gebhart/patrepeval huggingface dataset:
Gram-CTC: automatic unit selection and target decomposition for sequence labelling (2017)

Most existing sequence labelling models rely on a fixed decomposition of a target sequence into a sequence of basic units. These methods suffer from two major drawbacks: 1) the set of basic units is fixed, such as the set of words, characters or phonemes in speech recognition, and 2) the decomposition of target sequences is fixed. These drawbacks usually result in sub-optimal performance of modeling sequences. In this paper, we extend the popular CTC loss criterion to alleviate these limitations, and propose a new loss function called Gram-CTC. While preserving the advantages of CTC, Gram-CTC automatically learns the best set of basic units (grams), as well as the most suitable decomposition of target sequences. Unlike CTC, Gram-CTC allows the model to output variable number of characters at each time step, which enables the model to capture longer term dependency and improves the computational efficiency. We demonstrate that the proposed Gram-CTC improves CTC in terms of both performance and efficiency on the large vocabulary speech recognition task at multiple scales of data, and that with Gram-CTC we can outperform the state-of-the-art on a standard speech benchmark.
Discovery of Antibiotic ( <i>E</i> )-3-(3-Carboxyphenyl)-2-(4-cyanostyryl)quinazolin-4(3 <i>H</i> )-one (2015)

In the face of the clinical challenge posed by resistant bacteria, the present needs for novel classes of antibiotics are genuine. In silico docking and screening, followed by chemical synthesis of a library of quinazolinones, led to the discovery of (E)-3-(3-carboxyphenyl)-2-(4-cyanostyryl)quinazolin-4(3H)-one (compound 2) as an antibiotic effective in vivo against methicillin-resistant Staphylococcus aureus (MRSA). This antibiotic impairs cell-wall biosynthesis as documented by functional assays, showing binding of 2 to penicillin-binding protein (PBP) 2a. We document that the antibiotic also inhibits PBP1 of S. aureus, indicating a broad targeting of structurally similar PBPs by this antibiotic. This class of antibiotics holds promise in fighting MRSA infections.
ChemInform Abstract: Electrochemistry at Carbon Nanotubes: Perspective and Issues (2010)

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.
Identification of a New Class of Glucokinase Activators through Structure-Based Design (2013)

Glucose flux through glucokinase (GK) controls insulin release from the pancreas in response to high glucose concentrations. Glucose flux through GK also contributes to reducing hepatic glucose output. Because many individuals with type 2 diabetes appear to have an inadequacy or defect in one or both of these processes, compounds that can activate GK may serve as effective treatments for type 2 diabetes. Herein we report the identification and initial optimization of a novel series of allosteric glucokinase activators (GKAs). We discovered an initial thiazolylamino pyridine-based hit that was optimized using a structure-based design strategy and identified 26 as an early lead. Compound 26 demonstrated a good balance of in vitro potency and enzyme kinetic parameters and demonstrated blood glucose reductions in oral glucose tolerance tests in both C57BL/6J mice and high-fat fed Zucker diabetic fatty rats.
Development of online lines-scan imaging system for chicken inspection and differentiation (2006)

An online line-scan imaging system was developed for differentiation of wholesome and systemically diseased chickens. The hyperspectral imaging system used in this research can be directly converted to multispectral operation and would provide the ideal implementation of essential features for data-efficient high-speed multispectral classification algorithms. The imaging system consisted of an electron-multiplying charge-coupled-device (EMCCD) camera and an imaging spectrograph for line-scan images. The system scanned the surfaces of chicken carcasses on an eviscerating line at a poultry processing plant in December 2005. A method was created to recognize birds entering and exiting the field of view, and to locate a Region of Interest on the chicken images from which useful spectra were extracted for analysis. From analysis of the difference spectra between wholesome and systemically diseased chickens, four wavelengths of 468 nm, 501 nm, 582 nm and 629 nm were selected as key wavelengths for differentiation. The method of locating the Region of Interest will also have practical application in multispectral operation of the line-scan imaging system for online chicken inspection. This line-scan imaging system makes possible the implementation of multispectral inspection using the key wavelengths determined in this study with minimal software adaptations and without the need for cross-system calibration.
Diffusion-Weighted Magnetic Resonance Imaging in Alzheimer’s Disease (1999)

Diffusion-weighted imaging (DWI) is a powerful new magnetic resonance imaging technique for evaluating tissue pathophysiology in vivo. We performed DWI in three orthogonal spatial directions in 10 patients with mild to moderate Alzheimer's disease (AD) and 11 control subjects. Average apparent diffusion coefficients (ADCavg) were calculated for gray matter regions, and anisotropy indexes were calculated for white matter regions. Global measures of atrophy and white matter hyperintensities (WMH) were obtained on T2-weighted images to control for their potential confounding effects on ADCavg and anisotropy. The measures of atrophy and WMH differed between the groups and were used as covariates in the subsequent statistical analyses. Patients with AD demonstrated diminished anisotropy in the posterior white matter (p < 0.0001) and increased ADCavg in the hippocampus (p < 0.05) when compared to the control group. Diffusion measures did not correlate with the severity of dementia. DWI provides a unique, quantitative parameter that may be sensitive to the pathophysiological and/or microstructural abnormalities that occur in AD.
Effectiveness of a Smart Hydrogel in Well Leakage Remediation (2020)

Abstract Leakage in carbon storage and hydrocarbon wells continues to be an area of concern in the development and abandonment of reservoirs. Industry need for a leakage remediation sealant that can perform in systems beyond the capability of cement squeezes has driven the development of a CO2/pH activated "smart" gel. Exploratory laboratory tests and a mock field scale well test were performed to determine the effectiveness of the smart gel. Control of the smart gel particle size distribution was demonstrated through batch synthesis experiments. Microfluidic experiments show some of the mechanisms leading to the successful sealing of an engineered fracture system. Initial and subsequent testing of the deployed smart gel in a leaky mock well completion proves the effective scale up of the smart gel sealing capability and can further drive wider adoption of this unique technology.
Bacteriophage LM33_P1, a fast-acting weapon against the pandemic ST131-O25b:H4<i>Escherichia coli</i>clonal complex (2016)

<sec><st>Objectives</st> Amongst the highly diverse <it>Escherichia coli</it> population, the ST131-O25b:H4 clonal complex is particularly worrisome as it is associated with a high level of antibiotic resistance. The lack of new antibiotics, the worldwide continuous increase of infections caused by MDR bacteria and the need for narrow-spectrum antimicrobial agents have revived interest in phage therapy. In this article, we describe a virulent bacteriophage, LM33_P1, which specifically infects O25b strains, and provide data related to its therapeutic potential. </sec> <sec><st>Methods</st> A large panel of <it>E. coli</it> strains (<it>n</it>&hairsp;=&hairsp;283) was used to assess both the specificity and the activity of bacteriophage LM33_P1. Immunology, biochemistry and genetics-based methods confirmed this specificity. Virology methods and sequencing were used to characterize this bacteriophage <it>in vitro</it>, while three relevant mouse models were employed to show its <it>in vivo</it> efficacy. </sec> <sec><st>Results</st> Bacteriophage LM33_P1 exclusively infects O25b <it>E. coli</it> strains with a 70% coverage on sequence types associated with high antibiotic resistance (ST131 and ST69). This specificity is due to an interaction with the LPS mediated by an original tail fibre. LM33_P1 also has exceptional intrinsic properties with a high adsorption constant and produces over 300 virions per cell in <10 min. Using animal pneumonia, septicaemia and urinary tract infection models, we showed the <it>in vivo</it> efficacy of LM33_P1 to reduce the bacterial load in several organs. </sec> <sec><st>Conclusions</st> Bacteriophage LM33_P1 represents the first weapon that specifically and quickly kills O25b <it>E. coli</it> strains. Therapeutic approaches derived from this bacteriophage could be developed to stop or slow down the spread of the ST131-O25b:H4 drug-resistant clonal complex in humans. </sec>
Self‐Repairable Polyurethane Networks by Atmospheric Carbon Dioxide and Water (2014)

Sugar moieties were incorporated into cross-linked polyurethane (PUR) networks in an effort to achieve self-repairing in the presence of atmospheric carbon dioxide (CO2) and water (H2O). When methyl-α-D-glucopyranoside (MGP) molecules are reacted with hexamethylene diisocyanate trimer (HDI) and polyethylene glycol (PEG) to form cross-linked MGP-polyurethane (PUR) networks, these materials are capable of self-repairing in air. This process requires atmospheric amounts of CO2 and H2O, thus resembling plant behavior of carbon fixation during the photosynthesis cycle. Molecular processes responsible for this unique self-repair process involve physical diffusion of cleaved network segments as well as the formation of carbonate and urethane linkages. Unlike plants, MGP-PUR networks require no photo-initiated reactions, and they are thus capable of repair in darkness under atmospheric conditions.
A Novel Energy Efficient Coding-Aware Scheme in Wireless Sensor Networks (2015)

It is known that the network coding-aware routing could promote system performance by exploring network coding opportunities. In this paper, we analyze the benefits brought by the coding-aware routing in terms of energy efficiency. Specifically, we propose a novel Energy Efficient Coding-Aware Scheme (EECAS) that targets to minimize the total energy consumption of all nodes of wireless sensor networks for multiple unicast traffic-flow demands. Furthermore, by formulating a Minimum Time-cost Model (MTM), we propose a TDMA-based energy-efficient scheduling scheme at the MAC layer. Simulation results show that EECAS reduces at most 11% of energy compared to common routing scheme and 6% compared to traditional coding-aware routing scheme.
The Use of Polydimethylsiloxane Concave Microstructures Arrays to Enhance Light Extraction Efficiency of InGaN Quantum Wells Light-Emitting Diodes (2009)

Novel approach to improve light extraction efficiency of InGaN-based light emitting diodes with polydimethylsiloxane concave microstructures arrays was demonstrated, which leads to enhancement of extraction efficiency by 1.60-times in good agreement with simulation.
Virion Encapsidation of tRNA <sub>3</sub> <sup>Lys</sup> -Ribozyme Chimeric RNAs Inhibits HIV Infection (1998)

Retroviruses require a specific host cellular tRNA primer for initiation of first-strand DNA synthesis. This primer is bound by viral proteins and copackaged into virions. We have exploited this property in the design and testing of an antiviral ribozyme fused to tRNA(3Lys), the primer used for lentiviral replication, including human immunodeficiency virus (HIV-1 and HIV-2). The chimera consists of tRNA(3Lys) covalently attached to a hammerhead ribozyme, which is targeted to the region immediately upstream of the primer binding site of the HIV-1 genome. The tRNA-ribozyme chimeric transcript is catalytically active in vitro and is efficiently bound by HIV reverse transcriptase with an affinity similar to that of tRNA(3Lys). We have expressed the chimeric RNAs from either the tRNA(3Lys) intragenic RNA polymerase III promoter or from a human U6 snRNA promoter. The U6 promoter results in up to 10-fold enhanced expression of the tRNA-ribozyme. Most importantly, the tRNA(3Lys)-ribozymes are encapsidated in HIV-1 virions such that they are effective in substantially reducing the level of infectious virus produced from cells cotransfected with HIV-1 proviral DNA. These results demonstrate the feasibility of using this novel strategy to reduce HIV infectivity and more generally indicate the potential power of using the retroviral primer tRNAs as tools for expressing and delivering ribozymes and other antiretroviral RNAs to the virion capsid.
Enhanced Nodulation and Nitrogen Fixation by a Revertant of a Nodulation-Defective <i>Bradyrhizobium japonicum</i> Tryptophan Auxotroph (1990)

In greenhouse studies, the symbiotic properties of a prototrophic revertant (TA11 NOD) of a nodulation defective tryptophan auxotroph of Bradyrhizobium japonicum were compared with those of the normally nodulating wild-type strain, B. japonicum I-110 ARS. Strain I-110 ARS was the parent of auxotrophic mutant TA11. Plants inoculated with TA11 NOD contained significantly more nitrogen per plant than did plants inoculated with wild-type bacteria (275.9 +/- 35 versus 184 +/- 18 mg). Also, plants that received the revertant were larger, averaging 8.4 +/- 0.9 g (dry weight) versus 6.4 +/- 0.6 g for those that received the wild-type bacterial strain. Additionally, plants that received the NOD strain had 56% more nodules and 41% more nodule mass than did control plants. With both inocula, average nodule size and amount of nitrogen fixed per gram of nodule were about the same. These data indicated that the improvement in nitrogen fixation observed with the TA11 NOD resulted from an increase in the overall nodule number. The physiological basis for this increase in nodulation is not known, but enhanced tryptophan catabolism does not appear to be involved.
Microbial Oxidation of Sulfides by <i>Thiobacillus denitrificans</i> for Treatment of Sour Water and Sour Gases (1993)

It has been demonstrated that the bacterium Thiobacillus denitrificans may be cultured aerobically and anoxically in batch and continuous cultures on hydrogen sulfide (H2S) gas under sulfide-limiting conditions. Under these conditions sulfide concentrations in the culture medium were less than 1µM resulting in very low concentrations of H2S in the reactor-outlet gas. Heterotrophic contamination was shown to have negligible effect on reactor performance with respect to hydrogen-sulfide oxidation. In fact, growth of T. denitrificans in the presence of floc-forming heterotrophs produced a hydrogen-sulfide-active floc with excellent settling characteristics. Flocculated T. denitrificans has been used to remove H2S from gases and to remove sulfides from sour water at concentrations up to 25 mM. Reactors containing flocculated T. denitrificans have been operated for up to nine months continuously. A sulfide-tolerant strain (strain F) of T. denitrificans has also been shown to prevent the net production of H2S by sulfate-reducing bacteria in both liquid cultures and sandstone cores. As hydrogen sulfide was produced by sulfate-reducing bacteria, it was immediately oxidized to sulfate by T. denitrificans. Strain F has also been used to remove dissolved sulfides from formation water pumped from an underground gas storage facility.
Analysis of abnormal signals within the QRS complex of the high-resolution electrocardiogram (1997)

This paper presents a new, quantitative approach to measuring abnormal intra-QRS signals, using the high-resolution electrocardiogram (HRECG). These signals are conventionally known as QRS "notches and slurs." They are measured qualitatively and form the basis for the ECG identification of myocardial infarction. The HRECG is used for detection of ventricular late potentials (LP), which are linked with the presence of a reentry substrate for ventricular tachycardia (VT) after a myocardial infarction. LP's are defined as signals from areas of delayed conduction which outlast the normal QRS period. Our objective is to quantify very low-level abnormal signals that may not outlast the normal QRS period. In this work, abnormal intra-QRS potentials (AIQP) were characterized by removing the predictable, smooth part of the QRS from the original waveform. This was represented as the impulse response of an ARX parametric model, with model order selected empirically from a training data set. AIQP were estimated using the residual of the modeling procedure. Critical AIQP parameters to separate VT and non-VT subjects were obtained using discriminant functions. Results suggest that AIQP indexes are a new predictive index of the HRECG for VT. The concept of abnormal intra-QRS potentials permits the characterization of pathophysiological signals contained wholly within the normal QRS period, but related to arrhythmogenesis. The new method may have other applications, such as detection of myocardial ischemia and improved ECG identification of the site of myocardial infarction, particularly in the absence of Q waves.
A new polycrystalline silicon technology for integrated sensor applications (2002)

A novel metal-induced lateral crystallization (MILC) technique has been applied to the formation of polycrystalline silicon (poly-Si) with greatly enhanced material characteristics. Compared to conventional poly-Si, MILC poly-Si gives rise to much improved performance not only in sensors but also in thin film transistors. A variety of sensing and electronic devices can be realized simultaneously on MILC poly-Si, thus making MILC an enabling technology for integrated silicon micro-machining.
A novel approach for integration of dual metal gate process using ultra thin aluminum nitride buffer layer (2004)

We report and demonstrate a novel approach for dual metal gate CMOS process integration using an ultra thin aluminum nitride (AlN/sub x/) buffer layer between metal gate and gate dielectric. The buffer layer prevents the gate oxide from being exposed to a metal etching process and plays a key role in determining the work functions at the metal/dielectric interface. During annealing, this buffer layer is completely consumed through the reaction with metal gate and converted into a new metal alloy, resulting in no increase of EOT. The work functions of the original gate metals are modified as a result of this reaction, making this approach extremely attractive for dual metal gate CMOS applications.
A Modified Round Baler to Harvest Small-Diameter Woody Biomass (2008)

A round baler was modified to harvest woody crops with a basal stem diameter up to 75 mm at the point of cut. Two innovative headers were designed to cut, shred and feed the woody biomass into the round bale chamber. In 2006, a first header was designed and constructed, specifically for row-planted willow. It included a 1.97-m wide four-saw-blade horizontal cutter, a 1.55-m wide horizontal rotor shredder and a 1.2-m wide baler. The machine could harvest one or two willow rows at a time with continuous cutting and baling rates between 8 and 12 t wet matter/h. In 2006, more than 90 bales were harvested. Bale diameter ranged between 1.0 and 1.5 m; density between 220 and 300 kg wet/m3. The rotary saw blades used in the first header left a neat and clean cut stubble which favours rapid regrowth of plantations. However, the saw blades are expected to be less efficient in uneven land with natural shrubs and scattered rocks. In 2007, a second header was designed without saw blades; it used a more aggressive and wider rotary shredder (2.30 m) including 20 flail hammers or 60 flail knives able to simultaneously cut and shred the woody crop. This second header was used to harvest natural brushes on abandoned agricultural land, natural pasture with sporadic shrubs and forest understory vegetation. In the western Canadian prairie, the prototype harvested natural willow rings around marshes at rates from 5 to 7 t wet crop/h. This innovative “bio-baler” could therefore be used to harvest fast growing willow plantations or naturally growing woody brushes as new sources of biomass, in addition to rejuvenating the land from sometimes undesirable shrubs.
How to build a holographic television system (2013)

The ultimate three-dimensional television viewing experience will be autostereoscopic (requiring no glasses), provide smooth parallax rather than just two views, and support other real-world perceptual cues to depth such as visual accommodation (focusing). Holography meets these requirements, but it is often felt that the scene-acquisition, bandwidth, and display pixel count requirements for holographic television will prove insurmountable. We describe the characteristics of a “true” holographic television display, review the input, transmission, and output needs, and describe our experiments in creating an end-to-end holographic television system with costs in only the hundreds of dollars, based upon a combination of various current consumer-electronics technologies and a novel light-modulator chip.
Bicyclic Derivatives of Hexahydroaporphine: Novel Agents that Lower Intraocular Pressure (1997)

We have synthesized a number of novel bicyclic hexahydroaporphines containing a phenethylamine moiety for preliminary study as intraocular pressure lowering agents. The target molecules were synthesized in a twelve step process. The final products were secondary or tertiary amines containing either an aromatic methoxy or phenolic substituent. These molecules, in hydrochloride salt form, were assayed in doses ranging from 0.1-1.5%. All products and vehicle were administered topically to one eye of normotensive rabbits and intraocular pressure was measured in both eyes for up to six hours. Four of the five compounds examined produced a significant and, in some cases, prolonged, ocular hypotensive response. Secondary and N-methylated tertiary amines were equally effective, as were compounds containing either the 10-methoxy group of free phenol. Studies are currently in progress to optimize potency and identify functional and molecular mechanisms of action.
Source Deghosting and Demultiple for Calm and Rough Weather Conditions (2019)

Summary Source deghosting and demultiple algorithms have been extensively studied but mostly in the case of a flat sea-surface. In this work, we consider time-varying sea-surfaces in different types of weather conditions and derive an inversion approach for removal of sea-surface effects. Starting from Rayleigh's reciprocity theorem, we model seismic data including time-dependent wavefields scattered at the sea-surface, and highlight the temporal variation of these wavefields through simple synthetic examples, comparing two different weather conditions (calm and rough). We also reveal a limitation of source deghosting in the context of time-dependent wavefields: source deghosting affects the sea-surface multiples and can compromise the success of demultiple processing, which is applied in a later step. Results shows that this limitation is also important under calm weather conditions. To overcome this limitation, we propose simultaneously source deghosting and demultiple, therefore, removing all sea-surface effects in one-step. Synthetic data examples are shown using the Sigsbee2B geological model.