gebhart/patrepeval huggingface dataset:
Nanomechanical Control of an Optical Antenna (2007)

In this work we present a tunable bowtie optical antenna fabricated via a colloidal nanomask. The structure consists of two gold nanotriangles on a silica substrate. The feedgap can be continuously varied by manipulating an antenna arm with nanometer precision with an atomic force microscope (AFM). At the same time the optical response of the nanoantenna is determined with darkfield scattering spectroscopy.
Integration of corynebacteriophages beta tox+, omega tox+, and gamma tox- into two attachment sites on the Corynebacterium diphtheriae chromosome (1983)

The bacterial attachment sites of independently isolated Corynebacterium diphtheriae strains C7s and (belfanti)1030 lysogenic for corynebacteriophages beta tox+, omega tox+, and gamma tox- were determined by Southern blot analysis. Both corynebacterial strains contained two distinct bacterial attachment sites (attB1 and attB2). We found that infection by any of the three closely related corynebacteriophages may give rise to single, double, and triple lysogens. In the case of toxigenic C. diphtheriae strains C7s(beta tox+) and C7s(omega tox+), the final yields of diphtheria toxin produced under optimal conditions were equivalent and varied by one-, two-, or threefold depending upon the number of integrated prophage.
Synthesis of a protected C‐11/C‐17 segment of mycinolide‐V (1990)

Abstract Starting from D ‐ribonolactone, the cyclopentylidene‐protected dihydroxy ester 12 was prepared in five steps. Reaction of its enolate 13 with benzyloxymethyl iodide gave the esters 15 and 16 with modest selectivity. Each of these was converted into the desired mycinolide building block 32 in seven and six steps, respectively.
The effects of an immunomodulatory LFA3-IgG1 fusion protein on nonhuman primates. (1994)

LFA3TIP, a fusion protein comprised of the first extracellular domain of LFA-3 fused to the hinge, CH2 and CH3 domains of human IgG1, inhibits proliferation of human T cells in vitro. LFA3TIP also inhibits responses of human CD2 transgenic mice by rapidly and totally depleting peripheral T cells. These effects require binding of the LFA-3 and CH2 domains of LFA3TIP to CD2+ T cells and Fc gamma R+ accessory cells, respectively. As CD2 is well conserved in primate species, we evaluated the effects of LFA3TIP in nonhuman primates. We report in vitro results leading to the selection of the baboon as a model for analysis of LFA3TIP, and in vivo effects of single and multidose regimens of LFA3TIP administration. This is the first report of the in vivo administration of an immunomodulatory fusion protein to primates. LFA3TIP is shown to mediate effects on primate T lymphocytes without apparent related toxicities or immunogenicity. Results are discussed in context of potential mechanisms of LFA3TIP immunotherapy.
Temporal Bone Pathology in a Case of Amyloidosis with Hearing Loss and Vertigo (1995)

Temporal bone findings in a case of amyloidosis with hearing loss and vertigo are reported. The striking findings of the bilateral temporal bones were amyloid deposits observed in the facial nerve. To our knowledge, there are no cases with amyloid deposits in the temporal bones among amyloidosis cases reported in the literature. Dehiscence of the facial canal and the facial nerve protruding on to the stapes was observed bilaterally. Inflammation with ossification in the posterior semicircular canal and reduction in the number of spiral ganglion cells were observed in the left ear.
Patterning the Brain of the Zebrafish Embryo (1993)

The brain's default mode network consists of discrete, bilateral and symmetrical cortical areas, in the medial and lateral parietal, medial prefrontal, and medial and lateral temporal cortices of the human, nonhuman primate, cat, and rodent brains. Its ...Read More
SNA Distribution Services (1983)

This paper describes the IBM SNA Distribution Services (SNADS). Heretofore, SNA has focused on synchronous data distribution. Along with the advent of office systems and other distributed applications has come the requirement to provide a common architecture for interchanging data asynchronously among diverse systems and products. SNA Distribution Services provides a general asynchronous (delayed delivery) data distribution facility for SNA applications. The initial implementations are for office systems applications. Discussed are objectives for an asynchronous data distribution service, key architectural concepts, the relationship between SNADS and SNA synchronous communication architecture, and the interface between the distribution service and application transaction programs.
Staphylococcus aureus Endocarditis (2005)

S aureus is the leading cause of IE in many regions of the world. Characteristics of patients with S aureus IE vary significantly by region. Further studies are required to determine the causes of regional variation.
Learning to Diagnose with LSTM Recurrent Neural Networks (2015)

Clinical medical data, especially in the intensive care unit (ICU), consist of multivariate time series of observations. For each patient visit (or episode), sensor data and lab test results are recorded in the patient's Electronic Health Record (EHR). While potentially containing a wealth of insights, the data is difficult to mine effectively, owing to varying length, irregular sampling and missing data. Recurrent Neural Networks (RNNs), particularly those using Long Short-Term Memory (LSTM) hidden units, are powerful and increasingly popular models for learning from sequence data. They effectively model varying length sequences and capture long range dependencies. We present the first study to empirically evaluate the ability of LSTMs to recognize patterns in multivariate time series of clinical measurements. Specifically, we consider multilabel classification of diagnoses, training a model to classify 128 diagnoses given 13 frequently but irregularly sampled clinical measurements. First, we establish the effectiveness of a simple LSTM network for modeling clinical data. Then we demonstrate a straightforward and effective training strategy in which we replicate targets at each sequence step. Trained only on raw time series, our models outperform several strong baselines, including a multilayer perceptron trained on hand-engineered features.
A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning (2008)

Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome.
Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection (2010)

Any system, natural or human-made, is better understood if we analyze both its history and its structure. Here we combine structural analyses with a "Reconstructed Evolutionary Adaptive Path" (REAP) analysis that used the evolutionary and functional history of DNA polymerases to replace amino acids to enable polymerases to accept a new class of triphosphate substrates, those having their 3'-OH ends blocked as a 3(')-ONH(2) group (dNTP-ONH(2)). Analogous to widely used 2',3'-dideoxynucleoside triphosphates (ddNTPs), dNTP-ONH(2)s terminate primer extension. Unlike ddNTPs, however, primer extension can be resumed by cleaving an O-N bond to restore an -OH group to the 3'-end of the primer. REAP combined with crystallographic analyses identified 35 sites where replacements might improve the ability of Taq to accept dNTP-ONH(2)s. A library of 93 Taq variants, each having replacements at three or four of these sites, held eight variants having improved ability to accept dNTP-ONH(2) substrates. Two of these (A597T, L616A, F667Y, E745H, and E520G, K540I, L616A) performed notably well. The second variant incorporated both dNTP-ONH(2)sand ddNTPs faithfully and efficiently, supporting extension-cleavage-extension cycles applicable in parallel sequencing and in SNP detection through competition between reversible and irreversible terminators. Dissecting these results showed that one replacement (L616A), not previously identified, allows Taq to incorporate both reversible and irreversible terminators. Modeling showed how L616A might open space behind Phe-667, allowing it to move to accommodate the larger 3'-substituent. This work provides polymerases for DNA analyses and shows how evolutionary analyses help explore relationships between structure and function in proteins.
Translocation of double-strand DNA through a silicon oxide nanopore (2005)

We report double-strand DNA translocation experiments using silicon oxide nanopores with a diameter of about 10 nm . By monitoring the conductance of a voltage-biased pore, we detect molecules with a length ranging from 6557 to 48 500 base pairs. We find that the molecules can pass the pore both in a straight linear fashion and in a folded state. Experiments on circular DNA further support this picture. We sort the molecular events according to their folding state and estimate the folding position. As a proof-of-principle experiment, we show that a nanopore can be used to distinguish the lengths of DNA fragments present in a mixture. These experiments pave the way for quantitative analytical techniques with solid-state nanopores.
Science Translational Medicine Podcast: 27 April 2016 (2016)

Peptide-coated beads could be used for contraception or to select the sperm best suited for use in assisted reproduction.
Mucoadhesion of Polymer-coated Liposomes to Rat Intestine in vitro. (1994)

Multilamellar liposomes consisting of dipalmitoyl phosphatidylcholine (DPPC) and dicetyl phosphate (DCP) in a molar ratio of 8:2 (DPPC:DCP = 8:2) were coated with three different types of polymers: chitosan, polyvinyl alcohol having a long alkyl chain, and poly(acrylic acid) bearing cholesterols. The existence of polymer layers on the liposome surface was confirmed by measuring the zeta potential of the liposomal particles. The mucoadhesive function of the polymer-coated liposomes was evaluated in vitro using rat intestine. A particle counting method using the Coulter counter was adopted to evaluate the adhesive % of liposomes. Chitosan coated liposomes showed the highest adhesive % among the polymer-coated liposomes tested. No adhesive % was observed for the non-coated liposomes. The adhesion of chitosan-coated liposomes to the intestine wall was confirmed by fluorescence microscopy using pyrene loaded liposomes.
Alteration of the lipid profile in lymphomas induced by MYC overexpression (2014)

Overexpression of the v-myc avian myelocytomatosis viral oncogene homolog (MYC) oncogene is one of the most commonly implicated causes of human tumorigenesis. MYC is known to regulate many aspects of cellular biology including glucose and glutamine metabolism. Little is known about the relationship between MYC and the appearance and disappearance of specific lipid species. We use desorption electrospray ionization mass spectrometry imaging (DESI-MSI), statistical analysis, and conditional transgenic animal models and cell samples to investigate changes in lipid profiles in MYC-induced lymphoma. We have detected a lipid signature distinct from that observed in normal tissue and in rat sarcoma-induced lymphoma cells. We found 104 distinct molecular ions that have an altered abundance in MYC lymphoma compared with normal control tissue by statistical analysis with a false discovery rate of less than 5%. Of these, 86 molecular ions were specifically identified as complex phospholipids. To evaluate whether the lipid signature could also be observed in human tissue, we examined 15 human lymphoma samples with varying expression levels of MYC oncoprotein. Distinct lipid profiles in lymphomas with high and low MYC expression were observed, including many of the lipid species identified as significant for MYC-induced animal lymphoma tissue. Our results suggest a relationship between the appearance of specific lipid species and the overexpression of MYC in lymphomas.
The Drawing Assistant: Automated Drawing Guidance and Feedback from Photographs (2013)

International audience
TA-CD. Xenova. (2002)

TA-CD (formerly IPC-1010), a cocaine conjugate that stimulates the production of antibodies against cocaine, is under development by Xenova (formerly Cantab) for the potential treatment of cocaine dependence [176912], [414867], [449997]. The vaccine was originally discovered at Stanford University and exclusively licensed to ImmuLogic Pharmaceuticals as IPC-1010 [176908]. It was renamed TA-CD when ownership was transferred to Cantab [463510], [463511]. By April 2002, a second phase IIa dose escalation trial was underway [445298], which was ongoing in September 2002 [463866].
Fabrication of Cobalt and Cobalt Oxide/Graphene Composites: Towards High‐Performance Anode Materials for Lithium Ion Batteries (2009)

Pave a way to high-performance anode materials: Organic metal/graphene composites are fabricated through an in situ assembly of disc-shaped phthalocyanine molecules with graphene sheets during the chemical reduction of graphite oxide, which enables a homogenous dispersion of Co and Co3O4 nanoparticles in the sheets after simple pyrolysis and oxidation. The resulting Co3O4/graphene composites exhibit remarkable lithium storage performance. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Enhancing therapeutic glycoprotein production in Chinese hamster ovary cells by metabolic engineering endogenous gene control with antisense DNA and gene targeting (1999)

Recombinant glycoprotein therapeutics have proven to be invaluable pharmaceuticals for the treatment of chronic and life-threatening diseases. Although these molecules are extraordinarily efficacious, many diseases have high dosage requirements of several hundred milligrams of protein for each administration. Multiple doses at this level are often required for treatment. One of the major challenges currently facing the biotechnology industry is the development of large-scale, cost-effective production and manufacturing processes of these biologically synthesized molecules. Metabolic engineering of animal cell expression hosts promises to address this challenge by substantially enhancing recombinant protein quality, productivity, and biological activity. In this report, we describe a novel approach to metabolic engineering in Chinese hamster ovary cells by control of endogenous gene expression. Analysis of the advantages and limitations of using antisense DNA and gene targeting as a means of control are discussed and several gene candidates for regulation with these techniques are identified. Practical considerations for using these technologies to reduce the levels of the CHO cell sialidase (Warner et al., Glycobiology, 3, 455-463, 1993) as a model gene system for regulation are also presented.
Multisite management study of menorrhagia with abnormal laboratory haemostasis: a prospective crossover study of intranasal desmopressin and oral tranexamic acid (2009)

The optimal management of menorrhagia among women with abnormal laboratory haemostasis is uncertain. In a crossover study, 116 women with menorrhagia [pictorial blood assessment chart (PBAC) score >100], negative gynaecological evaluation and abnormal laboratory haemostasis were randomly assigned to either intranasal desmopressin (IN-DDAVP) or tranexamic acid (TA) therapy for two menstrual cycles. The subjects then crossed over to the second study drug for two additional cycles. Menstrual blood loss (MBL) was measured by PBAC scores at baseline and after each menstrual cycle. Quality of life (QOL) was assessed with four validated instruments. There was a statistically significant decrease in PBAC scores for both treatments. On average, the estimated decrease in the PBAC from baseline was -64.1 [95% confidence interval (CI) = -88.0, -40.3] for IN-DDAVP and -105.7 (95% CI = -130.5, -81.0) for TA. The decrease in PBAC score was greater for TA than IN-DDAVP (a difference of 41.6, P-value = 0.0002, 95% CI = 19.6, 63.6). The test for treatment-type effect was significant (P < 0.0001) suggesting a greater reduction in PBAC score with TA. Use of both IN-DDAVP and TA improved QOL by all four instruments. We conclude that both medications reduced MBL and improved QOL among females with menorrhagia and abnormal laboratory haemostasis, but TA proved more effective.
Characteristics of phosphate solubilization by an isolate of a tropical Penicillium rugulosum and two UV-induced mutants (1999)

After screening several fungal isolates obtained from Venezuelan soils, the isolate IR-94MF1 of Penicillium rugulosum was selected for its high mineral phosphate solubilizing activity (Mps+) with hydroxyapatite. Mutants with altered (Mps−) or amplified activity (Mps++) were obtained by UV irradiation of conidia. When glucose was used as the sole C source by the fungus, gluconic acid was associated with the hydroxyapatite activity. In solid media, in comparison to glucose and maltose, sucrose appeared to be the best C source for the solubilization of hydroxy-apatite and FePO4.
Clinical inertia in patients with T2DM requiring insulin in family practice. (2010)

Even in patients identified as being sufficiently high risk to warrant insulin therapy, a clinical care gap exists in physician efforts to achieve and sustain recommended HbA₁(c) target levels. Family physicians need strategies to facilitate earlier initiation and ongoing intensification of insulin therapy.
Oxygen effects on thermophilic microbial populations in biofilters treating nitric oxide containing off‐gas streams (2001)

Abstract Electricity generation from coal has increased by an average of 51 billion kWh per year over the past 3 years. For this reason cost‐effective strategies to control nitrogen oxides (NO x ) from coal‐fired power plant combustion gases must be developed. Compost biofilters operated at 55°C at an empty bed contact time (EBCT) of 13 seconds were shown to be feasible for removal of nitric oxide (NO) from synthetic flue gas. Denitrifying microbial populations in these biofilters were shown to reduce influent NO feeds by 90 to 95% at inlet NO concentrations of 500 ppmv. Oxygen was shown to have a significant effect on the NO removal efficiency demonstrated by these biofilters. Two biofilters were set up under identical conditions for the purpose of monitoring NO removal as well as changes in the microbial population in the bed medium under anaerobic and aerobic conditions. Changes in the microbial population were monitored to determine the maximum oxygen tolerance of a denitrifying biofilter as well as methods of optimizing microbial populations capable of denitrification in the presence of low oxygen concentrations. Nitric oxide removal dropped to between 10 and 20% when oxygen was present in the influent stream. The inactive compost used to pack the biofilters may have also caused the decreased NO removal efficiency compared to previous biofiltration experiments. Analysis of the bed medium microbial population using environmental scanning electron microscopy indicated significant increases in biomass populating the surface of the compost when compared to unacclimated compost.
Adaptive MIMO Transmission Scheme: Exploiting the Spatial Selectivity of Wireless Channels (2005)

We present a novel adaptive transmission technique for MIMO systems with the aim to enhancing the spectral efficiency for a target error rate performance and transmit power. This adaptive method employs the condition number of the spatial correlation matrix as an indicator of the spatial selectivity of the MIMO channel. The distribution of the condition number is then used to identify the prevailing channel environment. Depending on the identified channel state, our adaptive algorithm chooses the MIMO transmission method, among spatial multiplexing, D-STTD, and beamforming, which maximizes the spectral efficiency. Performance results show significant gains in throughput and reduced error rate compared to conventional fixed transmission schemes.
Negative Regulation of Immunoglobulin E–dependent Allergic Responses by Lyn Kinase (2004)

A role for Lyn kinase as a positive regulator of immunoglobulin (Ig)E-dependent allergy has long been accepted. Contrary to this belief, Lyn kinase was found to have an important role as a negative regulator of the allergic response. This became apparent from the hyperresponsive degranulation of lyn-/- bone marrow-derived mast cells, which is driven by hyperactivation of Fyn kinase that occurs, in part, through the loss of negative regulation by COOH-terminal Src kinase (Csk) and the adaptor, Csk-binding protein. This phenotype is recapitulated in vivo as young lyn-/- mice showed an enhanced anaphylactic response. In vivo studies also demonstrated that as lyn-/- mice aged, their serum IgE increased as well as occupancy of the high affinity IgE receptor (FcepsilonRI). This was mirrored by increased circulating histamine, increased mast cell numbers, increased cell surface expression of the high affinity IgE receptor (FcepsilonRI), and eosinophilia. The increased IgE production was not a consequence of increased Fyn kinase activity in lyn-/- mice because both lyn-/- and lyn-/- fyn-/- mice showed high IgE levels. Thus, lyn-/- mice and mast cells thereof show multiple allergy-associated traits, causing reconsideration of the possible efficacy in therapeutic targeting of Lyn in allergic disease.