gebhart/patrepeval huggingface dataset:
Nanopores in solid-state membranes engineered for single molecule detection (2010)

A nanopore is an analytical tool with single molecule sensitivity. For detection, a nanopore relies on the electrical signal that develops when a molecule translocates through it. However, the detection sensitivity can be adversely affected by noise and the frequency response. Here, we report measurements of the frequency and noise performance of nanopores </=8 nm in diameter in membranes compatible with semiconductor processing. We find that both the high frequency and noise performance are compromised by parasitic capacitances. From the frequency response we extract the parameters of lumped element models motivated by the physical structure that elucidates the parasitics, and then we explore four strategies for improving the electrical performance. We reduce the parasitic membrane capacitances using: (1) thick Si(3)N(4) membranes; (2) miniaturized composite membranes consisting of Si(3)N(4) and polyimide; (3) miniaturized membranes formed from metal-oxide-semiconductor (MOS) capacitors; and (4) capacitance compensation through external circuitry, which has been used successfully for patch clamping. While capacitance compensation provides a vast improvement in the high frequency performance, mitigation of the parasitic capacitance through miniaturization offers the most promising route to high fidelity electrical discrimination of single molecules.
Residue-specific bioincorporation of non-natural, biologically active amino acids into proteins as possible drug carriers: Structure and stability of the per -thiaproline mutant of annexin V (1998)

Residue-specific bioincorporation of 1,3-thiazolidine-4-carboxylic acid [thiaproline, Pro(S)], a non-natural amino acid analog of proline, into human recombinant annexin V was achieved with a proline-auxotrophic Escherichia coli strain by fermentation procedures in minimal medium. Quantitative replacement of proline with thiaproline was confirmed by mass-spectrometric, amino acid, and x-ray crystallographic analyses. The wild-type protein and its per-Pro(S) mutant were found to crystallize isomorphously and to show identical three-dimensional structures in crystals. In solution the dichroic properties of the wild-type and per-Pro(S) protein confirmed nearly identical overall folds. From thermal denaturation experiments, however, a reduced Tm (-4.5 K) value was determined whereas the van't Hoff enthalpy and entropy were not significantly affected. Therefore, protein mutants containing bioactive amino acid analogs like thiaproline at multiple sites would be expected to fully retain their functional properties, including immunogenicity, and thus could serve as promising vehicles for targeted drug delivery.
Genes of the T-Cell Antigen Receptor in Normal and Malignant T Cells (1987)

In this review, the germline genomic and cDNA structures and the evolution of the human TcR-alpha-, TcR-beta-, and Tc gamma-chain genes have been reviewed and discussed. The estimated V-gene segment repertoires established for the human TcR-alpha-, TcR-beta-, and Tc gamma-chain genes have also been summarized. The use of TcR and Tc gamma genes in the evaluation of hematopoietic malignancies and identification of chromosomal translocations has also been presented. It is hoped that such information will serve as a reference point from which the study of TcR genes can further progress. This will almost certainly include the use of TcR and perhaps Tc gamma genes in the study of the dual recognition of antigen and MHC gene products, the role of these genes in thymic education/selection, and the role(s) of these genes in oncogenesis processes and autoimmune settings.
Why have monitoring? (2001)

Distributed DC battery supported power systems are a requirement of many industries. The management and maintenance of such systems presents unique difficulties due to the quantity and distributed nature of the industries involved. Astute solutions are therefore required if we are to significantly reduce maintenance costs and improve the quality of service. The efficient application of technology to resolve the issues of managing these assets including the other services at each location, such as air-conditioning, generators and security will be discussed within a variety of different situations. The paper emphasises the importance of an integrated approach to remote site management and the application of central management platforms in decision making. Specific conclusions are reviewed and elaborated upon.
One packet suffices - Highly efficient packetized Network Coding With finite memory (2011)

Random Linear Network Coding (RLNC) has emerged as a powerful tool for robust high-throughput multicast. Projection analysis, a recently introduced technique, shows that the distributed packetized RLNC protocol achieves (order) optimal and perfectly pipelined information dissemination in many settings. In the original approach to RNLC intermediate nodes code together all available information. This requires intermediate nodes to keep considerable data available for coding. Moreover, it results in a coding complexity that grows linearly with the size of this data. While this has been identified as a problem, approaches that combine queuing theory and network coding have heretofore not provided a succinct representation of the memory needs of network coding at intermediates nodes. This paper shows the surprising result that, in all settings with a continuous stream of data, network coding continues to perform optimally even if only one packet per node is kept in active memory and used for computations. This leads to an extremely simple RLNC protocol variant with drastically reduced requirements on computational and memory resources. By extending the projection analysis, we show that in all settings in which the RLNC protocol was proven to be optimal its finite memory variant performs equally well. In the same way as the original projection analysis, our technique applies in a wide variety of network models, including highly dynamic topologies that can change completely at any time in an adversarial fashion.
Structure and Dynamics of Triazole‐Linked DNA: Biocompatibility Explained (2011)

Blending in: A triazole-modified DNA duplex is perturbed in structure and dynamics, but this is delocalized over five base pairs. The conformation remains B-DNA and hydrogen bonds between the DNA phosphate oxygen and polymerases can be mimicked by the triazole nitrogen (see figure). The results explain the surprising biocompatibility of triazole-linked DNA.
Multiple Access for 5G New Radio: Categorization, Evaluation, and Challenges (2017)

Next generation wireless networks require massive uplink connections as well as high spectral efficiency. It is well known that, theoretically, it is not possible to achieve the sum capacity of multi-user communications with orthogonal multiple access. To meet the challenging requirements of next generation networks, researchers have explored non-orthogonal and overloaded transmission technologies-known as new radio multiple access (NR-MA) schemes-for fifth generation (5G) networks. In this article, we discuss the key features of the promising NR-MA schemes for the massive uplink connections. The candidate schemes of NR-MA can be characterized by multiple access signatures (MA-signatures), such as codebook, sequence, and interleaver/scrambler. At the receiver side, advanced multi-user detection (MUD) schemes are employed to extract each user's data from non-orthogonally superposed data according to MA-signatures. Through link-level simulations, we compare the performances of NR-MA candidates under the same conditions. We further evaluate the sum rate performances of the NR-MA schemes using a 3-dimensional (3D) ray tracing tool based system-level simulator by reflecting realistic environments. Lastly, we discuss the tips for system operations as well as call attention to the remaining technical challenges.
Interferon-α Abrogates Tolerance Induction by Human Tolerogenic Dendritic Cells (2011)

IFN-α inhibits the induction of T cell tolerance by reversing the tolerogenic function of human DC.
A Platform for the Implementation of the Services of an Educational Network. (1998)

Multimedia and hypermedia had and still have a tremendous impact on the evolution of educational software. In this paper we propose a platform for the implementation of the services of an educational network over TCP/IP networks such as the Internet. Our proposal aims at providing an integrated communicational environment which supplies the communicative needs of one educational community, using the latest telecommunication and multimedia information processing technology. We propose various kinds of communication forms for the interaction between the participants.
Two-Component Regulatory Systems (2014)

Originally characterized for nitrogen regulation (NtrB-NtrC), chemotaxis (CheA-CheY-CheB), osmoregulation (EnvZ-OmpR), and regulation of phosphate uptake (PhoR-PhoB) in Escherichia coli and Salmonella typhimurium, the family of two-component systems has rapidly expanded, and new examples continue to emerge. More than 30 of these regulatory pairs have been identified in both gram-negative and gram-positive bacteria; they control functions ranging from virulence gene expression in Agrobacterium tumefaciens (VirA-VirG), S. typhimurium (PhoQ-PhoP), and Bordetella pertussis (BvgSBvgA) to complex developmental pathways such as sporulation (SpoIIJ-SpoOF-SpoOA) and competence for transformation by exogenous DNA (ComP-ComA and DegS-DegU) in Bacillus subtilis. These pairs are the focus of this chapter. Sequence similarities to other two-component systems suggest the conserved His-189 residue of the DegS protein kinase and Asp-56 residue of the DegU response regulator as likely candidates for the respective phosphorylation sites of the two proteins. A large number of proteins belonging to the histidine protein kinase-response regulator family have been characterized in gram-positive bacteria. It appears that a considerable amount of overlap exists between the different systems controlling postexponential-phase responses in B. subtilis. Thus, DegS-DegU, ComP-ComA, and SpoOA are all involved in controlling competence gene expression, and the SpoOA phosphorelay and DegS-DegU both control protease gene expression.
The Binding of Oxidized Low Density Lipoprotein (ox-LDL) to ox-LDL Receptor-1 Reduces the Intracellular Concentration of Nitric Oxide in Endothelial Cells through an Increased Production of Superoxide (2001)

Oxidized low density lipoprotein (ox-LDL) has been suggested to affect endothelium-dependent vascular tone through a decreased biological activity of endothelium-derived nitric oxide (NO). Oxidative inactivation of NO is regarded as an important cause of its decreased biological activity, and in this context superoxide (O(2)) is known to inactivate NO in a chemical reaction during which peroxynitrite is formed. In this study we examined the effect of ox-LDL on the intracellular NO concentration in bovine aortic endothelial cells and whether this effect is influenced by ox-LDL binding to the endothelial receptor lectin-like ox-LDL receptor-1 (LOX-1) through the formation of reactive oxygen species and in particular of O(2). ox-LDL induced a significant dose-dependent decrease in intracellular NO concentration both in basal and stimulated conditions after less than 1 min of incubation with bovine aortic endothelial cells (p < 0.01). In the same experimental conditions ox-LDL also induced O(2) generation (p < 0.001). In the presence of radical scavengers and anti-LOX-1 monoclonal antibody, O(2) formation induced by ox-LDL was reduced (p < 0.001) with a contemporary rise in intracellular NO concentration (p < 0.001). ox-LDL did not significantly modify the ability of endothelial nitric oxide synthase to metabolize l-arginine to l-citrulline. The results of this study show that one of the pathophysiological consequences of ox-LDL binding to LOX-1 may be the inactivation of NO through an increased cellular production of O(2).
lntegrated Environmental River Modelling - Recent Trends (2001)

Sustainable management of our rivers requires an in-depth understanding of river processes and their interaction and the application of an integrated management approach. While standard river modelling tools have enhanced and broadened the understanding of river processes they often do not facilitate the integrated approach required for today's river management. Recent trends in river modelling encompass the integration of different types of models ranging from 1D, 2D and 3D model integration to integration of surface water and ground water models and the development of more complex process modules. Examples describing the application of such integrated models and advanced process modules are presented.
Estimation of Heavy-Ion LET Thresholds in Advanced SOI IC Technologies From Two-Photon Absorption Laser Measurements (2010)

The laser energy thresholds for SEU for SOI 1-Mbit SRAMs built in Sandia's 0.35-μm SOI technology were measured using carrier generation by two-photon absorption. The laser measurements were correlated to heavy-ion threshold LET measurements to determine an empirical relationship between laser energy threshold and heavy-ion threshold LET. This empirical relationship was used to estimate the threshold LETs for other circuits built in Sandia's 0.35-μm SOI technology and SRAMs built in IBM's 45 and 65-nm SOI technologies. For an ASIC built in Sandia's 0.35-μm SOI technology the estimated threshold from laser measurements was close to the measured heavy-ion threshold LET. However, for a dual-port SRAM also built in Sandia's 0.35-μm SOI technology and for the 45- and 65-nm IBM SOI SRAMs, the threshold LETs estimated from laser measurements did not correlate to the measured heavy-ion threshold LETs. For the IBM SRAMs, the likely cause of the discrepancy between the threshold LETs estimated from laser measurements and the threshold LETs measured by heavy-ion testing is due to the laser pulse simultaneously injecting charge into multiple transistors within a memory cell and/or in adjacent memory cells. This is due to the relatively large size of the laser spot size compared to the size of the SEU sensitive volume of the IBM SOI devices. The hardness assurance implications of these results are discussed.
Polyamines: from Molecular Biology to Clinical Applications (1991)

The polyamines putrescine, spermidine and spermine represent a group of naturally occurring compounds exerting a bewildering number of biological effects, yet despite several decades of intensive research work, their exact physiological function remains obscure. Chemically these compounds are organic aliphatic cations with two (putrescine), three (spermidine) or four (spermine) amino or amino groups that are fully protonated at physiological pH values. Early studies showed that the polyamines are closely connected to the proliferation of animal cells. Their biosynthesis is accomplished by a concerted action of four different enzymes: ornithine decarboxylase, adenosylmethionine decarboxylase, spermidine synthase and spermine synthase. Out of these four enzyme, the two decarboxylases represent unique mammalian enzymes with an extremely short half life and dramatic inducibility in response to growth promoting stimuli. The regulation of ornithine decarboxylase, and to some extent also that of adenosylmethionine decarboxylase, is complex, showing features that do not always fit into the generally accepted rules of molecular biology. The development and introduction of specific inhibitors to the biosynthetic enzymes of the polyamines have revealed that an undisturbed synthesis of the polyamines is a prerequisite for animal cell proliferation to occur. The biosynthesis of the polyamines thus offers a meaningful target for the treatment of certain hyperproliferative diseases, most notably cancer. Although most experimental cancer models responds strikingly to treatment with polyamine antimetabolites--namely, inhibitors of various polyamine synthesizing enzymes--a real breakthrough in the treatment of human cancer has not yet occurred. It is, however, highly likely that the concept is viable. An especially interesting approach is the chemoprevention of cancer with polyamine antimetabolites, a process that appears to work in many experimental animal models. Meanwhile, the inhibition of polyamine accumulation has shown great promise in the treatment of human parasitic diseases, such as African trypanosomiasis.
INTELLIGENT TRANSPORTATION SYSTEMS FIELD OPERATIONAL TEST CROSS-CUTTING STUDY: ADVANCE TRAVELER INFORMATION SYSTEMS (1998)

Advanced Traveler Information Systems (ATIS) Cross-Cutting report summarizes and interprets the results exclusively of several Field Operational Tests (FOTs) that have traveler information components. The FOTs considered in this report include: Atlanta Kiosk, Genesis, Seattle Wide-Area Information For Travelers, TravInfo, TravLink, Trilogy, Atlanta Driver Advisory Service, Advanced Driver and Vehicle Navigation, Driver Information Radio Experimenting With Communication Technology, Herald II, Idaho Storm Warning System, TravTek, Travel-Aid and Transit En-Route Information. The analysis and results presented in this report are categorized as impacts, user response, technical lessons learned, institutional challenges and resolutions and cost to implement. The Traveler information systems faced a wide variety of institutional challenges. This report highlights the successes and problems these tests encountered while attempting to develop the technologies appropriate to establishing and implementing ATIS.
Antide and related antagonists of luteinizing hormone release with long action and oral activity. (1988)

Antide is the decapeptide N-Ac-D-Nal(2),D-Phe(pCl),D-Pal(3),Ser,Lys(Nic),D-Lys(Nic),Leu,Lys(iPr),P ro,D- Ala-NH2 [Nal(2) represents 3-(2-naphthyl)alanine; Phe(p-Cl) represents 3-(4-chlorophenyl)alanine; Pal(3) represents 3-(3-pyridyl)alanine; Lys(Nic) represents N epsilon-nicotinoyllysine; Lys-(iPr) represents N epsilon-isopropyllysine], which is an antagonist of luteinizing hormone-releasing hormone (LHRH), which has high antiovulatory activity, releases negligible histamine, and is scheduled for scale-up, safety testing, and evaluation in the experimental primate and in clinical medicine. Thirty-five more peptides were synthesized, designed on antide with variations in positions 5-8. Of these, N-Ac-D-Nal(2),D-Phe(pCl),D-Pal(3),Ser,Lys(Pic),cis-D- Ala(PzAC),Leu,Lys(iPr),Pro,D-Ala-NH2 [Lys(Pic) represents N epsilon-picoloyllysine; Ala(PzAC) represents 3-(4-pyrazinylcarbonylaminocyclohexyl)alanine] was not only the most potent but also had higher antiovulatory activity than antide--i.e., 73% per 0.25 microgram and 100% per 0.5 microgram vs. 36% per 0.5 microgram and 100% per 1.0 microgram. Antide showed significant (P less than 0.001) duration of action when injected at a dose of 10 micrograms 44 hr before injection of 50 ng of the agonist [D-Qal(3)6]LHRH [Qal(3) represents 3-(3-quinolyl)alanine]. Antide showed oral antiovulatory activity at 600 micrograms (73%) and at 1200 micrograms (100%) with negligible difference between water and corn oil oral formulations.
G-->A hypermutation of the human immunodeficiency virus type 1 genome: evidence for dCTP pool imbalance during reverse transcription. (1994)

The quasispecies model for RNA viruses predicts the existence of a replication error threshold beyond which there is a melting or total loss of sequence information. Retroviral G-->A hypermutation is probably an example. Here it is shown that G-->A transitions may occur in both GpG and GpA dinucleotide contexts. Transitions in GpG preferentially occur via base mispairing at the ends of runs of G residues, whereas G-->A transitions within GpA may result from temporary dislocation of the primer and template strands by a single base. The two circumstances may be related by the local dCTP substrate concentration. An in vitro elongation assay shows that primer/template dislocation is more frequent for the human immunodeficiency virus type 1 reverse transcriptase than for murine or avian retroviral enzymes. Taken together these data suggest that G-->A hypermutation is an example of induced mutation whereby the viral reverse transcriptase is forced into making errors by imbalances in the intracellular dCTP concentration.
Human cDNA clones for an alpha subunit of Gi signal-transduction protein. (1987)

Two cDNA clones were obtained from a lambda gt11 cDNA human brain library that correspond to alpha i subunits of G signal-transduction proteins (where alpha i subunits refer to the alpha subunits of G proteins that inhibit adenylate cyclase). The nucleotide sequence of human brain alpha i is highly homologous to that of bovine brain alpha i [Nukada, T., Tanabe, T., Takahashi, H., Noda, M., Haga, K., Haga, T., Ichiyama, A., Kangawa, K., Hiranaga, M., Matsuo, H. & Numa, S. (1986) FEBS Lett. 197, 305-310] and the predicted amino acid sequences are identical. However, human and bovine brain alpha i cDNAs differ significantly from alpha i cDNAs from human monocytes, rat glioma, and mouse macrophages in amino acid (88% homology) and nucleotide (71-75% homology) sequences. In addition, the nucleotide sequences of the 3' untranslated regions of human and bovine brain alpha i cDNAs differ markedly from the sequences of human monocyte, rat glioma, and mouse macrophage alpha i cDNAs. These results suggest there are at least two classes of alpha i mRNA.
The use of controlled reperfusion strategies in cardiac surgery to minimize ischaemia/reperfusion damage (2009)

Ischaemia and reperfusion occur during almost every cardiac operation, and one of the key elements to achieve a successful operation is to counteract the detrimental effects of induced ischaemia and reperfusion during the operation. The cardiac surgeon is in a unique position to protect the heart before ischaemia is induced and to avoid further damage during the reperfusion period. The surgeon can alter the composition of the reperfusate and the conditions of reperfusion so that the ischaemia/reperfusion injury is minimal, even after very complex procedures that require long aortic cross-clamp periods. This in turn allows him to perform a near-perfect surgical repair of the underlying disease without the pressure of time. The vast knowledge gained in this field over the years has led to application in other organs, such as the limbs (acute limb ischaemia), lungs (lung transplantation), kidney and liver (kidney and liver transplantation), and more recently even for the brain [acute cerebral artery occlusion (stroke)] and the whole body (cardiopulmonary resuscitation). Further improvements in reperfusion strategies will allow salvage of tissue and even whole body after ischaemic periods thought previously to be irreversibly damaged.
T‐cell development, doing it in a dish (2006)

The thymus provides a unique environment for the development of T lymphocytes from bone marrow-derived progenitor cells. Several environmental factors have been identified that influence the development of T cells in the thymus. In particular, the Notch pathway has emerged as critical for the induction of T-lineage commitment and differentiation. Until recently, however, the precise nature of the thymus-derived signals that drive T-cell development were unclear, and the only reliable in vitro culture system that supported T-cell differentiation required the use of thymus organ cultures. Here, we discuss recent advances in the identification of critical Notch receptor ligands that have facilitated the development of a simple in vitro model for the differentiation of T cells 'in a dish', providing an alternate approach for studying T lymphopoiesis.