gebhart/patrepeval huggingface dataset:
Not Ions Alone:  Barriers to Ion Permeation in Nanopores and Channels (2004)

A hydrophobic pore of subnanometer dimensions can appear impermeable to an ion even though its radius is still much wider than that of the ion. Pores of molecular dimensions can be found, for instance, in carbon nanotubes, zeolites, or ion channel proteins. We quantify this barrier to ion permeation by calculating the potential of mean force from umbrella-sampled molecular dynamics simulations and compare them to continuum-electrostatic Poisson-Boltzmann calculations. The latter fail to describe the ion barrier because they do not account for the properties of water in the pore. The barrier originates from the energetic cost to desolvate the ion. Even in wide pores, which could accommodate an ion and its hydration shell, a barrier of several kT remains because the liquid water phase is not stable in the hydrophobic pore. Thus, the properties of the solvent play a crucial role in determining permeation properties of ions in confinement at the molecular scale.
Knowledge-based analysis of microarray gene expression data by using support vector machines (2000)

We introduce a method of functionally classifying genes by using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines (SVMs). SVMs are considered a supervised computer learning method because they exploit prior knowledge of gene function to identify unknown genes of similar function from expression data. SVMs avoid several problems associated with unsupervised clustering methods, such as hierarchical clustering and self-organizing maps. SVMs have many mathematical features that make them attractive for gene expression analysis, including their flexibility in choosing a similarity function, sparseness of solution when dealing with large data sets, the ability to handle large feature spaces, and the ability to identify outliers. We test several SVMs that use different similarity metrics, as well as some other supervised learning methods, and find that the SVMs best identify sets of genes with a common function using expression data. Finally, we use SVMs to predict functional roles for uncharacterized yeast ORFs based on their expression data.
Charting the molecular network of the drug target Bcr-Abl (2009)

The tyrosine kinase Bcr-Abl causes chronic myeloid leukemia and is the cognate target of tyrosine kinase inhibitors like imatinib. We have charted the protein-protein interaction network of Bcr-Abl by a 2-pronged approach. Using a monoclonal antibody we have first purified endogenous Bcr-Abl protein complexes from the CML K562 cell line and characterized the set of most tightly-associated interactors by MS. Nine interactors were subsequently subjected to tandem affinity purifications/MS analysis to obtain a molecular interaction network of some hundred cellular proteins. The resulting network revealed a high degree of interconnection of 7 "core" components around Bcr-Abl (Grb2, Shc1, Crk-I, c-Cbl, p85, Sts-1, and SHIP-2), and their links to different signaling pathways. Quantitative proteomics analysis showed that tyrosine kinase inhibitors lead to a disruption of this network. Certain components still appear to interact with Bcr-Abl in a phosphotyrosine-independent manner. We propose that Bcr-Abl and other drug targets, rather than being considered as single polypeptides, can be considered as complex protein assemblies that remodel upon drug action.
Neurotrophin-regulated signalling pathways (2006)

Neurotrophins are a family of closely related proteins that were identified initially as survival factors for sensory and sympathetic neurons, and have since been shown to control many aspects of survival, development and function of neurons in both the peripheral and the central nervous systems. Each of the four mammalian neurotrophins has been shown to activate one or more of the three members of the tropomyosin-related kinase (Trk) family of receptor tyrosine kinases (TrkA, TrkB and TrkC). In addition, each neurotrophin activates p75 neurotrophin receptor (p75NTR), a member of the tumour necrosis factor receptor superfamily. Through Trk receptors, neurotrophins activate Ras, phosphatidyl inositol-3 (PI3)-kinase, phospholipase C-gamma1 and signalling pathways controlled through these proteins, such as the MAP kinases. Activation of p75NTR results in activation of the nuclear factor-kappaB (NF-kappaB) and Jun kinase as well as other signalling pathways. Limiting quantities of neurotrophins during development control the number of surviving neurons to ensure a match between neurons and the requirement for a suitable density of target innervation. The neurotrophins also regulate cell fate decisions, axon growth, dendrite growth and pruning and the expression of proteins, such as ion channels, transmitter biosynthetic enzymes and neuropeptide transmitters that are essential for normal neuronal function. Continued presence of the neurotrophins is required in the adult nervous system, where they control synaptic function and plasticity, and sustain neuronal survival, morphology and differentiation. They also have additional, subtler roles outside the nervous system. In recent years, three rare human genetic disorders, which result in deleterious effects on sensory perception, cognition and a variety of behaviours, have been shown to be attributable to mutations in brain-derived neurotrophic factor and two of the Trk receptors.
End-sequence profiling: Sequence-based analysis of aberrant genomes (2003)

Genome rearrangements are important in evolution, cancer, and other diseases. Precise mapping of the rearrangements is essential for identification of the involved genes, and many techniques have been developed for this purpose. We show here that end-sequence profiling (ESP) is particularly well suited to this purpose. ESP is accomplished by constructing a bacterial artificial chromosome (BAC) library from a test genome, measuring BAC end sequences, and mapping end-sequence pairs onto the normal genome sequence. Plots of BAC end-sequences density identify copy number abnormalities at high resolution. BACs spanning structural aberrations have end pairs that map abnormally far apart on the normal genome sequence. These pairs can then be sequenced to determine the involved genes and breakpoint sequences. ESP analysis of the breast cancer cell line MCF-7 demonstrated its utility for analysis of complex genomes. End sequencing of approximately 8,000 clones (0.37-fold haploid genome clonal coverage) produced a comprehensive genome copy number map of the MCF-7 genome at better than 300-kb resolution and identified 381 genome breakpoints, a subset of which was verified by fluorescence in situ hybridization mapping and sequencing.
System/370 Extended Architecture: Facilities for Virtual Machines (1983)

This paper describes the evolution of facilities for virtual machines on IBM System/370 computers, and presents the elements of a new architectural facility designed for the virtual-machine environment. Assists that have been added to various System/370 models to support the use of virtual machines are summarized, and a general facility for this purpose which was introduced with the System/370 Extended Architecture (370-XA) is described. A new instruction of the 370-XA architecture places the machine in a specific mode in which several special capabilities are enabled. These allow the machine to provide execution in the virtual-machine environment of most of the instructions (including many privileged instructions) and most of the facilities (such as dynamic address translation) of both the System/370 and the 370-XA architectures. The major features of this new facility are individually discussed and summarized.
Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon (2008)

These findings have serious implications for all PCR-based gene expression studies, including the relatively new PCR array method, and for both qualitative and quantitative PCR-based molecular diagnostic assays, suggesting that careful consideration should be given to inhibition compatibility when conducting PCR analyses. We have demonstrated unequivocally that it is not safe to assume that different PCR reactions are equally susceptible to inhibition by substances co-purified in nucleic acid extracts.
Physicochemical Characterization of a Synthetic Lipid Emulsion for Hepatocyte-Selective Delivery of Lipophilic Compounds: Application to Polyiodinated Triglycerides as Contrast Agents for Computed Tomography (1996)

A synthetic lipid emulsion (LE) has been developed with physicochemical properties that closely resemble those of a specific class of naturally-occurring lipoproteins known as chylomicron remnants. The formulation has the potential to serve as a hepatocyte-selective delivery system for any lipophilic or amphipathic compounds that can be associated with the internal lipid phase of the emulsion. In the present studies, a lipophilic polyiodinated triglyceride (ITG) was successfully incorporated into the delivery vehicle to form a stable chylomicron-remnant-like emulsion capable of localizing material to the liver following intravenous injection. The preferred ITG-LE formulation was shown to have a mean particle diameter of less than 200 nm and a particle size stability profile in excess of 12 months. The viscosity, pH, and osmolality of the formulation also appeared favorable for safe and convenient intravenous injection. The particle size profile, chemical properties, and high degree of incorporation of ITG into the emulsion suggest that the ITG-LE formulation holds substantial promise as a hepatocyte-selective imaging agent for computed tomography of the liver. Biodistribution, elimination, and computed tomography (CT) imaging results in animals corroborated the hepatocyte-selective nature of the ITG-LE formulation.
Polymerase chain reaction and Q beta replicase amplification (1991)

The polymerase chain reaction (PCR) and Q beta replicase are two methods in which nucleic acid polymerases are used for amplification. Although these approaches share many similar problems concerning target contamination and probe specificity, they differ dramatically in their mechanisms of action and modes of application. The PCR method amplifies target sequences between two priming oligonucleotides and in essence amplifies a portion of the analyte. Q beta replicase, on the other hand, amplifies a specific template molecule hybridized to target sequences and therefore amplifies a signal component of the system. For this reason, Q beta replicase amplification has applications in areas other than for the detection of nucleic acid sequences. The requirements for application and the advantages of both PCR and Q beta replicase amplification are reviewed.
Newly synthesized proinsulin/insulin and stored insulin are released from pancreatic B cells predominantly via a regulated, rather than a constitutive, pathway. (1987)

The pancreatic B cell has been used as a model to compare the release of newly synthesized prohormone/hormone with that of stored hormone. Secretion of newly synthesized proinsulin/insulin (labeled with [3H]leucine during a 5-min pulse) and stored total immunoreactive insulin was monitored from isolated rat pancreatic islets at basal and stimulatory glucose concentrations over 180 min. By 180 min, 15% of the islet content of stored insulin was released at 16.7 mM glucose compared with 2% at 2.8 mM glucose. After a 30-min lag period, release of newly synthesized (labeled) proinsulin and insulin was detected; from 60 min onwards this release was stimulated up to 11-fold by 16.7 mM glucose. At 180 min, 60% of the initial islet content of labeled proinsulin was released at 16.7 mM glucose and 6% at 2.8 mM glucose. Specific radioactivity of the released newly synthesized hormone relative to that of material in islets indicated its preferential release. A similar degree of isotopic enrichment of released, labeled products was observed at both glucose concentrations. Quantitative HPLC analysis of labeled products indicated that glucose had no effect on intracellular proinsulin to insulin conversion; release of both newly synthesized proinsulin and insulin was sensitive to glucose stimulation; 90% of the newly synthesized hormone was released as insulin; and only 0.5% of proinsulin was rapidly released (between 30 and 60 min) in a glucose-independent fashion. It is thus concluded that the major portion of released hormone, whether old or new, processed or unprocessed, is directed through the regulated pathway, and therefore the small (less than 1%) amount released via a constitutive pathway cannot explain the preferential release of newly formed products from the B cell.
Vaccine Potential of theNeisseria meningitidis2086 Lipoprotein (2004)

A novel antigen that induces cross-reactive bactericidal antibodies against a number of Neisseria meningitidis strains is described. This antigen, a approximately 28-kDa lipoprotein called LP2086, was first observed within a complex mixture of soluble outer membrane proteins (sOMPs) following a series of fractionation, protein purification, and proteomics steps. Approximately 95 different neisserial isolates tested positive by Western blotting and PCR screening methods for the presence of the protein and the gene encoding LP2086. The strains tested included isolates of N. meningitidis serogroups A, B, C, W135, and Y, Neisseria gonorrhoeae, and Neisseria lactamica. To better understand the microheterogeneity of this protein, the 2086 genes from 63 neisserial isolates were sequenced. Two different subfamilies of LP2086 were identified based on deduced amino acid sequence homology. A high degree of amino acid sequence similarity exists within each 2086 subfamily. The highest degree of genetic diversity was seen between the two subfamilies which share approximately 60 to 75% homology at the nucleic acid level. Flow cytometry (fluorescence-activated cell sorting) analyses and electron microscopy indicated that the LP2086 is localized on the outer surface of N. meningitidis. Antiserum produced against a single protein variant was capable of eliciting bactericidal activity against strains expressing different serosubtype antigens. Combining one recombinant lipidated 2086 (rLP2086) variant from each subfamily with two rPorA variants elicited bactericidal activity against all strains tested. The rLP2086 family of antigens are candidates worthy of further vaccine development.
Optical Communication Systems for Datacenter Networks (2017)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text D. V. Plant, M. Morsy-Osman, and M. Chagnon, "Optical Communication Systems for Datacenter Networks," in Optical Fiber Communication Conference, OSA Technical Digest (online) (Optica Publishing Group, 2017), paper W3B.1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
HIV Inhibitors Targeted at the Reverse Transcriptase (1992)

HIV inhibitors targeted at the virus-associated reverse transcriptase (RT) can be divided into two groups, depending on whether they are targeted at the substrate or nonsubstrate binding site. To the first group belong the 2',3'-dideoxynucleosides (i.e., DDC, DDI), 3'-azido-2',3'-dideoxynucleosides (i.e., AZT), 3'-fluoro-2',3'-dideoxynucleosides (i.e., FLT), 2',3'-didehydro-2',3'-dideoxynucleosides (i.e., D4C, D4T) and carbocyclic derivatives thereof (i.e., carbovir), 2'-fluoro-ara-2',3'-dideoxynucleosides, 1,3-dioxolane derivatives (i.e., 2',3'-dideoxyl-3'-thiacytidine), oxetanocin analogues and carbocyclic derivatives thereof (i.e., cyclobut-G) and the 9-(2-phosphonylmethoxyethyl)adenine (PMEA) and 9-(3-fluoro-2-phosphonylmethoxypropyl)adenine (FPMPA) derivatives. These compounds need to be phosphorylated intracellularly to their triphosphate forms before they act as competitive inhibitors or alternate substrates (chain terminators) of HIV RT. The second group includes the tetrahydro-imidazo[4,5,l-jk][1,4]-benzodiazepin-2(1H)one (TIBO), 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine (HEPT), dipyrido[3,2-b:2',3'-e]-[1,4]diazepin-6-one (nevirapine) and pyridin-2(1H)one derivatives, which interact as such, noncompetitively, with a specific allosteric binding site of HIV-1 RT. Compounds belonging to the two different groups may give rise to synergism which combined, and, likewise, viral resistance to the compounds may arise through different mutations, depending on the nature of the compounds and the group to which they belong.
Parameter-Free Radial Distortion Correction with Center of Distortion Estimation (2007)

We propose a method of simultaneously calibrating the radial distortion function of a camera and the other internal calibration parameters. The method relies on the use of a planar (or, alternatively, nonplanar) calibration grid which is captured in several images. In this way, the determination of the radial distortion is an easy add-on to the popular calibration method proposed by Zhang [24]. The method is entirely noniterative and, hence, is extremely rapid and immune to the problem of local minima. Our method determines the radial distortion in a parameter-free way, not relying on any particular radial distortion model. This makes it applicable to a large range of cameras from narrow-angle to fish-eye lenses. The method also computes the center of radial distortion, which, we argue, is important in obtaining optimal results. Experiments show that this point may be significantly displaced from the center of the image or the principal point of the camera.
A review of chemical structure retrieval systems (1987)

Abstract This paper decribes the development and current state‐of‐the‐art in computerized systems for the storage and retrieval of chemical structure information. The main types of machine‐readable structure representation — fragmentation codes, linear notations and connection tables — are described, together with the retrieval algorithms which are used to provide structure and substructure search facilities. Current research work in chemical structure retrieval includes the development of techniques for the representation and searching of the generic structures which occur in chemical patents, for searching files of three‐dimensional structures, for ranking searches designed to identify compounds structurally similar to a given query compound, and the use of parallel computers to increase the efficiency of substructure searching. Chemical structure handling techniques are also applicable in a range of application areas, including chemical reaction indexing, computer‐aided synthesis design and structure elucidation, and substructural analysis methods for the study of quantitative structure—activity relationships.
Peptide engineering allows cytotoxic T-cell vaccination against human papilloma virus tumour antigen, E6. (1995)

Major histocompatibility complex (MHC) class I allele-specific binding motifs have proved useful in predicting cytotoxic T-cell epitopes from immunogenic proteins. In a search of the E6 protein from human papilloma virus type 16 utilizing the Kb binding motif, we discovered four potential binding peptides. One peptide, E6.1 (sequence 50-57, YDFAFRDL), was poor in its ability to stabilize empty Kb on RMA-S cells, with a t1/2 = 33 min versus 30 min for empty Kb. This peptide subsequently proved to be non-immunogenic upon mouse in vivo vaccination. It was hypothesized that an isoleucine for aspartate substitution at position 2 would improve Kb stabilization kinetics and therefore immunogenic potential. The engineered peptide E6.1 I2 increased the Kb t1/2 to 100 min and was immunogenic upon in vivo vaccination. Cytolytic T lymphocytes (CTL) raised with the E6.1 I2 peptide responded to cells pulsed with either the wild-type peptide or the engineered peptide, implying a blindness to the substitution. More striking, these CTL also lysed a syngeneic cell line transfected with the E6 gene, implying that the E6.1 peptide was processed and presented. These data demonstrate that subimmunogenic peptides can be engineered to improve binding kinetics, which in turn improves immunogenicity. Provided that poor binding peptides are processed, the induction threshold for CTL activation can be achieved with engineered peptides, thus allowing for the kill of wild-type target cells. This approach may prove relevant to the design of subunit vaccines to virally induced tumours.
Estimating expected completion times with probabilistic job routing (2006)

A common problem in production environments is the need to estimate the remaining time in system for work-in-progress jobs. Simulation can be used to obtain the estimates. However, when the future path of a job is uncertain (due to stochastic events such as rework), using simulation to estimate the remaining cycle time of a job at step k can be imprecise; traditional confidence intervals on the estimated remaining cycle times may be too large to be of practical significance. We propose a response surface methodology-based approach to estimating conditional confidence intervals on the remaining cycle times as jobs progress through the system and more information is obtained on them. This method will provide more useful and accurate estimates of remaining cycle times at various stages of the process flow. Further, we outline two different simulation approaches for estimating the response surfaces used to generate the confidence intervals.
Interleukin‐4 and the interleukin‐4 receptor in allergic contact dermatitis (1998)

Cutaneous immune responses involving T helper (TH) type 1 (TH1) and type 2 (TH2) T cells, characterised by secretion of interferon-gamma (Ifn-gamma) and interleukin-4 (IL-4), respectively, have both been reported in allergic contact dermatitis (ACD). We used immunohistochemistry to localize expression of IL-4 in ACD lesions and unaffected skin. Atopic dermatitis (AD) and psoriasis biopsies provided positive and negative IL-4 immunoreactivity controls. To investigate the role of IL-4 in ACD, we investigated expression of IL-4 receptors in ACD, AD and psoriatic skin. IL-4 immunoreactivity was found in cells in the dermal infiltrate in 3 out of 7 ACD lesions, but not in unaffected skin from these patients. IL-4 immunoreactivity was found in the dermal infiltrate of all lesional and unaffected AD biopsies, but in none of the psoriatic biopsies. IL-4 receptor alpha chain immunoreactivity, associated with dermal mast cells, was found in all patients. Local expression of IL-4 in ACD indicates either TH2 or TH0 immunoregulation in some allergic contact dermatitis lesions. Our findings do not support exclusive TH1 or TH2 cutaneous immune responses in ACD. Expression of IL-4 receptors by cutaneous mast cells provides a route through which local effects of IL-4 might be mediated.