gebhart/patrepeval huggingface dataset:
Incorporation and washout of orally administeredn-3 fatty acid ethyl esters in different plasma lipid fractions (1999)

The aim of the present study was to quantify the incorporation of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) into plasma lipids after oral administration of n-3 fatty acid ethyl esters, since little is known about the rate and pattern of incorporation into plasma lipid fractions. In addition, we aimed to obtain preliminary information regarding EPA half-life, which is needed to establish an optimal dosing schedule. Five healthy volunteers ingested two 8.5 g doses of n-3 fatty acid ethyl esters daily for 7 d, supplying 6.0 g EPA/d and 5.3 g DHA/d. The fatty acid compositions of plasma phospholipids (PL), cholesteryl esters (CE) and triacylglycerols (TAG) were determined during supplementation and during a washout period of 7 d. Half-lives of EPA and DHA were calculated. The proportion of EPA in PL showed a 15-fold increase after 7 d (P < 0.001), while DHA showed a smaller increase (P < 0.01). In CE, EPA also increased (P < 0.05), while DHA did not increase at all. Remarkably, incorporation of DHA into TAG was even higher than that of EPA. Half-life of EPA in PL ranged from 1.63 to 2.31 d (mean 1.97 (SE 0.15) d), whereas mean half-life of EPA in CE was 3.27 (SE 0.56) d. In three subjects, washout of EPA and DHA from TAG seemed to follow a bi-exponential pattern, with a short half-life (< 1 d) in the initial phase and a half-life of several days in the second phase. In conclusion, EPA ethyl esters are rapidly incorporated into plasma lipids, especially into PL. The relatively long half-life of EPA in plasma would permit a dosing schedule with intervals of > or = 12 h in supplementation studies.
Type 2 Diabetes Comorbidities and Treatment Challenges: Rationale for DPP-4 Inhibitors (2010)

The management of type 2 diabetes is designed to reduce disease-related complications and improve long-term outcomes. Achieving glycemic control is a critical component of this process. The selection of drug therapy for reducing blood glucose is made more challenging when patients already have complications or comorbid conditions (eg, high risk for hypoglycemia, obesity, renal impairment). Dipeptidyl peptidase-4 (DPP-4) inhibitors are a new class of antihyperglycemic drugs that block degradation of incretin hormones. By enhancing and prolonging incretin effects, DPP-4 inhibitors stimulate glucose-dependent insulin secretion and also reduce glucagon secretion. This results in improved glycemic control, as reflected by decreases in glycated hemoglobin (HbA1c), fasting plasma glucose, and postprandial plasma glucose. Dipeptidyl peptidase-4 inhibitors also have the potential to improve beta-cell function. In randomized clinical trials, the DPP-4 inhibitors saxagliptin and sitagliptin reduced HbA1c by 0.5% to 0.8%, compared with placebo, whether used as monotherapy or in combination with another agent. As initial combination therapy with metformin, saxagliptin and sitagliptin have demonstrated reductions in HbA1c of 2.5% and 1.9%, respectively. The efficacy of the DPP-4 inhibitors was maintained during treatment for up to 2 years, and did not differ in the elderly compared with younger adults. Dipeptidyl peptidase-4 inhibitors offer efficacy similar to other drug classes, and are well tolerated with a lower risk of hypoglycemia, weight-neutral effects, and a low propensity for drug-drug interactions. On the basis of their clinical profiles, the DPP-4 inhibitors are emerging as an attractive option for improving glycemic control in patients with type 2 diabetes. Saxagliptin and sitagliptin are approved for use as initial therapy in combination with metformin, as monotherapy, as well as in combination with metformin, a sulfonylurea, or a thiazolidinedione in patients not adequately controlled by these agents alone.
Analysis of fast kV-switching in dual energy CT using a pre-reconstruction decomposition technique (2008)

Fast kV-switching is a dual energy acquisition technique in CT in which alternating views correspond to the low and high tube voltages. Its high temporal resolution and its suitability to a variety of source trajectories make it an attractive option for dual energy data acquisition. Its disadvantages include a one view mis-registration between the data for high and low voltages, the potential for poor spectrum separation because the fast kV-switching waveform may be more like a sine wave than the desired square wave, and the higher noise in the low voltage data because of the technical difficulty of swinging the tube current to counter the loss of x-ray production efficiency and loss of penetration at lower tube voltages. These issues are investigated with a recently developed pre-reconstruction decomposition method by the authors. Results include that symmetric view matching eliminates streaks from the view mis-registration, a sinusoidal waveform swinging between 80 and 135 kV gives sufficient spectrum separation, and that contrast-to-noise for the simulated imaging task maximizes at monochromatic energy of 75 keV.
Specifities of Rabbit Antisera to Multiple Antigen (MAP) Peptides (1995)

Two multiple antigen peptides consisting of 6 and 7 aminoa cid residues, respectively, plus a 12-residue fragment, used as a control, all linked to a polylysine core, were used as immunogens in rabbits in order to obtain an immune response. Rabbit antisera against such polymers were then tested in ELISA against a panel of antigens in order to analyze the specificities of the resulting antibodies. The responses were different for all three immunogens, being partially or totally directed, for two of the three compounds, including the 12-residue control MAP peptide, against the polylysyl core, which is considered as non immunogenic. The third MAP polymer was practically unable to elicit an immune response.
Drug screening in a zebrafish model of Duchenne muscular dystrophy (2011)

Two known zebrafish dystrophin mutants, sapje and sapje-like (sap(c/100)), represent excellent small-animal models of human muscular dystrophy. Using these dystrophin-null zebrafish, we have screened the Prestwick chemical library for small molecules that modulate the muscle phenotype in these fish. With a quick and easy birefringence assay, we have identified seven small molecules that influence muscle pathology in dystrophin-null zebrafish without restoration of dystrophin expression. Three of seven candidate chemicals restored normal birefringence and increased survival of dystrophin-null fish. One chemical, aminophylline, which is known to be a nonselective phosphodiesterase (PDE) inhibitor, had the greatest ability to restore normal muscle structure and up-regulate the cAMP-dependent PKA pathway in treated dystrophin-deficient fish. Moreover, other PDE inhibitors also reduced the percentage of affected sapje fish. The identification of compounds, especially PDE inhibitors, that moderate the muscle phenotype in these dystrophin-null zebrafish validates the screening protocol described here and may lead to candidate molecules to be used as therapeutic interventions in human muscular dystrophy.
Deep Learning in Bioinformatics (2016)

In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e., omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e., deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies.
Heterogenized “Ligand-Free” Lanthanide Catalysts for the Homo- and Copolymerization of Ethylene and 1,3-Butadiene (2005)

Silica-supported lanthanide catalysts have been prepared from the reaction of dehydroxylated silica and tris(bistrimethylsilyl)amido lanthanides Ln[N(SiMe3)2]3 (Ln = Sc, Y, La, Nd, Sm, Gd, Dy). On activation with AliBu3 (TIBA), the compounds catalyze the polymerization of ethylene, with the scandium catalyst showing the highest activity. There is an inverse relationship between ionic radius of the lanthanide metal and the activity of the resulting catalyst. The polymer produced was highly linear and of high molecular weight. Activation with magnesium alkyls was less effective but gave polyethylene of slightly higher molecular weight. The supported lanthanides, when activated with TIBA, were also active for the polymerization of 1,3-butadiene, with very high molecular weight polymers being produced. In all cases the polymer was found to be predominately 1,4-cis (typically 85−90% by diad analysis), with only scandium producing a much higher level of 1,4-trans units. The system was also shown to copolymerize ethylene and butadiene, with large differences in the polymeric products depending on the both the choice of the lanthanide and the feed ratio of the monomer. With both neodymium and dysprosium multiblock polymers consisting of 1,4-cis, 1,4-trans, and ethylene blocks were obtained. With scandium two distinct modes of polymerization were detected, with both multiblock 1,4-cis and a somewhat alternating ethylene/1,4-trans block structure observed in the 13C NMR spectra.
Isolation and Identification of β-Lysine as an Intermediate in Lysine Fermentation (1966)

Abstract Clostridium SB4 ferments lysine to acetate, butyrate, and 2 moles of ammonia. The fermenting system appears to be typical of those studied previously (1–7), except that α-ketoglutarate is required for fermentation by cell extracts rather than pyruvate. The omission of all required cofactors except α-ketoglutarate and coenzyme A results in the accumulation of a basic amino acid. The amino acid has been isolated in gram quantities and shown to be l-β,e-diaminocaproic acid (l-β-lysine). The conversion of l-lysine to l-β-lysine is readily reversible; the equilibrium constant (k = [β-lysine]/ [lysine]) is 5.7. The level of α-ketoglutarate influences both the rate and extent of conversion of lysine to β-lysine, but the system does not require substrate levels of α-ketoglutarate. Pyridoxal phosphate can be substituted for α-ketoglutarate when crude cell extracts are used, and α-ketoglutarate can be deleted from reaction mixtures without loss of activity when dialyzed extracts are used. A sulfhydryl compound, i.e. glutathione or mercaptoethanol, and coenzyme A are required for maximal rates of conversion of lysine to β-lysine when dialyzed cell extracts are used. Pyridoxal phosphate has a stimulating effect with such extracts. β-Lysine is fermented more rapidly than lysine by Clostridium SB4 extracts, and the addition of lysine does not inhibit β-lysine fermentation. Apparently β-lysine lies on or very close to the path of lysine fermentation.
Capsid Protein Synthesis from Replicating RNA Directs Specific Packaging of the Genome of a Multipartite, Positive-Strand RNA Virus (2005)

Flock house virus (FHV) is a bipartite, positive-strand RNA insect virus that encapsidates its two genomic RNAs in a single virion. It provides a convenient model system for studying the principles underlying the copackaging of multipartite viral RNA genomes. In this study, we used a baculovirus expression system to determine if the uncoupling of viral protein synthesis from RNA replication affected the packaging of FHV RNAs. We found that neither RNA1 (which encodes the viral replicase) nor RNA2 (which encodes the capsid protein) were packaged efficiently when capsid protein was supplied in trans from nonreplicating RNA. However, capsid protein synthesized in cis from replicating RNA2 packaged RNA2 efficiently in the presence and absence of RNA1. These results demonstrated that capsid protein translation from replicating RNA2 is required for specific packaging of the FHV genome. This type of coupling between genome replication and translation and RNA packaging has not been observed previously. We hypothesize that RNA2 replication and translation must be spatially coordinated in FHV-infected cells to facilitate retrieval of the viral RNAs for encapsidation by newly synthesized capsid protein. Spatial coordination of RNA and capsid protein synthesis may be key to specific genome packaging and assembly in other RNA viruses.
Modeling of a compliant joint in a Magnetic Levitation System for an endoscopic camera (2012)

Abstract. A novel compliant Magnetic Levitation System (MLS) for a wired miniature surgical camera robot was designed, modeled and fabricated. The robot is composed of two main parts, head and tail, linked by a compliant beam. The tail module embeds two magnets for anchoring and manual rough translation. The head module incorporates two motorized donut-shaped magnets and a miniaturized vision system at the tip. The compliant MLS can exploit the static external magnetic field to induce a smooth bending of the robotic head (0–80°), guaranteeing a wide span tilt motion of the point of view. A nonlinear mathematical model for compliant beam was developed and solved analytically in order to describe and predict the trajectory behaviour of the system for different structural parameters. The entire device is 95 mm long and 12.7 mm in diameter. Use of such a robot in single port or standard multiport laparoscopy could enable a reduction of the number or size of ancillary trocars, or increase the number of working devices that can be deployed, thus paving the way for multiple view point laparoscopy.
An Application of Holography to Interference Microscopy (1968)

An experimental two-beam interference microscope has been constructed which uses a hologram to generate one of the beams. This eliminates the need for selecting matched optics as required in conventional systems. Using the techniques described in this paper, one can modify a conventional bright field microscope to produce horizontal and oblique section interferograms in real or recorded time, or differential and totally doubled interferograms in real or recorded time. The optical configuration of the microscope is explained, and experimental results are given for the transmitted light case.
Domains involved in osmoregulation of the ompF gene in Escherichia coli (1985)

Expression of the ompF gene, which is under the control of the OmpR protein, is regulated by the osmolarity of the medium. To study the mechanism of osmoregulation, plasmids carrying two different types of chimeric genes were constructed. In one type, the coding region of the ompF gene was linked to the trp promoter (trpPO) preceding ompF, and in the other type the ompF upstream region, mostly composed of the region for regulation by OmpR and the promoter region, was linked to the lacZ gene by protein fusion. Expression of beta-galactosidase by the lacZ chimeric gene was OmpR dependent and osmoregulated as sensitively as that of the intact ompF gene. In the ompR20 background the direction of osmoregulation was opposite that of normal osmoregulation, as was the direction of osmoregulation of the intact ompF gene. Osmoregulation was also observed with trpPO-ompF chimeric genes. However, the regulation was not as sensitive to the osmolarity of the medium as was regulation of the intact ompF gene and was independent of OmpR. These results suggest that OmpR-dependent osmoregulation played a primary role in the osmoregulation of ompF expression and that ompR-independent osmoregulation most likely did not play a crucial role. Studies with a series of trpPO-ompF chimeric genes also suggest that the untranslated leader region, about 100 base pairs in length, between the transcription initiation site and the initiation codon was not required for osmoregulation.
Spread of a Novel Influenza A (H1N1) Virus via Global Airline Transportation (2009)

International air travelers departing from Mexico in March and April 2009 were unknowingly transporting a novel influenza A (H1N1) virus around the world. The purpose of this analysis was to show h...
Identification of the membrane glycoprotein that is the C3b receptor of the human erythrocyte, polymorphonuclear leukocyte, B lymphocyte, and monocyte (1980)

A human erythrocyte membrane glycoprotein of 205,000 mol wt (gp205) has been identified as the C3b receptor of the erythrocyte, polymorphonuclear leukocyte (PMN), B lymphocyte, and monocyte. Initially, gp205 was sought and characterized as a constituent of the human erythrocyte membrane that can impair activation of the alternative complement pathway by inducing loss of function of the properdin-stabilized amplification C3 convertase (C3b,Bb,P) through displacement of Bb from C3b and by promoting cleavage-inactivation of C3b by C3b inactivator. These inhibitory activities of gp205 suggested that this membrane glyeoprotein had an affinity for C3b and prompted an analysis of its possible identity as the C3b receptor of human peripheral blood cells. The F(ab')2 fragment of rabbit IgG anti-gp205 inhibited the formation of rosettes with sheep EC3b of human erythroeytes, B lymphocytes, monocytes and PMN in a dose-response manner; the 50 percent inhibitory doses were 0.13/mug/ml, 0.90 mug/ml, 1.25 mug/ml, and 1.20 mug/ml of F(ab')2, respectively. Anti-gp205 did not impair the formation of rosettes by monocytes and B lymphocytes with sheep EC3bi or with EC3d. Scatchard analysis of the number of specific (125)I-F(ab')(2) anti-gp205 binding sites/cell revealed 950 sites/erythrocyte, 21,000 sites/cell of B lymphocyte preparation, 57,000 sites/PMN, and 48,000 sites/monocyte, indicating that the higher concentrations of antibody that had been required for inhibition of rosette formation by the nucleated cells reflected larger numbers of receptors on these cells. Direct evidence for the identity of gp205 as the C3b receptor of the four cell types was obtained when detergent-solubilized membrane proteins of the surface-radioiodinated cells were reacted with anti- gp205 and the immunoprecipitate was analyzed by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. In each instance, the antigenic material reacting with anti-gp205 represented a single protein with an apparent 205,000 mol wt. Thus, gp205 is the C3b receptor of human erythrocytes, PMN, B lymphocytes, and monocytes.
The Pseudomonas aeruginosa phaG gene product is involved in the synthesis of polyhydroxyalkanoic acid consisting of medium-chain-length constituents from non-related carbon sources (2000)

We recently identified the phaG Pp gene encoding (R)-3-hydroxydecanoyl-ACP :CoA transacylase in Pseudomonas putida, which directly links the fatty acid de novo biosynthesis and polyhydroxyalkanoate (PHA) biosynthesis.An open reading frame (ORF) of which the deduced amino acid sequence shared about 57% identity with PhaG from P. putida was identified in the P. aeruginosa genome sequence.Its coding region (herein called phaG Pa ) was amplified by PCR and cloned into the vector pBBR1MCS-2 under lac promoter control.The resulting plasmid pBHR88 mediated PHA synthesis contributing to about 13% of cellular dry weight from non-related carbon sources in the phaG Pp -negative mutant P. putida PhaG N -21.The PHA was composed of 5 mol% 3-hydroxydodecanoate, 61 mol% 3-hydroxydecanoate, 29 mol% 3-hydroxyoctanoate and 5 mol% 3-hydroxyhexanoate.Furthermore, an isogenic phaG Pa knock-out mutant of P. aeruginosa was constructed by gene replacement.The phaG Pa mutant did not show any difference in growth rate, but PHA accumulation from gluconate was decreased to about 40% of wild-type level, whereas from fatty acids wild-type level PHA accumulation was obtained.These data suggested that PhaG from P. aeruginosa exhibits 3-hydroxyacyl-ACP:CoA transacylase activity and strongly enhances the metabolic flux from fatty acid de novo synthesis towards PHA MCL synthesis.Therefore, a function could be assigned to the ORF present in the P. aeruginosa genome, and a second PhaG is now known.
Virtual Router Redundancy Protocol (VRRP) Version 3 for IPv4 and IPv6 (2010)

This memo defines the Virtual Router Redundancy Protocol (VRRP) for
IPv4 and IPv6. It is version three (3) of the protocol and it is based
on VRRP (version 2) for IPv4 that is defined in RFC 3768 and on draft-
ieft-vrrp-ipv6-spec-08.txt. VRRP specifies an election protocol that
dynamically assigns responsibility for a virtual router to one of the
VRRP routers on a LAN. The VRRP router controlling the IPv4 or IPv6
address(es) associated with a virtual router is called the Master, and
forwards packets sent to these IPv4 or IPv6 addresses. VRRP Master
routers are configured with virtual IPv4 or IPv6 addresses and VRRP
Backup routers infer the address family of the virtual addresses being
carried based on the transport protocol. Within a VRRP router the
virtual routers in each of the IPv4 and IPv6 address families are a
domain unto themselves and do not overlap. The election process
provides dynamic fail over in the forwarding responsibility should the
Master become unavailable. For IPv4, the advantage gained from using
VRRP is a higher availability default path without requiring
configuration of dynamic routing or router discovery protocols on
every end-host. For IPv6, the advantage gained from using VRRP for
IPv6 is a quicker switch over to back up routers than can be obtained
with standard IPv6 Neighbor Discover (RFC 4861) mechanisms.
Thalassospiramides A and B, Immunosuppressive Peptides from the Marine BacteriumThalassospirasp. (2007)

[structure: see text] Two new cyclic peptides, thalassospiramides A and B (1 and 2), were isolated from a new member of the marine alpha-proteobacterium Thalassospira. The thalassospiramides, the structures of which were assigned by combined spectral and chemical methods, bear unusual gamma-amino acids and show immunosuppressive activity in an interleukin-5 production inhibition assay (IC50 = 5 muM for thalassospiramide B).
Real-time 3D Reconstruction and Semantic Segmentation using Multi-layer Heightmaps (2015)

The problem of identifying objects in images is an open problem in computer vision.Most current methods do not operate in real time, or directly on a 3D representation of a scene.In this thesis, we investigate various ways of using heightmaps to possibly improve on current methods of semantic segmentation, with the aim of implementing it on a Project Tango device, a tablet computer with built-in 3D depth acquisition support, for real-time usage.We focus on the four-class labelling problem defined in the NYUv2 dataset.
The pregnancy hormone relaxin is a player in human heart failure (2001)

Human congestive heart failure is characterized by complex neurohumoral activation associated with the up-regulation of vasoconstricting and salt-retaining mediators and the compensatory rise of counter-regulatory hormones. In the present study, we provide the first evidence that relaxin (RLX), known as a pregnancy hormone, represents a potential compensatory mediator in human heart failure: plasma concentrations of RLX and myocardial expression of the two RLX genes (H1 and H2) correlate with the severity of disease and RLX responds to therapy. The failing human heart is a relevant source of circulating RLX peptides, and myocytes as well as interstitial cells produce RLX. Elevation of ventricular filling pressure up-regulates RLX expression and the hormone acts as a potent inhibitor of endothelin 1, the most powerful vasoconstrictor in heart failure. Furthermore, RLX modulates effects of angiotensin II, another crucial mediator. Our data identify RLX as a new player in human heart failure with potential diagnostic and therapeutic relevance.