gebhart/patrepeval huggingface dataset:
Fine structure of negatively charged and neutral excitons in monolayer MoS$_{2}$ (2020)

We present experimental and theoretical results on the high-quality single-layer MoS$_{2}$ which reveal the fine structure of charged excitons, i.e., trions. In the emission spectra we resolve and identify two trion peaks, T$_{1}$ and T$_{2}$, resembling the pair of singlet and triplet trion peaks (T$_S$ and T$_{T}$) in tungsten-based materials. However, in polarization-dependent photoluminescence measurements we identify these peaks as novel intra- and inter-valley singlet trions, constituting the trion fine structure distinct from that already known in bright and dark 2D materials with large conduction-band splitting induced by the spin-orbit coupling. We show that the trion energy splitting in MoS$_{2}$ is a sensitive probe of inter- and intra-valley carrier interaction. With additional support from theory we claim that the existence of these singlet trions combined with an anomalous excitonic g-factor and the characteristic temperature dependence of the emission spectra together suggest that monolayer MoS$_{2}$ has a dark excitonic ground state, despite having "bright" single-particle arrangement of spin-polarized conduction bands.
Functional Network Construction in Arabidopsis Using Rule-Based Machine Learning on Large-Scale Data Sets (2011)

The meta-analysis of large-scale postgenomics data sets within public databases promises to provide important novel biological knowledge. Statistical approaches including correlation analyses in coexpression studies of gene expression have emerged as tools to elucidate gene function using these data sets. Here, we present a powerful and novel alternative methodology to computationally identify functional relationships between genes from microarray data sets using rule-based machine learning. This approach, termed "coprediction," is based on the collective ability of groups of genes co-occurring within rules to accurately predict the developmental outcome of a biological system. We demonstrate the utility of coprediction as a powerful analytical tool using publicly available microarray data generated exclusively from Arabidopsis thaliana seeds to compute a functional gene interaction network, termed Seed Co-Prediction Network (SCoPNet). SCoPNet predicts functional associations between genes acting in the same developmental and signal transduction pathways irrespective of the similarity in their respective gene expression patterns. Using SCoPNet, we identified four novel regulators of seed germination (ALTERED SEED GERMINATION5, 6, 7, and 8), and predicted interactions at the level of transcript abundance between these novel and previously described factors influencing Arabidopsis seed germination. An online Web tool to query SCoPNet has been developed as a community resource to dissect seed biology and is available at http://www.vseed.nottingham.ac.uk/.
Membrane pore size impacts performance of a xenogeneic bioartificial liver1 (2003)

The elicited immune response of healthy dogs to a xenogeneic BAL was blocked and BAL performance significantly improved by reducing the permeability of the BAL membrane.
DISEMINER : a distributional-semantics inference maker (2018)

Computer Science Department
The killing of Helicobacter pylori by low-power laser light in the presence of a photosensitiser (1996)

Helicobacter pylori is associated with various gastrointestinal disorders. Lethal photosensitisation was investigated as a possible technique for killing H. pylori which might offer a better alternative to antibiotics. The susceptibility of H. pylori to lethal photosensitisation was determined by mixing suspensions of H. pylori with various photosensitisers and plating out on blood agar before irradiation with low-power laser light. Five sensitisers were studied further by mixing them with H. pylori in a tissue-culture plate and counting survivors after irradiation as a function of laser exposure time, dye concentration and pre-irradiation time. Crystal violet and thionine were ineffective as sensitisers, but zones of inhibition appeared with methylene blue (MB), protoporphyrin IX (PPIX), haematoporphyrin derivative (HPD), toluidine blue O (TBO) and disulphonated aluminium phthalocyanine (S2). Laser light or sensitiser alone did not affect bacterial viability. S2 (100 microg/ml) with a laser light energy density of 16 J/cm2, HPD (10O microg/ml) with 160 J/cm2, MB (100 microg/ml) with 21 J/cm2, PPIX (150 microg/ml) with 320 J/cm2 and TBO (50 microg/ml) with 160 J/cm2 all reduced bacterial viability by >99%. The killing of sensitised H. pylori by laser light offers a new approach to the treatment of localised infections when all colonised areas are accessible to light.
Improved Dispenser Cathodes (2006)

Variations in emission current from dispenser cathodes can be caused by variations in temperature and work function over the surface. This paper described research to reduce these variations using improved mechanical designs and controlled porosity cathodes made from sintered tungsten wires. The program goal is to reduce current emission variations to less than 5% over the surface of magnetron injection guns operating temperature limited.
FPGA-Based Sensorless PMSM Speed Control Using Reduced-Order Extended Kalman Filters (2014)

This paper presents the design and implementation of a field-programmable gate array (FPGA)-based architecture for the speed control of sensorless permanent-magnet synchronous motor (PMSM) drives. For the reduction of computation resources, as well as accuracy improvement in the rotor position estimation, a parallel reduced-order extended Kalman filter (EKF) is proposed in this work. Compared with an EKF, the system order is reduced and the iteration process is greatly simplified, resulting in significant savings of resource utility, while maintaining high estimation performance. The whole control system includes a current-control-and-coordinate-transformation unit, a proportional-integral (PI) speed controller, and other accessory modules, all implemented in a single FPGA chip. A hardware description language is adopted to describe advantageous features of the proposed control system. Moreover, the finite-state-machine method is applied with the purpose to reduce logic elements used in the FPGA chip. The validity of the approach is verified through simulation based on the Modelsim/Simulink cosimulation method. Finally, experimental results are obtained on an FPGA platform with an inverter-fed PMSM to show the feasibility and effectiveness of the proposed system-on-programmable-chip for PMSM drives.
SAMMate: a GUI tool for processing short read alignments in SAM/BAM format (2011)

With just a few mouse clicks, SAMMate will provide biomedical researchers easy access to important alignment information stored in SAM/BAM files. Our software is constantly updated and will greatly facilitate the downstream analysis of NGS data. Both the source code and the GUI executable are freely available under the GNU General Public License at http://sammate.sourceforge.net.
Asymmetric stacked autoencoder (2017)

Traditional stacked autoencoders have an equal number of encoders and decoders. However, while fine-tuned as a deep neural network the decoder portion is detached and never used. This begs the question: ‘do we need equal number of decoders and encoders’? In this study we explore asymmetric autoencoders — unequal number of encoders and decoders. We specifically address two tasks — 1. Classification capacity as deep neural network and 2. Compressibility of stacked autoencoder. For both the problems, our asymmetric autoencoders have several encoders but a single decoders. We find that such autoencoders are more accurate compared to traditional symmetrically stacked autoencoders for classification accuracy and also yield slightly better results on compression problems.
Direct numerical simulation of hypersonic boundary-layer transition over blunt leading edges. I - A new numerical method and validation (1997)

This paper presents and tests a new high-order upwind finite difference shock fitting method for the direct simulations of hypersonic flows with strong bow shocks. There are three main aspects of the new method: a simple unsteady shock fitting formulation, new upwind high-order finite difference schemes for spatial discretization, and new third-order semi-implicit Runge-Kutta schemes for temporal discretization. The results of accuracy tests of the new fifth-order shock-fitting method are presented for four test cases: 1D wave equation, 2D direct numerical simulation (DNS) of stability of supersonic Couette flow, steady viscous hypersonic flow over a circular cylinder, and the DNS of receptivity to freestream acoustic disturbances for hypersonic boundary layers over a parabola. (Author)
Analysis of a Steam Drive Project, Inglewood Field, California (1969)

This is the first reported California field data on the vertical extent and residual oil saturation of the steam swept zone. Field-derived data on reservoir heat distribution support the published theoretical data. The Inglewood field, discovered in 1924, occupies a faulted anticline along the Newport-Inglewood Fault System on the western edge of the Los Angeles basin (Fig. 1). The Upper Investment zone, UB sand, selected for this test is the shallowest producing reservoir in the field and lies about 1,000 ft below surface ( 650 subsea). The UB sand productive limit are defined by an updip sand pinchout, the Inglewood Fault, and by down-dip water. The UB sand is 40 to 60 ft thick, consists of fine- to coarse-grain sand with occasional pebbles, ranges from soft to unconsolidated, is overlain by a thick siltstone section and has bottom water. The reservoir properties are shown in Table 1, and electric log characteristics in Fig. 2. The air permeability ranges from 3.3 to 14.3 darcies in the top 40 ft of the reservoir, and porosity averages 39 percent. The primary producing mechanism is pressure depletion with primary producing mechanism is pressure depletion with water encroachment. Oil in place at start of project was 1,930 bbl/acre-ft. The Investment zone oil is asphalt base, 14 degrees API gravity with an in-situ viscosity of 1,200 cp. The high oil viscosity, low reservoir pressure, shallow depth and high oil saturation are all favorable for application of thermal recovery methods. Preliminary laboratory studies of steamflooding in Inglewood cores indicated that residual oil saturations of approximately 20 percent could be achieved with throughput of 1 PV of water converted to steam. Chevron Oil Field Research Co. and Standard Oil Co. of California, WOI conducted the Investment zone lost to learn if the low laboratory residual saturations could be obtained in the field and to determine the oil displacement efficiency in the project area. The test was designed to obtain data on vertical and areal coverage, heat losses, and rate of steam front advance, and to evaluate producing problems associated with continuous steam injection. Design Project Area Project Area Fig. 3 shows the steamflood pilot layout. It is an inverted six-spot containing 2.6 acres within the five first-line producing wells. The project area of the reservoir has essentially no dip. Injection Well 270 and Temperature Observation Wells 271, 272, 273 and 293, were newly drilled for the project. The location of Wells 304 and 304A, which were drilled specifically to obtain post-steam saturation, is also shown in Fig. 3.
Influence of ZrO2 Structure and Copper Electronic State on Activity of Cu/ZrO2 Catalysts in Methanol Synthesis from CO2 (2014)

Cu/ZrO2 catalysts obtained by impregnation of ZrO2 and complexation with citric acid were studied for CO2 hydrogenation to methanol. The catalyst structure, texture, and active copper surface were determined using XRD, BET, and reactive adsorption of N2O, respectively. The XPS and Auger spectroscopies were used to determine the surface structure and copper electronic state. FT-IR pyridine adsorption was studied to determine acidity of the catalysts. The results of quantum-chemical calculations concerning the formation of oxygen vacancies in monoclinic and tetragonal ZrO2 have been also presented. It was found that selection of the appropriate conditions of the catalyst preparation influences the degree of copper dispersion, its electronic state, and contents of the zirconia polymorphic phases (tetragonal and monoclinic). The presence of oxygen vacancies stabilizes both the thermodynamically unstable t-ZrO2 phase and Cu1+ cations, which are present in the vicinity of oxygen vacancies. Complexes formed preferentially on tetragonal ZrO2 built from Cu cations and oxygen vacancies are the acid centers active in methanol synthesis reaction; therefore the catalytic activity toward methanol increases with increasing t-ZrO2 content. The implications of the obtained results for the mechanism of the catalytic hydrogenation of CO2 are discussed.
Gas-phase Raman spectroscopy of phosphorus, arsenic, and saturated sulphur vapours (1969)

The gas-phase Raman spectra of P4, As4, P2, and As2 are recorded and compared with literature values for P2 and As2 derived from electronic spectroscopy, and for sulphur, the gas-phase Raman spectra of S8 and S6 are obtained, together with a polarized band at 237 cm.–1 which is probably due to S7.
Probing the Laser Ablation of Black Phosphorus by Raman Spectroscopy (2021)

Laser ablation in conjunction with Raman spectroscopy can be used to attain a controllable reduction of the thickness of exfoliated black phosphorus flakes and simultaneous measurement of the local temperature. However, this approach can be affected by several parameters, such as the thickness-dependent heat dissipation. Optical, thermal, and mechanical effects in the flakes and the substrate can influence the laser ablation and may become a source of artifacts on the measurement of the local temperature. In this work, we carry out a systematic investigation of the laser thinning of black phosphorus flakes on SiO<sub>2</sub>/Si substrates. The counterintuitive results from Raman thermometry are analyzed and elucidated with the help of numerical solutions of the problem, laying the groundwork for a controlled thinning process of this material.
Drastic Effect of Lattice Propionitrile Molecules on the Spin-Transition Temperature of a 2,2′-Dipyridylamino/s-triazine-Based Iron(II) Complex (2014)

Reaction of iron(II) selenocyanate (obtained from Fe(ClO4)2 and KNCSe) with 2-(N,N-bis(2-pyridyl)amino)-4,6-bis(pentafluorophenoxy)-(1,3,5)triazine (L1(F)) in propionitrile produces the compound [Fe(L1(F))2(NCSe)2]·2CH3CH2CN (1(NCSe)·2PrCN), which shows spin-crossover (SCO) properties characterized by a T(1/2) of 283 K and a ΔT80 (i.e., temperature range within which 80% of the transition considered occurs) of about 65 K. Upon air exposure, 1(NCSe)·2PrCN gradually converts to a new SCO species that exhibits different properties, as reflected by T(1/2) = 220 K and ΔT80 = 70 K. Various characterization techniques, namely, IR spectroscopy, thermogravimetric analysis, and thermodiffractometric studies, reveal that the new phase is obtained through the loss of the lattice propionitrile molecules within several days upon air exposure or several hours upon heating above 390 K.
Faculty Opinions recommendation of Human Olfaction without Apparent Olfactory Bulbs. (2019)

The olfactory bulbs (OBs) are the first site of odor representation in the mammalian brain, and their unique ultrastructure is considered a necessary substrate for spatiotemporal coding of smell. Given this, we were struck by the serendipitous observation at MRI of two otherwise healthy young left-handed women, yet with no apparent OBs. Standardized tests revealed normal odor awareness, detection, discrimination, identification, and representation. Functional MRI of these women's brains revealed that odorant-induced activity in piriform cortex, the primary OB target, was similar in its extent to that of intact controls. Finally, review of a public brain-MRI database with 1,113 participants (606 women) also tested for olfactory performance, uncovered olfaction without anatomically defined OBs in ∼0.6% of women and ∼4.25% of left-handed women. Thus, humans can perform the basic facets of olfaction without canonical OBs, implying extreme plasticity in the functional neuroanatomy of this sensory system.Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved. PMID: 31706696 Funding information This work was supported by: NIMH NIH HHS, United States Grant ID: U54 MH091657
Hollow Silica Nanoparticles Penetrate the Peripheral Nerve and Enhance the Nerve Blockade from Tetrodotoxin (2017)

The efficacy of tetrodotoxin (TTX), a very potent local anesthetic, is limited by its poor penetration through barriers to axonal surfaces. To address this issue, we encapsulated TTX in hollow silica nanoparticles (TTX-HSN) and injected them at the sciatic nerve in rats. TTX-HSN achieved an increased frequency of successful blocks, prolonged the duration of the block, and decreased the toxicity compared to free TTX. In animals injected with fluorescently labeled HSN, the imaging of frozen sections of nerve demonstrated that HSN could penetrate into nerve and that the penetrating ability of silica nanoparticles was highly size-dependent. These results demonstrated that HSN could deliver TTX into the nerve, enhancing efficacy while improving safety.
Physical mapping and YAC-cloning connects four genetically distinct 4qter loci (D4S163, D4S139, D4F35S1 and D4F104S1) in the FSHD gene-region (1993)

We have constructed a long-range restriction map of the region on chromosome 4q that contains the gene for facioscapulohumeral muscular dystrophy (FSHD). This region contains the linkage group cen ... D4S163-D4S139-D4F35S1-D4F104S1-FSHD ... 4qter, which spans a genetic distance of about 5 cM. Pulse field gel electrophoresis (PFGE) mapping indicated that these loci span a region not more than 1 Mb. STSs were developed for several of these loci, which served to isolate four overlapping yeast artificial chromosomes (YACs). These YACs confirmed the PFGE map and have allowed us to generate a more detailed restriction map using cosmid contig mapping. The physical distances were smaller than was expected on the basis of the genetic map. Two potential HTF islands have been detected within the cloned region. One HTF island maps about 100 kb centromeric from the tandem repeats involved in the FSHD mutation, whereas the other maps within these tandem repeats.
Anti-Biofilm Strategies: How to Eradicate Candida Biofilms? (2011)

In nature, microorganisms prefer to reside in structured microbial communities, termed biofilms, rather than as free-floating planktonic cells. Advantageous for the microorganisms, but disadvantageous for human health, is the increased resistance/tolerance of the biofilm cells to antimicrobial treatment. In clinically relevant biofilms, Candida albicans is one of the most frequently isolated microorganisms in biofilms. This review primarily elaborates on the activity of the currently used antimycotics against Candida biofilms, the potential of antifungal lock therapy and sheds more light on new promising compounds resulting from the gradual shift of anti-biofilm research activities to natural products, plants and their extracts.
Iron Transporter Protein Expressions in Children with Celiac Disease (2021)

Anemia is a frequent finding in children with celiac disease but the detailed pathophysiological mechanisms in the intestine remain obscure. One possible explanation could be an abnormal expression of duodenal iron transport proteins. However, the results have so far been inconsistent. We investigated this issue by comparing immunohistochemical stainings of duodenal cytochrome B (DCYTB), divalent metal transporter 1 (DMT1), ferroportin, hephaestin and transferrin receptor 1 (TfR1) in duodenal biopsies between 27 children with celiac disease and duodenal atrophy, 10 celiac autoantibody-positive children with potential celiac disease and six autoantibody-negative control children. Twenty out of these 43 subjects had anemia. The expressions of the iron proteins were investigated with regard to saturation and the percentage of the stained area or stained membrane length of the enterocytes. The results showed the stained area of ferroportin to be increased and the saturation of hephaestin to be decreased in celiac disease patients compared with controls. There were no differences in the transporter protein expressions between anemic and non-anemic patients. The present results suggest an iron status-independent alteration of ferroportin and hephaestin proteins in children with histologically confirmed celiac disease.
Nut and legume consumption and human health: an umbrella review of observational studies (2021)

Consumption of nuts and legumes has been associated with several health benefits. The aim of this study was to systematically review existing meta-analyses of observational studies on nut and legume intake and non-communicable diseases, and assess the level of evidence. Out of the six meta-analyses focussed on legume and 15 on nut intake, a possible association with decreased risk of colorectal adenoma and coronary heart disease was found for higher legume consumption, and a decreased risk of cardiovascular and cancer mortality, colon cancer, hypertension and ischaemic stroke for higher nut consumption. The association between legume consumption and cardiovascular diseases (CVDs), as well as nut consumption and risk of cancer, CVD incidence and all-cause mortality, was deemed as "limited" due to heterogeneity between results and/or potential confounding factors. General benefit towards better health can be observed for nut and legume consumption. Further studies are needed to better elucidate potential confounding factors.
Audiometric Threshold Screening Method Using Envelope Detection Filters of Intensity Ramping Click Auditory Steady-State Responses (2006)

The Auditory Steady-state Responses (ASSR) elicited by click stimuli can be utilized for hearing screening as is traditionally done with click-evoked Auditory Brainstem Responses (ABR). In a typical ASSR or ABR hearing screening, several recordings at different intensities are required to find the response threshold. In this study the use of binaural click stimulus with time ramping intensity produces dual-ear evoked potentials in only one recording session, decreasing significantly the recording time. To achieve this performance a one second sweep consisting of repetitive click stimuli, with logarithmically ramping up intensity, is presented to one or both ears simultaneously. Unique repetition frequencies for each ear are used in order to differentiate the responses coming from each ear. The stimuli sweep is repeated and the EEG data corresponding to each sweep is averaged until a pre-specified residual noise level is achieved. Hilbert-transform-based envelope detection filters in the time domain are used to estimate the signal and noise energy around the main stimulation rate. Because the stimulus time-intensity functions are known, thresholds can be estimated from the response onset time position by estimating the significance of the signal to noise ratio. Preliminary results indicate a strong agreement of the obtained thresholds with behavioral thresholds.