gebhart/patrepeval huggingface dataset:
Regulation of muscle malonyl‐CoA levels in the nutritionally insulin‐resistant desert gerbil, Psammomys obesus† (2002)

Since non-diabetic Psammomys on a LE diet already show insulin resistance in the fed state, the sustained low malonyl-CoA levels in these animals imply a readiness for the oxidation of fatty acids. In a desert gerbil, adjusted to a food-scarce environment, such a continuing utilization of fatty acids as energy substrate by muscle would preserve the available glucose for glucose-dependent tissues and would diminish the need for gluconeogenesis.
Elucidation of the Metabolic Fate of Glucose in the Filamentous Fungus Trichoderma reesei Using Expressed Sequence Tag (EST) Analysis and cDNA Microarrays (2002)

Despite the intense interest in the metabolic regulation and evolution of the ATP-producing pathways, the long standing question of why most multicellular microorganisms metabolize glucose by respiration rather than fermentation remains unanswered. One such microorganism is the cellulolytic fungus Trichoderma reesei (Hypocrea jecorina). Using EST analysis and cDNA microarrays, we find that in T. reesei expression of the genes encoding the enzymes of the tricarboxylic acid cycle and the proteins of the electron transport chain is programmed in a way that favors the oxidation of pyruvate via the tricarboxylic acid cycle rather than its reduction to ethanol by fermentation. Moreover, the results indicate that acetaldehyde may be channeled into acetate rather than ethanol, thus preventing the regeneration of NAD(+), a pivotal product required for anaerobic metabolism. The studies also point out that the regulatory machinery controlled by glucose was most probably the target of evolutionary pressure that directed the flow of metabolites into respiratory metabolism rather than fermentation. This finding has significant implications for the development of metabolically engineered cellulolytic microorganisms for fuel production from cellulose biomass.
Localization of Protein A in the Bacteria (1972)

Staphylococcus aureus , strain Cowan I, contains 1.7% protein A and its isolated cell walls contain 6.7%. Removal of contaminating cytoplasmic membrane fragments from the cell walls does not decrease the content of protein A. Extraction of cell walls with trichloroacetic acid releases teichoic acid but not protein A. Extractions with high concentrations of LiCl do not remove protein A. Only bacteriolytic enzymes can release the protein. Protein A isolated from bacteria after lysozyme digestion contains peptidoglycan constituents. More effective bacteriolytic enzymes such as lysostaphin release peptidoglycan fragments from this protein A preparation. We conclude from these results that protein A is a cell wall component of S. aureus and is covalently linked to the peptidoglycan structure.
Implantable multichannel electrode array based on soi technology (2003)

This work presents a new method of fabricating implantable multielectrode arrays on lightly doped single-crystal silicon. Such arrays are essential tools for electrical stimulation and recording of nerve signals. Our new microfabrication process, based on silicon-on-insulator (SOI) technology, inherently has excellent control over the final probe thickness without wet etching. The needle shanks are 6 mm long and 80 μm wide. Here the thickness of the probe, 25 μm, is defined by the device layer thickness on the SOI wafer. Our new sprinkler fluidic channel, which has holes spaced 50 μm apart along its 6 mm length, permits the perfusion of a large area of tissue with any desired neurotransmitter or other drug. The probes fabricated here are tested in the cat primary visual cortex; data recorded from adjacent neurons was used to characterize their orientation tuning. The sprinkler channel was characterized, and flowrate through the channel is a linear function of the applied pressure.
Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation (2004)

MS-based proteomics usually involves the fragmentation of tryptic peptides (tandem MS or MS(2)) and their identification by searching protein sequence databases. In ion trap instruments fragments can be further fragmented and analyzed, a process termed MS/MS/MS or MS(3). Here, we report that efficient ion capture in a linear ion trap leads to MS(3) acquisition times and spectra quality similar to those for MS(2) experiments with conventional 3D ion traps. Fragmentation of N- or C-terminal ions resulted in informative and low-background spectra, even at subfemtomol levels of peptide. Typically C-terminal ions are chosen for further fragmentation, and the MS(3) spectrum greatly constrains the C-terminal amino acids of the peptide sequence. MS(3) spectra allow resolution of ambiguities in identification, a crucial problem in proteomics. Because of the sensitivity and rapid scan rates of the linear ion trap, several MS(3) spectra per peptide can be obtained even when sequencing very complex mixtures. We calculate the probability that an experimental MS(3) spectrum originates from fragmentation of a given N- or C-terminal ion of a peptide under consideration. This MS(3) identification score can be combined with the MS(2) scores of the precursor peptide from existing search engines. When MS(3) is performed on the linear ion trap-Fourier transform mass spectrometer combination, accurate peptide masses further increase confidence in peptide identification.
The female reproductive cycle is an important variable in the response to trauma-hemorrhage (2000)

Although immune functions in proestrus females are maintained after hemorrhage as opposed to decreased responses in males, it remains unknown whether such a sexual dimorphism also exists with regard to cardiovascular and hepatocellular functions under those conditions. To study this, male and female (estrus and proestrus) rats underwent a 5-cm midline laparotomy and were bled to and maintained at a mean blood pressure of 40 mmHg until 40% of the maximal bleed-out volume was returned in the form of Ringer lactate (RL). Rats were then resuscitated with four times the shed blood volume with RL. At 24 h thereafter, cardiac index; heart performance; hepatocellular function; and plasma estradiol, testosterone, and prolactin levels were measured. Cardiovascular and hepatocellular functions were depressed in males and estrus females (P < 0.05) but were not depressed in proestrus females after resuscitation. Plasma estradiol and prolactin levels were highest in proestrus females (P < 0.05), whereas males had high testosterone and the lowest estradiol levels (P < 0.05). Thus the female reproductive cycle is an important variable in the response to hemorrhage. Because low testosterone and high estradiol and prolactin levels appear to be beneficial for organ functions after trauma-hemorrhage, antagonism of testosterone receptors and/or increases in estradiol and prolactin levels in males and estrus females, respectively, may be novel approaches for improving organ functions under such conditions.
Small-Molecule Inhibitors of the TLR3/dsRNA Complex (2011)

The protein-RNA interface has been regarded as "undruggable" despite its importance in many biological processes. The toll-like receptor 3 (TLR3)/double-stranded RNA (dsRNA) complex provides an exciting target for a number of infectious diseases and cancers. We describe the development of a series of small-molecule probes that were shown to be competitive inhibitors of dsRNA binding to TLR3 with high affinity and specificity. In a multitude of assays, compound 4a was profiled as a potent antagonist to TLR3 signaling and also repressed the expression of downstream signaling pathways mediated by the TLR3/dsRNA complex, including TNF-α and IL-1β.
Cloning and structure-function analysis of the Leishmania donovani kinetoplastid membrane protein-11 (1995)

This report describes the complete translated gene sequence, predicted secondary structure and lipid bilayer association of a novel kinetoplastid membrane protein (KMP-11) from Leishmania donovani promastigotes. KMP-11 was previously referred to as the lipophosphoglycan-associated protein (LPGAP). The isolation, species distribution and chemical characterization, including a partial protein sequence analysis and post-translational modifications, of this major membrane component have been described [Jardim, Funk, Caprioli and Olafson (1995) Biochem. J. 305, 307-313]. C.d. measurements of KMP-11 indicated a very high helical content estimated to be approximately 86% in trifluoroethanol. This was in agreement with computer-based secondary-structure analyses which predicted KMP-11 to be almost exclusively alpha-helical, with the protein adopting a helix-loop-helix motif. Arrangement of the residues located in the putative helical regions on an Edmundson helical wheel showed that this molecule could have a strongly amphipathic conformation and provided an explanation for how such a highly charged protein might be inserted into the plasma membrane. Evidence in support of KMP-11 association with lipid bilayers was provided by showing that KMP-11 could mediate carboxyfluorescein release from liposomes. These findings suggested that KMP-11 may function in part to increase bilayer pressure, stabilizing molecules such as lipophosphoglycan within the parasite pellicular membrane.
Structured multimedia authoring (2005)

Authoring context sensitive, interactive multimedia presentations is much more complex than authoring either purely audiovisual applications or text. Interactions among media objects need to be described as a set of spatio-temporal relationships that account for synchronous and asynchronous interactions, as well as on-demand linking behavior. This article considers the issues that need to be addressed by an authoring environment. We begin with a partitioning of concerns based on seven classes of authoring problems. We then describe a selection of multimedia authoring environments within four different authoring paradigms: structured, timeline, graph and scripting. We next provide observations and insights into the authoring process and argue that the structured paradigm provides the most useful framework for presentation authoring. We close with an example application of the structured multimedia authoring paradigm in the context of our own structure-based system GRiNS.
Differences in Serum Phospholipid Fatty Acid Compositions and Estimated Desaturase Activities between Japanese Men with and without Metabolic Syndrome (2008)

Decreases in minor saturated fatty acids, accumulation of C20:3n-6 and C20:4n-3 and low estimated D5D activity were confirmed to be associated with MetS.
Synthesis and Some Properties of Sulfate Esters and Sulfamates of Iodothyronines* (1985)

In the present study, convenient methods have been developed for the synthesis of sulfate derivatives of iodothyronines. Reaction with chlorosulfonic acid in dimethylformamide gave rise to formation of the sulfate ester with the phenolic hydroxyl group. Reaction with the sulfurtrioxide-trimethylamine complex in alkaline medium afforded the sulfamate with the alpha-amino group of the alanine side chain. The sulfated products were isolated by adsorption onto Sephadex LH-20 in acidic medium, followed by desorption with water. Iodide was not retarded on these columns, whereas elution of native iodothyronines required alkaline ethanol mixtures. The yield of both reactions varied between 70-90%. The sulfates and sulfamates of T4, T3, rT3, and 3,3'-diiodothyronine could be separated by reverse phase HPLC. The sulfamates exhibited high cross-reactivities with antibodies against free iodothyronines, in contrast to the low activities of the sulfates. Products were further characterized by proton nuclear magnetic resonance, TLC, and hydrolysis by acid or sulfatase activity. The availability of large quantities of pure iodothyronine sulfates and sulfamates should facilitate the study of the importance of sulfate conjugation in the metabolism of thyroid hormone.
A Vascular Stent as an Active Component for Locally Enhanced Magnetic Resonance Imaging (2003)

The expandable active MRI stent produces local signal enhancement in MRA and MR flow measurements after catheter placement and thus may improve assessment of the stented vessel segment by MR imaging.
Growth rate of fractal copper electrodeposits: Potential and concentration effects (1991)

Experiments are reported on fractal copper electrodeposits. An electrochemical cell was designed in order to obtain a potentiostatic control on the quasi-two-dimensional electrodeposition process. The aim was focused on the analysis of the growth rate of the electrodeposited phase, in particular its dependence on the electrode potential and electrolyte concentration.
Adjunct quetiapine xr in patients with major depressive disorder: a pooled analysis of data from patients with anxious depression (2011)

Objective This pooled analysis evaluated efficacy of adjunct quetiapine XR (QTP-XR) in subgroups of patients with anxious depression and lower levels of anxiety. Methods Pooled data from two 6-week, double-blind, randomised, placebo-controlled trials (D1448C00006/D1448C00007) in patients with inadequate response to antidepressants were analysed. Patients received adjunct QTP-XR (150 or 300 mg/day) or placebo+antidepressant (SSRI or SNRI). Using criteria defined in the STAR*D study, analyses conducted in patients with anxious depression or lower baseline anxiety levels (HAM-D anxiety/somatic factor score &gt;/ = 7 and &lt; 7, respectively) included LSM change at Week 6 in: MADRS total (primary endpoint), HAM-A and CGI-S total scores. Results For patients with anxious depression (n = 697; 76% patients), adjunct QTP-XR 150mg/day (-14.44, p &lt; 0.01) and 300 mg/day (-15.09, p &lt; 0.001) significantly improved MADRS total scores versus placebo+antidepressant (-11.78) at Week 6, with significant improvement demonstrated from Week 1 onwards. Significant improvements were seen in HAM-A (QTP-XR 150 mg/day: -9.05, p &lt; 0.01; 300 mg/day -9.43, p &lt; 0.01) and CGI-S total scores (QTP-XR 150 mg/day: -1.60, p&lt; 0.001; 300 mg/day -1.63, p &lt; 0.001) versus placebo+antidepressant (-7.40, -1.22, respectively) at Week 6. A smaller subgroup (n = 222; 24% patients) had lower baseline anxiety levels. At Week 1, adjunct QTP-XR (150 mg/day -9.09; p &lt; 0.01; 300 mg/day -8.60; p &lt; 0.05) significantly improved MADRS total score versus placebo+antidepressant (-5.93). At Week 6 there were no significant changes (QTP-XR 150 mg/day -14.49; p = 0.243; 300 mg/day -14.01; p = 0.388) versus placebo+antidepressant (-12.78). Conclusions For patients with anxious depression, adjunct QTP-XR (150 and 300 mg/day) was effective at reducing symptoms of anxiety and depression, with symptom improvement observed from Week 1 onwards. AstraZeneca funded.
Serial Assessment of Human Tumor Burdens in Mice by the Analysis of Circulating DNA (2007)

Internal human xenografts provide valuable animal models to study the microenvironments and metastatic processes occurring in human cancers. However, the use of such models is hampered by the logistical difficulties of reproducibly and simply assessing tumor burden. We developed a high-sensitivity assay for quantifying human DNA in small volumes of mouse plasma, enabling in-life monitoring of systemic tumor burden. Growth kinetics analyses of various xenograft models showed the utility of circulating human DNA as a biomarker. We found that human DNA concentration reproducibly increased with disease progression and decreased after successful therapeutic intervention. A marked, transient spike in circulating human tumor DNA occurred immediately after cytotoxic therapy or surgery. This simple assay may find broad utility in target validation studies and preclinical drug development programs.
Ikaros regulates neutrophil differentiation (2003)

The Ikaros gene encodes a zinc finger transcription factor that is selectively expressed by all hematopoietic cells. Although Ikaros is required for lymphocyte differentiation, its role in the myeloid lineage is unclear. We show here that Ikaros expression is temporally regulated during neutrophil differentiation: Ikaros is primarily expressed at immature stages and significantly less so in mature neutrophils. Furthermore Ik(L/L) mice, harboring a hypomorphic mutation at the Ikaros locus, exhibit several defects during neutrophil differentiation. (1) Ik(L/L) fetal livers contain high numbers of neutrophil lineage cells, and this increase is reflected in the number of GM-CSF-dependent progenitor cells. (2) The migratory potential and survival of neutrophil progenitors is altered in vitro. (3) Expression of the Gr-1 marker is delayed and repressed. In contrast, neutrophil function appears normal. These data demonstrate that Ikaros regulates early neutrophil differentiation but is dispensable in mature neutrophils.
An embryogenic model to explain cytogenetic inconsistencies observed in chorionic villus versus fetal tissue (1988)

While the fetus and placenta have a common ancestry, chorionic villus tissue does not always reflect fetal genotype. Data are presented from 15 CVS subjects in whom cytogenetic inconsistencies were observed when comparing (1) cultured chorionic villi, (2) direct chromosome preparations of intact villi, and (3) cultured fetal tissue. Embryogenic models are presented to explain these discrepancies. Mosaicism confined to direct chromosome preparations was the most commonly observed inconsistency. This can be explained by postzygotic non-disjunction limited to cytotrophoblast. In all but one instance, the abnormal cell line was limited to the placenta, with the normal cell line reflecting fetal genotype. Analysis of direct chromosome preparations from multiple individually processed villus fragments may be helpful in recognizing mosaicism confined to the placenta. While both direct chromosome preparations and villus cultures can be misleading, the latter are more likely to reflect fetal genetic status since they are derived from the extraembryonic mesoderm.
S-Linked Ganglioside Analogues for Use in Conjugate Vaccines (2004)

[structure: see text] Glycosidase resistant thioglycoside precursors of the melanoma-associated ganglioside GM(2) have been synthesized starting from lactose. Syntheses of several analogues of ganglioside GM(3) and a positional isomer have been developed. These compounds contain thio-linked sialic acid residues and a modified ceramide aglycon functionalized for coupling to proteins, surfaces, or matrices. The hydrolytic stability of these oligosaccharides enhances the immunogenicity of the corresponding conjugate vaccines by ensuring their integrity in the acidic compartments of antigen processing cells.
Fault-tolerance in the Borealis distributed stream processing system (2005)

We present a replication-based approach to fault-tolerant distributed stream processing in the face of node failures, network failures, and network partitions. Our approach aims to reduce the degree of inconsistency in the system while guaranteeing that available inputs capable of being processed are processed within a specified time threshold. This threshold allows a user to trade availability for consistency: a larger time threshold decreases availability but limits inconsistency, while a smaller threshold increases availability but produces more inconsistent results based on partial data. In addition, when failures heal, our scheme corrects previously produced results, ensuring eventual consistency.Our scheme uses a data-serializing operator to ensure that all replicas process data in the same order, and thus remain consistent in the absence of failures. To regain consistency after a failure heals, we experimentally compare approaches based on checkpoint/redo and undo/redo techniques and illustrate the performance trade-offs between these schemes.
Enzymes as Working or Inspirational Electrocatalysts for Fuel Cells and Electrolysis (2008)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTEnzymes as Working or Inspirational Electrocatalysts for Fuel Cells and ElectrolysisJames A. Cracknell, Kylie A. Vincent, and Fraser A. Armstrong∗View Author Information Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom∗ To whom correspondence should be addressed. E-mail: [email protected]Cite this: Chem. Rev. 2008, 108, 7, 2439–2461Publication Date (Web):July 11, 2008Publication History Received1 February 2008Published online11 July 2008Published inissue 1 July 2008https://pubs.acs.org/doi/10.1021/cr0680639https://doi.org/10.1021/cr0680639review-articleACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views12265Altmetric-Citations885LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Carbohydrates,Electrodes,Fuel cells,Peptides and proteins,Redox reactions Get e-Alerts
Taking Guns Seriously: Common Sense Gun Control to Keep Guns Out of the Hands of Kids and Criminals (1999)

We have a responsibility to the victims of crime and violence.It is a responsibility to think not only of our own convenience but of the tragedy of sudden death.It is a responsibility to put away childish things -to make the possession and use of firearms a matter undertaken only by serious people who will use them with the restraint and maturity that their dangerous nature deserves -and demands.For too long we have dealt with these deadly weapons as if they were harmless toys.Yet their very presence, the ease of their acquisition, and familiarity of their appearance have led to thousands of deaths each year . . .It is past time that we wipe this stain of violence from our land." 1
A scalable MPEG-4 video codec architecture for IMT-2000 multimedia applications (2002)

A scalable MPEG-4 video codec architecture is proposed to achieve low power consumption and high cost-effectiveness for IMT-2000 multimedia applications. The MPEG-4 video codec consists of a 16-bit multimedia-extended RISC processor and dedicated hardware accelerators, which bring about both low power consumption and programmability. The proposed architecture is extended and applied for the development of two MPEG-4 LSIs. One is an MPEG-4 video codec LSI, which performs an MPEG-4 video encoding and decoding at 15 frames per second with quarter common intermediate format. The other is an MPEG-4 audiovisual LSI, containing three 16-bit RISC processors and a 16-Mbit embedded DRAM, executes the major functions of 3GPP 3G-324M video telephony for IMT-2000 applications. By introducing the optimization of the embedded DRAM configuration, clock gating technique, and low power motion estimation, the MPEG-4 audiovisual LSI consumes only 240 mW when it activates MPEG-4 video SP@L1 codec, the AMR speech codec, and the H.223 annex B multiplex at 60 MHz clock rate.