gebhart/patrepeval huggingface dataset:
Chromatin interaction networks and higher order architectures of eukaryotic genomes (2011)

Eukaryotic genome is, not only linearly but also spatially, organized into non-random architecture. Though the linear organization of genes and their epigenetic descriptors are well characterized, the relevance of their spatial organization is beginning to unfold only recently. It is increasingly being recognized that physical interactions among distant genomic elements could serve as an important mean to eukaryotic genome regulation. With the advent of proximity ligation based techniques coupled with next generation sequencing, it is now possible to explore whole genome chromatin interactions at high resolution. Emerging data on genome-wide chromatin interactions suggest that distantly located genes are not independent entities and instead cross-talk with each other in an extensive manner, supporting the notion of "chromatin interaction networks". Moreover, the data also advance the field to "3-dimensional (3D) chromatin structure and dynamics", which would enable molecular biologists to explore the spatiotemporal regulation of genome. In this article, we introduce a stepwise topological transformation of genome from 1-dimension (1D, linear) to 2-dimension (2D, networks) to 3-dimension (3D, architecture) and discuss how such transformations could advance our understanding of genome biology.
pH response of human dental plaque to chewing gum supplemented with low molecular chitosan. (1994)

The effects of low molecular chitosan (LMCS) on pH responses of human dental plaque following exposure to fermentable carbohydrates were investigated by an ion-sensitive field-effect transistor electrode system. After the plaque pH values were minimized by direct application of 5% glucose solution or consumption of sugared caramel, the subjects started chewing the test gums containing 0 (control), 1 or 3% (w/w) LMCS for three minutes. The pH response was monitored until it recovered to over pH5.5. In the case of the glucose solution, chewing 3% LMCS gum caused significantly more rapid pH recovery toward the resting level than did the control gum. Initial pH rising rate during gum chewing was faster with either of the two LMCS gums than with the control gum. In the case of caramel, additional effects of LMCS were observed numerically as LMCS content increased. The findings indicated that LMCS had a potential to promote recovery of plaque pH after acidogenic challenge and to maintain the plaque pH around neutrality.
CH+(1–0) and13CH+(1–0) absorption lines in the direction of massive star-forming regions (2010)

We report the detection of the ground-state rotational transition of the methylidyne cation CH<sup>+<sup/> and its isotopologue <sup>13<sup/>CH<sup>+<sup/> toward the remote massive star-forming regions W33A, W49N, and W51 with the HIFI instrument onboard the <i>Herschel<i/> satellite. Both lines are seen only in absorption against the dust continuum emission of the star-forming regions. The CH<sup>+<sup/> absorption is saturated over almost the entire velocity ranges sampled by the lines-of-sight that include gas associated with the star-forming regions (SFR) and Galactic foreground material. The CH<sup>+<sup/> column densities are inferred from the optically thin components. A lower limit of the isotopic ratio [ <sup>12<sup/>CH<sup>+<sup/>] /[ <sup>13<sup/>CH<sup>+<sup/>] <i>><i/> 35.5 is derived from the absorptions of foreground material toward W49N. The column density ratio, <i>N<i/>(CH<sup>+<sup/>)/<i>N<i/>(HCO<sup>+<sup/>), is found to vary by at least a factor 10, between 4 and <i>><i/>40, in the Galactic foreground material. Line-of-sight <sup>12<sup/>CH<sup>+<sup/> average abundances relative to total hydrogen are estimated. Their average value, <i>N<i/>(CH<sup>+<sup/>)/<i>N<i/><sub>H<sub/> > 2.6×10<sup>-8<sup/>, is higher than that observed in the solar neighborhood and confirms the high abundances of CH<sup>+<sup/> in the Galactic interstellar medium. We compare this result to the predictions of turbulent dissipation regions (TDR) models and find that these high abundances can be reproduced for the inner Galaxy conditions. It is remarkable that the range of predicted <i>N<i/>(CH<sup>+<sup/>)/<i>N<i/>(HCO<sup>+<sup/>) ratios, from 1 to ~50, is comparable to that observed.
A General Method for Data Averaging of Anisotropic Elastic Constants (1993)

Redundant experimental data are usually required to determine the best value for the whole set of compliances of an anisotropic laminate. A method is presented here to optimize the compliance tensor values using the five invariants of fourth-rank compliance tensors. A vectorial representation of those invariants is given. It provides a compact presentation of the data and reveals the experimental scatter. Experimental data obtained with bending tests on plates are used as an example to optimize the flexural compliance tensor of a laminate and to show the relevance of the method in practice.
Ontology-aware Prescription Recommendation in Treatment Pathways Using Multi-evidence Healthcare Data (2023)

For care of chronic diseases (e.g., depression, diabetes, hypertension), it is critical to identify effective treatment pathways that aim to promptly update the medication following the change of patient state and disease progression. This task is challenging because the optimal treatment pathway for each patient needs to be personalized due to the significant heterogeneity among individuals. Therefore, it is naturally promising to investigate how to use the abundant electronic health records to recommend effective and safe prescriptions. However, prescription recommendation needs to consider multiple aspects of life-critical evidence, such as the information relevance in terms of medical concepts, the health condition in terms of diagnosis history, and the further constraint in terms of side information (e.g., patient demographics and drug side effects). To this end, in this article, we propose a novel prescription recommendation framework named OntoPath to predict the next drug in disease treatment pathways, by building an ontology-aware hierarchical-attention model that integrates multiple medical evidence from domain knowledge guidance, medical history profiling, and side information utilization. Specifically, our method can be characterized from three aspects: (1) by incorporating the longitudinal diagnosis history, we enrich the profiling of patients in terms of comprehensive health conditions, which can largely influence a drug’s outcome on individual patients; (2) using the hierarchical disease and drug ontology structures, we are able to model the domain-specific relevance between patients and drugs at multiple levels of granularity and achieve in-depth collaborative filtering; (3) we introduce a pre-training stage to enhance the discriminativeness of network representations, which helps us obtain a premium model initialization to further boost the final recommendation training. We perform extensive experiments on a large-scale depression cohort with over 37,000 patients from a real-world medical claims database. The quantitative and qualitative results demonstrate the effectiveness of OntoPath through the consistent outperformance over state-of-the-art prescription recommendation baselines and the interpretation of model mechanism in case studies.
Scintillating Fiber Imager for RLGS (2003)

The Scintillating Fiber Imager reported last year was upgraded. The readout configuration and fiber size were optimized for Restriction Landmark Genomic Scanning (RLGS) technology. The background counts were reduced by the anti-coincidence plastic scintillator. The detection efficiency was improved about 5 times, and the spatial resolution good enough for RLGS was achieved.
Vibration control of a PZT actuated suspension dual-stage servo system using a PZT sensor (2003)

Structural resonance modes of the head stack and suspension assembly are one of the major limiting factors for achieving higher head-positioning servo performance in hard disk drives. This paper discusses the vibration suppression control of a PZT actuated suspension dual-stage servo system. A PZT strip on a PZT actuated suspension is utilized as a vibration sensor to control both the voice coil motor (VCM) actuator butterfly mode and the suspension sway mode. The vibration suppression controller is designed using the H/sub /spl infin// control design method. Experimental results show that an attenuation of 15 dB can be achieved for both the suspension sway mode and the VCM butterfly mode, and the rms of the head off-track motion due to airflow excited vibration can be reduced by approximately 30% with the proposed vibration suppression control scheme.
A Nanocomposite of Halloysite/Surfactant/Wax to Inhibit Surfactant Adsorption onto Reservoir Rock Surfaces for Improved Oil Recovery (2020)

Surfactant adsorption onto reservoir rock surfaces is a major issue in enhanced oil recovery (EOR) applications, decreasing the economic success of an EOR project. A method to minimize loss of surfactant is to encapsulate the surfactant and deliver it directly to the oil–water interface. This can be done through the use of naturally occurring clay nanotubes known as halloysites, where surfactants can be encapsulated in the lumen of the nanotubes. Halloysite nanotubes are about 1 μm in length with an outer diameter of about 70 nm and a lumen diameter of about 50 nm. These natural clay nanotubes are thermally stable, inexpensive, abundantly available, and environmentally friendly. An interesting aspect of the halloysite is that it has a predominantly negatively charged outer silica surface and a positively charged inner alumina surface. The surfactants are loaded into the halloysite nanotubes (HNTs) and coated with a thin layer of paraffin wax through a vacuum suction and solvent evaporation method. A thin paraffin wax coating/skin over the surfactant-loaded halloysites prevents the premature release of surfactants until they are in contact with oil, which promotes dissolution of the wax, releasing the surfactant. Imbibition experiments are carried out by measuring oil recovered after pushing injection fluids containing the HNTs through a capillary packed tightly with fresh and crude oil-saturated crushed shale cores. At 70 °C, the wax-coated surfactant-loaded halloysites system exhibited 40% oil recovery, compared to just 16% for surfactant alone and 3% for wax-coated halloysite (no surfactant). A much lower oil recovery for the surfactant alone (16%) can be attributed to excessive surfactant adsorption to the fresh core (85% adsorption), making these adsorbed surfactants unavailable to be in contact with the oil for enhancing the recovery. The method of surfactant encapsulation in wax-coated halloysites therefore leads to a targeted, stimulus-responsive delivery system to the oil–water interface in shale reservoirs with the potential to enhance oil recovery.
Silica-based photonic crystal fiber for the generation of broad band UV radiation (2019)

We report a small-core UV-grade silica multimode photonic crystal fiber for nonlinear frequency conversion in the ultraviolet spectral region. The fiber has been fabricated using F110 UV-Grade glass from Heraeus, which features excellent transmission and low solarization in the UV window. Pumping the fiber core at 355 nm with picosecond laser pulses, we observe the appearance of parametric sidebands in several spatial modes up to 380 nm. We modelled this process using intermodal phase-matching conditions and obtained excellent agreement between calculations and the measured data. We further report frequency conversion pumping into the fiber microstructured cladding where broadband cascaded Raman scattering spanning up to 391 nm is observed. These results represent a significant step towards the efficient and stable generation of UV supercontinuum spectra in an all-silica fiber platform.
The Law of Interspousal Immunity in Ohio (1979)

The purpose of this note will be to discuss Ohio's current position on interspousal immunity as well as the problems that are created by the retention of that doctrine.
Interactions between listening effort and masker type on the energetic and informational masking of speech stimuli (2013)

In most cases, normal-hearing listeners perform better when a target speech signal is masked by a single irrelevant speech masker than they do with a noise masker at an equivalent signal-to-noise ratio (SNR). However, this relative advantage for segregating target speech from a speech masker versus a noise masker may not come without a cost: segregating speech from speech may require the allocation of additional cognitive resources that are not required to segregate speech from noise. The cognitive resources required to extract a target speech signal from different backgrounds can be assessed by varying the complexity of the listening task. Examples include: (1) contrasting the difference between the detection of a speech signal and the correct identification of its contents; (2) contrasting the difference between single-task diotic and dual-task dichotic listening tasks; and (3) contrasting the difference between standard listening tasks and one-back tasks where listeners must keep one response in memory during each stimulus presentation. By examining performance with different kinds of maskers in tasks with different levels of complexity, we can start to determine the impact that the informational and energetic components of masking have on the listening effort required to understand speech in complex environments.
Local Connectivity Solution over Bluetooth and Wi-Fi (2007)

In this paper a local connectivity solution is presented in which smart phones and PDA-s can connect to the enterprise intranet using either Bluetooth or Wi-Fi proximity networking via access points. The contribution highlights the differences at various levels of the implementation between the Bluetooth-based and Wi-Fi based components in our attempt to create a unified service level for Bluetooth-based, Wi-Fi based and both Bluetooth- and Wi-Fi based terminals (newer generation smart phones). Finally use cases and a list of applications are presented that can benefit from our solution in the enterprise segment.
Trees That Grow. (2016)

We study the notion of extensibility in functional data types, as a new approach to the problem of decorating abstract syntax trees with additional information. We observed the need for such extensibility while redesigning the data types representing Haskell abstract syntax inside Glasgow Haskell Compiler (GHC). Specifically, we describe a programming idiom that exploits type-level functions to allow a particular form of extensibility.  The approach scales to support existentials and generalised algebraic data types, and we can use pattern synonyms to make it quite convenient in practice.
QLB: Collision-Aware Quasi-Newton Solver with Cholesky and L-BFGS for Nonlinear Time Integration (2021)

We advocate for the straightforward applications of the Cholesky and the Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithms in the context of nonlinear time integration of deformable objects with dynamic collisions. At the beginning of each time step, we form and factor the Hessian matrix, accounting for all internal forces while omitting the implicit cross-coupling terms from the collision forces between multiple dynamic objects or self collisions. Then during the nonlinear solver iterations of the time step, we implicitly update this Hessian with L-BFGS. This approach is simple to implement and can be readily applied to any nonlinear time integration scheme, including higher-order schemes and quasistatics. We show that this approach works well in a wide range of settings involving complex nonlinear materials, including heterogeneity and anisotropy, as well as collisions, including frictional contact and self collisions.
Lithospheric structure of the Labrador Sea from constrained 3-D gravity inversion (2013)

Regional inversions of free air gravity data constrained by bathymetric and sediment thickness information were undertaken over the Labrador Sea and its margins to generate 3-D density anomaly models to investigate broad-scale crustal structural variations across the extinct spreading centre. Benchmarked against independent seismic Moho depth constraints, a density anomaly isosurface within the inverted volumes was selected as a Moho-proxy and regional maps of Moho structure were developed. Inversions using two different sources for depth to basement constraints revealed similar Moho structures with a depth to Moho of 12 km beneath the Labrador Sea which deepens to 20 km and greater towards Davis Strait and beneath the offshore extension of the Grenville Province. Density anomaly slices through the models corresponding to seismic lines show good agreement between the inverted Moho-proxy and the seismic Moho, with the only exceptions occurring where a high velocity lower crustal zone or underplate has been modelled from wide-angle reflection/refraction profiling studies. The inverted depth to Moho estimates were combined with depth to basement constraints to investigate crustal thickness, both for the full crust and for individual crustal layers, revealing that the crust of the Labrador Sea is generally 5–10 km thick but thickens to 20–25 km towards Davis Strait and beneath the offshore extension of the Grenville Province, not taking into account high density underplates or anomalously high density lower crust. Sediment and crustal thickness variations were investigated to compute stretching factors, β, across the Labrador Sea and to identify zones which deviate from local isostatic compensation. Assuming both an initial unstretched crustal thickness of 35 km and using a variable unstretched crustal thickness model, much of the Labrador Sea has experienced 70–90 per cent thinning. The derived β values suggest that embrittlement of the entire crust and serpentinization of the upper mantle are likely to have occurred for large portions of the central and southern Labrador Sea, inboard of known oceanic crust. Isostatic considerations reveal sediment excess and deficiency on the Labrador and Greenland margins, respectively, possibly reflecting fundamental rheological asymmetry, with the Greenland margin appearing weaker than the Labrador margin. A strong gradient from sediment deficiency to excess, exclusive to the Labrador margin, may reveal the southwestern limit of a regional graben bounding listric detachment or of a zone of distributed faults and detachments.
Regulation of HGT by natural transformation in Ralstonia solanacearum (2008)

International audience
Systemic TLR2 tolerance enhances central nervous system remyelination (2019)

Our results suggest that reducing TLR2 signaling in vivo by inducing TLR2 tolerance significantly enhances myelin repair. Furthermore, the enhanced remyelination resulting from TLR2 tolerance induction is associated with a shift in corpus callosum microglia from a pro-inflammatory iNOS<sup>+</sup> phenotype to a non-inflammatory/pro-repair Arg1<sup>+</sup> phenotype. While deletion of TLR2 would be an impractical approach in vivo, reducing innate immune signaling through TLR2 tolerance induction may represent a novel, two-pronged approach for treating both inflammatory and myelin repair components of MS.
2-Axis Magnetometers Based on Full Wheatstone Bridges Incorporating Magnetic Tunnel Junctions Connected in Series (2012)

Full Wheatstone Bridge incorporating a serially connected ensemble of Magnetic tunnel junctions was produced, targeting an application as a magnetic field compass. To that end, MTJs with <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\rm RxA}\sim 10\ {\rm k}\Omega\ \mu{\rm m}^{2}$</tex></formula> , <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">${\rm TMR}\sim 150$</tex></formula> –200%, <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\rm Hf}=5\ {\rm Oe}$</tex></formula> and <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">${\rm Hf}=5\ {\rm Oe}$</tex></formula> were produced. In order to achieve a full bridge signal, two stacks with an asymmetric SAF reference structure where used to produce MTJs with opposite dR/dH upon annealing in the same substrate. The resulting Bridges exhibit sensitivities between 13.5–32 mV/V/Oe depending on the field range and provide a significantly advantageous alternative to AMR and GMR based bridges.
An acid-stable laccase from Sclerotium rolfsii with potential for wool dye decolourization (2003)

The plant pathogen basidiomycete S. rolfsii secretes two laccases (SRL1 and SRL2) with molecular weights of 55 and 86 kDa, respectively. Laccase production was shown to be inducible by the addition of 2,5-xylidine to the cultural media. After treatment with a combination of chitinase and β-1,3-glucanase, two different laccases were isolated from the sclerotia depending on the stage of sclerotia development. The more prominent laccase, SRL1, was purified and found to decolourize the industrially important wool azo dye Diamond Black PV 200 without the addition of redox mediators. The enzyme (pI 5.2) was active in the acidic pH range, showing an optimal activity at pH 2.4, with ABTS as substrate. The optimum temperature for activity was determined to be 62 °C. Enzyme stability studies revealed that SRL1 was notably stable at 18 °C and pH 4.5, retaining almost full activity after a week. Oxidation of tyrosine was not detectable under the reaction conditions but the enzyme did oxidize a variety of the usual laccase substrates. SRL1 was strongly inhibited by sodium azide and fluoride. Dye solutions decolourized with the immobilized laccase were successfully used for redyeing.
STUDIES ON THE CHEMISTRY OF GROUP III AND V ELEMENTS. (1969)

The research had the stated objectives (1) to develop new organometallic carbene precursors and new carbene chemistry, and (2) to study new reactions found with regard to scope and mechanism. Results and conclusions are very briefly summarized and a listing of publications, lectures, and scientific personnel associated with the project is provided. (Author)
Metal Nitride and Metal Carbide Nanoparticles by a Soft Urea Pathway (2009)

An easy way to produce several metal nitrides and metal carbides at relatively low temperature (800 °C) using simple and mainly nontoxic precursor is presented. The procedure has been shown to be rather general and it was possible to synthesize TiN, VN, NbN, GaN, Mo2N, W2N, CrN, NbC(N), TiC(N), WC, Mo2C, and Cr3C2 nanoparticles using urea or close derivatives as both nitrogen or carbon source and the growth controlling system. In every case, a homogeneous gel-like starting product has been formed that is converted by calcination into the corresponding metal nitride or metal carbide (including mixed species), without any preliminary treatments or further purifications. Samples were characterized by XRD, TEM, SEM, EA, and BET, and the products were shown to be well-defined and rather homogeneous.