gebhart/patrepeval huggingface dataset:
Vector Green's function for S-parameter measurements of the electromagnetic volume integral equation (2011)

We present a variation of the electric-field volume integral equation (VIE) for inhomogeneous media that is tailored for microwave S-parameter measurements. The kernel of the standard VIE is a dyadic Green's function that can relate fields in the object domain to observed scattered fields outside the object domain. Here, we derive a kernel we call a vector Green's function that gives, instead of observed fields, observed S-parameter measurements that would be obtained in a bistatic antenna setup. This formulation directly links the object properties to microwave measurements in a way that is useful to many microwave applications. This derivation uses an antenna model based on the source-scattering matrix formulation. We show how this vector Green's function can be obtained from simulation and validate this model with several experiments.
Protease-Triggered Dispersion of Nanoparticle Assemblies (2007)

We present a new highly sensitive method for detection of proteases based on triggered dispersion of gold nanoparticle assemblies. Copyright © 2007 American Chemical Society.
The use of 2D fingerprint methods to support the assessment of structural similarity in orphan drug legislation (2014)

Measures of structural similarity based on 2D fingerprints can provide a useful source of information for the assessment of orphan drug status by regulatory authorities.
The Sphingolipidoses (1966)

THE sphingolipidoses comprise a group of inherited metabolic diseases characterized by the accumulation of excessive quantities of certain glycolipids or phospholipids in various tissues of the body. These lipids have a common basic structure called ceramide (Fig. 1, line 1) consisting of the long-chain amino alcohol sphingosine acylated with a fatty acid on the nitrogen atom of sphingosine.Recent significant advances have provided considerable insight into the nature of the metabolic aberrations in several of the sphingolipidystrophies. This progress is due to a large extent to the application of newly developed technics for the chemical synthesis of specifically labeled sphingolipids. . . .
The Role of Microglia in Antibody-Mediated Clearance of Amyloid-Beta from the Brain (2009)

Immunotherapy has emerged as a leading new approach to the reduction of amyloid deposits in the brains of Alzheimer patients. At least 4 distinct actions of anti-Abeta antibodies have been proposed as contributing to the inhibition of amyloid deposition and its clearance. Critically, each of these proposed mechanisms may be acting simultaneously, and it is feasible that different antibodies may utilize each mechanism to a different extent. One of these proposed mechanisms involves the activation of microglia and the phagocytosis of Abeta peptide. In general this is assumed to proceed through the Fcgamma-receptor binding by antibody opsonized Abeta aggregates, however modifying the microglial phenotype into one with a greater propensity for phagocytosing Abeta is also feasible, as microglia avidly phagocytose Abeta in vitro without antibody present. Evidence is presented supporting arguments that microglial activation does play a role in amyloid removal, particularly compacted amyloid deposits, under certain conditions. In addition to the specific antibody used, other considerations in comparing different reports of antibody action in APP mice include the age of the mice, the extent of pre-existing amyloid when therapy is initiated, the time point when the effects of the therapy are examined and the route of antibody administration. Future questions will consider the source of the activated microglia near the plaques after antibody administration (resident or peripheral) and the extent to which shifts in the microglial phenotype mediate some of the amyloid lowering actions of immunotherapy.
Angiogenin expression and prognosis in primary breast carcinoma. (1998)

Angiogenin is a protein originally isolated as an inducer of new blood vessel growth, and it has been reported to be an effective substrate for tumor cell adhesion. To understand the role of angiogenin in cancer progression, we evaluated the expression of angiogenin in 459 cases with primary breast carcinoma and in 40 benign breast specimens using an immunoassay. Higher angiogenin concentrations were observed in carcinomas in comparison with fibrocystic disease (mean, 17.3 versus 10.9 ng/mg; P = 0.008), but not with fibroadenomas. We selected 5 ng/mg cytosol protein of angiogenin as the normal cutoff for primary breast carcinoma. Eighty-eight percent of carcinomas expressed elevated angiogenin levels and 12% had low levels. We observed an association between elevated levels of angiogenin and low/ moderate histological grade (P = 0.001) and small tumor size (P = 0.026), but not with age, menopausal status, lymph node status, stage of disease, or hormonal receptor status. With a median follow-up of 31 months, breast cancer patients with elevated angiogenin levels had significantly longer disease-free survival (DFS) than patients with low angiogenin (log-rank, P = 0.003). This effect was equally observed in node-negative and node-positive cases. In a multivariate analysis of DFS, only angiogenin, tumor size, and histological grade showed statistical significance. A multivariate analysis of overall survival showed that angiogenin and tumor size were the only significant variables. Serum samples from the breast cancer patients at the time of surgery were available in 194 cases. We evaluated the levels of circulating angiogenin using the same immunoassay as in tumor tissue. Serum angiogenin levels were higher in cancer patients than in 40 healthy controls (mean, 401.2 versus 206.0 ng/ml; P < 0.0001). In breast cancer patients, we observed no correlation between the serum concentrations and the tissue levels of angiogenin (r = 0.115; P = 0.110). In addition, serum levels of angiogenin did not have a prognostic impact on the DFS of breast cancer patients (log-rank, P = 0.581). Our results indicate that elevated levels of tissue angiogenin, but not of circulating angiogenin, are a favorable prognostic factor in primary breast carcinoma, which is consistent with a role of angiogenin as a cancer cell substrate.
The Chemistry of Organic Silicon Compounds (1989)

Historical overview and comparison of silicon with carbon, J.Y.Corey theoretical aspects of organosilicon compounds, Y.Apeloig structural chemistry of organic silicon compounds, W.S.Sheldrick dynamic stereochemistry at silicon, R.J.P.Corriu et al thermochemistry, R.Walsh analysis of organosilicon compounds, T.R.C.Crompton positive and negative ion chemistry of silicon-containing molecules in the gas phase, H.Schwarz NMR spectroscopy of organosilicon compounds, E.A.Williams photoelectron spectra of silicon compounds, H.Bock and B.Solouki general synthetic pathways to organosilicon compounds, L.Birkofer and O.Stuhl recent synthetic application of organosilanes, G.L.Larson acidity, basicity and complex formation of organosilicon compounds, A.R.Bassindale and P.G.Taylor reaction mechanisms of nucleophilic attacks at silicon, A.R.Bassindale and P.G.Taylor activating and directive effects of silicon, A.R.Bassindale and P.G.Taylor the photochemistry of organosilicon compounds, A.G.Brook trivalent silyl ions, J.B.Lambert and W.J.Schulz Jr multiple bonds to silicon, G.Raabe and J.Michl bio-organic chemistry, R.Tacke and J.Linoh polysilanes, R.West hypervalent silicon compounds, R.J.P.Corriu and J.C.Young siloxane polymers and copolymers, T.C.Kendrick organosilicon derivatives of phosphorus arsenic, antimony and bismuth, D.A.Armitage chemistry of compounds with silicon-sulphur, silicon-selenium and silicon-tellurium bonds, D.A.Armitage transition-metal silyl derivatives, T.D.Tilley the hydrosilylation reaction, I.Ojima.
Rethinking the duration requirement for generalized anxiety disorder: evidence from the National Comorbidity Survey Replication (2005)

A large number of people suffer from a GAD-like syndrome with episodes of < 6 months duration. Little basis for excluding these people from a diagnosis is found in the associations examined here.
The Effect of Two New Dressings on Epidermal Wound Healing (1982)

The effects of a Polyethylene oxide hydrogel dressing and a co-polymer starch hydrogel dressing upon the rate of re-epithelization were evaluated in a study using Yorkshire pigs. The polyethylene oxide hydrogel dressing significantly promoted re-epithelization by 44% as compared to untreated control wounds, while the copolymer starch hydrogel dressing significantly promoted epidermal healing by 24%. A possible mechanism of action is presented for the quicker healing induced by these dressings.
State‐of‐the‐Art Clinical Article: Pharmacokinetic/Pharmacodynamic Parameters: Rationale for Antibacterial Dosing of Mice and Men (1998)

Investigations over the past 20 years have demonstrated that antibacterials can vary markedly in the time course of antimicrobial activity. These differences in pharmacodynamic activity have implications for optimal dosage regimens. The results of more recent studies suggest that the magnitude of the pharmacokinetic/pharmacodynamic parameters required for efficacy are relatively similar in animal infection models and in human infections. However, there is still much to learn. Additional studies are needed to further correlate pharmacokinetic/pharmacodynamic parameters for many antibacterials with therapeutic efficacy in a variety of animal infection models and in human infections. The potential value of using pharmacokinetic/pharmacodynamic parameters as guides for establishing optimal dosing regimens for new and old drugs and for new emerging pathogens and resistant organisms, for setting susceptibility breakpoints, and for reducing the cost of drug development should make the continuing search for the therapeutic rationale of antibacterial dosing of mice and men worthwhile.
Three epidermal and one simple epithelial type II keratin genes map to human chromosome 12 (1991)

We have localized the genes which encode the human type II epidermal keratins K5, K6a, and K6b and the simple epithelial keratin K7 (KRT5, KRT6A, KRT6B, and KRT7, respectively) to chromosome 12 using Southern blot analysis of somatic cell hybrids. In addition, we have sublocalized the genes for K6a and K7 to bands 12q12----q14 on the long arm of this chromosome by in situ hybridization of metaphase chromosomes.
Endocrinologic response to vasopressin infusion in advanced vasodilatory shock* (2004)

The preliminary results of this study indicate that a combined AVP and NE infusion increases prolactin plasma concentrations in advanced vasodilatory shock. Hemodynamic effects of AVP infusion are independent of baseline plasma AVP concentrations.
The vermiform appendix impacts the risk of developing Parkinson’s disease (2018)

The pathogenesis of Parkinson's disease (PD) involves the accumulation of aggregated α-synuclein, which has been suggested to begin in the gastrointestinal tract. Here, we determined the capacity of the appendix to modify PD risk and influence pathogenesis. In two independent epidemiological datasets, involving more than 1.6 million individuals and over 91 million person-years, we observed that removal of the appendix decades before PD onset was associated with a lower risk for PD, particularly for individuals living in rural areas, and delayed the age of PD onset. We also found that the healthy human appendix contained intraneuronal α-synuclein aggregates and an abundance of PD pathology-associated α-synuclein truncation products that are known to accumulate in Lewy bodies, the pathological hallmark of PD. Lysates of human appendix tissue induced the rapid cleavage and oligomerization of full-length recombinant α-synuclein. Together, we propose that the normal human appendix contains pathogenic forms of α-synuclein that affect the risk of developing PD.
Squeezed-state effect on bound–continuum transitions (1993)

An atomic model is discussed that contains one structured continuum interacting with an electromagnetic field of quantum nature. It is assumed that the field is initially in a squeezed state. Three kinds of squeezed state are discussed: (1) the squeezed vacuum state, (2) the squeezed state with a strong coherent component, and (3) the Holstein–Primakoff SU(1, 1) coherent state. A derivation is given of a fully analytical formula for the probability of finding the system in the continuum in a long-time regime. This result is obtained by a nonperturbative method and hence is valid for arbitrary field strengths. The result is discussed for various values of the parameters describing the electromagnetic field and its interaction with the atomic model and exhibits a strong dependence of the probability on the type and the squeezing parameters of the squeezed state.
Mass Spectrometry-Based Sequencing of Lignin Oligomers (2010)

Although the primary structure of proteins, nucleic acids, and carbohydrates can be readily determined, no sequencing method has been described yet for the second most abundant biopolymer on earth (i.e. lignin). Within secondary-thickened plant cell walls, lignin forms an aromatic mesh arising from the combinatorial radical-radical coupling of monolignols and many other less abundant monomers. This polymerization process leads to a plethora of units and linkage types that affect the physicochemical characteristics of the cell wall. Current methods to analyze the lignin structure focus only on the frequency of the major monomeric units and interunit linkage types but do not provide information on the presence of less abundant unknown units and linkage types, nor on how linkages affect the formation of neighboring linkages. Such information can only be obtained using a sequencing approach. Here, we describe, to our knowledge for the first time, a sequencing strategy for lignin oligomers using mass spectrometry. This strategy was then evaluated on the oligomers extracted from wild-type poplar (Populus tremula x Populus tremuloides) xylem. In total, 134 lignin trimers to hexamers were observed, of which 36 could be completely sequenced. Interestingly, based on molecular mass data of the unknown monomeric and dimeric substructures, at least 10 unknown monomeric units or interunit linkage types were observed, one of which was identified as an arylglycerol end unit.
Targeting Activated Akt with GDC-0068, a Novel Selective Akt Inhibitor That Is Efficacious in Multiple Tumor Models (2013)

GDC-0068 is a highly selective, orally bioavailable Akt kinase inhibitor that shows pharmacodynamic inhibition of Akt signaling and robust antitumor activity in human cancer cells in vitro and in vivo. Our preclinical data provide a strong mechanistic rationale to evaluate GDC-0068 in cancers with activated Akt signaling.
An improved procedure for the synthesis of glycine and taurine conjugates of bile acids (1977)

Glycine and taurine conjugates of 5beta-cholanic acids have been synthesized using improved procedures based on the peptide coupling reagent, N-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline. The conjugates are obtained in chromatographically pure form in yields higher than 90%. The use of this procedure in the large scale preparation of cholyl[1,2-13C2]glycine is described.
A Fibre Optic Multi-Component Seismic Acquisition System for Permanent Reservoir Monitoring (2008)

Abstract A fibre optic multi-component seismic acquisition system for permanent installation on the sea floor has been developed and tested. Permanent seafloor seismic installations are an alternative to other marine seismic acquisition methods for time-lapse (or 4D) seismic reservoir monitoring. 4D seismic can assist reservoir engineers to monitor fluid injection and drainage of the reservoir, and help determine detailed reservoir fluid-flow models. The new fibre optic system uses a Dense Wavelength Division Multiplexing telemetry scheme to optically power the seismic sensors. This methodology allows for channel counts in excess of 2000 per cable. Furthermore, the fibre optic system has a very broad processing bandwidth that yields exceptional dynamic range (&amp;gt; 140dB), which together with low channel crosstalk and distortion, will produce high quality seismic images. The multi-component sensors at each receiver station are optical transducers made using Michelson interferometers. Avoiding in-sea electronics creates a safe and robust system, and utilisation of standard telecommunication components ensures an economically viable reservoir monitoring tool. Field trials conducted in hydrocarbon provinces demonstrate the reliability and excellent response of the fibre optic system to the seismic source. The seismic data acquired by the new fibre optic acquisition system show good correlation with data acquired in parallel using a conventional electrical seafloor acquisition system.
Somatic Frameshift Mutations in the BAX Gene in Colon Cancers of the Microsatellite Mutator Phenotype (1997)

Cancers of the microsatellite mutator phenotype (MMP) show exaggerated genomic instability at simple repeat sequences. More than 50 percent (21 out of 41) of human MMP+ colon adenocarcinomas examined were found to have frameshift mutations in a tract of eight deoxyguanosines [(G)8] within BAX, a gene that promotes apoptosis. These mutations were absent in MMP- tumors and were significantly less frequent in (G)8 repeats from other genes. Frameshift mutations were present in both BAX alleles in some MMP+ colon tumor cell lines and in primary tumors. These results suggest that inactivating BAX mutations are selected for during the progression of colorectal MMP+ tumors and that the wild-type BAX gene plays a suppressor role in a p53-independent pathway for colorectal carcinogenesis.
Reevaluation of the Harboe Assay as a Standardized Method of Assessment for the Hemolytic Performance of Ventricular Assist Devices (2012)

The Harboe spectrophotometric assay is regarded as one of the safest and most reproducible methods for measuring plasma free hemoglobin (pfHb). However, there is still some ambiguity in the application of the assay when assessing the hemolytic performance of ventricular assist devices (VADs). The purpose of this study was to reexamine and compare values of pfHb obtained using different concentrations of plasma diluent (Na(2) CO(3) ) as cited by various studies such that a standard practice may be recommended for the application of the Harboe assay in the hemolytic evaluation of VADs, allowing reliable comparisons to be made between laboratories. As a means to examine the Harboe assay, a BioMedicus BPX-80 was tested using both whole blood and a washed suspension of red blood cells (RBCs). Results show that for whole blood, the pfHb may be underestimated by 13-23%, dependent upon the concentration of Na(2) CO(3) diluent solution. This trend was not observed for the washed suspension of RBCs. Furthermore, it is shown that the concentration of diluent influences the stability of a sample. The results of this study show that the problems associated with the incongruity of pfHb readings are a direct result of the precipitation of proteins from the plasma under alkaline conditions; as the molarity of the diluent controls pH, it becomes essential to use the appropriate concentration of Na(2) CO(3) diluent in order to avoid turbidity of the solution and the consequent misrepresentation of pfHb values. Such standardization is pertinent when measuring the very low levels of pfHb observed during the in vivo testing of modern ventricular assist devices.
Hardware Translation Coherence for Virtualized Systems (2017)

To improve system performance, operating systems (OSes) often undertake activities that require modification of virtual-to-physical address translations. For example, the OS may migrate data between physical pages to manage heterogeneous memory devices. We refer to such activities as page remappings. Unfortunately, page remappings are expensive. We show that a big part of this cost arises from address translation coherence, particularly on systems employing virtualization. In response, we propose hardware translation invalidation and coherence or HATRIC, a readily implementable hardware mechanism to piggyback translation coherence atop existing cache coherence protocols. We perform detailed studies using KVM-based virtualization, showing that HATRIC achieves up to 30% performance and 10% energy benefits, for per-CPU area overheads of 0.2%. We also quantify HATRIC's benefits on systems running Xen and find up to 33% performance improvements.
Upphaf Þjóðólfs 1848 (1998)

Þjóðólfur, the first modern newspaper published in Iceland, started to come out in 1848, 150 years ago. A bimonthly publication, Þjóðólfur flourished for more than half a century until forced to give way to the daily newspapers in the second decade of the 20th century. Early accounts of the establishment of Þjóðólfur are examined critically and an attempt is made to draw up a new and clearer picture as to how it came ínto being.
MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion (2009)

One of the most interesting challenges facing paleobiologists is explaining the Cambrian explosion, the dramatic appearance of most metazoan animal phyla in the Early Cambrian, and the subsequent stability of these body plans over the ensuing 530 million years. We propose that because phenotypic variation decreases through geologic time, because microRNAs (miRNAs) increase genic precision, by turning an imprecise number of mRNA transcripts into a more precise number of protein molecules, and because miRNAs are continuously being added to metazoan genomes through geologic time, miRNAs might be instrumental in the canalization of development. Further, miRNAs ultimately allow for natural selection to elaborate morphological complexity, because by reducing gene expression variability, miRNAs increase heritability, allowing selection to change characters more effectively. Hence, miRNAs might play an important role in shaping metazoan macroevolution, and might be part of the solution to the Cambrian conundrum.
Neutron single crystal diffraction: techniques and applications in molecular systems (2005)

Abstract Single crystal neutron diffraction is a powerful method for the investigation of molecular structure, and in many cases is found to be an excellent complement to X-ray diffraction. The ability of neutron diffraction to determine the position of the atomic nucleus, rather than the electron density, is key to its use in structural studies. Among other advantages, this lends the neutron the ability to determine accurately the positions (and displacement parameters) of light atoms. In the context of molecular systems, neutron diffraction is thus very well suited to the determination of hydrogen atom parameters, which are key to many applications in molecular structure determination, including hydrogen bonded systems, organometallic materials and in macromolecular structures. This article briefly summarises some of the applications to which single crystal neutron diffraction has been put in the study of molecular structure, together with an account of the techniques and instrumentation used for these experiments. Particular account is taken of recent developments in instrumentation, and the new scientific applications that have resulted from these, along with a forward look to some of the exciting developments currently taking place in this field. These include instruments with dramatically enhanced detector arrays, other optimisations to improve count-rate and performance, the construction of new neutron sources and exciting new instruments being planned for these sources.
Antisense PMO Found in Dystrophic Dog Model Was Effective in Cells from Exon 7-Deleted DMD Patient (2010)

Antisense PMOs, the effectiveness of which has been demonstrated in a dog model, achieved multi-exon skipping of dystrophin gene on the FACS-aided MyoD-transduced fibroblasts from an exon 7-deleted DMD patient, suggesting the feasibility of systemic multi-exon skipping in humans.