gebhart/patrepeval huggingface dataset:
Structural study on the free lipid A isolated from lipopolysaccharide of Porphyromonas gingivalis (1995)

The chemical structure of lipid A isolated from Porphyromonas gingivalis lipopolysaccharide was elucidated by compositional analysis, mass spectrometry, and nuclear magnetic resonance spectroscopy. The hydrophilic backbone of free lipid A was found to consisted of beta(1,6)-linked D-glucosamine disaccharide 1-phosphate. (R)-3-Hydroxy-15-methylhexadecanoic acid and (R)-3-hydroxyhexadecanoic acid are attached at positions 2 and 3 of the reducing terminal residue, respectively, and positions 2' and 3' of the nonreducing terminal unit are acylated with (R)-3-O-(hexadecanoyl)-15-methylhexadecanoic acid and (R)-3-hydroxy-13-methyltetradecanoic acid, respectively. The hydroxyl group at position 4' is partially replaced by another phosphate group, and the hydroxyl groups at positions 4 and 6' are unsubstituted. Considerable heterogeneity in the fatty acid chain length and the degree of acylation and phosphorylation was detected by liquid secondary ion-mass spectrometry (LSI-MS). A significant pseudomolecular ion of lipid A at m/z 1,769.6 [M-H]- corresponding to a diphosphorylated GlcN backbone bearing five acyl groups described above was detected in the negative mode of LSI-MS. Predominant ions, however, were observed at m/z 1,434.9 [M-H]- and m/z 1,449.0 [M-H]-, each representing monophosphoryl lipid A lacking (R)-3-hydroxyhexadecanoic and (R)-3-hydroxy-13-methyltetradecanoic acids, respectively. The presence of mono- and diphosphorylated lipid A species was also confirmed by LSI-MS of de-O-acylated lipid A (m/z 955.3 and 1,035.2, respectively).
Three-Year Efficacy of Complex Insulin Regimens in Type 2 Diabetes (2009)

Patients who added a basal or prandial insulin-based regimen to oral therapy had better glycated hemoglobin control than patients who added a biphasic insulin-based regimen. Fewer hypoglycemic episodes and less weight gain occurred in patients adding basal insulin. (Current Controlled Trials number, ISRCTN51125379.)
Membrane Stresses Induced by Overproduction of Free Fatty Acids in Escherichia coli (2011)

Microbially produced fatty acids are potential precursors to high-energy-density biofuels, including alkanes and alkyl ethyl esters, by either catalytic conversion of free fatty acids (FFAs) or enzymatic conversion of acyl-acyl carrier protein or acyl-coenzyme A intermediates. Metabolic engineering efforts aimed at overproducing FFAs in Escherichia coli have achieved less than 30% of the maximum theoretical yield on the supplied carbon source. In this work, the viability, morphology, transcript levels, and protein levels of a strain of E. coli that overproduces medium-chain-length FFAs was compared to an engineered control strain. By early stationary phase, an 85% reduction in viable cell counts and exacerbated loss of inner membrane integrity were observed in the FFA-overproducing strain. These effects were enhanced in strains endogenously producing FFAs compared to strains exposed to exogenously fed FFAs. Under two sets of cultivation conditions, long-chain unsaturated fatty acid content greatly increased, and the expression of genes and proteins required for unsaturated fatty acid biosynthesis were significantly decreased. Membrane stresses were further implicated by increased expression of genes and proteins of the phage shock response, the MarA/Rob/SoxS regulon, and the nuo and cyo operons of aerobic respiration. Gene deletion studies confirmed the importance of the phage shock proteins and Rob for maintaining cell viability; however, little to no change in FFA titer was observed after 24 h of cultivation. The results of this study serve as a baseline for future targeted attempts to improve FFA yields and titers in E. coli.
A CNTFET based Multi-Stage Transimpedance Amplifier for Blood Glucose Monitoring Systems (2018)

In this paper, the design of an ultra-low-power, low noise carbon nanotube field effect transistor (CNTFET) based transimpedance amplifier (TIA) is presented for an amperiometric based blood glucose monitoring system for wearable devices. The proposed cascode common source multistage transimpedance amplifier circuit is designed and implemented in CNTFET technology. It has been demonstrated that the performance of the proposed TIA can be enhanced by considering an optimum number of CNTs, the CNT pitch and CNT diameter. The TIA shows a significant increase in transimpedance gain, 572 MΩ, with a bandwidth of 200 MHz and an input referred current noise of 8.3 fA√Hz for an input current of 2 nA. The total power consumption is 11 pW with a 1.8 V supply.
Glutamate modulators as novel interventions for mood disorders (2005)

Pharmacological approaches that modulate components of the glutamate system offer novel targets for severe, recurrent mood disorders. Controlled studies are necessary.
RNA Interference-Based Therapeutics: New Strategies to Fight Infectious Disease (2008)

For many years, there has been an ongoing search for new compounds that can selectively alter gene expression as a new way to treat human disease by addressing targets that are otherwise "undruggable" with traditional pharmaceutical approaches involving small molecules or proteins. RNA interference (RNAi) strategies have raised a lot of attention and several compounds are currently being tested in clinical trials. Viruses are the obvious target for RNAi-therapy, as most are difficult to treat with conventional drugs, they become rapidly resistant to drug treatment and their genes differ substantially from human genes, minimizing side effects. Antisense strategy offers very high target specificity, i.e., any viral sequence could potentially be targeted using the complementary oligonucleotide sequence. Consequently, new antisense-based therapeutics have the potential to lead a revolution in the anti-infective drug development field. Additionally, the relatively short turnaround for efficacy testing of potential RNAi molecules and that any pathogen is theoretically amenable to rapid targeting, make them invaluable tools for treating a wide range of diseases. This review will focus on some of the current efforts to treat infectious disease with RNAi-based therapies and some of the obstacles that have appeared on the road to successful clinical intervention.
Fungal Decay of Wood: Soft Rot—Brown Rot—White Rot (2008)

Wood decay by fungi is typically classified into three types: soft rot, brown rot and white rot. Brown rot fungi are the most prevalent with regard to attack on coniferous, structural wood products in North America. The wood decayed by brown rot fungi is typically brown and crumbly and it is degraded via both non-enzymatic and enzymatic systems. A series of celluloytic enzymes are employed in the degradation process by brown rot fungi, but no lignin degrading enzymes are typically involved. White rot fungi are typically associated with hardwood decay and their wood decay patterns can take on different forms. White rotted wood normally has a bleached appearance and this may either occur uniformly, leaving the wood a spongy or stringy mass, or it may appear as a selective decay or a pocket rot. White rot fungi possess both cellulolytic and lignin degrading enzymes and these fungi therefore have the potential to degrade the entirety of the wood structure under the correct environmental conditions. Soft rot fungi typically attack higher moisture, and lower lignin content wood and can create unique cavities in the wood cell wall. Less is known about the soft rot degradative enzyme systems, but their degradative mechanisms are reviewed along with the degradative enzymatic and non-enzymatic systems known to exist in the brown rot and white rot fungi. As we learn more about the non-enzymatic systems involved in both brown and white rot degradative systems, it changes our perspective on the role of enzymes in the decay process. This in turn is affecting the way we think about controlling decay in wood preservation and wood protection schemes, as well as how we may apply fungal decay mechanisms in bioindustrial processes.
Prognostic implications of cyclins (D1, E, A), cyclin‐dependent kinases (CDK2, CDK4) and tumor‐suppressor genes (pRb, p16INK4A) in childhood acute lymphoblastic leukemia (1997)

Immunohistochemistry was used to analyze samples of 40 newly diagnosed childhood acute lymphoblastic leukemias (ALL) for their expression of cyclins (D1, E, A), cyclindependent kinases (cdk2, cdk4) and tumor-suppressor genes (pRb, p16 INK4A ), in order to discover whether or not the expression of these various proteins may be of prognostic relevance for the survival of children with ALL.Patients with ALL who were strongly positive for cyclin D1 had a lower probability of remaining in first continuous remission than ALL patients who were negative or weakly positive for this trait.There was also a significant correlation between expression of cyclin D1 and frequency of recurrence.For cyclin E and cyclin A, in contrast, there was no difference in the duration of relapse-free-intervals or the frequency of recurrence in patients.Children with cdk4-positive ALL had a lower probability of remaining in first continuous remission than children with cdk4-negative ALL.No prognostic relevance was found for cdk2.Patients with ALL who expressed pRb had a higher probability and patients who expressed p16 a lower probability of remaining in first continuous remission, but the results were not statistically significant.This investigation demonstrated that cyclin D1 and cdk4 were the most important prognostic factors for children with ALL, and that the combination of them showed the strongest prognostic relevance.
Force Constants of Nickel Carbonyl from Vibrational Spectra of Isotopic Species (1968)

The infrared spectra of gaseous Ni(13CO)4 and Ni(C18O)4 and the infrared and Raman spectra of CCl4 solutions of these isotopic molecules were recorded. General quadratic valence force constants have been calculated from the frequencies of the normal species and the two isotopic species. The resulting force constant solution is similar to that obtained previously assuming a pi electron interaction potential function. These results put the force constants of metal carbonyls on a firmer basis.
CO2 Thermosiphon for Competitive Geothermal Power Generation (2008)

Engineered geothermal systems represent a significant unutilized energy source, with the potential to assist in meeting growing energy demands with clean, renewable energy. Traditional geothermal systems use water as the working fluid. An alternative working fluid is carbon dioxide which offers potential benefits including favorable thermodynamic and transport properties and the potential for sequestration. An important feature is that CO2 does not dissolve mineral salts, and this will serve to reduce fouling and corrosion problems which afflict piping and surface equipment in conventional water cycles. Our modeling shows that a CO2-based power plant has net electricity production comparable to the traditional approach, but with a much simpler design, and demonstrates the comparative efficacy of CO2 as a heat extraction and working fluid. While the economic viability of a CO2-based system remains to be proven, this analysis provides a starting point for more detailed thermodynamic and economic models of engineered geothermal systems power conversion utilizing CO2.
Durable solgel antireflective films with high laser-induced damage thresholds for inertial confinement fusion (2005)

We tested the use of two hydrophobic methyl-substituted silane precursors, methyltriethoxysilane and dimethyldiethoxysilane, to synthesize methyl-modified silica sols by a two-step method and a cohydrolysis method to produce durable antireflective films with high laser-induced-damage thresholds (LIDTs). Using small-angle x-ray scattering technology, we obtained details of the microstructure of clusters in sol and found various double fractal structural characteristics in the methyl-modified silica clusters; our findings were confirmed by transmission-electron micrographs. Through a ^29 Si magic-angle spin nuclear magnetic resonance study of the corresponding xerogels, we determined the double-fractal microstructure, which we then related to the LIDTs of AR films. The distribution configuration of methyls in clusters determined the double-fractal microstructure of clusters and then the LIDTs of AR films. The LIDTs of films produced by the cohydrolysis method (the highest was 38 J/cm² for 1-ns, 1064-nm laser action) were much higher than those from the two-step method because of the loose netlike clusters in the former configuration. During the 220-day aging, the transmittance of hydrophobic AR film decreased &#8764;0.2%. So it is practicable to prepare durable AR films with higher LIDTs than those of normal AR SiO2 films only by introducing hydrophobic methyls into a Si-O-Si matrix of clusters if an appropriate hydrophobic precursor is chosen.
Unimolecular Micelles based on Hydrophobically Derivatized Hyperbranched Polyglycerols: Biodistribution Studies (2008)

We recently reported the synthesis and testing of a new class of unimolecular micelles based on hyperbranched polyglycerols as second generation synthetic plasma expanders and as general drug delivery vehicles. A detailed biodistribution study of two derivatized hyperbranched polyglycerols of different molecular weights derivatized with hydrophobic groups and short poly(ethylene glycol) chains is reported in this article. In mice, these materials are nontoxic with circulation half-lives as high as 31 h, controllable by manipulating the molecular weight and the degree of PEG derivatization. Organ accumulation is low, presumably due to the "pegylation" effect. Thermal degradation and hydrolysis data suggest that these polymers are highly stable with a long shelf life, a major advantage for a pharmaceutical product. Degradation under acidic conditions has been observed for these polymers.
Making sense of cancer genomic data (2011)

High-throughput tools for nucleic acid characterization now provide the means to conduct comprehensive analyses of all somatic alterations in the cancer genomes. Both large-scale and focused efforts have identified new targets of translational potential. The deluge of information that emerges from these genome-scale investigations has stimulated a parallel development of new analytical frameworks and tools. The complexity of somatic genomic alterations in cancer genomes also requires the development of robust methods for the interrogation of the function of genes identified by these genomics efforts. Here we provide an overview of the current state of cancer genomics, appraise the current portals and tools for accessing and analyzing cancer genomic data, and discuss emerging approaches to exploring the functions of somatically altered genes in cancer.
Comparison of Changes in Ejection Fraction to Changes in Impedance Cardiography Cardiac Index and Systolic Time Ratio (2004)

Ejection fraction (EF) is the most common measure of left ventricular function in patients with heart failure. However, serial measurements of EF are costly and not practical for guiding frequent management decisions. Impedance cardiography (ICG) provides noninvasive hemodynamic measures with proven validity. The purpose of this study was to assess how changes in ICG parameters compared with changes in EF in heart failure subjects enrolled in a comprehensive outpatient management program. Retrospective chart review identified 13 subjects with two sets of paired echocardiography and ICG measurements (before and after treatment in an outpatient heart failure clinic setting). Mean age was 69+/-11 years, etiology was 54% ischemic heart disease, and mean New York Heart Association class was 2.5+/-0.5. The mean time between pre- and posttreatment EF measurements was 198+/-161 days. Changes in cardiac index and systolic time ratio by ICG were compared with changes in EF by echocardiography. From entry to final measurement, mean EF improved 9%+/-13%. Seven (54%) subjects had >5% improvement in EF, three (23%) had >5% decrease, and three had <5% change. Changes in ICG cardiac index and systolic time ratio were highly correlated with changes in EF (0.85, -0.73). ICG may be a practical, reliable, and cost-effective method of monitoring left ventricular function and guiding management decisions.
Soft Combination and Detection for Cooperative Spectrum Sensing in Cognitive Radio Networks (2008)

In this letter, we consider cooperative spectrum sensing based on energy detection in cognitive radio networks. Soft combination of the observed energies from different cognitive radio users is investigated. Based on the Neyman-Pearson criterion, we obtain an optimal soft combination scheme that maximizes the detection probability for a given false alarm probability. Encouraged by the performance gain of soft combination, we further propose a new softened hard combination scheme with two-bit overhead for each user and achieve a good tradeoff between detection performance and complexity.
Reclassification of Eubacterium formicigenerans Holdeman and Moore 1974 as Dorea formicigenerans gen. nov., comb. nov., and description of Dorea longicatena sp. nov., isolated from human faeces. (2002)

Two strains of a gram-positively staining, obligately anaerobic, non-spore-forming, rod-shaped bacterium, designated strains 111-13A and 111-35T, were isolated from human faeces. Analysis of the 16S rRNA gene sequences indicated that these strains were members of the Clostridium coccoides rRNA group of organisms. The nearest relatives of the unknown bacterium were Eubacterium formicigenerans (having a sequence similarity of 94%) and an uncultured bacterium (similarity > 99%). Characterization studies indicated that the unidentified faecal bacterium was biochemically distinct from Eubacterium formicigenerans, members of the Clostridium coccoides group and all other described Eubacterium species. On the basis of the data from these studies, it is proposed that the hitherto unknown rod-shaped bacterium be designated a species of a novel genus, namely Dorea longicatena gen. nov., sp. nov., and that Eubacterium formicigenerans be transferred to this genus as Dorea formicigenerans gen. nov., comb. nov.
Multiple proteins interact at a unique cis-element in the 3'-untranslated region of amyloid precursor protein mRNA. (1994)

Growing evidence suggests that Alzheimer's disease results from dysregulated production and deposition of beta-amyloid in the central nervous system. beta-Amyloid is derived from proteolytic processing of one of multiple amyloid precursor protein (APP) isoforms. The production of APP in many somatic tissues and tumor cell lines provides a more accessible model to study the regulation of APP gene expression. Recent data suggest that APP mRNAs accumulate in activated lymphocytes and neuronal tumor lines. We are interested in defining the contribution of alterations in stability to changes in steady-state APP mRNA levels in these model systems. Herein we demonstrate by mobility shift assay that the 3'-untranslated region of APP RNAs which contain a contiguous 29-base region interacts in vitro with multiple mRNA-binding proteins found in cytosolic lysates prepared from normal and transformed human cells. UV cross-linking of radiolabeled APP RNAs to cytosolic protein extracts followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis identified six distinct RNA-protein complexes of 42, 47, 65, 73, 84, and 104 kDa. Competition assays with APP, AU-rich, or irrelevant RNAs demonstrated that binding was specific and in some cases preferential for AU- or U-rich sequences by which we tentatively place the binding site of the proteins along the 29-base region. APP mRNA-binding proteins were constitutively active in all tumor lines examined as well as at diminished levels in whole human brain cytosolic lysates. The core element is AU-rich and highly conserved between human and some murine APP mRNAs. In the accompanying paper (Zaidi, S. H. E. and Malter, J. S. (1994) J. Biol. Chem. 269, 24007-24013) we show that this 29-base element in the 3'-untranslated region regulates the stability of APP mRNA. Cumulatively these data suggest that steady-state APP mRNA levels are modulated by cytosolic protein-RNA interactions.
Identification of a Highly Encapsulated, Genetically Related Group of Invasive Type III Group B Streptococci (1998)

Type III group B streptococci (GBS) isolated from Tokyo and Salt Lake City were classified according to the similarity of HindIII and Sse83871 restriction digest patterns (RDPs) of bacterial DNA. The bacteria were clustered into three RDP types, with excellent correlation between subtyping based on the two enzymes. The majority (91%) of invasive isolates obtained from neonates were RDP type III-3. The mean sialic acid content of the III-3 strains was higher than that of other type III strains. Closely related isolates were concordant for expression of the bacterial enzyme C5a-ase, but invasive strains were no more likely to be C5a-ase positive than were strains isolated from the genitourinary tract of pregnant women. These data indicate that a group of genetically related organisms with increased capsule production causes the majority of invasive type III GBS disease.
The VP16 transcription activation domain is functional when targeted to a promoter-proximal RNA sequence. (1992)

Among eukaryotic transcription trans-activators, the human immunodeficiency virus type 1 (HIV-1) Tat protein is exceptional in that its target site TAR is an RNA rather than a DNA sequence. Here, we confirm that fusion of Tat to the RNA-binding domain of the HIV-1 Rev protein permits the efficient activation of an HIV-1 long terminal repeat (LTR) promoter in which critical TAR sequences have been replaced by RNA sequences derived from the HIV-1 Rev response element (RRE). An RRE target sequence as small as 13 nucleotides is shown to form an effective in vivo target for Rev binding. More important, a fusion protein consisting of Rev attached to the VP16 transcription activation domain was also observed to efficiently activate the HIV-1 LTR from this nascent RNA target. These data demonstrate that trans-activation of transcription by acidic activation domains does not require a stable interaction with the promoter DNA and suggest that VP16, like Tat, can act on steps subsequent to the formation of the HIV-1 LTR preinitiation complex. The finding that the activation domains of VP16 and Tat are functionally interchangeable raises the possibility that these apparently disparate viral trans-activators may nevertheless act via similar mechanisms.
Schottky-to-Ohmic Crossover in Carbon Nanotube Transistor Contacts (2013)

For carbon nanotube transistors, as for graphene, the electrical contacts are a key factor limiting device performance. We calculate the device characteristics as a function of nanotube diameter and metal work function. Although the on-state current varies continuously, the transfer characteristics reveal a relatively abrupt crossover from Schottky to Ohmic contacts. We find that typical high-performance devices fall surprisingly close to the crossover. Therefore, tunneling plays an important role even in this regime, so that current fails to saturate with gate voltage as was expected due to "source exhaustion."
Iterative decoding and channel estimation (2002)

We investigate iterative decoding and channel estimation for multiple-access channels. Results are obtained concerning the fixed points of such iterations.