gebhart/patrepeval huggingface dataset:
Effect of H-NS on the elongation and compaction of single DNA molecules in a nanospace (2013)

The effect of the bacterial heat-stable nucleoid-structuring protein (H-NS) on the conformation of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. With increasing concentration of H-NS, the DNA molecules either elongate or contract. The conformational response is related to filamentation of H-NS on DNA through oligomerization and H-NS mediated bridging of distal DNA segments and is controlled by the concentration and ionic composition of the buffer. Confinement in a nanochannel also facilitates compaction of DNA into a condensed form for over-threshold concentrations of H-NS. Divalent ions such as magnesium facilitate but are not required for bridging nor condensation. The time scale of the collapse after exposure to H-NS was determined to be on the order of minutes, which is much shorter than the measured time required for filamentation of around one hour. We found that the effect of H-NS is not only related to its binding properties but also the confinement is of paramount importance. The interplay between confinement, H-NS-mediated attraction, and filamentation controls the conformation and compaction of DNA. This finding might have implications for gene silencing and chromosome organisation, because the cross-sectional dimensions of the channels are comparable to those of the bacterial nucleoid.
Synthesizing Realistic Vehicular Mobility for More Precise Simulation of Inter-vehicle Communication (2007)

Recently many researches about transmission of traffic information among vehicles by using inter-vehicle communication without any load side infrastructures have been studied. In order to evaluate performance of such inter-vehicle communication, traffic simulators are widely used. However, in most of existing traffic simulators, distance between two following vehicles is modeled as equals based on statistical flow rates. Such mobility models do not reflect real performance of inter-vehicle communication, In this paper, we extract particular characteristics of real vehicular mobility from several traces of vehicular movement, formulate them formally, implement the formulated realistic vehicular mobility on an existing traffic simulator and obtain more real performance of inter-vehicle communication. In the extracted vehicular mobility, each vehicle runs at a different speed, with different distance from the vehicle ahead, and with different vehicular density/distribution while the bottleneck capacity and saturation flow rate of the target roads are preserved as the same as those on the original one. We have shown that performance of inter-vehicle communication is rather different between the proposed mobility and original mobility by evaluating the reachable hop counts of multi-hop communication and performance of the DSR protocol.
Molecular cloning, testicular postnatal expression, and oocyte-activating potential of porcine phospholipase Cζ (2006)

The molecular mechanism by which sperm triggers Ca2+ oscillation, oocyte activation, and early embryonic development has not been clarified. Recently, oocyte activation has been shown to be induced by sperm-specific phospholipase Czeta (PLCzeta). The ability of PLCzeta to induce oocyte activation is highly conserved across vertebrates. In the present study, porcine PLCzeta cDNA was identified and the nucleotide sequence was determined. The expression pattern of porcine PLCzeta mRNA during the period of postnatal testicular development was shown to be similar to that of mouse PLCzeta. PLCzeta mRNA expression in the pig and mouse was detected only in the testes when the elongated spermatids had differentiated, and was detected from day 96 after birth in the pig. Histological examination of porcine testis during the period of postnatal development revealed the presence of spermatozoa from day 110 after birth. These findings suggest that the synthesis of PLCzeta mRNA starts when spermiogenesis is initiated. Microinjection of porcine PLCzeta complementary RNA into porcine oocytes demonstrated that porcine PLCzeta has the ability to trigger repetitive Ca2+ transients in porcine oocytes similar to that observed during fertilization. It was also found that porcine PLCzeta cRNA has the potential to induce oocyte activation and initiate embryonic development up to the blastocyst stage.
Brain TRF Immunoreactivity during Various Physiological and Stress Conditions in the Rat (1979)

Methanol extracts of several rat tissues (hypothalamus, amygdala, the rest of the forebrain, brain stem and pancreas) were partially purified in SP-cation exchange chromatography and measured in TRF radioimmunoassay. It was found that hypothalamic and amygdaloid TRF contents were highest during the light period of the day, but brain stem TRF had an opposite rhythm. Hypothalamic TRF content rose after 10 min by 14% (p less than 0.05) when the rats were exposed to transfer stress. During short-time immobilization stress tests, hypothalamic TRF rose by 41% (p less than 0.05) after a 10-sec immobilization. Cold exposure did not produce any changes in hypothalamic TRF contents within 45 min. Handling stress and time of day appear to be the most important factors influencing the hypothalamic TRF content and have to be taken into account when measuring TRF.
Automated Honeynet Deployment for Dynamic Network Environment (2013)

One of the challenges facing information technology (IT) security professionals is the laborious task of sifting through numerous log files in an attempt to identify malicious traffic and conduct a forensics analysis to determine an appropriate course of action. This process is complicated significantly by the volume of traffic that can be associated with a production device environment. A honey net can provide a mechanism to identify much of the forensically interesting traffic by creating a representative system to collect traffic data. However, it is challenging to maintain an accurate representation of a dynamic system in order to consistently collect the appropriate data of interest. This research effort addresses a current challenge identified by researchers at the Honey net Project by describing a methodology for automatically creating and dynamically updating a honey net in order to facilitate IDS support.
IC‐P‐049: AMYLOIDOSIS CHANGES ASSOCIATIONS BETWEEN HIPPOCAMPUS VOLUME AND BRAIN METABOLIC DECLINES (2014)

The cerebral metabolic rate of glucose measured by Positron Emission Tomography (PET) using [18 F]FDG is often used as a biomarker of neurodegeneration in Alzheimer's disease (AD) and healthy aging. Mechanism underlying hypometabolism in these populations has been attributed to brain amyloidosis, tauopathy or cell depletion. Here, we investigate the link between hippocampal volume and regional hypometabolism in normal and an AD animal model (transgenic rat McGill-R-Thy1-APP) harbouring brain amyloidosis. This model shows the effects of amyloidosis on biomarkers in the absence of tauopathy or cell depletion. We hypothesized a distinct association pattern between rate of metabolic decline in hippocampal projections and hippocampal volume in TG animals. A total of 15 rats with a mean age of 16.6 months were used for this study. Hippocampus volumes were computed using structural Magnetic Resonance Imaging (MRI). The images [18F]FDG were acquired using PET at baseline and follow-up. Then the percent change of FDG values were calculated with respect to the baseline values. Whole brain images were obtained by MRI using Fast Imaging with Steady State Precession. PET images were then correlated at a voxel level with the hippocampus volume from the MRI images. In WT, average volumes in total brain and hippocampus (mm3) at baseline were 2418.91 ± 142.68 and 78.76 ± 5.98, respectively. In TG, average volume in total brain and hippocampus were 2390.31 ± 210.00 and 81.68 ± 8.28, respectively. In WT, average follow-up total brain volume and hippocampus were 2454.45 ± 131.99 and 76.9875 ± 2.67, respectively; and 2392.13 ± 208.64 and 75.48 ± 8.75, respectively in TG. Changes in FDG and hippocampal volume in WT were -0.72 ± 6.7% and 5.3 ± 5.0%, respectively and in TG were 6.1 ± 11% and 6.2 ± 3.4%, respectively. In WT, 6-month hypometabolism in frontal, temporal, cingulate cortex and striatum were associated with individual baseline hippocampal volumes. In TG, 6-month hypometabolism in the amygdala, basal forebrain, cingulate cortex and striatum were associated with individual baseline hippocampal volumes.
Effects of multi-walled fullerene-like particles on tribological properties of a-C:H DLCs under boundary lubrication (2023)

Suitable friction modifiers and anti-wear additives for hydrogenated amorphas carbon (a-C:H) films have been investigated by many research groups for a decade since it is well-known that the combination of the a-C:H film and the conventional additives hardly exhibits good tribological performances under boundary lubrication. In this study, to confirm the effectiveness of nano-carbon additives for improving the tribological performance of a-C:H films, the tribological performances of the combination of the a-C:H film and multi-walled fullerenes (MWFs) containing oil was investigated under boundary lubrication. Especially, we compared the effects of the MWFs on the tribological performances of two DLCs: a-C:H and tetrahedral amorphous carbon (ta-C) using a ball-on disk tribometer and in-contact Raman tribometer that can monitor the chemical structure of frictional interfaces. All our results suggest that the combination of a-C:Hs and MWFs exhibits an ultralow friction and remarkable wear reduction compared to non-MWF added oils due to the formation of MWF tribofilms uniformly at the frictional interfaces.
Seismic stimulation for enhanced oil recovery (2008)

Thepore-scaleeffectsofseismicstimulationontwo-phase flow are modeled numerically in random 2D grain0pack geometries.Seismicstimulationaimstoenhanceoilproduction by sending seismic waves across a reservoir to liberate immobile patches of oil. For seismic amplitudes above a welldefined analytically expressed dimensionless criterion, the force perturbation associated with the waves indeed can liberateoiltrappedoncapillarybarriersandgetitflowingagain under the background pressure gradient. Subsequent coalescence of the freed oil droplets acts to enhance oil movement further because longer bubbles overcome capillary barriers more efficiently than shorter bubbles do. Poroelasticity theory defines the effective force that a seismic wave adds to the background fluid-pressure gradient. The lattice-Boltzmann model in two dimensions is used to perform pore-scale numerical simulations. Dimensionless numbers groups of material and force parameters involved in seismic stimulation aredefinedcarefullysothatnumericalsimulationscanbeapplied to field-scale conditions. Using the analytical criteria defined in the paper, there is a significant range of reservoir conditionsoverwhichseismicstimulationcanbeexpectedto enhanceoilproduction.
JiTI: A Robust Just in Time Instrumentation Technique (2000)

In this paper, we describe JiTI, a novel technique for instrumenting program binaries. The technique correctly deals with programs that contain traditionally hard to instrument features such as data in code, code in data, and self-modifying code. The technique does not require reverse engineering, program understanding tools or heuristics about the compiler or linker used. The basic is that a running process is cloned in memory, and that the cloned process is completely instrumented (code + data). By using the code of the instrumented process (clone) on the data of the original process, we can guarantee a correct instrumentation of the full code while keeping the process data untouched. JiTI has been completely implemented for SPARC processors and is used in a data race detector.
Sildenafil Improves the Beneficial Haemodynamic Effects of Intravenous Nitrite Infusion during Acute Pulmonary Embolism (2008)

Acute pulmonary embolism produces acute pulmonary hypertension, which can be counteracted by activating the nitric oxide-cyclic guanosine 3',5'-monophosphate (cGMP) pathway. While previous studies have shown that sildenafil (an inhibitor of cGMP-specific phosphodiesterase type 5) or nitrite (a storage molecule for nitric oxide) produces beneficial effects during acute pulmonary embolism, no previous study has examined whether the combination of these drugs can produce additive effects. Here, we expand previous findings and examine whether sildenafil enhances the beneficial haemodynamic effects produced by a low-dose infusion of nitrite in a dog model of acute pulmonary embolism. Haemodynamic and arterial blood gas evaluations were performed in non-embolized dogs treated with saline (n = 4), and in embolized dogs (intravenous injections of microspheres) that received nitrite (6.75 micromol/kg intravenously over 15 min. followed by 0.28 micromol/kg/min.) and sildenafil (0.25 mg/kg over 30 min.; n = 8), or nitrite followed by saline (n = 8), or saline followed by sildenafil (n = 7), or only saline (n = 8). Plasma thiobarbituric acid-reactive substances (TBARS) concentrations were determined using a fluorometric method. Acute pulmonary embolism increased pulmonary artery pressure by approximately 24 mmHg. While the infusion of nitrite or sildenafil infusions reversed this increase by approximately 42% (both P < 0.05), the combined infusion of both drugs reversed this increase by approximately 58% (P < 0.05). Similar effects were seen on the pulmonary vascular resistance index. Nitrite or sildenafil alone produced no significant hypotension. However, the combined infusion of both drugs caused transient hypotension (P < 0.05). Both drugs, either alone or combined, blunted the increase in TBARS concentrations caused by acute pulmonary embolism (all P < 0.05). These results suggest that sildenafil improves the beneficial haemodynamic effects of nitrite during acute pulmonary embolism.
Annual Morphological Cycles of Testis and Thumb Pad of the Male Frog (Rana ridibunda) (2008)

In this study, Rana ridibunda was used as samples because of their wide use in Turkey. Male frogs were collected in the East Marmara region each month throughout 1 year. Frogs from every monthly collection were used to analyze structural components of the thumb pads and testes. Spermatogenetic activity of Rana ridibunda living in the East Marmara region was determined to be "potentially continuous" type. Generally, the increase in the number and the size of nuclei of Leydig cells was inversely proportional to the fluctuation of spermatogenetic activity. The lumen of the seminiferous tubules in testes contained, in addition to the spermatogenic cells, a Periodic-acid Schiff-positive granular material. The amount of this material varied throughout the year, and that finding suggested a function related to spermiation. The components of thumb pads exhibited structural changes with respect to the activities of Leydig cells. During the periods where the Leydig cells were active, mucus glands (also called breeding glands) of thumb pads were also developed. On the other hand, we observed mixed glands with unknown function, which as first reported by us, and were poison glands in the thumb pads. The results suggest structural changes in the thumb pads are linked to changes in the testes.
Contribution of Bradykinin B1 and B2 Receptors in Allergen-induced Bronchial Hyperresponsiveness (1999)

Bradykinin (BK) is a peptide mediator generated at sites of inflammation and its effects are mediated through constitutively expressed B(2) receptor or through induction of B(1) receptors. We examined the role of these receptors in bronchial hyperresponsiveness (BHR). Brown-Norway rats sensitized with ovalbumin (OA) and Al(OH)(3) intraperitoneally, were exposed 3 wk later to either saline or OA aerosol. B(1) receptor antagonist desArg(10)[Hoe140] (200 nmol/kg or 1 micromol/kg, intraperitoneally) or B(2) receptor antagonist Hoe140 (200 nmol/kg, intraperitoneally) was administered 30 min before allergen exposure. Hoe140 had no effect on OA-induced BHR to acetylcholine (ACh) and bronchoalveolar lavage fluid (BALF) cellular profiles, but inhibited bronchoconstriction to BK (p < 0.04). At both doses, desArg(10)[Hoe140] dose-dependently inhibited allergen-induced BHR to ACh (p < 0.01), but had no effect on bronchoconstriction to BK or baseline ACh responsiveness. The inflammatory cells in BALF were not affected apart from reduced lymphocyte numbers at the highest dose. B(1) receptor mRNA expression measured by Northern analysis was increased after allergen exposure in sensitized lungs, with a peak at 2 to 6 h after exposure, whereas B(2) receptor mRNA expression remained unchanged. Newly induced BK B(1) receptors may be involved in allergen-induced BHR to ACh, whereas constitutive B(2) receptors mediate BK-induced bronchoconstriction.
Energy-efficient C-dump converters for switched reluctance motors (1997)

Two energy-efficient converter topologies, derived from the conventional C-dump converter, are proposed for switched reluctance motor (SRM) drives. The proposed topologies overcome the limitations of the conventional C-dump converter, and could reduce the overall cost of the SRM drive. The voltage ratings of the dump capacitor and some of the switching devices in the proposed converters are reduced to the supply voltage (V/sub dc/) level compared to twice the supply voltage (2V/sub dc/) in the conventional C-dump converter. Also, the size of the dump inductor is considerably reduced. The converters have simple control requirements, and allow the motor phase current to freewheel during chopping mode. Simulation and experimental results of the converters are presented and discussed.
Exercise-induced Bronchoconstriction: Reproducibility of Hyperpolarized3He MR Imaging (2012)

The reported measures of reproducibility of HPHe MR imaging may help in the design and interpretation of single- and multicenter studies of patients with exercise-induced bronchoconstriction.
Supplementary Figure 2 from Combining ABCG2 Inhibitors with IMMU-132, an Anti–Trop-2 Antibody Conjugate of SN-38, Overcomes Resistance to SN-38 in Breast and Gastric Cancers (2023)

&lt;p&gt;Molecular Structure of IMMU-132&lt;/p&gt;
Supplementary Report from Robust Gene Expression Signature from Formalin-Fixed Paraffin-Embedded Samples Predicts Prognosis of Non–Small-Cell Lung Cancer Patients (2023)

&lt;p&gt;PDF file - 315K, Sweave Report&lt;/p&gt;
Philips 3D Solutions: From Content Creation to Visualization (2006)

Philips is realizing an end-to-end 3D display solution from 3D content creation to visualization. This development fits in our long-standing tradition of combining expertise in video processing with our strength in display development to create the most exciting and best viewing experience. Philips developed several high-quality 3D displays, ranging in resolution, viewing angle, depth experience, and sizes from 4" to 40" and up. Backwards compatibility with 2D content is enabled via signal processing or opto-electronic 3D & 2D dual mode displays. Content creation and conversion methods are provided, which are a key factor for the success of 3D displays. Fully automatic conversion from monoscopic 2D content into 3D enables the re-use of all existing 2D video material. Further methods enable 3D animation/design, 2D to 3D conversion in post- production and live capture of new 3D content. Our efforts in MPEG standardization towards the "2D-plus-depth" format for 3D video enables a flexible interface between the variety in 3D content creation methods and the range in 3D displays. Furthermore, the 3D format is compatible with existing 2D content, standards and infrastructure. Currently, Philips offers several commercial 3D products for professional use such as digital signage, and progress is being made towards consumer products such as 3DTV.
Un prototipo di Gait Trainer (2011)

Le disabilità motorie sono impedimenti importanti dell’individuo, siano esse temporanee o permanenti, e sono causa di limitazioni alle attività del vivere quotidiano. Le disabilità motorie sono causate da lesioni vertebrali, da malattie cerebrovascolari,da malattie neurologiche, ecc. Il numero di persone che ci soffre è in crescita in tutto il mondo, a causa dell’aumento della popolazione e dell’invecchiamento. Se si fa riferimento alle sole persone con lesione midollare, il Ministero della Salute stima il loro numero intorno alle 70.000, con un trend in aumento di circa 2.500 nuovi casi ogni anno. In Italia le cause più frequenti sono gli incidenti stradali e gli infortuni sul lavoro.
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality (2016)

The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of reference genomes can impact comprehensive annotation of metatranscriptomes. Consequently, beyond the application of standardized pipelines, additional caution must be taken when interpreting their output and performing downstream, microbiome-specific, analyses. The pipeline used in these analyses along with a tutorial has been made freely available for download from our project website: http://www.compsysbio.org/microbiome .
A Novel Hybrid Approach to Selecting Marker Genes for Cancer Classification Using Gene Expression Data (2007)

Selecting a subset of marker genes from thousands of genes is an important topic in microarray experiments for diseases classification and prediction. In this paper, we proposed a novel hybrid approach that combines gene ranking, heuristic clustering analysis and wrapper method to select marker genes for tumor classification. In our method, we firstly employed gene filtering to select the informative genes; secondly, we extracted a set of prototype genes as the representative of the informative genes by heuristic K-means clustering; finally, employed SVM- RFE to find marker genes from the representative genes based on recursive feature elimination. The performance of our method was evaluated by AML/ALL microarray dataset. The experimental results revealed that our method could find very small subset of marker genes with minimum redundancy but got better classification accuracy.
Intelligence Communication in the Digital Era (2015)

This edited volume argues that producers of analysis need to shift from producing static, narrative products to much more dynamic, digitally-based platforms in order to remain competitive and relevant
Reproductive Biology of the Cigarette Beetle, Lasioderma serricorne1 2. Ovarian Development and Female Sexual Maturity2,3,4 (1973)

Journal Article Reproductive Biology of the Cigarette Beetle, Lasioderma serricorne 2. Ovarian Development and Female Sexual Maturity,, Get access James A. Coffelt, James A. Coffelt 5 5Graduate Research Assistant, Department of Entomology, University of Wisconsin, Madison. Present address: Agricultural Research Service, USDA, P.O. Box 14S6S, Gainesville, Fla. 32601. Search for other works by this author on: Oxford Academic Google Scholar W. E. Burkholder W. E. Burkholder 6Investigations Leader. Agricultural Research Service, USDA, University of Wisconsin, Madison 53706. Search for other works by this author on: Oxford Academic Google Scholar Annals of the Entomological Society of America, Volume 66, Issue 2, 15 March 1973, Pages 368–372, https://doi.org/10.1093/aesa/66.2.368 Published: 15 March 1973 Article history Received: 30 August 1972 Published: 15 March 1973