gebhart/patrepeval huggingface dataset:
A longitudinal study of pupillary light reflex in 6- to 24-month children (2020)

Pupillary light reflex (PLR) is an involuntary response where the pupil size changes with luminance. Studies have shown that PLR response was altered in children with autism spectrum disorders (ASDs) and other neurological disorders. However, PLR in infants and toddlers is still understudied. We conducted a longitudinal study to investigate PLR in children of 6-24 months using a remote pupillography device. The participants are categorized into two groups. The 'high risk' (HR) group includes children with one or more siblings diagnosed with ASDs; whereas the 'low risk' (LR) group includes children without an ASD diagnosis in the family history. The participants' PLR was measured every six months until the age of 24 months. The results indicated a significant age effect in multiple PLR parameters including resting pupil radius, minimal pupil radius, relative constriction, latency, and response time. In addition, the HR group had a significantly larger resting and minimal pupil size than the LR group. The experimental data acquired in this study revealed not only general age-related PLR changes in infants and toddlers, but also different PLRs in children with a higher risk of ASD.
Coherent image annotation by learning semantic distance (2008)

Conventional approaches to automatic image annotation usually suffer from two problems: (1) They cannot guarantee a good semantic coherence of the annotated words for each image, as they treat each word independently without considering the inherent semantic coherence among the words; (2) They heavily rely on visual similarity for judging semantic similarity. To address the above issues, we propose a novel approach to image annotation which simultaneously learns a semantic distance by capturing the prior annotation knowledge and propagates the annotation of an image as a whole entity. Specifically, a semantic distance function (SDF) is learned for each semantic cluster to measure the semantic similarity based on relative comparison relations of prior annotations. To annotate a new image, the training images in each cluster are ranked according to their SDF values with respect to this image and their corresponding annotations are then propagated to this image as a whole entity to ensure semantic coherence. We evaluate the innovative SDF-based approach on Corel images compared with Support Vector Machine-based approach. The experiments show that SDF-based approach outperforms in terms of semantic coherence, especially when each training image is associated with multiple words.
Roadmap to an Efficient Germanium-on-Silicon Laser: Strain vs. n-Type Doping (2012)

We provide a theoretical analysis of the relative merits of tensile strain and n-type doping as approaches to realizing an efficient low-power germanium laser. Ultimately, tensile strain offers threshold reductions of over 200x, and significant improvements in slope efficiency compared with the recently demonstrated 0.25% strained electrically pumped germanium laser. In contrast, doping offers fundamentally limited benefits, and too much doping is harmful. Moreover, we predict that tensile strain reduces the optimal doping value and that experimentally demonstrated doping has already reached its fundamental limit. We therefore theoretically show large (>; 1%) tensile strain to be the most viable path to a practical germanium-on-silicon laser.
A Low-Computation-Cycle Design of Input-Decimation Technique for RIDFT Algorithm (2019)

In this paper, a low-computation-cycle and energy-efficient design of input-decimation technique for the recursive inverse discrete Fourier transform (RIDFT) algorithm is proposed for the high-speed broadband communication systems. It is crucial that the input-decimation technique is presented to decrease the number of input sequences for the recursive filter so that the computation cycle of RIDFT can be shortened to meet the computing time requirement (3.6 μs). Therefore, the input-decimation RIDFT algorithm is able to carry out at least 55.5% reduction of the total computation cycles compared with the considered algorithms. Holding the advantages of input-decimation technique, the computational complexities of the real-multiplication and -addition are reduced to 41.3% and 22.2%, respectively. Finally, the physical implementation results show that the core area is 0.37× 0.37mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> with 0.18 μm CMOS process. The power consumption is 5.16 mW with the supply voltage of 1.8 V and the operating clock of 40 MHz. The proposed design can achieve 258 million of computational efficiency per unit area (CEUA) and really outperform the previous works.
Linear fitting of multi-threshold counting data with a pixel-array detector for spectral X-ray imaging (2014)

Experiments and modeling are described to perform spectral fitting of multi-threshold counting measurements on a pixel-array detector. An analytical model was developed for describing the probability density function of detected voltage in X-ray photon-counting arrays, utilizing fractional photon counting to account for edge/corner effects from voltage plumes that spread across multiple pixels. Each pixel was mathematically calibrated by fitting the detected voltage distributions to the model at both 13.5 keV and 15.0 keV X-ray energies. The model and established pixel responses were then exploited to statistically recover images of X-ray intensity as a function of X-ray energy in a simulated multi-wavelength and multi-counting threshold experiment.
Cloning the vaccinia virus genome as a bacterial artificial chromosome in <i>Escherichia coli</i> and recovery of infectious virus in mammalian cells (2002)

The ability to manipulate the vaccinia virus (VAC) genome, as a plasmid in bacteria, would greatly facilitate genetic studies and provide a powerful alternative method of making recombinant viruses. VAC, like other poxviruses, has a linear, double-stranded DNA genome with covalently closed hairpin ends that are resolved from transient head-to-head and tail-to-tail concatemers during replication in the cytoplasm of infected cells. Our strategy to construct a nearly 200,000-bp VAC-bacterial artificial chromosome (BAC) was based on circularization of head-to-tail concatemers of VAC DNA. Cells were infected with a recombinant VAC containing inserted sequences for plasmid replication and maintenance in Escherichia coli; DNA concatemer resolution was inhibited leading to formation and accumulation of head-to-tail concatemers, in addition to the usual head-to-head and tail-to-tail forms; the concatemers were circularized by homologous or Cre-loxP-mediated recombination; and E. coli were transformed with DNA from the infected cell lysates. Stable plasmids containing the entire VAC genome, with an intact concatemer junction sequence, were identified. Rescue of infectious VAC was consistently achieved by transfecting the VAC-BAC plasmids into mammalian cells that were infected with a helper nonreplicating fowlpox virus.
Tomographic migration‐velocity analysis using common angle image gathers (2008)

Tomographic migration‐velocity analysis (TMVA) allows to reconstruct the macro‐model of complex geological structures. The common angle imaging (CAI) framework provides an efficient way for TMVA. In this paper, we present a new approach to tomographic migration‐velocity analysis in the form of residual‐curvature analysis under the CAI framework. This new method extends the capability of residual migration‐velocity analysis (RMVA) based on the vertical update from the measured residual moveout on CAI gathers. Examples from the synthetic dataset and real dataset show a significant improvement of the velocity updating with this new method.
Rhomboid Proteases and their Biological Functions (2008)

The rhomboids are a well-conserved family of intramembrane serine proteases, which are unrelated to the classical soluble serine proteases. Their active site is buried within the plane of the membrane, and they cleave substrates in or near transmembrane domains. Although recently discovered, it is becoming clear that rhomboids control many important cellular functions. This review briefly describes recent biochemical and structural work that begins to explain how proteolysis occurs in a hydrophobic environment, but then focuses more extensively on the emerging biological functions of rhomboids. Although the function of most rhomboids is not yet known, they have already been implicated in growth factor signaling, mitochondrial function, host cell invasion by apicomplexan parasites, and protein translocation across membranes in bacteria. By exploiting cellular membrane trafficking machinery, rhomboids have evolved novel strategies to regulate proteolysis.
Diffractive optical networks and computational imaging without a computer (2023)

We will discuss diffractive optical networks designed by deep learning to all-optically implement various complex functions as the input light diffracts through spatially-engineered surfaces. These diffractive processors complete their computational task at the speed of light propagation through thin, passive optical layers and have various applications, e.g., all-optical image analysis, feature detection, object classification, computational imaging and seeing through diffusers. They also enable task-specific camera designs and new optical components for, e.g., spatial, spectral and temporal beam shaping, polarization engineering and spatially-controlled wavelength division multiplexing. These deep learning-designed diffractive networks broadly impact (1) all-optical statistical inference engines, (2) computational cameras and microscopes, and (3) inverse design of optical systems that are task-specific.
Decoding sequence-level information to predict membrane protein expression (2017)

Summary The expression of integral membrane proteins (IMPs) remains a major bottleneck in the characterization of this important protein class. IMP expression levels are currently unpredictable, which renders the pursuit of IMPs for structural and biophysical characterization challenging and inefficient. Experimental evidence demonstrates that changes within the nucleotide or amino-acid sequence for a given IMP can dramatically affect expression; yet these observations have not resulted in generalizable approaches to improved expression. Here, we develop a data-driven statistical predictor named IMProve, that, using only sequence information, increases the likelihood of selecting an IMP that expresses in E. coli. The IMProve model, trained on experimental data, combines a set of sequence-derived features resulting in an IMProve score, where higher values have a higher probability of success. The model is rigorously validated against a variety of independent datasets that contain a wide range of experimental outcomes from various IMP expression trials. The results demonstrate that use of the model can more than double the number of successfully expressed targets at any experimental scale. IMProve can immediately be used to identify favorable targets for characterization.
Actuation in Crosslinked Polymers via Photoinduced Stress Relaxation (2006)

Photoinduced polymer actuation by relieving stress unevenly through the thickness of a chemically crosslinked, rubbery polymer upon light exposure is demonstrated (see figure). The sensitivity of this method to light is greater than previously developed photoinduced actuation techniques, as the recurring chain-transfer reactions amplify the effects of each absorbed photon and subsequently generated radical on the stress-relief and actuation processes.
A Novel Structure to Improve the Viewing Angle Characteristics of Twisted-Nematic Liquid Crystal Displays (1999)

A numerical simulation of a novel wide viewing angle twisted-nematic liquid crystal display (TN-LCD) structure has been performed. The simulated results indicate that this new structure can provide an excellent gray level separation and a 50 : 1 contrast ratio that extends up to around ±60° along both the vertical (V) and horizontal (H) directions. No reverse image is expected over the ±65°H/±80°V range. No excessively dark or excessively bright images are observed over the entire viewing angle range of the display. The fabrication process to achieve this novel structure is also proposed.
Red-green-blue printing using luminescence-upconversion inks (2014)

Recent advances in producing pre-defined 2D patterns of upconversion nanophosphors via photolithography and printing techniques present new opportunities for the use of these materials in security applications. Here, we demonstrate an RGB additive-color printing system that produces highly-resolved pre-defined patterns that are invisible under ambient lighting, but which are viewable as luminescent multi-color images under NIR excitation. Patterns are generated by independent deposition of three primary-color (red, green and blue) upconverting inks using an aerosol jet printer. The primary-color inks are printed as isolated and overlapping features to produce images that simultaneously emit red, green, blue, cyan, magenta, yellow and white upconversion luminescence. The dependence of the chromaticity of certain secondary colors (cyan and magenta) and white on NIR excitation power density can be exploited as an additional authentication feature. The development of an RGB upconversion printing system paves the way for an entirely new arena in security printing.
Constitutive production of leukemia differentiation, colony- stimulating, erythroid burst-promoting, and pluripoietic factors by a human hepatoma cell line: characterization of the leukemia differentiation factor (1985)

Conditioned medium (CM) obtained from a human hepatoma cell line, SK-HEP-1, contains colony-stimulating factors (CSFs) active on murine and human bone marrow-derived granulocyte and macrophage colony-forming units (CFU-GM) and a factor capable of inducing granulocyte-macrophage differentiation (GM-DF) of murine myelomonocytic leukemic cells WEHI-3B(D+) and human promyelocytic leukemic cells HL-60 when assayed in semisolid agar cultures. The human active granulocyte-macrophage colony-stimulating factor (GM-CSF) for day 7 CFU-GM and the GM-DF for WEHI-3B(D+) and for HL-60 are not separable by acrylamide agarose column chromatography, eluting at an apparent molecular weight between 20,000 and 35,000 daltons, or by isoelectric focusing (isoelectric point, pH 5.4). In addition, SK-HEP-1 CM contains erythroid burst-promoting activity (BPA) and a factor that promotes the growth of human mixed colonies. SK-HEP-1 cells, which grow as an adherent monolayer, appear not to be endothelial or monocytic in origin since by immunofluorescent staining they are negative for Ia (HLA-DR), monocyte antigen 1 and 2, lysozyme, and factor VIII-related antigen. Positive immunofluorescent staining for keratin and fibronectin suggests the possibility that SK-HEP-1 is an epithelial cell line. Constitutive production of GM-DF as well as other hematopoietic activities including GM-CSF, erythroid BPA, and an activity that promotes the growth of human mixed colony progenitors by a human epithelial tumor cell line, SK-HEP-1, suggests that this cell line is a valuable resource for both large-scale production of these factors and the cloning of the gene(s) that code for these regulators.
Expression of the adrenomedullin binding protein, complement factor H, in the pancreas and its physiological impact on insulin secretion (2001)

Adrenomedullin (AM) is a ubiquitous peptide hormone which, among other functional roles, reduces insulin secretion in the pancreas. Recently we have described the interaction between AM and the complement regulator protein factor H, which results in mutual modulation of their respective functions. Here we identify the expression of factor H in the beta cells of the rat pancreatic islets by immunohistochemistry and multiple immunofluorescence followed by confocal microscopy. In addition, double immunogold staining under the electron microscope showed coexistence of insulin and factor H immunoreactivities within the same secretory granules; interestingly, factor H staining was found in the electron-lucent haloes whereas the insulin antibody labeled preferentially the dense cores. The existence of factor H mRNA in the pancreas was confirmed by RT-PCR and in situ hybridization. The function of factor H in the pancreas was investigated with an insulin secretion assay. Addition of factor H to freshly isolated islets in the presence of AM resulted in a further reduction in insulin secretion with a concomitant elevation of cAMP, suggesting that factor H increases AM function in glucose homeostasis. The expression of factor H in the pancreas may play other important roles such as protection against complement-mediated cell lysis.
Development of a Simultaneous PET/MRI Scanner (2005)

A combined magnetic resonance imaging (MRI) and positron emission tomography (PET) scanner would be a great benefit to nuclear medicine. The anatomical detail given by MRI and spectroscopy available with magnetic resonance spectroscopy (MRS) complement the quantitative physiological imaging obtained with PET. Such a device has not become a reality because of the incompatibilities of photomultiplier tubes (PMTs) and their associated electronics with MRI's high magnetic fields, as well as significant constraints on PET camera size due to the limited patient port of MR scanners. Recent advances in solid-state electronics have opened the possibility of replacing photomultiplier tubes with avalanche photodiodes (APDs) that are compact and do not share the vulnerabilities of PMTs to magnetic fields. Currently, we are planning to build a miniature PET tomograph using only solid-state electronics to give a combination MRI/PET scanner for small animals. This technology, once developed, can be extended to human scanner designs.
Noise Attenuation Based on Wave Vector Characteristics (2018)

Polarization filtering has been widely used to enhance signal-to-noise ratios for multicomponent seismic data. Polarization filters routinely depend on the ellipticity and directionality of spatial particle motions. However, factors such as noise and formation heterogeneity often make the polarization characteristics of body waves hard to distinguish. Here, we introduce a technique in the time domain for the separation of valid body waves and noise based on wave vector characteristics. First, we characterise the ground-roll polarization by the median wave vectors derived in large-scale moving time windows. For the suppression of ground roll, we fit the particle trajectory of ground roll by the least square method using all components simultaneously. Second, we apply three-stage smoothing to the ground-roll-removed multicomponent records. In each stage, we use mean or median vectors derived in small-scale moving-time or moving-trace windows to attenuate random noise and other non-ground-roll related coherent noise. The filter in the proposed method is not devised according to ellipticity and directionality. Instead, we use the wave vector decomposition to distinguish between noise and valid signals. Synthetic data and field data examples confirm that the proposed method can effectively suppress noise without damaging the high and low frequencies of a valid signal.
Polarization modulation imaging ellipsometer (2006)

The polarization modulation technique was successfully combined with parallel synchronous detection using a switching light source and a CCD camera to realize full-frame measurement of ellipsometric parameters. The detected thickness of a monolayer film of n-octadecylsiloxane agreed well with theoretical and reported experimental values. The thickness resolution for imaging and the temporal noise in parallel thickness measurements were smaller than +/-0.1 nm and smaller than +/-0.02 nm, respectively.
Experimental xenoimplantation of antlerogenic cells into mandibular bone lesions in rabbits: two-year follow-up. (2010)

Different types of cells require activation, and take part in annual, dynamic growth of deer antlers. Stem cells play the most important role in this process. This report shows the results of a two-year long observation of xenogenic implant of antlerogenic stem cells (cell line MIC-1). The cells were derived from growing antler of a deer (Cervus elaphus), seeded onto Spongostan and placed in postoperative lesions of mandibular bones of 15 experimental rabbits. The healing process observed in the implantation sites in all rabbits was normal, and no local inflammatory response was ever observed. Histological and immunohistochemical evaluations were performed after 1, 2, 6, 12 and 24 months, and confirmed the participation of xenogenic cells in the regeneration processes, as well as a lack of rejection of the implants. The deficiencies in the bones were replaced by newly formed, thick fibrous bone tissue that underwent mineralization and was later remodelled into lamellar bone. The results of the experiment with rabbits allow us to believe that antlerogenic cells could be used in reconstruction of bone tissues in other species as well.
High-speed Interferometric Synthetic Aperture Microscopy on a Graphics Processing Unit (2012)

Interferometric synthetic aperture microscopy (ISAM) is a computed imaging technique that achieves spatially-invariant transverse resolution in optical coherence tomography. We demonstrate a high speed, memory efficient implementation of 3D-ISAM using the graphics processing unit (GPU) on a 1300 nm spectral domain optical coherence tomography (SD-OCT) system which is several orders of magnitude faster than previously reported ISAM processing on a CPU.
Predictors of early immunotherapy response in head and neck cancer: Per lesion analysis of a prospective randomized trial with nivolumab. (2019)

6041 Background: The capacity for radiation and checkpoint inhibitors to elicit clinical responses is impacted by tumor immunogenicity and the immune microenvironment. We sought to determine whether head and neck primary site and metastatic tumor location was associated with initial response in non-irradiated lesions. Methods: We evaluated response in 144 non-irradiated lesions from 59 patients with metastatic head and neck cancer enrolled on a phase II randomized controlled trial of nivolumab with stereotactic body radiotherapy (n=30) vs. nivolumab alone (n=29). Nivolumab was administered 3 mg/kg intravenously every 2 weeks. Radiated lesions were treated with 27 Gy / 3 fractions to a single lesion within 14 days of the first dose of nivolumab. Non-target lesion progression was defined ≥30% increase in the greatest axial diameter 8 weeks after enrollment. Fisher’s exact test with nested bootstrap resampling was used for univariate analysis. Logistic regression with a mixed random effects term was used for multivariate analysis. Results: Primary tumor site, metastatic tumor organ sites, and the unadjusted likelihood of progressive disease by site are listed in the table. On multivariate logistic regression controlling for PD-L1 status (p=0.66) and viral status (p=0.29), lymph node metastases (OR 0.79, p=0.0064) were associated with decreased risk of progression, while liver metastases (OR 1.39, p=0.014) and oral cavity primaries (OR 1.56, p=0.018) were associated with increased risk of progression at 8 weeks, using lung metastases and larynx/hypopharynx primaries as reference. Conclusions: Primary tumor subsite and metastasis location were predictors of response or stable disease following treatment with nivolumab. Metastases from oral cavity primaries and metastases to the liver were at increased risk of early progression. Clinical trial information: NCT02684253. [Table: see text]