gebhart/patrepeval huggingface dataset:
Robust Kernel Regression for Restoration and Reconstruction of Images from Sparse Noisy Data (2006)

We introduce a class of robust non-parametric estimation methods which are ideally suited for the reconstruction of signals and images from noise-corrupted or sparsely collected samples. The filters derived from this class are locally adapted kernels which take into account both the local density of the available samples, and the actual values of these samples. As such, they are automatically steered and adapted to both the given sampling "geometry", and the samples' "radiometry". As the framework we proposed does not rely upon specific assumptions about noise or sampling distributions, it is applicable to a wide class of problems including efficient image upscaling, high quality reconstruction of an image from as little as 15% of its (irregularly sampled) pixels, super-resolution from noisy and under-determined data sets, state of the art denoising of images corrupted by Gaussian and other noise, effective removal of compression artifacts; and more.
Protein-DNA Complexes Containing DNA-Dependent Protein Kinase in Crude Extracts from Human and Rodent Cells (1999)

The DNA-dependent protein kinase (DNA-PK) is composed of a large catalytic subunit (DNA-PKcs) and a DNA-binding protein, Ku. Cells lacking DNA-PK activity are radiosensitive and are defective in DNA double-strand break repair and V(D)J recombination. Although much information regarding the interactions of Ku with DNA ends is available, relatively little is known about the interaction of DNA-PKcs with DNA-bound Ku. Here we show, using electrophoretic mobility shift assays, that chemical crosslinkers enhance the formation of protein-DNA complexes containing DNA-PKcs, Ku and other proteins in extracts from cells of normal human cell lines. Extracts from cells of the radiosensitive human cell line M059J, which lacks DNA-PKcs, are not competent to form these protein-DNA complexes, while addition of purified DNA-PKcs protein restores complex formation. This assay may be useful for screening for DNA-PK function in cells of human cell lines and for identifying proteins that interact with the DNA-PK-DNA complex. We also show that Ku protein in rodent cells can interact with human DNA-PKcs; however, this assay may be less useful for studying Ku/DNA-PKcs interactions in cells of rodent cell lines due to the low abundance of DNA-PKcs in these cells.
Optimizing IC Design for Manufacturability - 2011 Update (2012)

Integrating Circuit Design for Manufacturability (IC DfM) involves various methodologies, techniques, and tools to improve semiconductor reliability and fab yield metrics by optimizing device design or layout. Recent years have seen propagation of IC DfM into the multiple aspects of semiconductor product definition. In addition to the traditional, mainstream DfM related to the corrections of circuit layout by the different types of pattern resolution enhancement techniques, recent DfM disclosures related to stacked die verification, 3D die packaging, floorplanning, and wiring have been proposed to help with the growing number of IC applications. These extended categories of DfM would be useful especially for Systems-on-Chip as well as for the further pursuit of IC shrinkability, e.g. by double patterning. In this work, we discuss nineteen representative IC DfM disclosures filed or published in 2011 and 2012. Similarly, as in the previous review [1], we divided the patents into the ones pertaining to DfM definition, DfM execution, and DfM verification. The focus of the first group of patents (definition) was the correct-by-construction (CBC) architecture, e.g., of layout (active devices, metal routing), die floorplan, or package. The second group (execution) pertained to process proximity correction (mostly OPC), and the third group (verification) concentrated on process model calibration and identifying the sources of process variability. These directions of DfM development, consistent over the recent years, show the validity of the existing DfM approach to solve future design problems.
Large-effective-area ten-core fiber with cladding diameter of about 200 μm (2011)

A multicore fiber with two-pitch layout is proposed to overcome the trade-off between core number and a cladding diameter of a standard hexagonal layout with a single-core pitch. A fabricated ten-core fiber simultaneously realizes effective area of about 120 μm(2) at 1550 nm, small crosstalk, and cladding diameter of 204 μm. The crosstalk between the center core and outer cores is about 30 dB smaller than that between outer cores. The small crosstalk of the center core would help to keep the transmission quality of the center core at the same level as that of the outer cores.
Facile N-Arylation of Amines and Sulfonamides (2003)

[reaction: see text] A facile, transition-metal-free N-arylation procedure for amines and sulfonamides has been developed, which affords good to excellent yields of arylated products under very mild reaction conditions. A methoxy-substituted aryl triflate affords N-arylated products in high yields with excellent regioselectivity. This chemistry tolerates a variety of functional groups.
Multiparameter classifications of optical tomographic images (2008)

This research study explores the combined use of more than one parameter derived from optical tomographic images to increase diagnostic accuracy which is measured in terms of sensitivity and specificity. Parameters considered include, for example, smallest or largest absorption or scattering coefficients or the ratios thereof in an image region of interest. These parameters have been used individually in a previous study to determine if a finger joint is affected or not affected by rheumatoid arthritis. To combine these parameters in the analysis we employ here a vector quantization based classification method called Self-Organizing Mapping (SOM). This method allows producing multivariate ROC-curves from which sensitivity and specificities can be determined. We found that some parameter combinations can lead to higher sensitivities whereas others to higher specificities when compared to singleparameter classifications employed in previous studies. The best diagnostic accuracy, in terms of highest Youden index, was achieved by combining three absorption parameters [maximum(µa), minimum(µa), and the ratio of minimum(µa) and maximum(µa)], which result in a sensitivity of 0.78, a specificity of 0.76, a Youden index of 0.54, and an area under the curve (AUC) of 0.72. These values are higher than for previously reported single parameter classifications with a best sensitivity and specificity of 0.71, a Youden index of 0.41, and an AUC of 0.66.
Tumour growth inhibition by an imidazoquinoline is associated with c‐Myc down‐regulation in urothelial cell carcinoma (2008)

Imidazoquinolines can inhibit c-Myc expression and directly affect cell growth and tumorigenesis of bladder cancer cells, independent of an immune response. These direct effects might be synergistic with previously described immunogenic actions of imidazoquinolines. Our findings could broaden the potential application of imidazoquinoline therapy beyond dermatological malignancies, and further clinical studies are warranted.
Redox properties of extracellular polymeric substances (EPS) from electroactive bacteria (2016)

Although the capacity for electroactive bacteria to convert environmental metallic minerals and organic pollutants is well known, the role of the redox properties of microbial extracellular polymeric substances (EPS) in this process is poorly understood. In this work, the redox properties of EPS from two widely present electroactive bacterial strains (Shewanella oneidensis and Pseudomonas putida) were explored. Electrochemical analysis demonstrates that the EPS extracted from the two strains exhibited redox properties. Spectroelectrochemical and protein electrophoresis analyses indicate that the extracted EPS from S. oneidensis and P. putida contained heme-binding proteins, which were identified as the possible redox components in the EPS. The results of heme-mediated behavior of EPS may provide an insight into the important roles of EPS in electroactive bacteria to maximize their redox capability for biogeochemical cycling, environmental bioremediation and wastewater treatment.
Responses of thoracic spinoreticular and spinothalamic cells to intracardiac bradykinin (1984)

The response characteristics of spinoreticular and spinothalamic cells to intracardiac injection of bradykinin were determined in cats anesthetized with chloralose. Extracellular potentials of individual spinoreticular and spinothalamic cells were recorded from the T2-T4 segments of the spinal cord. Only those cells with cardiopulmonary sympathetic afferent input were tested for responses to intracardiac bradykinin (1-6 micrograms/kg). Thirty-seven of the 64 cells studied responded to bradykinin; 36 were excited and one was inhibited. For excited cells, discharge rate increased from 4 +/- 1.0 (SE) spikes/s to a peak of 20 +/- 2.4 spikes/s, a fivefold increase. Latency to onset of cell response was 13 +/- 1.1 s, and latency to peak response was 24 +/- 1.4 s after drug injection. Tachyphylaxis to additional doses of bradykinin was observed in 17 of 32 cells. Occurrence of tachyphylaxis was sometimes altered after bilateral cervical vagotomy. The projection sites in the caudal medulla and thalamus were similar for responsive and nonresponsive cells. Laminar cell locations in the spinal cord had no significant influence on likelihood of cell response to bradykinin. We conclude that spinoreticular and spinothalamic cells have a role in transmitting noxious information from the heart to the brain.
Corpus-Guided Sentence Generation of Natural Images (2011)

We propose a sentence generation strategy that describes images by predicting the most likely nouns, verbs, scenes and prepositions that make up the core sentence structure. The input are initial noisy estimates of the objects and scenes detected in the image using state of the art trained detectors. As predicting actions from still images directly is unreliable, we use a language model trained from the English Gigaword corpus to obtain their estimates; together with probabilities of co-located nouns, scenes and prepositions. We use these estimates as parameters on a HMM that models the sentence generation process, with hidden nodes as sentence components and image detections as the emissions. Experimental results show that our strategy of combining vision and language produces readable and descriptive sentences compared to naive strategies that use vision alone. 1
The modified weighted gauss-fitting algorithm for structured-illumination microscopy (2021)

Structured-illumination microscopy (SIM) is a novel instrument for measuring surface topography. After images captured by SIM, optical-sectioned images can be acquired by sectioned by section algorithm. Finally, the peak point can be obtained by gauss fitting algorithm based on sectioned images. However, classical gauss-fitting is an inaccurate method since it is sensitive to noise. In this paper, the modified weighted-gauss fitting algorithm (MWGFA) is applied to peak extract. Through simulation and wafer measurement experiment, MWGFA is demonstrated to be an effective method to fitting the SIM z-axis response curve obviously. Compared with CM, MWGFA behaves better in accuracy. Thus it is suitable for SIM well enough and improve the measurement accuracy in mirror and wafer with steps.
Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011: Phylogeny, Selection Pressure and Evolutionary Time-Scale Analysis (2013)

West Nile virus (WNV), an arbovirus maintained in a bird-mosquito enzootic cycle, can infect other vertebrates including humans. WNV was first reported in the US in 1999 where, to date, three genotypes belonging to WNV lineage I have been described (NY99, WN02, SW/WN03). We report here the WNV sequences obtained from two birds, one mosquito, and 29 selected human samples acquired during the US epidemics from 2006-2011 and our examination of the evolutionary dynamics in the open-reading frame of WNV isolates reported from 1999-2011. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses and selection pressure analyses were conducted with the HyPhy package. Phylogenetic analysis identified human WNV isolates within the main WNV genotypes that have circulated in the US. Within genotype SW/WN03, we have identified a cluster with strains derived from blood donors and birds from Idaho and North Dakota collected during 2006-2007, termed here MW/WN06. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. The mean nucleotide substitution rate for WNV isolates obtained from humans was calculated to be 5.06×10(-4) substitutions/site/year (s/s/y). The Bayesian skyline plot shows that after a period of high genetic variability following the introduction of WNV into the US, the WNV population appears to have reached genetic stability. The establishment of WNV in the US represents a unique opportunity to understand how an arbovirus adapts and evolves in a naïve environment. We describe a novel, well-supported cluster of WNV formed by strains collected from humans and birds from Idaho and North Dakota. Adequate genetic surveillance is essential to public health since new mutants could potentially affect viral pathogenesis, decrease performance of diagnostic assays, and negatively impact the efficacy of vaccines and the development of specific therapies.
"Birth of Planet Earth" fulldome excerpt (2019)

Scientific visualization of the energy harvesting process of an early photosynthetic organelle called a chromatophore.
Intake of Ultra-Processed Food and Ectopic-, Visceral- and Other Fat Depots: A Cross-Sectional Study (2022)

Energy intake from UPF is not associated with ectopic fat, SAT or total fat after adjustment for multiple confounders in this population having overall healthy food habits. However, a positive association between UPF and VAT was observed which was driven by women.
The notions of consistency and predicate locks in a database system (1976)

In database systems, users access shared data under the assumption that the data satisfies certain consistency constraints. This paper defines the concepts of transaction, consistency and schedule and shows that consistency requires that a transaction cannot request new locks after releasing a lock. Then it is argued that a transaction needs to lock a logical rather than a physical subset of the database. These subsets may be specified by predicates. An implementation of predicate locks which satisfies the consistency condition is suggested.
Autonomous High Precision Positioning of Surgical Instruments in Robot-Assisted Minimally Invasive Surgery under Visual Guidance (2010)

Despite the fact that minimally invasive robotic surgery provides many advantages for patients, complex tasks are still time-consuming, error-prone and lead to quicker fatigue of the surgeon. Automating recurrent tasks could greatly reduce total surgery time for patients. While surgeons gain most of the information which is necessary to perform the operation from the visual feedback of cameras, there is only little work on autonomous systems utilizing visual information to generate movement commands. A major step towards automated tasks is the autonomous positioning of surgical instruments with high precision inside the situs. In this paper, we tackle the challenges arising from automated positioning by employing visual servoing techniques in two ways: On one hand, a calibration of all system components has to be performed to enable position-based servoing in Cartesian space. On the other hand, lever effects which appear due to the nature of laparoscopic surgery and intrinsic system imprecisions may not be overcome with calibrations. Therefore, the instruments can also be servoed image-based. Combining both approaches to a switching scheme allows for autonomous high precision positing of surgical instruments in a complex setup with four robots.
A hierarchical MHT approach to ESM-radar fusion (2012)

This paper describes a fusion architecture that enables multi-level object tracking. The motivation is provided by the fusion of active and passive data, where multiple passive contacts may originate from the same platform at a given time. This poses a significant challenge to those target-tracking algorithms that are based on the assumption that each sensor provides at most one contact per target per scan or processing interval. For example, while each object has a unique radar return (except when considering extended objects with multiple reflectors), multiple passive contacts may arise when multiple emitter modes are onboard. Simulation results demonstrate the potential of the proposed architecture.
[Biomechanics of stress distribution and resistance of biological tissues: why use prostheses for the treatment of genital prolapse?]. (2003)

Our findings illustrate pelvic tissue failure observed in patients with genital prolapse. Individual maximal resistance of the pelvic ligaments is vary variable, between ligaments and between subjects, and even between sides in a given subject. Pelvic ligaments used for cure of genital prolapse are moderately resistant with wide interindividual variability. The mechanical properties of vaginal tissue are also very variable, illustrating why these tissues may exhibit a certain resistance against dissociation when exposed to loading but much less resistance when exposed to traction by a surgical suture. These findings suggest a revision of classical surgical procedures.
A Controlled Study of Transesophageal Echocardiography to Guide Central Venous Catheter Placement in Congenital Heart Surgery Patients (1999)

Transesophageal echocardiography can be used to guide central venous catheter placement in congenital heart surgery. Central venous catheters that seem to be located high in the right atrium by chest radiograph in these patients are often actually in the superior vena cava and pose little risk of cardiac perforation.
Public-key cryptography and password protocols (1999)

We study protocols for strong authentication and key exchange in asymmetric scenarios where the authentication server possesses ~a pair of private and public keys while the client has only a weak human-memorizable password as its authentication key. We present and analyze several simple password authentication protocols in this scenario, and show that the security of these protocols can be formally proven based on standard cryptographic assumptions. Remarkably, our analysis shows optimal resistance to off-line password guessing attacks under the choice of suitable public key encryption functions. In addition to user authentication, we describe ways to enhance these protocols to provide two-way authentication, authenticated key exchange, defense against server's compromise, and user anonymity. We complement these results with a proof that strongly indicates that public key techniques are unavoidable for password protocols that resist off-line guessing attacks. As a further contribution, we introduce the notion of public passwords that enables the use of the above protocols in situations where the client's machine does not have the means to validate the server's public key. Public passwords serve as "hand-held certificates" that the user can carry without the need for specal computing devices.
Epithelial-to-mesenchymal change of differentiation. From embryogenetic mechanism to pathological patterns. (1995)

In embryonic morphogenesis, dramatic changes from one state of differentiation to another take place, and some epithelia transform into mesenchymal cells endowed with the ability to migrate and to form connective tissue. In vitro model systems have been developed which have provided new insights into crucial aspects of this differentiation change. Triggered perhaps by either extracellular matrix or growth factors, this phenotypic conversion involves a reorganization of the cytoskeleton, and changes in both cell-cell and cell-matrix interactions. As embryonic and adult tissues contain the same, albeit differently expressed, genetic information, one could expect, under particular circumstances, conversion to mesenchyme from epithelium to occur in adult tissues too. Indeed, there is evidence that this change really occurs in human diseases: some tissue reactions to injury; the process of tumour invasion and metastasis; and the development of carcinosarcomas, are all pathological conditions in which an epithelial conversion into mesenchyme probably plays a role. Here, recent observations on embryonic and in vitro epithelial-mesenchymal conversion are reviewed, and these data are compared with findings from some pathological situations. Many similarities emerge which further strengthen the belief that this change in differentiation is involved in the pathogenesis, and underlies the pathological pattern of some diseases.
Literal Solutions for Optimal Design of Microwave Absorbing Composites (2021)

This paper proposes a new approach for the optimal design of microwave absorbing composites backed by a PEC layer and characterized by frequency dependent permeability and permittivity. The reflection coefficient is expressed as a function of the difference between the absorber hyperbolic input impedance and the free space wave impedance, considering an impinging plane wave with either normal or oblique incidence angle. The impedance matching condition for the selected frequency and incidence angle is solved in terms of literal expression of the optimal thickness, which is compared with the one quarter wavelength thickness given by a new accurate expression. The optimal thickness is used for the design of microwave absorbers made by dielectric-magnetic and dielectric composite materials. The frequency spectra of the absorber input impedances and reflection coefficients are computed in the frequency range from 2 GHz up to 18 GHz and for an incidence angle ranging between 0° and 30°. The obtained results prove the validity of the literal expression of the composite optimal thickness which explicitly shows the crucial parameters for the absorbing performances, obscured in common numerical procedures.