroxy-l-tryptophan into mammalian proteins in response to the codon, TGA. This amino acid can be used as a fluorescence probe and also undergoes electrochemical oxidation in situ to generate an efficient protein crosslinking.
Fundamental thermal fluctuations in microspheres (2004)

We present a theoretical analysis and the results of measurements of thermorefractive noise in microcavities. These measurements may be considered direct observations of fundamental fluctuations of temperature in solid media. Our experimentally measured noise spectra are in agreement with our theoretical model.
Morphological Differentiation of Neurons on Microtopographic Substrates Fabricated by Rolled‐Up Nanotechnology (2010)

Abstract Arrays of transparent rolled‐up microtubes can easily be mass‐produced using a combination of conventional photolithography, electron beam depositioning, and chemical etching techniques. Here, we culture primary mouse motor neurons and immortalised CAD cells, a cell line derived from the central nervous system, on various microtube substrates to investigate the influence of topographical surface features on the growth and differentiation behaviour of these cells. Our results indicate that the microtube chips not only support growth of both cell types but also provide a well‐defined, geometrically confined 3D cell culture scaffold. Strikingly, our micropatterns act as a platform for axon guidance with protruding cell extensions aligning in the direction of the microtubes and forming complex square‐shaped grid‐like neurite networks. Our experiments open up a cost‐efficient and bio‐compatible way of analysing single cell behaviour in the context of advanced micro‐/nanostructures with various biological applications ranging from neurite protection studies to cell sensor development.