gebhart/patrepeval huggingface dataset:
Secreted and cell surface genes expressed in benign and malignant colorectal tumors. (2001)

Serial analysis of gene expression was used to identify transcripts encoding secreted or cell surface proteins that were expressed in benign and malignant tumors of the colorectum. A total of 290,394 tags were analyzed from normal, adenomatous, and cancerous colonic epithelium. Of the 21,343 different transcripts observed, 957 were found to be differentially expressed between normal tissue and adenoma or between normal tissue and cancer. Forty-nine transcripts were elevated > or =20-fold in adenomas, 40 transcripts were elevated > or =20-fold in cancers, and 9 transcripts were elevated > or =20-fold in both. Products of six of these nine transcripts (TGFBI, LYS, RDP, MIC-1, REGA, and DEHL) were predicted to be secreted or to reside on the cell surface, and these were analyzed in more detail. The abnormal expression levels predicted by serial analysis of gene expression were confirmed by quantitative PCR analyses of each of these six genes. Moreover, the cell types responsible for the elevated expression were identified by in situ hybridization and by PCR analyses of epithelial cells immunoaffinity purified from primary tumors. This study extends knowledge of the differences in gene expression that underlie various stages of neoplasia and suggests specific diagnostic approaches that may be useful for the early detection of colorectal neoplasia.
Training a quantum optimizer (2016)

We study a variant of the quantum approximate optimization algorithm [E. Farhi, J. Goldstone, and S. Gutmann, arXiv:1411.4028] with a slightly different parametrization and a different objective: rather than looking for a state which approximately solves an optimization problem, our goal is to find a quantum algorithm that, given an instance of the maximum 2-satisfiability problem (MAX-2-SAT), will produce a state with high overlap with the optimal state. Using a machine learning approach, we chose a ``training set'' of instances and optimized the parameters to produce a large overlap for the training set. We then tested these optimized parameters on a larger instance set. As a training set, we used a subset of the hard instances studied by Crosson, Farhi, C. Y.-Y. Lin, H.-H. Lin, and P. Shor (CFLLS) (arXiv:1401.7320). When tested, on the full set, the parameters that we find produce a significantly larger overlap than the optimized annealing times of CFLLS. Testing on other random instances from 20 to 28 bits continues to show improvement over annealing, with the improvement being most notable on the hardest instances. Further tests on instances of MAX-3-SAT also showed improvement on the hardest instances. This algorithm may be a possible application for near-term quantum computers with limited coherence times.
Bacterial leaching of toxic metals from municipal sludge: influence of sludge characteristics (1993)

ABSTRACT: The presence of high concentrations of heavy metals in wastewater sludge is one of the most important factors that limit the application of sludge on agricultural land. In the last few years, the microbiological process of heavy metals removal from wastewater sludge has been studied in a batch mode. In the present study, the effects of metals, solids concentration, and initial pH on indigenous sulfur‐oxidizing thiobacilli growth and metal solubilization were examined. The results obtained indicate that metals removal is possible even in high sludge solids concentration (70 g/L). The rate of sulfuric acid production through the oxidation of added elemental sulfur is increased by the increased sludge solids concentration. The initial pH of the sludge (7.0–3.0) does not affect the capacity of metal leaching. The high concentration of metallic ions (Cu 2+ and Zn 2+ ) adjusted in the sludge did not greatly affect the microbiological activity of metal‐leaching bacteria. The leaching tests conducted with metal sulfides as substrate (chalcocite, galena, pyrite, sphalerite) showed that metals solubilization from sulfides occurred by an indirect mechanism (production of acid followed by metal solubilization due to the action of the acid produced). No evidence of direct oxidation of metal sulfides was observed.
A murine leukemia virus derived retroviral vector with a rat VL30 packaging psi sequence. (1992)

A rat VL30 packaging Psi sequence of 168 nucleotides has been characterized. It bears little or no homology to the Murine Leukemia Virus (MLV) Psi sequence, is much smaller in size and at least as efficient for packaging. The use of this small VL30 Psi sequence in MLV derived retroviral vectors should render even more unlikely recombinations possibly generating replication competent MLV viruses. Thus, utilization of the rat VL30 Psi sequence should improve the biological safety of MLV derived vectors for human gene transfer.
A rat incisor dentin matrix protein can induce neonatal rat muscle fibroblasts, in culture, to express phenotypic products of chondroblastic cells. (1991)

Demineralized dentin matrix induces the ectopic formation of bone, in vivo, when implanted subcutaneously or in muscle pouches. In these situations the bone induction follows a chondrogenic pathway. As part of the strategy for the assay and isolation of the factors responsible for initiating induction, we have developed a cell culture system in which the addition of soluble factors extracted from the dentin matrix appears to initiate chondrogenesis. Indicators of chondrogenesis, relative to control cultures, were taken as an increase of 35S-sulfate incorporation into proteoglycan (PG), an altered size of the PG, production of type II collagen, and changes in cell morphology and matrix histochemistry. Our studies have taken two directions: the use of the cell culture system under standard conditions to select fractions inducing one or more of the above indica-tors; and, the purification and characterization of the in vitro chondrogenesis inducing factor(s). Here we report the identification of a peptide fraction which acts in culture to satisfy each of the above indicators of chondrogenesis. An EDTA extract of rat incisor dentin was fractionated by CaCl2 precipitation, Sephacryl S-100 chromatography, and reverse phase HPLC. A single peptide fraction from the HPLC, evidenced by the existence of a single spot on 2-D Gel Electrophoresis, was found to be a potent enhancer of 35S-sulfate incorporation during the standard assay, with maximal activity in the 1-10 ng/ml range. Further detailed studies showed that the heightened incorporation occurred without any increase in cell number. The neonatal rat muscle explant fibroblasts exposed to this fraction for 7 days in monolayer culture formed dense cell nodules which stained intensely with Alcian blue relative to controls.(ABSTRACT TRUNCATED AT 250 WORDS)
Reliability of the compensation comparison method for measuring retinal stray light studied using Monte-Carlo simulations (2006)

Recently the psychophysical compensation comparison method was developed for routine measurement of retinal stray light. The subject's responses to a series of two-alternative-forced-choice trials are analyzed using a maximum-likelihood (ML) approach assuming some fixed shape for the psychometric function (PF). This study evaluates the reliability of the method using Monte-Carlo simulations. Various sampling strategies were investigated, including the two-phase sampling strategy that is used in a commercially available instrument. Results are given for the effective dynamic range and measurement accuracy. The effect of a mismatch of the shape of the PF of an observer and the fixed shape used in the ML analysis was analyzed. Main outcomes are that the two-phase sampling scheme gives good precision (Standard deviation = 0.07 logarithmic units on average) for estimation of the stray light value. Bias is virtually zero. Furthermore, a reliability index was derived from the responses and found to be effective.
Improvement of dimensional measurement accuracy of microstructures with high aspect ratio with a spherical coupling fiber probe (2014)

A specially designed and developed spherical coupling fiber probe was proposed to improve the dimensional measurement accuracy of microstructures with high aspect ratio. The effectiveness of the proposed probe was verified through simulation and experiment. Our simulation results indicated that the maximum deformation was less than 40 µm during the measurement and, therefore, the shaft of the proposed probe did not touch the sidewall of a micro hole. Our experimental results indicated that a static centroid stability of 1.76 µm could be achieved with a resolution of 30 nm in directions X and Y, which meant that the special light path arrangement of the proposed probe overcame the shadowing effect and improved the dimensional measurement accuracy of microstructures with high aspect ratio. It was, therefore, concluded that the proposed probe was suitable for the dimensional measurement of microstructures with a high aspect ratio.
An Integrated Circuit for Simultaneous Extracellular Electrophysiology Recording and Optogenetic Neural Manipulation (2017)

A single IC to measure and control action potentials using optogenetic proteins is realized so that more complicated behavioral neuroscience research and the translational neural disorder treatments become possible in the future.
Preclinical characterization of therapeutic antibodies targeted at the carboxy-terminus of Sonic hedgehog (2018)

The Sonic Hedgehog (Shh) signaling pathway has been implicated in the development and tumor progression of a number of human cancers. Using synthetic peptide mimics to mount an immune response, we generated a mouse mAb to the carboxy (C)-terminus of the Shh protein and characterized its preclinical antitumor effects. <i>In vitro</i> screening guided selection of the best candidate for mAb scale-up production and therapeutic development. C-term anti-Shh, Ab 1C11-2G4 was selected based on ELISA screens, Western blotting, and flow cytometric analyses. Purified Ab 1C11-2G4 was shown to recognize and bind both Shh peptide mimics and cell surface Shh. Administration of Ab 1C11-2G4 not only reduced cell viability in 7 cancer cell lines but also significantly inhibitted tumor growth in a xenograft model of A549 lung cancer cells. <i>Ex vivo</i> analyses of xenograft tumors revealed a reduction in Shh signal transduction and apoptosis in 2G4-treated mice. Collectively, our results provide early demonstration of the antitumor utility of antibodies specific for the C-terminal region of Shh, and support continued development to evaluate their potential efficacy in cancers in which Shh activity is elevated.
Cross-linked Polymersome Membranes:  Vesicles with Broadly Adjustable Properties (2002)

Massively cross-linked and property-tunable membranes have been fabricated by free radical polymerization of self-assembled, block copolymer vesicles − polymersomes. Similar efforts with cross-linkable lipids would appear frustrated in the past due to at least two factors: limited reactivity and membrane fragility under local stresses of nano-confined cross-linking. We describe here a diblock copolymer of poly(ethylene oxide)-polybutadiene that has a hydrophilic weight fraction like that of lipids and forms robust fluid phase membranes in water. The polymersomes sustain free radical polymerization of the hydrophobic butadiene, thereby generating a semipermeable nano-shell. Cross-linked giant vesicles prove stable in chloroform and can also be dehydrated and re-hydrated without rendering the ∼9 nm thick membrane core; the results imply defect-free membranes many microns-squared in area. Surface elastic moduli as well as sustainable wall stresses up to 103 Atm, orders of magnitude greater than any natural lipid membrane, appear consistent with strong tethering between close-packed neighbors. The enormous stability of the giant vesicles can be tuned down for application: blending in the hydrogenated analogue poly(ethylene oxide)-polyethylethylene modulates the effective elastic constants as well as the rupture strength by orders of magnitude. The results appear consistent with rigidity percolation through a finite-layer stack of two-dimensional lattices. Moreover, below the percolation limit, a regime of hyper-instability emerges, reflecting perhaps nanoscale demixing and suggestive of the limitations encountered with low reactivity lipids. The results provide general insights into covalent cross-linking within self-assembled nanostructures.
Poly(enamine‐ketones) from aromatic diacetylenic diketones and aromatic diamines (1986)

Abstract Novel poly(enamine‐ketones) were prepared with inherent viscosities as high as 1.99 dL/g using the Michael‐type addition of various diamines to 1,1′‐(1,3 or 1,4‐phenylene)bis(3‐phenyl‐2‐propyn‐1‐one) in m ‐cresol at 60–130°C. Tough, clear, amber films with tensile strengths of 12, 400 psi and tensile moduli of 397, 000 psi were cast from solutions of the polymers in chloroform. The polymers exhibited T g s as high as 235°C and weight losses of 14% after aging at 232°C in circulating air for 60 h. The synthesis and characterization of several poly(enamine‐ketones) are discussed.
Unified Measure of Goodness and Optimal Design of Spectral (2002)

To evaluate and optimally design spectral sensitivity functions for color input devices, a metric that incorporates practical, significant requirements is desired. The candidate metrics are Vora–Trussell's μ-factor, a metric based on geometrical difference, and the proposed Unified Measure of Goodness, or UMG, which simultaneously considers the imaging noise and its propagation, colorimetric reproduction accuracy and multi-illuminant color correction. A systematic approach is presented to searching for an optimal set of spectral sensitivity functions from among the complete combinations of the given filter components. Comparative computation results show that μ-factor is not a competent metric for the optimal design of camera spectral sensitivity functions while UMG is able to pick out the optimum successfully. Furthermore, the ultimate optimal set has been obtained by selecting the set with highest μ-factor value from the sub-optimal collection obtained with UMG. This hierarchical approach comprehensively considers the advantages of both quality metrics. The candidates of the optimal sets based on the given filter components are experimentally tested and presented in the end of the article.
A Simple, Robust, and Wide-range Chromatic Dispersion Monitor in Coherent Receivers (2009)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text L. Liu, Z. Tao, W. Yan, S. Oda, T. Hoshida, and J. C. Rasmussen, "A Simple, Robust, and Wide-range Chromatic Dispersion Monitor in Coherent Receivers," in Optical Fiber Communication Conference and National Fiber Optic Engineers Conference, OSA Technical Digest (CD) (Optica Publishing Group, 2009), paper JWA36. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Differential Requirements for Semaphorin 3F and Slit-1 in Axonal Targeting, Fasciculation, and Segregation of Olfactory Sensory Neuron Projections (2004)

The formation of precise stereotypic connections in sensory systems is critical for defining accurate internal representations of the external world; however, the molecular mechanisms underlying the formation of sensory maps are poorly understood. Here, we examine the roles of two structurally unrelated repulsive guidance cues, semaphorin 3F (Sema3F) and Slit-1, in olfactory sensory axon fasciculation, targeting, and segregation. Using sema3F-/- mice, we show that Sema3F is critical for vomeronasal sensory neuron axonal fasciculation and for segregation of these sensory afferents from the main olfactory system; however, Sema3F plays only a minor role in targeting of apical vomeronasal neuron axons to the anterior accessory olfactory bulb (AOB). In addition, we show that Sema3F is required for lamina-specific targeting of olfactory sensory axons within the main olfactory system. In contrast to Sema3F, Slit-1 is dispensable for fasciculation of basal vomeronasal neuron axons but is critical for targeting these axons to the posterior AOB. These results reveal discrete and complementary roles for secreted semaphorins and slits in axonal targeting, fasciculation, and segregation of olfactory sensory neuron projections.
Effects of Gear Dimensions and Tooth Surface Modifications on the Loaded Transmission Error of a Helical Gear Pair (1998)

Analysis of the loaded transmission error proved that the actual contact ratio and the effective contact ratios are the valid indices. In order to calculate the loaded transmission error, deformations of a pair of teeth are estimated using Hertzian formulas for the approach deformation and approximate formulas based on the FEM for the bending deflection. The actual contact ratio εr is defined using the rotational angle during which a tooth pair is actually in contact with each other. εr increases with the increase of applied loads. The effective contact ratio, εn, is determined geometrically by gear dimensions and modified tooth surfaces based on the path of contact. Adopting these ratios, the following characteristics are derived. 1) The loaded transmission error correlates to εr when it is smaller than εn and correlates to εn when εr exceeds εn. 2) Loaded transmission errors have their minimums and maximums at the same values of εr. 3) No load transmission error is the largest among the maximums. 4) Gear pairs with higher values of εn show lower loaded transmission error.
Detection of organic materials by spectrometric radiography method (2008)

In this paper we report a spectrometric approach to dual-energy digital radiography that has been developed and applied to identify specific organic substances and discern small differences in their effective atomic number. An experimental setup has been designed, and a theoretical description proposed based on the experimental results obtained. The proposed method is based on application of special reference samples made of materials with different effective atomic number and thickness, parameters known to affect X-ray attenuation in the low-energy range. The results obtained can be used in the development of a new generation of multi-energy customs or medical X-ray scanners.
Exploiting sensors on mobile phones to improve wide-area localization (2012)

In this paper, we discuss how the sensors available in modern smartphones can improve 6-degree-of-freedom (6DOF) localization in wide-area environments. In our research, we focus on phones as a platform for largescale Augmented Reality (AR) applications. Thus, our aim is to estimate the position and orientation of the device accurately and fast – it is unrealistic to assume that users are willing to wait tenths of seconds before they can interact with the application. We propose supplementing vision methods with sensor readings from the compass and accelerometer available in most modern smartphones. We evaluate this approach on a largescale reconstruction of the city center of Graz, Austria. Our results show that our approach improves both accuracy and localization time, in comparison to an existing localization approach based solely on vision. We finally conclude our paper with a real-world validation of the approach on an iPhone 4S. 1.
Grafts in myringoplasty: utilizing a silk fibroin scaffold as a novel device (2009)

Chronic perforations of the eardrum or tympanic membrane represent a significant source of morbidity worldwide. Myringoplasty is the operative repair of a perforated tympanic membrane and is a procedure commonly performed by otolaryngologists. Its purpose is to close the tympanic membrane, improve hearing and limit patient susceptibility to middle ear infections. The success rates of the different surgical techniques used to perform a myringoplasty, and the optimal graft materials to achieve complete closure and restore hearing, vary significantly in the literature. A number of autologous tissues, homografts and synthetic materials are described as graft options. With the advent and development of tissue engineering in the last decade, a number of biomaterials have been studied and attempts have been made to mimic biological functions with these materials. Fibroin, a core structural protein in silk from silkworms, has been widely studied with biomedical applications in mind. Several cell types, including keratinocytes, have grown on silk biomaterials, and scaffolds manufactured from silk have successfully been used in wound healing and for tissue engineering purposes. This review focuses on the current available grafts for myringoplasty and their limitations, and examines the biomechanical properties of silk, assessing the potential benefits of a silk fibroin scaffold as a novel device for use as a graft in myringoplasty surgery.
Enhanced machine recognition of speech through the integration of handwriting side information. (1991)

At last year’s ASA Fall Meeting the authors proposed a new approach for the correction of errors introduced by an automatic speech recognizer (ASR) during the decoding of difficult, large vocabulary speech tasks. This approach involves overwriting the incorrectly decoded words (or character strings) using a pressure-sensitive pen, on a transparent paperlike interface (PLI) capable of recognizing handwriting on-line. This solution combines the best features of both keyboard entry and mouse selecting: It is appropriate even for out-of-vocabulary words, yet the user’s attention remains concentrated on the screen at all times. In fact, further analysis shows that four intrinsic forms of complementarity between speech and handwriting add to the viability of this solution. Here evidence of complementarity in information, performance, functionality, and robustness is presented. Such complementarity contributes to the relative speed and ease of use of PLI to correct ASR errors. This in turn suggests an extension of this idea toward a jointuse of both ASR and PLI inputs. In this situation, ASR and PLI are used simultaneously, and the results of handwriting recognition are fed to the speech recognition module as apriori information to help reject unlikely possibilities and thereby guide the selection of promising candidates. Experimental results indicate that this approach may lead to substantially higher message recognition accuracy. As it requires users to speak and write consistent messages, psychological experiments that demonstrate this willingness are reported provided the increase in recognition accuracy effectively eliminates the need for error correction.