gebhart/patrepeval huggingface dataset:
Small Nuclear RNA Genes Transcribed by Either RNA Polymerase II or RNA Polymerase III in Monocot Plants Share Three Promoter Elements and Use a Strategy To Regulate Gene Expression Different from That Used by Their Dicot Plant Counterparts (1994)

RNA polymerase (Pol) II- and RNA Pol III-transcribed small nuclear RNA (snRNA) genes of dicotyledonous plants contain two essential upstream promoter elements, the USE and TATA. The USE is a highly conserved plant snRNA gene-specific element, and its distance from the -30 TATA box, corresponding to approximately three and four helical DNA turns in Pol III and Pol II genes, respectively, is crucial for determining RNA Pol specificity of transcription. Sequences upstream of the USE play no role in snRNA gene transcription in dicot plants. Here we show that for expression of snRNA genes in maize, a monocotyledonous plant, the USE and TATA elements are essential, but not sufficient, for transcription. Efficient expression of both Pol II- and Pol III-specific snRNA genes in transfected maize protoplasts requires an additional element(s) positioned upstream of the USE. This element, named MSP (for monocot-specific promoter; consensus, RGCCCR), is present in one to three copies in monocot snRNA genes and is interchangeable between Pol II- and Pol III-specific genes. The efficiency of snRNA gene expression in maize protoplast is determined primarily by the strength of the MSP element(s); this contrasts with the situation in protoplasts of a dicot plant, Nicotiana plumbaginifolia, where promoter strength is a function of the quality of the USE element. Interestingly, the organization of monocot Pol III-specific snRNA gene promoters closely resembles those of equivalent vertebrate promoters. The data are discussed in the context of the coevolution of Pol II- and Pol III-specific snRNA gene promoters within many eukaryotic organisms.
Special Section Guest Editorial: Artificial Intelligence in Medical Imaging (2018)

This editorial provides an overview of the articles in the special section.
Transport properties of uniaxially oriented aliphatic polyketone (2004)

Abstract The oxygen, carbon dioxide, and water‐transport properties of a uniaxially oriented aliphatic polyketone were determined. The polyketone was drawn to 5–10 times its original length. The transport properties were related to changes in crystallinity estimated by differential scanning calorimetry and density measurements and by changes in the molecular and crystal orientation assessed by, respectively, infrared and X‐ray spectroscopy. The film structures were characterized by confocal scanning laser microscopy and scanning electron microscopy. Stress‐strain tests on the drawn specimens enabled the impacts of orientation on the transport and mechanical properties to be compared. A draw‐induced increase in crystallinity and molecular orientation yielded permeabilities at a draw ratio of 10 that were 30–40% of the original value, and the percentage decrease was basically independent of the type of gas/vapor molecule. Also, the diffusivities of oxygen and carbon dioxide decreased by an order of magnitude. The fact that the amorphous permeability was peaking at a draw ratio of about 5 was a consequence of a peak in amorphous solubility, which was very high for oxygen and absent for water. It was suggested that the peak in solubility was mainly caused by the destruction of the polymer hydrogen‐bond network during drawing and crystal reorientation. The impact of structural reorganization within the polymer and presence of surface valleys seemed to have less impact on the mechanical properties than on the transport properties. This suggested that transport data are more sensitive than mechanical data in probing material defects and changes in molecular packing and morphology. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 947–955, 2004
ChainQueen: A Real-Time Differentiable Physical Simulator for Soft Robotics (2019)

Physical simulators have been widely used in robot planning and control. Among them, differentiable simulators are particularly favored, as they can be incorporated into gradient-based optimization algorithms that are efficient in solving inverse problems such as optimal control and motion planning. Therefore, rigid body simulators and recently their differentiable variants are studied extensively. Simulating deformable objects is, however, more challenging compared to rigid body dynamics. The underlying physical laws of deformable objects are more complex, and the resulting systems have orders of magnitude more degrees of freedom and there-fore they are significantly more computationally expensive to simulate. Computing gradients with respect to physical design or controller parameters is typically even more computationally challenging. In this paper, we propose a real-time, differentiable hybrid Lagrangian-Eulerian physical simulator for deformable objects, ChainQueen, based on the Moving Least Squares Material Point Method (MLS-MPM). MLS-MPM can simulate deformable objects with collisions and can be seamlessly incorporated into soft robotic systems. We demonstrate that our simulator achieves high precision in both forward simulation and backward gradient computation. We have successfully employed it in a diverse set of inference, control and co-design tasks for soft robotics.
A model for a fly-wheel driven by a grid connected Switch Reluctance Machine (2008)

This paper presents a PSCAD based simulation model for a grid-connected Switch Reluctance Machine (SRM), which drives a fly-wheel. The system can be used as an effective means to improve power quality issues, such as LVRT, voltage sags, sudden load demands, etc., that encountered in typical power networks. The proposed PSCAD model consists of two separate modules- one for the SRM and the other for the grid side power interface. The SRM module has the flexibility to operate both in motoring and generating modes whereas the power interface module facilitates the bidirectional power flow between the grid and the flywheel in accordance with the mode of operation of the SRM. During standby operation of the flywheel, both modules ensure that the speed of the flywheel is maintained at the desired constant value by operating the SRM machine in the motoring mode. In the event of grid supply failure or voltage sag or sudden load increase, the modules change their mode of operation to generation, during which the flywheel provides its stored kinetic energy back into the grid. Results, for both motoring and generating, are presented as a proof of the validity of proposed simulation module, which can be considered as a valuable tool for investigating grid-connected SRM machines.
Material discrimination by heat flow sensing (2009)

We propose a heat flow sensing device with a heat source to discriminate a contact object. The device was a three-layered structure separated by 600 mum-thick PDMS (Polydimethylsiloxane) spacer, and consisted of a micro heater and three resistance-temperature detectors (RTD). We detected transient heat flow with pulse-heating method when 10 mm-cubic blocks of cork, acrylic and aluminum were on contact with the device. Temperature gradient induced by heat flow differed by materials of contact objects. We also evaluated the surface temperature from two RTDs. Our device identified relative difference in thermal effusivity of materials.
Transparent Radio–Fiber–Radio–Fiber System in 100-GHz Band for Indoor Uplink Signal Transmission in Beyond 5G (2023)

We demonstrate the first radio–fiber–radio–fiber system for transparent delivery of 100-GHz radio signals from indoor to a central station. We successfully transmitted 16-QAM single-carrier and OFDM signals with line rates of approximately 30 and 40 Gb/s over the system consisting of two cascaded wireless–RoF links in the 100-GHz band.
Endo-lysosomal dysregulations and late-onset Alzheimer’s disease: impact of genetic risk factors (2019)

Increasing evidence supports that cellular dysregulations in the degradative routes contribute to the initiation and progression of neurodegenerative diseases, including Alzheimer's disease. Autophagy and endolysosomal homeostasis need to be maintained throughout life as they are major cellular mechanisms involved in both the production of toxic amyloid peptides and the clearance of misfolded or aggregated proteins. As such, alterations in endolysosomal and autophagic flux, as a measure of degradation activity in these routes or compartments, may directly impact as well on disease-related mechanisms such as amyloid-β clearance through the blood-brain-barrier and the interneuronal spreading of amyloid-β and/or Tau seeds, affecting synaptic function, plasticity and metabolism. The emerging of several genetic risk factors for late-onset Alzheimer's disease that are functionally related to endocytic transport regulation, including cholesterol metabolism and clearance, supports the notion that in particular the autophagy/lysosomal flux might become more vulnerable during ageing thereby contributing to disease onset. In this review we discuss our current knowledge of the risk genes APOE4, BIN1, CD2AP, PICALM, PLD3 and TREM2 and their impact on endolysosomal (dys)regulations in the light of late-onset Alzheimer's disease pathology.
La biosurveillance des micropolluants : Comment en sommes nous arrivés à encager des gammares? (2017)

[Departement_IRSTEA]Eaux [TR1_IRSTEA]BELCA
Search for vectorlikeBquarks in events with one isolated lepton, missing transverse momentum, and jets ats=8  TeVwith the ATLAS detector (2015)

A search has been performed for pair production of heavy vectorlike down-type ($B$) quarks. The analysis explores the lepton-plus-jets final state, characterized by events with one isolated charged lepton (electron or muon), significant missing transverse momentum, and multiple jets. One or more jets are required to be tagged as arising from $b$ quarks, and at least one pair of jets must be tagged as arising from the hadronic decay of an electroweak boson. The analysis uses the full data sample of $pp$ collisions recorded in 2012 by the ATLAS detector at the LHC, operating at a center-of-mass energy of 8 TeV, corresponding to an integrated luminosity of $20.3\text{ }\text{ }{\mathrm{fb}}^{\ensuremath{-}1}$. No significant excess of events is observed above the expected background. Limits are set on vectorlike $B$ production, as a function of the $B$ branching ratios, assuming the allowable decay modes are $B\ensuremath{\rightarrow}Wt/Zb/Hb$. In the chiral limit with a branching ratio of 100% for the decay $B\ensuremath{\rightarrow}Wt$, the observed (expected) 95% C.L. lower limit on the vectorlike $B$ mass is 810 GeV (760 GeV). In the case where the vectorlike $B$ quark has branching ratio values corresponding to those of an $SU(2)$ singlet state, the observed (expected) 95% C.L. lower limit on the vectorlike $B$ mass is 640 GeV (505 GeV). The same analysis, when used to investigate pair production of a colored, charge $5/3$ exotic fermion ${T}_{5/3}$, with subsequent decay ${T}_{5/3}\ensuremath{\rightarrow}Wt$, sets an observed (expected) 95% C.L. lower limit on the ${T}_{5/3}$ mass of 840 GeV (780 GeV).
Identification of a Signal Peptide for Unconventional Secretion (2007)

Homeoproteins are a class of transcription factors defined by the structure of their DNA-binding domain, the homeodomain. In addition to their nuclear cell-autonomous activities, homeoproteins transfer between cells, thanks to two separate steps of secretion and internalization, which both rely on unconventional mechanisms. Internalization is driven by the third helix of the homeodomain (Penetratin) through a non-vesicular and endocytosis-independent mechanism. In contrast, homeoprotein secretion involves vesicular compartments and requires the presence of a sequence of 11 amino acids (Sec sequence) spanning between the second and third helix of the homeodomain. In this study, we report that the SecPen polypeptide, which combines the two identified domains, Penetratin and Sec, bears all of the necessary information to go in and out of cells. We have analyzed key mechanisms and demonstrated that this peptide can efficiently cross a tight junction epithelium.
Method and apparatus for measuring purity of noble gases (2023)

A device for detecting impurities in a noble gas includes a detection chamber and a source of pulsed ultraviolet light. The pulse of the ultraviolet light is transferred into the detection chamber and onto a photocathode, thereby emitting a cloud of free electrons into the noble gas within the detection chamber. The cloud of electrons is attracted to the opposite end of the detection chamber by a high positive voltage potential at that end and focused onto a sensing anode. If there are impurities in the noble gas, some or all of the electrons within the cloud will bond with the impurity molecules and not reach the sensing anode. Therefore, measuring a lower signal at the sensing anode indicates a higher level of impurities while sensing a higher signal indicates fewer impurities. Impurities in the range of one part per billion can be measured by this device.
Do Shales Swell? A Critical Review of Available Evidence (1995)

Abstract A vast majority of drilling problems occur in shales. The traditional explanation is that Shales swell when contacted with water. As the use of oil based muds becomes more difficult, recent years have seen a large numberof publications dedicated to the study of water/shale interaction.Unfortunately, this large body of evidence contains too many contradictions to be trusted as a sound basis for engineering. A two years long critical review of this material was therefore undertaken revealing that most experimental observations performed in the laboratory were not representative of downhole conditions as air or water vapor had been introduced in the samples, leading to capillary phenomena which have been mistaken for swelling. Further observations revealed that true swelling is unlikely to be an issue downhole. Upon contact with drilling fluids, the occurrence of mineralogical transformations affecting the shale was identified and it was further shown that such transformations will affect the mechanical response of the rock.
Improvement of audio-visual score following in robot ensemble with human guitarist (2012)

Our goal is to create an ensemble between human guitarists and music robots, e.g., singing and playing instruments robots. Such robots need to detect the tempo and beat time of the music. Score following and beat tracking, which requires and does not requires a score, are commonly used for this purpose. Score following is an incremental audio-to-score alignment. Although most score following methods assume that players have a precise score, most scores for guitarists have only melody and chord sequences without any beat patterns. An audio-visual beat tracking for guitarists is reported that improves the accuracy of beat detection. However, the result of this method is still insufficient because it uses only onset information, not pitch information, and because the hand tracking shows low accuracy. In this paper, we report a multimodal score following for a guitar performance, an extension of an audio-visual beat tracking method. The main difference is to use chord sequences to improve tracking of audio signals and depth information to improve tracking of guitar playing. Chord sequences are used for the calculation of chord correlation between the input and a score. Depth information is used in the guitar plane masking by three dimensional Hough transform, for the stable detection of a hand. Finally, the system extracts score positions and tempos by a particle-filter based integration of audio and visual features, The resulting score following system improves the tempo and the score position of a performance by 0.2 [sec] compared to an existing system.
ChemInform Abstract: Synthesis of Stoichiometric Cadmium Selenide Films via Sequential Monolayer Electrodeposition. (1992)

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.
Gradient-based blind iterative techniques for I/Q imbalance compensation in digital radio receivers (2007)

This paper considers the radio implementation related I/Q imbalance problem and its digital compensation in direct-conversion and low-IF type radio receivers. In general, I/Q imbalances result in mirror-frequency interference and can severely limit the receiver dynamic range and sensitivity, if not taken properly into account. Here the compensation algorithm developments build on the so-called circular nature of complex-valued communications waveforms which is known to hold only under perfect I/Q balance. A well-behaving non-circularity measure is first formed which is then minimized iteratively using gradient-descent type approach. The derived compensator is computationally simple and operates blindly on the received signal, meaning that no known training or pilot data is needed. The compensation performance of the proposed method is analyzed using extensive computer simulations and is shown to outperform the state-of-the-art adaptive reference techniques by several dB's, when measured in terms of the obtained overall mirror-frequency attenuation.
Neutron scattering in the biological sciences: progress and prospects (2018)

The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
Comparisons of a computer-based propagation prediction tool with experimental data collected in urban microcellular environments (1997)

Engineers designing and installing outdoor and indoor wireless communications systems need effective and practical tools to help them determine base station antenna locations for adequate signal coverage. Computer-based radio propagation prediction tools are now often used in designing these systems. We assess the performance of such a propagation tool based on ray-tracing and advanced computational methods. We have compared its predictions with outdoor experimental data collected in Manhattan and Boston (at 900 MHz and 2 GHz). The comparisons show that the computer-based propagation tool can predict signal strengths in these environments with very good accuracy. The prediction errors are within 6 dB in both mean and standard deviation. This shows that simulations, rather than costly field measurements, can lead to accurate determination of the coverage area for a given system design.
Carbon Ion Therapy: on the importance of target size for selective boosting of hypoxic tumor subvolumina (2010)

On the importance of choice of target size for selective boosting of hypoxic tumor subvolumina in carbon ion therapy<br/><br/><br/>Purpose:<br/>Functional imaging methods in radiotherapy are maturing and can to some extent uncover radio resistant structures found within a tumour entity. Selective boost of identified hypoxic subvolumina with high-LET radiation may in principle lead to increased tumour control due to LET-dependence of the oxygen enhancement ratio (OER). Here, we demonstrate the importance of minimizing field sizes in order not to dilute the dose average LET by quantifying the OER as a function of PTV size and PTV position.<br/><br/>Methods:<br/>Several treatment plans are produced with TRiP, using a 256x256x256 mm&lt;sup&gt;3&lt;/sup&gt; water phantom and SOBP optimization on physical dose. Box formed PTV volumes between 0.15 - 1010 cm&lt;sup&gt;3&lt;/sup&gt;, and PTV positions ranging from 3 cm to 200 cm depth (relative to the surface where the beam enters) are examined. For each plan the minimum, maximum and the dose averaged LET of the PTV is calculated. The numbers are translated to OER using several sets of data found in literature for various cell lines.<br/><br/>Results:<br/>We find a strong dependence of the dose average LET and OER as a function of PTV volume. Dose averaged LET varies between 41 keV/µm (1010 cm&lt;sup&gt;3&lt;/sup&gt;) and 110 keV/µm (0.15 cm&lt;sup&gt;3&lt;/sup&gt;). The respective OERs range from 2.2 to 1.3 (Barendsen et al. 1966) and from 2.9 to 1.8 (Furusawa et al. 2000, both HSG and V79 data). Varying the position of the PTV for a 127.5 cm&lt;sup&gt;3&lt;/sup&gt; volume we find 52 keV/µm at 30 cm depth and 60 keV/µm at 200 cm depth.<br/><br/>Conclusion:<br/>In order to maximize effects of high-LET radiation, fields should be kept small and confined to hypoxic structures of the tumour entity. Deep seated tumours may additionally reduce the possible achievable effect. All cell lines investigated here did not reach an OER of 1, even for the smaller structures, which may indicate that the achievable dose average LET of carbon ions is too low, and heavier ions than carbon may be considered for functional LET-painting. <br/><br/><br/>
P1‐413: The first results of amyloid imaging in Japanese Alzheimer's Disease Neuroimaging Initiative (J‐ADNI) study (2010)

Alzheimer's Disease Neuroimaging Initiative in Japan (J-ADNI) project has been launched enacting a harmonized protocol with US and world-wide ADNI studies. Thirty-eight clinical sites recruit a total of 600 subjects: 300 mild cognitive impairements (MCI), 150 Alzheimer's disease (AD), and 150 cognitively normals (CN), and candidates of surrogate markers such as MRI, FDG-PET, PiB-PET, BF227-PET, CSF biomarkers are being accumulated. Among registered 296 subjects as of January 2010, amyloid PET was acquired in 45%, and FDG-PET was obtained in 75% of the total participants. Here we demonstrate the first preliminary results of amyloid PET in J-ADNI. The first 75 baseline PiB scans from 9 PET centers were analyzed with demographic information including APOE genotype. A bolus injection of [C-11]PiB (537 ± 70 MBq) was followed by a 70-min 3D dynamic scan. A sum image of 50-70 min and a parametric image of distribution volume by Logan graphical analysis were created in each subject, and evaluated in reference to the cerebellar cortex measures, that is SUVR and DVR, for both visual diagnosis and quantitative measurements of neocortical regions. We estimated an optimal cut-off value for SUVR as 1.47, with which the discrimination well corresponds to the visual diagnosis. The prevalence of PiB positivity was 93% in AD (age and ratio of APOE4 carrier; 73 ± 5.3, 50.0%), 70% of MCI (71 ± 5.6, 57.9%), and 32% of CN (67 ± 5.1, 43.8%). The PiB positive ratio in APOE4 carrier in AD, MCI and CN groups were 100%, 100%, and 54%, whereas those in non-carriers remain 88%, 40%, and 22%. A significant positive effect of APOE4 for PiB accumulation was observed even in early 60s (Figure 1). Among 3 cases out of 33 subjects diagnosed as PiB-negative with SUVR images, we found distinct cortical deposition of PiB in DVR images, but none of the reverse. We observed a PiB positive ratio in Japanese population equivalent to the US, Australia and EU studies. A significant APOE4 effect was found to push up amyloid-beta deposition even in young-old subjects. A dynamic PiB-PET analysis may give us more sensitive assessment for a small amount of amyloid deposition.