gebhart/patrepeval huggingface dataset:
Hyperinsulinemia of obesity is due to decreased clearance of insulin (1983)

The hyperinsulinemia of obesity could result from a decrease in the metabolic clearance rate of insulin (MCR-I), an increase in the secretory rate of insulin (SR-I), or a combination of both these processes. Because C-peptide and insulin are secreted in an equimolar ratio, the plasma concentrations of C-peptide (C) and insulin (I) are inversely proportional to their rates of metabolic clearance (C/I = MCR-I/MCR-C). We obtained 24-h integrated concentrations (IC) of insulin (IC-I) and C-peptide (IC-C) in 23 obese and 45 nonobese subjects over a period of normal activity and food intake. The IC-I was 69% higher in the obese subjects (P less than 0.0001). A 13% increase in the IC-C (P = 0.04), with a constant rate of C-peptide clearance, indicates a proportionate increase in SR-I. A 33% decrease in the IC-C/IC-I in the obese group (P less than 0.005) reflects a decrease in MCR-I; hence, 75% of the hyperinsulinemia is due to a decrease in the clearance of insulin. Because peripheral MCR-I (pMCR-I) is similar in obese and nonobese subjects, the decrease in MCR-I may be due to a decrease in the hepatic clearance of insulin. This conclusion was supported by our comparison of 24-h IC-C/IC-I ratios in the obese and nonobese subjects. Whereas the 24-h IC-C/IC-I of the nonobese resembled the fasting state, the 24-h IC-C/IC-I of the obese resembled the postprandial state, when insulin removal by the liver is known to be suppressed. These data are consistent with a decreased 24-h hepatic MCR-I (hMCR-I) as the cause of the hyperinsulinemia of obesity.
EDITORIAL: RETHINKING ASSISTANCE FOR AFRICA (2006)

Africa is currently a fragile mess. So was Europe in 1945. The USA supported Europe through security, trade and governance policies that complemented aid. Africa needs the same co‐ordinated approach from Europe now.
Free space optical communications routing performance in highly dynamic airspace environments (2004)

Airborne networking environments utilizing high speed free space optical communications are being proposed as a method of providing immediate high speed network access and communications in a tactical environment where access is otherwise unavailable. Frequent link failures and recoveries due to wing obstruction and the dead zone produced by the wake vortex of the aircraft characterize the links. Many links additionally have large delay due both to coding/interleaving and propagation characteristics. Network availability from a user perspective is predicated on the fast response to link outages and recoveries by the routing protocol. The routing protocol must converge very quickly to ensure that the network is highly available and that traffic is not disrupted. In this work, we considered two different architectures/topologies that meet these requirements and analyzed the performance of OSPF and EIGRP on each using simulation. We fixed the scenarios such that an end-to-end path was always available through the network. We varied the input parameters for OSPF and EIGRP to maximize network availability. We determined that OSPF is limited by its minimum HELLO interval and results in gaps in path availability on the order of seconds and EIGRP may respond quickly to achieve subsecond gaps in path availability, but at a cost of increased network traffic. We have additionally introduced an analytical methodology for selection of HELLO interval lengths and router dead times which quantifies the cost and benefit of a particular selection. Scalability of the different approaches to a complete network needs further exploration.
Exploiting streams in instruction and data address trace compression (2004)

Novel research ideas in computer architecture are frequently evaluated using trace-driven simulation. The large size of traces incited different techniques for trace reduction. These techniques often combine standard compression algorithms with trace-specific solutions, taking into account the tradeoff between reduction in the trace size and simulation slowdown due to compression. This paper introduces SBC, a new algorithm for instruction and data address trace compression based on instruction streams. The proposed technique significantly reduces trace size and simulation time, and can be successfully combined with general compression algorithms. The SBC technique combined with gzip reduces the size of SPEC CPU2000 traces 59-97930 times, and combined with Sequitur 65-185599 times.
Disentangling Oil Weathering at a Marine Seep Using GC×GC: Broad Metabolic Specificity Accompanies Subsurface Petroleum Biodegradation (2008)

Natural seeps contribute nearly half of the oil entering the coastal ocean. However, environmental fate studies generally monitor fewer than 5% of these petroleum compounds. Hence, the rates and relevance of physical, chemical, and biological weathering processes are unknown for the large majority of hydrocarbons, both released from natural seeps and also from human activities. To investigate the specific compositional changes occurring in petroleum during subsurface degradation and submarine seepage, we studied the natural oil seeps offshore Santa Barbara, California with comprehensive, two-dimensional gas chromatography (GC x GC). With this technique, we quantified changes in the molecular diversity and abundance of hydrocarbons between subsurface reservoirs, a proximal sea floor seep, and the sea surface overlying the seep. We also developed methods to apportion hydrocarbon mass losses due to biodegradation, dissolution, and evaporation, for hundreds of tracked compounds that ascended from the subsurface to the sea floor to the sea surface. The results provide the first quantitative evidence of broad metabolic specificity for anaerobic hydrocarbon degradation in the subsurface and reveal new trends of rapid hydrocarbon evaporation at the sea surface. This study establishes GC x GC as a powerful technique for differentiating biological and physical weathering processes of complex mixtures at a molecular level.
High Density Smart Cards: New Security Challenges and Applications (2007)

High Density cards represent the next generation of secure portable and removable tokens for the mobile and wireless markets. What makes these cards so particular is that, in addition to the traditional ISO 7816 interface to the Subscriber Identity Module, there are hundreds of megabytes of non-volatile Flash Memory available on the same token. This is a small revolution when compared to current EEPROM cards which allow for only a few hundreds of kilobytes of memory both for applications and data. Flash memory can be accessed either via a USB (Universal Serial Bus) or an MMC (MultiMediaCard) high speed interface. Therefore two different ecosystems co-exist on the same chip, which makes the security aspects of these cards particularly interesting and challenging. In this paper we examine the specific security aspects of such high density cards and explain what potential security issues a manufacturer has to face and how he can overcome them. We discuss specifically how flash memory interacts with other memory on board, how it is organised, what it is used for. We contrast this approach with the memory architecture and organization of conventional smart cards such as those used in GSM and EMV payment applications. Since there is no ROM memory at all on these cards, we explain where the proprietary and highly sensitive operating system of the card manufacturer and the proprietary algorithms of the telecommunications operators will reside, how they can be protected and what the challenges are for initializing the whole system. Current secure smart card personalization techniques will have to be revisited and new procedures need to be put in place to securely instantiate this new generation of (SIM) cards. New algorithms for EEPROM emulation and anti-tearing (the fact that data is not lost when power is lost abruptly) need to be developped, one-time programmable areas need to be provided to boot-up securely. Initial program loader techniques and public key schemes are required for secure personalization. The high speed interface has to be secured and separated from access to the main memory on chip. We also discuss security aspects of single die architectures, platform security for flash memory cards and security aspects of cryptographic hardware cores including the necessity to protect them against side-channel attacks as on traditional smart cards. These security features in turn allow considering high density cards for enhanced security applications such as secure data storage thanks to on-the-fly encryption at the megabyte rate, enterprise DRM, DRM agents for mobile TV, mobile payment and m-commerce. New applications which require huge storage capacity and sophisticated security features at the same time are enabled with this new generation of smart removable devices.
Molecular single cell studies of normal and transformed lymphocytes. (1997)

The polymerase chain reaction allows the characterization of RNA and DNA sequences from single cells. Methods were established to analyse single cells isolated from suspension or by multicolour flow cytometry. We established a method to isolate single immunostained cells from frozen tissue sections and to analyse those cells for immunoglobulin gene rearrangements. This method was first used to study B cell differentiation within human germinal centres. In another series of experiments, Hodgkin and Reed-Sternberg (HRS) cells from a total of 14 cases of HD were analysed for B lineage derivation and clonality. In 13 of the 14 cases, clonal V gene rearrangements were identified. This shows that HRS cells generally represent the outgrowth of a clonal population of B cells. The detection of somatic mutations in all VH gene rearrangements amplified from HRS cells and the nature of those mutations identifies a GC B cell as the HRS precursor.
Stem Morphological and Cell Wall Traits Associated with Divergent In Vitro Neutral Detergent Fiber Digestibility in Alfalfa Clones (2006)

Poor cell wall digestibility of alfalfa ( Medicago sativa L.) stems limits available energy to ruminants. This study compared alfalfa clones identified as either low or high rapid (16 h), or low or high potential (96 h) stem in vitro neutral detergent fiber digestibility (IVNDFD) for stem detergent fiber, cell wall, and morphology traits. Clones were established in replicated field plots at two sites in Minnesota during 2001 and harvested twice (primary spring growth and first summer regrowth) in the two following years. Presence of flowers, stem length, internode number, mean internode length, and number of elongating internodes was determined on 10 stems from each plot at every harvest. Herbage was dried and the stem fraction was analyzed for 16‐ and 96‐h IVNDFD, detergent fiber components, and cell wall concentration and composition (Klason lignin, individual neutral sugars, and total uronic acids). Stem neutral detergent fiber (NDF) and cell wall concentration were lower for the high rapid than low rapid IVNDFD clones, but the high and low potential IVNDFD clonal groups did not differ. Lignin and pectin concentrations of the cell wall were lower and higher, respectively, for both high IVNDFD groups than their corresponding low groups. The low rapid and high potential IVNDFD groups had longer stem and internode lengths than their corresponding groups.
Tunneling discharge of positive trapped oxide charge in p-channel field effect transistors (2011)

Negative bias temperature instability has been studied in 130 nm and 90 nm channel length, SiO2 gate insulator field effect transistors at room temperature. Pulsed voltage stressing and subsequent recovery using times starting in the tens of microsecond regime were employed together with a single point data acquisition time ∼4 μs. Threshold voltage shifts were characteristic of oxide charge trapping as opposed to interface state generation. Recovery of the threshold voltage was modeled assuming quantum mechanical tunneling of trapped charges from the dielectric to the Si substrate.
Laser-generated ultrasound with optical fibres using functionalised carbon nanotube composite coatings (2014)

Optical ultrasound transducers were created by coating optical fibres with a composite of carbon nanotubes (CNTs) and polydimethylsiloxane (PDMS). Dissolution of CNTs in PDMS to create the composite was facilitated by functionalisation with oleylamine. Composite surfaces were applied to optical fibres using dip coating. Under pulsed laser excitation, ultrasound pressures of 3.6 MPa and 4.5 MPa at the coated end faces were achieved with optical fibre core diameters of 105 and 200 μm, respectively. The results indicate that CNT-PDMS composite coatings on optical fibres could be viable alternatives to electrical ultrasound transducers in miniature ultrasound imaging probes.
Improved transcriptional activators and their use in mis‐expression traps in Arabidopsis (2005)

The synthetic transcription factor LhG4 has been used in numerous mis-expression studies in plants. We show that the sequence encoding the LhG4 activation domain, derived from Saccharomyces cerevisiae GAL4, contains several cryptic polyadenylation signals in Arabidopsis. The GAL4-derived sequence was modified according to preferred Arabidopsis codon usage, generating LhG4AtO which was faithfully transcribed in Arabidopsis plants. In protoplasts, LhG4AtO achieved maximum transactivation of the pOp promoter with 10-fold less input DNA than LhG4. The same methods were used to compare 10 other LhG4 derivatives that carried alternative natural or synthetic activation domains. Lh214 and Lh314, which contain synthetic activation domains comprising trimers of a core acidic activation domain, directed threefold more GUS expression from the pOp promoter with 20-fold less input DNA than LhG4. In contrast, when expressed from the CaMV 35S promoter in transgenic plants carrying a pOp-GUS reporter, Lh214 and Lh314 yielded transformants with substantially lower GUS activities than other constructs including LhG4AtO and LhG4 which performed similarly. When incorporated into an enhancer-trapping vector, however, LhG4AtO and Lh314 yielded enhancer traps with approximately twice the frequency of LhG4, suggesting that the modified activation domains offer improved performance when expressed from weaker transcription signals. To increase the number of LhG4 patterns available for mis-expression studies, we describe a population of enhancer-trap lines obtained with LhG4AtO in a pOp-GUS background. We show that enhancer-trap lines can transactivate an unlinked pOp-green fluorescent protein (pOp-GFP) reporter in the pattern predicted by staining for GUS activity.
Protein kinase C agonist and antagonist effects in normal human epidermal keratinocytes (1993)

Several lines of evidence implicate protein kinase C (PKC) in the development of basal cell and squamous cell carcinomas, tumors which originate from epidermal keratinocytes. To examine PKC in a model relevant to human skin, we exposed normal human epidermal keratinocytes (NHEK) in serum-free media to a variety of PKC agonists and antagonists. NHEK PKC activity increased up to 10-fold within the 1st hour of exposure to tetradecanoyl phorbol acetate (TPA), and gradually returned to control values within 72 h. TPA-induced PKC activity was enhanced by pretreatment of cultures with protein and RNA synthesis inhibitors. TPA-induced growth arrest and differentiation was antagonized by staurosporine. Down-regulation by bryostatin pretreatment blocked TPA-stimulated differentiation. Our overall conclusion is that activation of PKC in cultured human keratinocytes is required for differentiation. These results are crucial to the analysis of compounds suspected of promoting or inhibiting epidermal tumors.
Inter-User Interference in Body Sensor Networks: Preliminary Investigation and an Infrastructure-Based Solution (2009)

Inter-user interference is the interference in communication when several body sensor networks (BSNs) operate in the same vicinity. As BSN users congregate in an area, interference due to concurrently communicating BSNs will increase, resulting in poor performance. In this paper, we conduct a preliminary investigation of the impact of inter-user interference and investigate its behavior with respect to parameters such as number of networks and the rates at which these networks communicate. Inter-user interference, is seen to reduce packet delivery ratio by almost 35% in cases of 8 or more high-rate networks operating in the same location. We also propose a system to mitigate the adverse effects of inter-user interference. Our solution uses a fixed network infrastructure to monitor and identify BSNs that are likely to interfere with each other. The network then recommends changes to the BSN protocol to lessen interference between them. We also implement an instance of our system using a wireless sensor network (WSN) infrastructure to reduce interference. The system is shown to significantly decrease the impact of inter-user interference.
Video-Based Tracking, Learning, and Recognition Method for Multiple Moving Objects (2013)

This paper presents an extended Markov chain Monte Carlo (MCMC) method for tracking and an extended hidden Markov model (HMM) method for learning/recognizing multiple moving objects in videos with jittering backgrounds. A graphical user interface (GUI) with enhanced usability is also proposed. Previous MCMC and HMM-based methods are known to suffer performance impairments, degraded tracking and recognition accuracy, and higher computation costs when challenged with appearance and trajectory changes such as occlusion, interaction, and varying numbers of moving objects. This paper proposes a cost reduction method for the MCMC approach by taking moves, i.e., birth and death, out of the iteration loop of the Markov chain when different moving objects interact. For stable and robust tracking, an ellipse model with stochastic model parameters is used. Moreover, our HMM method integrates several different modules in order to cope with multiple discontinuous trajectories. The GUI proposed herein offers an auto-allocation module of symbols from images and a hand-drawing module for efficient trajectory learning and for interest trajectory addition. Experiments demonstrate the advantages of our method and GUI in tracking, learning, and recognizing spatiotemporal smooth and discontinuous trajectories.
Endothelin-1, a Regulator of Angiogenesis in the Chick Chorioallantoic Membrane (2001)

We investigated the angiogenic properties of endothelin-1 (ET-1) using a novel experimental approach involving the constant production and release of ET-1, which was achieved by grafting stably transfected Chinese hamster ovary (CHO) (CHO-ET-1) cell aggregates onto the chorioallantoic membrane (CAM) ectoderm. Macroscopic observation showed that CHO-ET-1 cell aggregates formed highly vascularized nodules surrounded by radially rearranged vessels, with a strong angiogenic response. 5-Bromo-2'-deoxy-uridine (BrdU) studies showed an increase in endothelial cell proliferation in the CAM vasculature around CHO-ET-1 nodules. An angiogenic response was also observed with gelatin sponges containing conditioned medium from CHO-ET-1 cells. The specific involvement of ET-1 in the angiogenic effect mediated by CHO-ET-1 was demonstrated by the reduction or abolition of neovascularized CHO-ET-1 nodules by (1) bosentan, a mixed antagonist of ET(A)/ET(B) receptors, (2) an ET(A) receptor antagonist (Ru69986) and (3) phosporamidon, an inhibitor of endothelin-converting enzyme-1 (ECE-1). We also demonstrated that VEGF was involved in CHO-ET-1-mediated angiogenesis, by using a specific inhibitor of VEGF tyrosine kinase receptor activity (PTK787/ZK 222584), which abolished CHO-ET-1 nodule formation and CAM neovascularization. Thus, our results show that exogenous ET-1 mediates angiogenesis in vivo.
Fine Specificity of T Cells Reactive to Human Pdc–E2 163–176 Peptide, the Immunodominant Autoantigen in Primary Biliary Cirrhosis: Implications for Molecular Mimicry and Cross–Recognition Among Mitochondrial Autoantigens (2000)

The anti-mitochondrial antibody response in primary biliary cirrhosis (PBC) is primarily directed at E2 components of PDC, OGDC, and BCOADC, and E3BP. Previous work has shown that the immunodominant autoreactive T- cell epitope is the PDC-E2 163-176 peptide, restricted by HLA DR53. To address molecular mimicry and cross-recognition among mitochondrial autoantigens, we analyzed reactivity, including agonism and antagonism assays, to a series of single amino acid-substituted peptides using cloned T-cell lines in PBC and controls. Interestingly, fine specificities were unique for every single T-cell clone, but the clones could be categorized into two distinct groups based on recognition motifs of the T-cell receptor (TCR) ligand: group A (170)ExDK(173) and group B (168)EIExD(172). (170)E is the most critical TCR contact residue for both groups of cloned T-cell lines, whereas (173)K and (168)E are the critical TCR contact residues for group A and group B cloned T-cell lines, respectively. More importantly, some group A-cloned T-cell lines cross-reacted to human E3BP 34-47, human OGDC-E2 100-113, and several peptides derived from various microbial proteins carrying an ExDK motif, whereas group B-cloned T-cell lines reacted only to E3BP 34-47 carrying an EIExD motif. Furthermore, an RGxG motif was exclusively found in the complementarity-determining region (CDR3) of the TCR Vbeta in the group B-cloned T-cell lines, while G, S, and/or R were frequently found in the CDR3 of the TCR Vbeta in the group A-cloned T-cell lines. These data provide a framework for understanding molecular mimicry among mitochondrial antigens.
Autophosphorylation of the protein kinase dependent on double-stranded RNA. (1987)

The double-stranded RNA (dsRNA)-dependent protein kinase (p68 kinase) from interferon-treated human cell is a Mr 68,000 protein induced by interferon. By the use of a specific monoclonal antibody, we have been able to study the two distinct protein kinase activities characteristic of purified p68 kinase. The first activity is functional for endogenous phosphorylation of the enzyme (p68 kinase), whereas the second one is responsible for the phosphorylation of exogenous substrates such as eukaryotic initiation factor 2 and histone. When activated by dsRNA in the presence of Mn2+ and ATP, p68 kinase is autophosphorylated and is then capable of catalyzing phosphorylation of histone in the absence of dsRNA. Whereas binding of 8-azido-[alpha-32P] ATP (8-N3ATP) to p68 kinase is dependent on both dsRNA and Mn2+, phosphorylated p68 kinase binds 8-N3ATP independent of dsRNA. This is consistent with a dsRNA requirement for the autophosphorylation of p68 kinase, but not for the phosphorylation of exogenous substrates. p68 kinase is mainly associated with the ribosomal pellet. It could be recovered efficiently by a buffer containing both high salt and a nonionic detergent. Synthesis of p68 kinase is induced several-fold by interferon in different types of human cells. Partial proteolysis of [35S]methionine and an 8-N3ATP-labeled p68 kinase preparation by Staphylococcus aureus V8 protease indicated the presence of a major Mr 48,000 polypeptide (p48) with a specific ATP-binding site. p48 probably contains the catalytic unit of p68 kinase and is analogous to a similar protein which we have previously described as a distinct protein present in a complexed form with p68 kinase. We now believe that the presence of p48 in previously purified kinase preparations was due to partial degradation of p68 kinase.