gebhart/patrepeval huggingface dataset:
Co-planar light-actuated optoelectrowetting microfluidic device for droplet manipulation (2021)

We report on a co-planar light-actuated digital microfluidics device that features a metal mesh grid integrated on the device surface to allow droplets to be exposed from above. We discuss a theoretical circuit model for our co-planar optoelectrowetting (OEW) design that allows for the optimization of droplet actuation while maintaining reliable droplet movement. Basic droplet manipulations such as merging and parallel actuation of droplets are achieved at speeds of up to 4.5 cm / s. The co-planar OEW device design benefits from having an open top design that allows for a wider range of system integration configurations than previous generations of OEW devices. A droplet-on-demand dispensing system from above is integrated with the co-planar OEW device to demonstrate the versatility of this optofluidic platform. The ability to inject, collect, and position individual droplets to form large-scale droplet arrays of up to 20 × 20 is achieved.
Molecular Evolution of H6 Influenza Viruses from Poultry in Southeastern China: Prevalence of H6N1 Influenza Viruses Possessing Seven A/Hong Kong/156/97 (H5N1)-Like Genes in Poultry (2002)

The A/teal/Hong Kong/W312/97 (H6N1) influenza virus and the human H5N1 and H9N2 influenza viruses possess similar genes encoding internal proteins, suggesting that H6N1 viruses could become novel human pathogens. The molecular epidemiology and evolution of H6 influenza viruses were characterized by antigenic and genetic analyses of 29 H6 influenza viruses isolated from 1975 to 1981 and 1997 to 2000. Two distinct groups were identified on the basis of their antigenic characteristics. Phylogenetic analysis revealed that all H6N1 viruses isolated from terrestrial poultry in 1999 and 2000 are closely related to A/teal/Hong Kong/W312/97 (H6N1), and the nucleotide sequences of these viruses and of A/Hong Kong/156/97 (H5N1) were more than 96% homologous. The hemagglutinin (HA) of the 1999 and 2000 terrestrial viruses does not have multiple basic amino acids at the site of cleavage of HA1 to HA2; however, a unique insertion of aspartic acid in HA1 between positions 144 and 145 (H3 numbering) was found. The neuraminidase of these terrestrial H6N1 viruses has a deletion of 19 amino acids characteristic of A/Hong Kong/156/97 (H5N1). Evolutionary analysis suggested that these H6N1 viruses coevolved with A/quail/Hong Kong/G1/97-like H9N2 viruses and became more adapted to terrestrial poultry. These terrestrial 1999 and 2000 A/teal/Hong Kong/W312/97 (H6N1)-like viruses, along with the H9N2 viruses, could have been involved in the genesis of the pathogenic H5N1 influenza viruses of 1997. The presence of H6N1 viruses in poultry markets in Hong Kong that possess seven of the eight genes of the A/Hong Kong/156/97 (H5N1) virus raises the following fundamental questions relevant to influenza pandemic preparedness: could the pathogenic H5N1 virus reemerge and could the H6N1 viruses directly cross the species barrier to mammals?
Development of the Brinell Sandwich Passive Transducer (1976)

Abstract : Passive stress gages can provide a cost-effective method of measuring peak stress in soil and on a soil-structure interface. Ideally, the deformation characteristics of a soil stress gage should match the soil as closely as possible. However, a flat, disc-shaped gage whose stiffness is greater than that of the soil is not very sensitive to variations in soil properties. Since pretest predictions of peak stress resulting from nuclear and high-explosive detonations are often very inaccurate, the widest possible sensing range is clearly advantageous. For maximum usefulness when dealing with pulses of different rise times and durations, the gage should be free of rate effects over as broad a range of pulse shapes as possible.
Countermeasureing Zero Day Attacks: Asset-Based Approach (2017)

There is no doubt that security issues are on the rise and defense mechanisms are becoming one of the leading subjects for academic and industry experts. In this paper, we focus on the security domain and envision a new way of looking at the security life cycle. We utilize our vision to propose an asset-based approach to countermeasure zero day attacks. To evaluate our proposal, we built a prototype. The initial results are promising and indicate that our prototype will achieve its goal of detecting zero-day attacks.
Continuous and Discrete Data Rebinning in Time-of-Flight PET (2008)

This paper investigates data compression methods for time-of-flight (TOF) positron emission tomography (PET), which rebin the 3-D TOF measurements into a set of 2-D TOF data for a stack of transaxial slices. The goal of this work is to develop rebinning algorithms that are more accurate than the TOF single-slice-rebinning (TOF-SSRB) method proposed by Mullani in 1982. Two approaches are explored. The first one is based on a partial differential equation, which expresses a consistency condition for TOF-PET data with a Gaussian TOF profile. From this equation we derive an analytical rebinning algorithm, which is unbiased in the limit of continuous sampling. The second approach is discrete: each 2-D rebinned data sample is calculated as a linear combination of the 3-D TOF samples in the same axial plane parallel to the axis of the scanner. The coefficients of the linear combination are precomputed by optimizing a cost function which enforces both accuracy and good variance reduction, models the TOF profile, the axial PSF of the LORs, and the specific sampling scheme of the scanner. Measurements of a thorax phantom on a prototype TOF-PET scanner with a resolution of 550 ps show that the proposed discrete method improves the bias-variance trade-off and is a promising alternative to TOF-SSRB when data compression is required to achieve clinically acceptable reconstruction time.
Design, Synthesis, and Structure−Activity Relationship of Tropane Muscarinic Acetylcholine Receptor Antagonists (2009)

Novel tropane derivatives were characterized as muscarinic acetylcholine receptor antagonists (mAChRs). Through optimization of the structure-activity relationship around the tropane scaffold, the quaternary ammonium salt 34 was identified as a very potent M(3) mAChR antagonist. The compound was functionally active and displayed greater than 24 h duration of action in a mouse model of bronchoconstriction.
Chained System: A Linear Combination of Different Types of Statistical Machine Translation Systems (2009)

The paper explores a way to learn post-editing fixes of raw MT outputs automatically by combining two different types of statistical machine translation (SMT) systems in a linear fashion. Our proposed system (which we call a chained system) consists of two SMT sys-tems: (i) a syntax-based SMT system and (ii) a phrase-based SMT system (Koehn, 2004). We first translate source sentences of the bi-text training data into a target language, using the syntax-based SMT. This provides us the monolingual parallel data that consist of the raw MT outputs and their corresponding hu-man translations. We then build a phrase-based SMT system, using the monolingual pa-rallel corpus. Our system is thus a chain of a syntax-based SMT system and a phrase-based SMT system. The benefit of the chained sys-tem is to learn post-editing fixes automatically via a phrase-based SMT system (Simard, et al., 2007a/b). We investigated the impact from the chained system on the initial SMT system in terms of BLEU, using typologically differ-ent language pairs. The results of our experi-ments strongly indicate that the second part of the chained system can compensate the weak-nesses of the initial SMT system in a robust way by providing human-like fixes. 1
Raising the baseline for high-precision text classifiers (2007)

Many important application areas of text classifiers demand high precision andit is common to compare prospective solutions to the performance of Naive Bayes. This baseline is usually easy to improve upon, but in this work we demonstrate that appropriate document representation can make out performing this classifier much more challenging. Most importantly, we provide a link between Naive Bayes and the logarithmic opinion pooling of the mixture-of-experts framework, which dictates a particular type of document length normalization. Motivated by document-specific feature selection we propose monotonic constraints on document term weighting, which is shown as an effective method of fine-tuning document representation. The discussion is supported by experiments using three large email corpora corresponding to the problem of spam detection, where high precision is of particular importance.
MiddlewareandPerformanceIssuesfor ComputationalFinanceApplicationsonBlueGene/L (2007)

We discuss real-world case studies involving the implementation of a web services middleware tier for the IBM Blue Gene/L supercomputer to support financial business applications. These programs that are representative of a class of modern financial analytics that take part in distributed business workflows and are heavily database-centric with input and output data stored in external SQL data warehouses. We describe the design issues related to the development of our middleware tier that provides a number of core features, including an automated SQL data extraction and staging gateway, a standardized high-level job specification schema, awell-defined web services (SOAP)APIforinteroperability with other applications, and a secure HTML/JSP web-based interface suitable for general users. Further, we provide observations on performance optimizations to support the relevant data movement requirements.
Potent nonpeptide angiotensin II receptor antagonists. 2. 1-(Carboxybenzyl)imidazole-5-acrylic acids (1993)

The further evolution of the imidazole-5-acrylic acid series of nonpeptide angiotensin II receptor antagonists is detailed (for Part 1, see: J. Med. Chem. 1992, 35, 3858). Modifications of the N-benzyl ring substitution were undertaken in an effort to mimic the Tyr4 residue of angiotensin II. Introduction of a p-carboxylic acid on the N-benzyl ring resulted in the discovery of compounds with nanomolar affinity for the receptor and good oral activity. SAR studies of these potent antagonists revealed that the thienyl ring, the (E)-acrylic acid, and the imidazole ring in addition to the two acid groups were important for high potency. Also, overlay comparisons of the parent diacid with both angiotensin II and a representative biphenylyltetrazole nonpeptide angiotensin II receptor antagonist are presented. The parent diacid analog, SK&F 108566 or (E)-3-[2-butyl-1-(4-carboxybenzyl)-1H-imidazole-5-yl]-2-[(2- thienyl)methyl]propenoic acid, is currently in clinical development for the treatment of hypertension.
An Interpenetrated Framework Material with Hysteretic CO<sub>2</sub> Uptake (2009)

A new, twofold interpenetrated metal-organic framework (MOF) material has been synthesized that demonstrates dramatic steps in the adsorption and hysteresis in the desorption of CO(2). Measurement of the structure by powder X-ray diffraction (PXRD) and pair distribution function (PDF) analysis indicates that structural changes upon CO(2) sorption most likely involve the interpenetrated frameworks moving with respect to each other.
In vitro and in vivo evaluation of carboranyl uridines as boron delivery agents for neutron capture therapy. (1996)

The purpose of the present study was to evaluate 2' and 5'-O-(o-carboran-1-ylmethyl)uridine (CBU-2' and CBU-5') as delivery agents for Boron Neutron Capture Therapy (BNCT) of brain tumors. The in vitro cellular uptake, persistence, subcellular distribution and cytotoxicity, and in vivo biodistribution of CBU-2' have been studied as follows. Cellular uptake studies were carried out with the F98 rat glioma, U-87 MG human glioma, B16 melanoma, SP2/0 myeloma and MDCK fibroblasts. All tumor and non-tumor cell lines had high uptake of CBU-2' (46-75 ppm), indicating that uptake was not selective for neoplastic cells and was independent of cell proliferation. In vitro persistence studies showed high cellular retention of CBU-2' compared to sodium borocaptate (BSH), when cells were transferred from boron-containing to boron-free medium and cultured for an additional 24-48 hours. Subcellular fractionation revealed 75.6% of the recoverable boron was cell membrane associated, 15.6% was in the cytosol, and 8.8% was in the nuclear fraction, but no boron was detectable in the RNA and DNA fractions. F98 glioma cells were cultured in the presence of 3 metabolic inhibitors (rotenone, dipyridamole and NBMPR ¿6-[(4-nitrobenzyl)thio]-9-beta-D-ribofuranosylpurine¿) and none of these blocked the cellular uptake of CBU-2' suggesting that uptake was neither energy nor nucleoside transport dependent. In vivo studies in F98 glioma bearing rats showed that CBU-2' in tumor attained concentrations of 8.0 +/- 2.1 micrograms B/g tissue, which was 13 x greater than that in normal brain of the ipsilateral and contralateral cerebral hemispheres (0.6 +/- 0.2 microgram B/g). The B levels, however, were still lower than the minimum 20-35 microgram B/g, which are required for in vivo BNCT. In summary, our in vitro and in vivo data indicate that CBU-2' was not sufficiently selective for in vivo targeting of brain tumors. However, CBU-2' and CBU-5' were highly toxic for F98 glioma cells in vitro (IC50 = 3 - 13 x 10(-5) M), as determined by measuring the uptake of 3H-thymidine, and the survival of F98 glioma cells using a clonogenic assay, which suggests that these compounds should be further evaluated as potential cytoreductive chemotherapeutic agents.
A kinetic model for vessel‐encoded dynamic angiography with arterial spin labeling (2012)

The ability to visualize blood flow in a vessel-selective manner is of importance in a range of cerebrovascular diseases. Conventional X-ray methods are invasive and carry risks to the patient. Recently, a noninvasive dynamic angiographic MRI-based technique has been proposed using vessel-encoded pseudocontinuous arterial spin labeling, yielding vessel-selective angiograms of the four main brain-feeding arteries. In this study, a novel kinetic model for the signal evolution in such acquisitions is derived and applied to healthy volunteers and to a patient with Moya-Moya disease. The model incorporates bolus dispersion, T(1) decay and radio frequency effects and is applicable to other angiographic methods based on continuous or pseudocontinuous arterial spin labeling. The model fits the data well in all subjects and yields parametric maps relating to blood volume, arrival time, and dispersion, changes to which may indicate disease. These maps are also used to generate synthesized images of blood inflow without bias from T(1) decay and radio frequency effects, greatly improving collateral vessel visibility in the patient with Moya-Moya disease. Relative volume flow rates in downstream vessels are also quantified, showing the relative importance of each feeding artery. This framework is likely to be of use in assessing collateral blood flow in patient groups.
Restoration of Peroxisomal Catalase Import in a Model of Human Cellular Aging (2007)

Peroxisomes play an important role in human cellular metabolism by housing enzymes involved in a number of essential biochemical pathways. Many of these enzymes are oxidases that transfer hydrogen atoms to molecular oxygen forming hydrogen peroxide. The organelle also contains catalase, which readily decomposes the hydrogen peroxide, a potentially damaging oxidant. Previous work has demonstrated that aging compromises peroxisomal protein import with catalase being particularly affected. The resultant imbalance in the relative ratio of oxidases to catalase was seen as a potential contributor to cellular oxidative stress and aging. Here we report that altering the peroxisomal targeting signal of catalase to the more effective serine-lysine-leucine (SKL) sequence results in a catalase molecule that more strongly interacts with its receptor and is more efficiently imported in both in vitro and in vivo assays. Furthermore, catalase-SKL monomers expressed in cells interact with endogenous catalase subunits resulting in altered trafficking of the latter molecules. A dramatic reduction in cellular hydrogen peroxide levels accompanies this increased peroxisomal import of catalase. Finally, we show that catalase-SKL stably expressed in cells by retroviral-mediated transduction repolarizes mitochondria and reduces the number of senescent cells in a population. These results demonstrate the utility of a catalase-SKL therapy for the restoration of a normal oxidative state in aging cells.
Model predictive BESS control for demand charge management and PV-utilization improvement (2018)

Adoption of battery energy storage systems for behind-the-meters application offers valuable benefits for demand charge management as well as increasing PV-utilization. The key point is that while the benefit/cost ratio for a single application may not be favorable for economic benefits of storage systems, stacked services can provide multiple revenue streams for the same investment. Under this framework, we propose a model predictive controller to reduce demand charge cost and enhance PV-utilization level simultaneously. Different load patterns have been considered in this study and results are compared to the conventional rule-based controller. The results verified that the proposed controller provides satisfactory performance by improving the PV-utilization rate between 60% to 80% without significant changes in demand charge (DC) saving. Furthermore, our results suggest that batteries can be used for stacking multiple services to improve their benefits. Quantitative analysis for PV-utilization as a function of battery size and prediction time window has also been carried out.
Fabrication and Wire Extrusion of Ceramic Superconductors (1989)

Many applications of high-temperature superconductors (HTSs) will depend on the ability to fabricate these materials into long lengths with suitable electrical and mechanical properties maintained over the entire length. The program described in this paper is focused on improvement of the relevant material properties of HTSs and on development of fabrication methods that can be transferred to industry for production of commercial conductors. Our research has resulted in advances in fabrication methods that improve the performance of long lengths of polycrystalline HTS wires and tapes. We have examined the Y-Ba-Cu-O (YBCO), Bi-Sr-Ca-Cu-O (BSCCO), and Tl-Ba-Ca-Cu-O (TBCCO) classes of HTSs. Significant results from our research and work by contemporaries are reported in the various sections of the paper.
Heterostructure integrated thermionic coolers (1997)

Thermionic emission in heterostructures is proposed for integrated cooling of high power electronic and optoelectronic devices. This evaporative cooling is achieved by selective emission of hot electrons over a barrier layer from the cathode to the anode. It is shown that with available high electron mobility and low thermal conductivity materials, and with optimized conduction band offsets in heterostructures, single-stage room temperature cooling of up to 20°–40° over thicknesses of the order of microns is possible.
Cornelia de Lange syndrome: Clinical review, diagnostic and scoring systems, and anticipatory guidance Am J Med Genet Part A 143A:1287–1296 (2008)

DOI 10.1002/ajmg.a.31757 In publishing the manuscript, the affiliation of one of the contributors was not completely listed. The correct author affiliation for Angelo Selicorni should have read: 8Clinical Genetics, Department of Pediatrics, IRCCS Policlinico Foundation, Milan, Italy The corresponding author regrets the error.
Ultrasound Matrix Imaging-Part II: The Distortion Matrix for Aberration Correction Over Multiple Isoplanatic Patches. (2022)

This is the second article in a series of two which report on a matrix approach for ultrasound imaging in heterogeneous media. This article describes the quantification and correction of aberration, i.e. the distortion of an image caused by spatial variations in the medium speed-of-sound. Adaptive focusing can compensate for aberration, but is only effective over a restricted area called the isoplanatic patch. Here, we use an experimentally-recorded matrix of reflected acoustic signals to synthesize a set of virtual transducers. We then examine wave propagation between these virtual transducers and an arbitrary correction plane. Such wave-fronts consist of two components: (i) An ideal geometric wave-front linked to diffraction and the input focusing point, and; (ii) Phase distortions induced by the speed-of-sound variations. These distortions are stored in a so-called distortion matrix, the singular value decomposition of which gives access to an optimized focusing law at any point. We show that, by decoupling the aberrations undergone by the outgoing and incoming waves and applying an iterative strategy, compensation for even high-order and spatially-distributed aberrations can be achieved. After a numerical validation of the process, ultrasound matrix imaging (UMI) is applied to the in-vivo imaging of a gallbladder. A map of isoplanatic modes is retrieved and is shown to be strongly correlated with the arrangement of tissues constituting the medium. The corresponding focusing laws yield an ultrasound image with drastically improved contrast and transverse resolution. UMI thus provides a flexible and powerful route towards computational ultrasound.
Evolution and Association Analysis of Ghd7 in Rice (2012)

Plant height, heading date, and yield are the main targets for rice genetic improvement. Ghd7 is a pleiotropic gene that controls the aforementioned traits simultaneously. In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise π and θ in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.