gebhart/patrepeval huggingface dataset:
Biofilm Producing Salmonella Typhi: Chronic Colonization and Development of Gallbladder Cancer (2017)

<i>Salmonella enterica</i> subspecies <i>enterica</i> serovar Typhi is the aetiological agent of typhoid or enteric fever. In a subset of individuals, <i>S</i>. Typhi colonizes the gallbladder causing an asymptomatic chronic infection. Nonetheless, these asymptomatic carriers provide a reservoir for further spreading of the disease. Epidemiological studies performed in regions where <i>S.</i> Typhi is endemic, revealed that the majority of chronically infected carriers also harbour gallstones, which in turn, have been indicated as a primary predisposing factor for the onset of gallbladder cancer (GC). It is now well recognised, that <i>S.</i> Typhi produces a typhoid toxin with a carcinogenic potential, that induces DNA damage and cell cycle alterations in intoxicated cells. In addition, biofilm production by <i>S.</i> Typhi may represent a key factor for the promotion of a persistent infection in the gallbladder, thus sustaining a chronic local inflammatory response and exposing the epithelium to repeated damage caused by carcinogenic toxins. This review aims to highlight the putative connection between the chronic colonization by highly pathogenic strains of <i>S</i>. Typhi capable of combining biofilm and toxin production and the onset of GC. Considering the high risk of GC associated with the asymptomatic carrier status, the rapid identification and profiling of biofilm production by <i>S</i>. Typhi strains would be key for effective therapeutic management and cancer prevention.
Tonality detection methods for wheezes recognition system (2012)

In this paper a comparison of some known and new features used for signal tonality detection in pulmonary wheezes recognition systems is presented. In the article, the Tonal Index is compared to Kurtosis (K), Energy Ratio (ER), two types of correlation feature (CF), Difference to Mean ratio (D2M), Eigen Value Decomposi-tion feature (EVD) and Linear Prediction feature (LP). The analy-sis of efficiency related to complexity of descriptors is presented as well. Experiments have been conducted on artificially generated wheezes-like signals that have been embedded in real pulmonary noise (a hybrid signal) as well as on recorded real wheezes.
Large-Scale Estimation in Cyberphysical Systems Using Streaming Data: A Case Study With Arterial Traffic Estimation (2013)

Controlling and analyzing cyberphysical and robotics systems is increasingly becoming a Big Data challenge. We study the case of predicting drivers' travel times in a large urban area from sparse GPS traces. We present a framework that can accommodate a wide variety of traffic distributions and spread all the computations on a cluster to achieve small latencies. Our framework is built on Discretized Streams, a recently proposed approach to stream processing at scale. We demonstrate the usefulness of Discretized Streams with a novel algorithm to estimate vehicular traffic in urban networks. Our online EM algorithm can estimate traffic on a very large city network (the San Francisco Bay Area) by processing tens of thousands of observations per second, with a latency of a few seconds.
Thrombospondin-1 Contributes to Mortality in Murine Sepsis through Effects on Innate Immunity (2011)

TSP-1 deficiency was protective in two murine models of peritoneal sepsis, independent of TGFβ1 activation. Our studies suggest TSP-1 expression is associated with decreased phagocytosis and possibly bacterial clearance, leading to increased peritoneal inflammation and mortality in WT mice. These data support the contention that TSP-1 should be more fully explored in the human condition.
Bioaccumulation of triclocarban in <i>Lumbriculus variegatus</i> (2009)

The antimicrobial triclocarban (TCC) has been detected in streams and municipal biosolids throughout the United States. In addition, TCC and potential TCC transformation products have been detected at high levels (ppm range) in sediments near major cities in the United States. Previous work has suggested that TCC is relatively stable in these environments, thereby raising concerns about the potential for bioaccumulation in sediment-dwelling organisms. Bioaccumulation of TCC from sediments was assessed using the freshwater oligochaete Lumbriculus variegatus. Worms were exposed to TCC in sediment spiked to 22.4 ppm to simulate the upper bound of environmental concentrations. Uptake from laboratory-spiked sediment was examined over 56 d for TCC and 4,4'-dichlorocarbanilide (DCC), a chemical impurity in and potential transformation product of TCC. The clearance of TCC from worms placed in clean sediment was also examined over 21 d after an initial 35-d exposure to TCC in laboratory-spiked sediment. Concentrations of TCC and DCC were monitored in the worms, sediment, and the overlying water using liquid chromatography/tandem mass spectrometry. Experimental data were fitted using a standard biodynamic model to generate uptake and elimination rate constants for TCC in L. variegatus. These rate constants were used to estimate steady-state lipid (lip)- and organic carbon (OC)-normalized biota-sediment accumulation factors (BSAFs) for TCC and DCC of 2.2+/-0.2 and 0.3+/-0.1 g OC/g lip (goc/glip), respectively. Alternatively, directly measured BSAFs for TCC and DCC after 56 d of exposure were 1.6+/-0.6 and 0.5+/-0.2 goc/glip, respectively. Loss of TCC from pre-exposed worms followed first-order kinetics, and the fitted elimination rate constant was identical to that determined from the uptake portion of the present study. Overall, study observations indicate that TCC bioaccumulates from sediments in a manner that is consistent with the traditional hydrophobic organic contaminant paradigm.
A robust implementation and application of antileakage Fourier transform interpolation (2018)

Abstract One major difficulty in land seismic data processing is noise related to a complex near surface. The presence of sand dunes and loose deposits overlaying relatively high velocity layers leads to the generation of strong near-surface noise that travels at low velocities. This energy is often aliased despite the small shot and geophone spacing of modern 3D wide-azimuth seismic surveys. Direct application of velocity-based filtering in frequency-wavenumber (f-k) or Radon domains is not effective in suppressing this noise. Seismic data need to be interpolated and regularized to dealias the slow-traveling near-surface arrivals before denoising technologies are applied. In this work, we utilized an f-k domain seismic data interpolation technique similar to the antileakage Fourier transform method for its ability to remove leaked energy in the f-k domain arising from gaps and irregularities during data acquisition. To deal with aliasing in the input data, we implemented an antialiasing weighting function based on piecewise linearity of the seismic data. Seismic images obtained from processing with data regularization show significant signal-to-noise ratio improvement over previous results. Because of the uplift brought by this new interpolation technology and workflow, data interpolation and regularization have become an integral part of Saudi Aramco's land 3D data processing workflow.
Estimation of fracture parameters from reflection seismic data—Part II: Fractured models with orthorhombic symmetry (2000)

Abstract Existing geophysical and geological data indicate that orthorhombic media with a horizontal symmetry plane should be rather common for naturally fractured reservoirs. Here, we consider two orthorhombic models: one that contains parallel vertical fractures embedded in a transversely isotropic background with a vertical symmetry axis (VTI medium) and the other formed by two orthogonal sets of rotationally invariant vertical fractures in a purely isotropic host rock. Using the linear-slip theory, we obtain simple analytic expressions for the anisotropic coefficients of effective orthorhombic media. Under the assumptions of weak anisotropy of the background medium (for the first model) and small compliances of the fractures, all effective anisotropic parameters reduce to the sum of the background values and the parameters associated with each fracture set. For the model with a single fracture system, this result allows us to eliminate the influence of the VTI background by evaluating the differences between the anisotropic parameters defined in the vertical symmetry planes. Subsequently, the fracture weaknesses, which carry information about the density and content of the fracture network, can be estimated in the same way as for fracture-induced transverse isotropy with a horizontal symmetry axis (HTI media) examined in our previous paper (part I). The parameter estimation procedure can be based on the azimuthally dependent reflection traveltimes and prestack amplitudes of P-waves alone if an estimate of the ratio of the P- and S-wave vertical velocities is available. It is beneficial, however, to combine P-wave data with the vertical traveltimes, NMO velocities, or AVO gradients of mode-converted (PS) waves. In each vertical symmetry plane of the model with two orthogonal fracture sets, the anisotropic parameters are largely governed by the weaknesses of the fractures orthogonal to this plane. For weak anisotropy, the fracture sets are essentially decoupled, and their parameters can be estimated by means of two independently performed HTI inversions. The input data for this model must include the vertical velocities (or reflector depth) to resolve the anisotropic coefficients in each vertical symmetry plane rather than just their differences. We also discuss several criteria that can be used to distinguish between the models with one and two fracture sets. For example, the semimajor axis of the P-wave NMO ellipse and the polarization direction of the vertically traveling fast shear wave are always parallel to each other for a single system of fractures, but they may become orthogonal in the medium with two fracture sets.
Simple finite-element model accounts for wide range of cardiac dysrhythmias. (1984)

A simple finite-element model of ventricular conduction processes that explicitly incorporates spatial dispersion of refractoriness was developed. This model revealed that spatial dispersion of refractoriness is a sufficient condition to produce self-sustained reentry even in the absence of unidirectional block, inhomogeneity in local conduction velocities, or the presence of ectopic pacemakers. The model displayed a wide variety of rhythm disturbances qualitatively similar to clinically familiar cardiac dysrhythmias. Electrical stability of the model was determined as a function of the model parameters including ventricular stimulation rate, conduction velocity, and mean refractory period as well as standard deviation of refractory periods. We conclude that spatial dispersion of refractoriness is a sufficient condition to initiate reentrant dysrhythmias but that other physiologic variables such as ventricular rate and conduction velocity strongly influence the dysrhythmogenic effect of spatial dispersion of refractoriness.
Calcium Effects on Phosphorus Absorption: Implications for the Prevention and Co-Therapy of Osteoporosis (2002)

As calcium intake increases without a corresponding increase in phosphorus intake, phosphorus absorption falls and the risk of phosphorus insufficiency rises. Intakes with high Ca:P ratios can occur with use of supplements or food fortificants consisting of non-phosphate calcium salts. Older patients with osteoporosis treated with current generation bone active agents should receive at least some of their calcium co-therapy in the form of a calcium phosphate preparation.
Frequent promoter hypermethylation of Wnt pathway inhibitor genes in malignant astrocytic gliomas (2009)

Aberrant activation of wingless (Wnt) signaling is involved in the pathogenesis of various cancers. Recent studies suggested a role of Wnt signaling in gliomas, the most common primary brain tumors. We investigated 70 gliomas of different malignancy grades for promoter hypermethylation in 8 genes encoding members of the secreted frizzled-related protein (SFRP1, SFRP2, SFRP4, SFRP5), dickkopf (DKK1, DKK3) and naked (NKD1, NKD2) families of Wnt pathway inhibitors. All tumors were additionally analyzed for mutations in exon 3 of the beta-catenin gene (CTNNB1). While none of the tumors carried CTNNB1 mutations, we found frequent promoter hypermethylation of Wnt pathway inhibitor genes, with at least one of these genes being hypermethylated in 6 of 16 diffuse astrocytomas (38%), 4 of 14 anaplastic astrocytomas (29%), 7 of 10 secondary glioblastomas (70%) and 23 of 30 primary glioblastomas (77%). Glioblastomas often demonstrated hypermethylation of 2 or more analyzed genes. Hypermethylation of SFRP1, SFRP2 and NKD2 each occurred in more than 40% of the primary glioblastomas, while DKK1 hypermethylation was found in 50% of secondary glioblastomas. Treatment of SFRP1-, SFRP5-, DKK1-, DKK3-, NKD1- and NKD2-hypermethylated U87-MG glioblastoma cells with 5-aza-2'-deoxycytidine and trichostatin A resulted in increased expression of each gene. Furthermore, SFRP1-hypermethylated gliomas showed significantly lower expression of the respective transcripts when compared with unmethylated tumors. Taken together, our results suggest an important role of epigenetic silencing of Wnt pathway inhibitor genes in astrocytic gliomas, in particular, in glioblastomas, with distinct patterns of hypermethylated genes distinguishing primary from secondary glioblastomas.
Functional changes in salivary glands of autoimmune disease-prone NOD mice (1992)

Lymphocytic infiltration of the salivary glands in autoimmune diseases results in the human condition known as xerostomia. To date, an animal model for the autoimmune development of salivary gland dysfunction has yet to be described. With the autoimmune diabetes-prone nonobese diabetic (NOD) mouse strain, salivary flow rates and total saliva protein concentration in both male and female mice showed a progressive decline in the nondiabetic and diabetic states. Submandibular gland weight decreased from control mice with the progression to onset of diabetes in both sexes, whereas the weight of the parotid gland remained unchanged. The level of saliva amylase activity, when measured relative to unit volume, decreased in nondiabetic males but increased upon onset of diabetes to control values. When expressed relative to protein concentration in saliva, amylase activity was depressed for both sets of NOD mice but was higher upon diabetes onset than in the nondiabetic animals. In females a similar pattern was observed except that amylase activity expressed relative to unit volume was not significantly depressed in either set of NOD mice. The same observations were made for glandular amylase activity. The level of epidermal growth factor (a product of the ductal cells of the submandibular gland) was reduced over 500- and 18-fold for male and female diabetic mice, respectively. Sodium dodecyl sulfate polyacrylamide gels of total saliva showed changes in mobility as well as concentration of several proteins in the NOD mice.(ABSTRACT TRUNCATED AT 250 WORDS)
Rising through the Crisis: the Impact of Emerging Countries on the Future Distribution of Power (2014)

The article reviews the economic performance of the main emerging countries before and throughout the global economic and financial crisis as well as some projections regarding their economic performance in future. It argues that the rising powers’ likely impact upon the future global economic landscape would be a move towards multipolarity, although its outlook presents still many uncertainties.
An algorithm for the display of nucleic acid secondary structure (1982)

A simple algorithm is presented for the graphic display of nucleic acid secondary structure. Examples of secondary structure displays are given for tRNA, 5S RNA and part of the 16S RNA. Due to its speed, this algorithm could easily be used in conjunction with secondary structure programs which calculate various alternate structures.
PixonVision real-time Deblurring Anisoplanaticism Corrector (DAC) (2007)

DigiVision, Inc. and PixonImaging LLC have teamed to develop a real-time Deblurring Anisoplanaticism Corrector (DAC) for the Army. The DAC measures the geometric image warp caused by anisoplanaticism and removes it to rectify and stabilize (dejitter) the incoming image. Each new geometrically corrected image field is combined into a running-average reference image. The image averager employs a higher-order filter that uses temporal bandpass information to help identify true motion of objects and thereby adaptively moderate the contribution of each new pixel to the reference image. This result is then passed to a real-time PixonVision video processor (see paper 6696-04 note, the DAC also first dehazes the incoming video) where additional blur from high-order seeing effects is removed, the image is spatially denoised, and contrast is adjusted in a spatially adaptive manner. We plan to implement the entire algorithm within a few large modern FPGAs on a circuit board for video use. Obvious applications are within the DOD, surveillance and intelligence, security and law enforcement communities. Prototype hardware is scheduled to be available in late 2008. To demonstrate the capabilities of the DAC, we present a software simulation of the algorithm applied to real atmosphere-corrupted video data collected by Sandia Labs.
Revisiting ligand-induced conformational changes in proteins: essence, advancements, implications and future challenges (2012)

Ligand-induced conformational changes are of immense importance for the biological activity of a protein. An in-depth understanding of salutary and deleterious effects of ligand-induced conformational alterations in single- and multi-chain proteins would lend a hand in human welfare. Unlike single-chain proteins, the function of multichain proteins depends upon the inherent properties of the subunit interfaces. The interfaces of temporary oligomeric proteins and the active sites of enzymes are of similar characteristics but the interfaces are more conservative than the active sites. Therefore, these interfaces may possibly be represented as drug targets by inhibition or induction of the oligomerization process. Thus without detailed structural understanding of ligand-induced conformational changes in a protein, structure-based rational drug designing is a great challenging task. So the purpose of this review is to clarify or enlighten the reader at the degree of internal motions related to protein backbone and side-chain flexibility which occur on binding of small molecule to a protein target. This can prove helpful to improve the conformational prediction for a protein-ligand complex. Besides a detailed description of protein-ligand interaction, this review also focuses on structure-activity relationships of protein which will surely help in the rational drug designing.
Protein N-arginine methyltransferase 5 promotes the tumor progression and radioresistance of nasopharyngeal carcinoma (2015)

Radiotherapy resistance is the main cause of the the poor prognosis of some nasopharyngeal carcinoma (NPC) patients. Yet, the exact mechanism is still elusive. In the present study, we explored the clinical and biological role of protein arginine methyltransferase 5 (PRMT5) in NPC. Our results revealed that PRMT5 was overexpressed in NPC tissues when compared with that in adjacent non-tumor tissues by quantitative RT-PCR and immunoblotting. High expression of PRMT5 was correlated with adverse outcomes of NPC patients as determined by the scoring of a tissue microarray. Silencing of PRMT5 promoted the radiosensitivity of 5-8F and CNE2 cells as determined by cell proliferation and colony formation assays. Furthermore, fibroblast growth factor receptor 3 (FGFR3) was identified as one of the downstream targets of PRMT5, and the silencing of PRMT5 decreased the mRNA and protein levels of FGFR3 in the 5-8F and CNE2 cells. Silencing of FGFR3 induced similar phenotypes as the inhibition of PRMT5, and re-expression of FGFR3 in 5-8F/shPRMT5 and CNE2/shPRMT5 cells restored the proliferation and colony formation ability induced by irradiation exposure. Our results indicate that PRMT5 is a marker of poor prognosis in NPC patients. PRMT5 promoted the radioresistance of NPC cells via targeting FGFR3, at least partly if not totally. PRMT5 and its downstream effector FGFR3 may be potential targets for anticancer strategy.
ChemInform Abstract: Phthalylglycine and Phthalylalanine in Heterocyclic Synthesis: Synthesis and Reactions of 4‐Substituted‐phthalazinones. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
An Inverter-Based Analog Front-End for a 56-Gb/s PAM-4 Wireline Transceiver in 16-nm CMOS (2018)

This letter describes an inverter-based analog receiver front-end that was evaluated within a complete ADC-based 56-Gb/s four pulse-amplitude modulation wireline transceiver system. The frontend contains hybrid continuous-time linear equalizers with lowand high-frequency peaking as well as inverter-based programmable gain amplifiers that serve as buffers for the 32× time-interleaved SAR ADC. The inductorless design achieves high bandwidth through a reduced number of equalizer stages (with fewer parasitic poles) and active peaking techniques. The transceiver that contains the analog front-end (AFE) achieves . 10-6 BER over a backplane channel with 35-dB loss at 14 GHz and with 2-mVrms input crosstalk noise. The AFE core occupies 0.00425 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in 16-nm fin field effect transistor CMOS and consumes 165 mW.
ATOMIC IODINE PHOTODISSOCIATION LASER (1964)

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A simple method for the separation and quantification of urinary porphyrins. (1982)

A simple routine method for the separation and quantification of urinary coproporphyrin and uroporphyrin using anion-exchange resin columns is described. The coproporphyrin is first removed from the urine by ether extraction. The anion exchange resin column is then used to isolate the uroporphyrin from the aqueous residue. The proposed method is compared with an existing method developed by Rimington in terms of recovery and reproducibility. Results from 15 urine specimens analysed by both methods are compared. The proposed method yielded lower values for coproporphyrin and higher values for uroporphyrin than the established method, but there was a good correlation between the two methods. This and its relative simplicity make it suitable for routine use.