gebhart/patrepeval huggingface dataset:
The Ubiquitin-Proteasome Pathway Mediates the Regulated Degradation of Mammalian 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase (2000)

3-Hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR), the key regulatory enzyme in the mevalonate (MVA) pathway, is rapidly degraded in mammalian cells supplemented with sterols or MVA. This accelerated turnover was blocked by N-acetyl-leucyl-leucyl-norleucinal (ALLN), MG-132, and lactacystin, and to a lesser extent by N-acetyl-leucyl-leucyl-methional (ALLM), indicating the involvement of the 26 S proteasome. Proteasome inhibition led to enhanced accumulation of high molecular weight polyubiquitin conjugates of HMGR and of HMGal, a chimera between the membrane domain of HMGR and beta-galactosidase. Importantly, increased amounts of polyubiquitinated HMGR and HMGal were observed upon treating cells with sterols or MVA. Cycloheximide inhibited the sterol-stimulated degradation of HMGR concomitantly with a marked reduction in polyubiquitination of the enzyme. Inhibition of squalene synthase with zaragozic acid blocked the MVA- but not sterol-stimulated ubiquitination and degradation of HMGR. Thus, similar to yeast, the ubiquitin-proteasome pathway is involved in the metabolically regulated turnover of mammalian HMGR. Yet, the data indicate divergence between yeast and mammals and suggest distinct roles for sterol and nonsterol metabolic signals in the regulated ubiquitination and degradation of mammalian HMGR.
MEG and EEG data analysis with MNE-Python (2013)

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne.
Diagnosis and treatment of impetigo. (2007)

Impetigo is a highly contagious, superficial skin infection that most commonly affects children two to five years of age. The two types of impetigo are nonbullous impetigo (i.e., impetigo contagiosa) and bullous impetigo. The diagnosis usually is made clinically, but rarely a culture may be useful. Although impetigo usually heals spontaneously within two weeks without scarring, treatment helps relieve the discomfort, improve cosmetic appearance, and prevent the spread of an organism that may cause other illnesses (e.g., glomerulonephritis). There is no standard treatment for impetigo, and many options are available. The topical antibiotics mupirocin and fusidic acid are effective and may be superior to oral antibiotics. Oral antibiotics should be considered for patients with extensive disease. Oral penicillin V is seldom effective; otherwise there is no clear preference among antistaphylococcal penicillins, amoxicillin/clavulanate, cephalosporins, and macrolides, although resistance rates to erythromycin are rising. Topical disinfectants are not useful in the treatment of impetigo.
Sputtered II-VI Alloys and Structures forTandem PV: Final Subcontract Report, 9 December 2003 - 30 July 2007 (2008)

This report elaborates on Phase 3 and provides summaries of the first two Phases. Phase 3 research work was divided into five task areas covering different aspects of the II-VI tandem cell.
Synthesis, phosphorylation, and degradation of multiple forms of the platelet-derived growth factor receptor studied using a monoclonal antibody. (1987)

We have developed a monoclonal antibody, designated PR7212 (IgG1), which specifically recognizes the platelet-derived growth factor receptor (PDGFR) of primate cells. The antibody recognizes an extracellular epitope of the receptor, demonstrated by its ability to bind to intact cells. Using this antibody, we have detected three forms of PDGFR of approximately 180, 164, and 130 kDa. All three of the forms were detected by Western blot analysis of human dermal fibroblasts. Immunoprecipitates of 32P-labeled membrane extracts of human dermal fibroblasts demonstrate that phosphorylation of all three forms of the receptor is stimulated by PDGF. In addition, several smaller molecules were detected, ranging in size from 113 to 49 kDa, which are also phosphorylated in response to PDGF addition. These smaller molecules may be either PDGFR kinase substrates or partially degraded PDGFR. Only the 180- and the 164-kDa forms of the receptor are detectable from immunoprecipitates of soluble extracts of 35S-metabolically labeled cells. Pulse-chase experiments demonstrate that the 164-kDa form is a precursor of the 180-kDa molecule. After PDGF binding at 37 degrees C, the 180-kDa form disappears from the cell surface in parallel with a decrease in 125I-PDGF binding, providing evidence that occupation results in internalization of PDGFR rather than inactivation.
Circulating Insulin and Insulin Growth Factor-1 Are Independent Determinants of Left Ventricular Mass and Geometry in Essential Hypertension (1999)

These data indicate that insulin and IGF-1 are powerful independent determinants of LV mass and geometry in untreated subjects with essential hypertension and normal glucose tolerance.
Gain and saturation characteristics of dual-wavelength-pumpedsilica-fibre Raman amplifiers (1999)

Dual-wavelength-pumped silica-fibre Raman amplifiers operating at wavelengths around 1.55 µm and with gain bandwidths around 60 nm have been constructed. An experimental comparison is made between dual and single stage configurations and the spectral gain tilt due to inhomogeneous saturation under large signal conditions has been characterised.
Interactive simulation of solid rigid bodies (1995)

The article describes the implementation of an interactive system for simulating rigid bodies with contact and friction. The system can simulate moderately complex mechanical systems at interactive rates (20-30 Hz on low end Silicon Graphics workstations). New objects and user specified constraints can be added into the simulation environment on the fly. The system uses analytical methods to compute contact forces, as opposed to the penalty methods common in other interactive systems. Currently, the system's weakest feature is that it can fail to detect high speed collisions. Objects that move at high speeds (relative to the step size of the simulation) are subject to a form of aliasing and may tunnel through other objects without causing a collision. Other simplifications of the system involve approximating collision times and locations by interpolation methods, and periodic error correction adjustments of geometric tolerances. It is difficult to try to quantify the error incurred by a given approximation or tradeoff. Some of the design choices will likely curtail the system's use for highly predictive applications. However, they do not seriously affect simulating the basic dynamics of a mechanism like a feeder. In general, the system performs with sufficient accuracy and realism to be considered a viable interactive simulation environment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Growth hormone treatment of growth hormone-deficient adults results in a marked increase in Lp(a) and HDL cholesterol concentrations. (1993)

The effects of growth hormone treatment of adults with adult-onset pituitary insufficiency on lipoproteins and apolipoproteins were investigated. Nine patients, one women and eight men (age range, 34-58 years), who had been treated for pituitary tumors were studied. They had complete pituitary insufficiency with a duration of at least 1 year. All patients received replacement therapy with thyroid hormones, glucocorticoids, and gonadal steroids. The study had a double-blind, placebo-controlled, crossover design for active treatment with recombinant human growth hormone (0.25-0.5 units/kg per week s.c. given each evening) for 6 months. Fasting serum levels of cholesterol; triglycerides; high density lipoprotein and low density lipoprotein cholesterol; apolipoproteins A-I, B, and E; and lipoprotein (a) were measured before and after 6 and 26 weeks of treatment. Lipoprotein (a) concentrations increased markedly during treatment and were about twice as high compared with pretreatment levels. Serum cholesterol and low density lipoprotein cholesterol concentrations were decreased after 6 weeks of treatment, but levels had returned to pretreatment levels after 26 weeks. High density lipoprotein cholesterol concentrations increased during treatment and were significantly higher than pretreatment levels after 26 weeks of treatment. Serum triglyceride concentrations did not change significantly, but in two patients with marked hypertriglyceridemia, growth hormone treatment resulted in a marked decrease. Serum concentrations of apolipoproteins A-I, B, and E did not change significantly, but changes in apolipoprotein A-I and B concentrations were in parallel to those observed for high density lipoprotein cholesterol and low density lipoprotein cholesterol, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Recent advances of biomaterials in biotherapy (2016)

Biotherapy mainly refers to the intervention and the treatment of major diseases with biotechnologies or bio-drugs, which include gene therapy, immunotherapy (vaccines and antibodies), bone marrow transplantation and stem-cell therapy. In recent years, numerous biomaterials have emerged and were utilized in the field of biotherapy due to their biocompatibility and biodegradability. Generally, biomaterials can be classified into natural or synthetic polymers according to their source, both of which have attracted much attention. Notably, biomaterials-based non-viral gene delivery vectors in gene therapy are undergoing rapid development with the emergence of surface-modified or functionalized materials. In immunotherapy, biomaterials appear to be attractive means for enhancing the delivery efficacy and the potency of vaccines. Additionally, hydrogels and scaffolds are ideal candidates in stem-cell therapy and tissue engineering. In this review, we present an introduction of biomaterials used in above biotherapy, including gene therapy, immunotherapy, stem-cell therapy and tissue engineering. We also highlighted the biomaterials which have already entered the clinical evaluation.
ChemInform Abstract: Total Chemical Synthesis of Proteins: Evolution of Solid Phase Synthetic Methods Illustrated by Total Chemical Synthesis of the HIV‐1 Protease (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Antitumor mechanisms of Eubacterium lentum and its components. (1995)

In the present study, some antitumor mechanisms of Eubacterium lentum (TYH-11) and bacterial components having antitumor effects were investigated. E.lentum induced maximum NK cell activity in C3H/He mice on day 1 after injection (90.6% against 33.9% of control at E:T ratio 50:1) and the activity was kept at a level of 48.6% on day 7. Tumoricidal peritoneal macrophages were induced 9 days after E.lentum injection into BALB/c mice (56.2% against 10.1% control at E:T ratio 10:1). Tumoricidal macrophage activity persisted at the same level for at least 11 days. Cytotoxic T lymphocyte (CTL) activity was induced only in tumor bearing mice treated with E.lentum, 4 weeks after tumor inoculation. Antitumor activity was observed in the cell wall (CW) and membrane fractions (CM) of E.lentum. CW induced NK cell activity; the activity was transient while the kinetics of NK activity by CM showed 2 peaks, on day 1 and day 7. Tumoricidal macrophages were induced by CW and the activity level was the same as that induced by whole body, while that induced by CM was at a lower level. Neither CW nor CM induced CTL in tumor bearing mice.
A novel, low-cost deep trench decoupling capacitor for high-performance, low-power bulk CMOS applications (2008)

We present an overview and electrical results for a novel deep trench decoupling capacitor. The process of this decoupling capacitor borrows from the regular embedded DRAM trench process, but with significant process simplification for decoupling use which provide reduced cost and reduced process cycle time. This capacitor can provide significant chip-level area savings, using only 1/8 silicon real estate to fabricate the same capacitance as standard planar gate oxide capacitors. Additionally, the trench decap demonstrates a dramatic improvement in leakage compared to standard planar gate oxide capacitors - as much as 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> improvement in leakage can be realized using trench decaps instead of conventional planar decap designs.
Statistical approach to vocal tract transfer function estimation based on factor analyzed trajectory HMM (2008)

In this paper, we describe a novel statistical approach to the vocal tract transfer function (VTTF) estimation of a speech signal based on a factor analyzed trajectory hidden Markov model (HMM). Because speech is a quasi-periodic signal, there are many missing frequency components between adjacent F <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> harmonics. The proposed method determines a time-varying VTTF sequence based on the maximum a posteriori (MAP) estimation considering not only harmonic components observed at each analyzed frame but also those at other frames for stochastically interpolating the missing frequency parts.
Human PD-L1-overexpressing porcine vascular endothelial cells induce functionally suppressive human CD4+CD25hiFoxp3+ Treg cells (2011)

ABSTRACT In xenotransplantation models, direct activation of hCD4+ T cells by porcine VECs leads to a robust proliferation of T cells. To investigate the underlying mechanisms, human antiporcine MLEC culture was used to investigate cross-species cell interactions, proliferation of hCD4+ T cells, and induction of human cytokines. We report that xenoantigen presentation by PIEC expands hCD4+ Foxp3+ Tregs and hCD4+ Foxp3– Teffs, and this process is dependent on porcine MHC-II antigen expression. Stable transfection of hPD-L1 into PIEC inhibits Teff proliferation, but Treg proliferation is not affected. Surprisingly, IL-10 production by hCD4+ T cells is augmented significantly by PIEChPD-L1. Notably, hPD-L1-induced Tregs have higher suppressive potency and mediate suppressive function partially through IL-10 and CD73. This study opens the possibility of using hPD-L1-overexpressing porcine VECs as a novel therapeutic to allow tolerance of xenotransplants and also supports the possibility of using hPD-L1 transgenic pigs as xenotransplant donors.
Rapid and highly efficient inducible cardiac gene knockout in adult mice using AAV-mediated expression of Cre recombinase (2014)

AAV9-mediated expression of Cre is a promising approach for rapid and efficient conditional cardiac gene knockout in adult mice.
IL-10 Directly Activates and Expands Tumor-Resident CD8+ T Cells without De Novo Infiltration from Secondary Lymphoid Organs (2012)

The presence of activated intratumoral T cells correlates clinically with better prognosis in patients with cancer. Although tumor vaccines can increase the number of tumor-specific CD8(+) T cells in systemic circulation, they frequently fail to increase the number of active and tumor reactive T cells within the tumor. Here we show that treatment with the pleiotropic cytokine interleukin-10 (IL-10) induces specific activation of tumor-resident CD8(+) T cells as well as their intratumoral expansion in several mouse tumor models. We found that inhibition of T-cell trafficking from lymphoid organs did not impair IL-10-induced tumor rejection or the activation of tumor-resident CD8(+) T cells. Tumor-resident CD8(+) T cells expressed elevated levels of the IL-10 receptor and were directly activated by IL-10, resulting in prominent phosphorylation of STAT3 and STAT1. Although CD4(+) T cells, regulatory T cells, NK cells, and dendritic cells have been reported as prominent targets of IL-10 in the tumor microenvironment, we found that expression of the IL-10R was required only on CD8(+) T cells to facilitate IL-10-induced tumor rejection as well as in situ expansion and proliferation of tumor-resident CD8 T cells. Together, our findings indicate that IL-10 activates CD8(+) T-cell-mediated tumor control and suggest that IL-10 may represent a potential tumor immunotherapy in human patients with cancer.
Phosphorylation of the c-Fos transrepression domain by mitogen-activated protein kinase and 90-kDa ribosomal S6 kinase. (1993)

Phosphorylation of the C terminus of c-Fos has been implicated in serum response element-mediated repression of c-fos transcription after its induction by serum growth factors. The growth-regulated enzymes responsible for this phosphorylation in early G1 phase of the cell cycle and the sites of phosphorylation have not been identified. We now provide evidence that two growth-regulated, nucleus- and cytoplasm-localized protein kinases, 90-kDa ribosomal S6 kinase (RSK) and mitogen-activated protein kinase (MAP kinase), contribute to the serum-induced phosphorylation of c-Fos. The major phosphopeptides derived from biosynthetically labeled c-Fos correspond to phosphopeptides generated after phosphorylation of c-Fos in vitro with both RSK and MAP kinase. The phosphorylation sites identified for RSK (Ser-362) and MAP kinase (Ser-374) are in the transrepression domain. Cooperative phosphorylation at these sites by both enzymes was observed in vitro and reflected in vivo by the predominance of the peptide phosphorylated on both sites, as opposed to singly phosphorylated peptides. This study suggests a role for nuclear RSK and MAP kinase in modulating newly synthesized c-Fos phosphorylation and downstream signaling.
Monitoring Blood Glucose Changes in Cutaneous Tissue by Temperature-modulated Localized Reflectance Measurements (2003)

Blood glucose concentrations alter thermally modulated optical signals, presumably through physiologic and physical effects. Temperature changes drive cutaneous vascular and refractive index responses in a way that mimics the effect of changes in glucose concentration. Run-to-run differences are attributable to site-to-site structural differences.
An integrated approach based on cross-layer optimization - Designing a mobile broadband wireless access network (2004)

In this paper, a new OFDM-based air interface technology for a mobile broadband wireless system is described. The technology leverages the standard Internet protocol (IP) network elements to build the system and deploys a new air interface technology based on OFDMA. Cross-layer optimization played a major role in the design where the choices made in the physical, MAC, and link layers are also driven by the goal of extending the Internet to the wireless space. A major physical layer benefit of this air interface comes from the orthogonality property that the results in the elimination of in-cell interference are averaged and a worst-case interferer does not limit the system performance. The physical layer features not only result in high capacity but also provide very fine granularity of allocating air link resources, which improves the MAC and link-layer efficiency. The MAC and link layer provide contention-free, fast control channels between the RAR and the WTs. These channels are used to ferry a variety of signaling such as assignments of traffic channel, acknowledgements, channel quality, and traffic request reports. This holistic approach allows for a scheduler that could not only achieve high spectral efficiency but also allow for a fine control over QoS attributes such as latency, reliability, and service differentiation.
Mutations in the Drosophila Gene Encoding Ribosomal Protein S6 Cause Tissue Overgrowth (1993)

We have characterized two P-element-induced, lethal mutations in Drosophila melanogaster which affect the larval hemocytes, mediators of the insect immune response. Each mutant displays larval melanotic tumors characteristic of mutations affecting the insect cellular immune system, and the moribund animals develop grossly hypertrophied hematopoietic organs because of increased cell proliferation and extra rounds of endoreduplication in some hematopoietic cells. Surprisingly, these mutations are due to P element insertions in the 5' regulatory region of the Drosophila gene encoding ribosomal protein S6 and cause a reduction of S6 transcript abundance in mutant larvae.
Improving Throughput in Multihop Wireless Networks (2006)

One of the main characteristics of wireless ad hoc networks is their node-centric broadcast nature of communication, leading to interferences and spatial contention between adjacent wireless links. Due to such interferences, pessimistic concerns have been recently raised with respect to the decreasing network capacity in wireless ad hoc networks when the number of nodes scales to several orders of magnitude higher. Such studies assume uniformly distributed nodes in the network and randomized traffic patterns. In this paper, we argue that in all cases of end-to-end data communications-including one-to-k unicast and multicast data dissemination as well as k-to-one data aggregation-the maximum achievable end-to-end data throughput (measured on the sources) heavily depends on the strategy of arranging the topology of transmission between sources and destinations, as well as possible per-node operations such as coding. An optimal strategy achieves better end-to-end throughput than an arbitrary one. We present theoretical studies and critical insights with respect to how these strategies may be designed so that end-to-end throughput may be increased. After all, under all circumstances-in either a lightly loaded or a congested network-increasing end-to-end throughput from its baseline is always beneficial to applications using ad hoc networks to communicate.