gebhart/patrepeval huggingface dataset:
The impact of industrial biotechnology (2006)

In this review, the impact of industrial (or "white") biotechnology can have on our society and economy is discussed. An overview is given of industrial biotechnology and its applications in a number of product categories ranging from food ingredients, vitamins, bio-colorants, solvents, plastics and biofuels. The use of fossil resources is compared with renewable resources as the preferred feedstock for industrial biotechnology. A brief discussion is also given of the expected changes in society and technology, ranging from the shift in the supply of resources, the growing need for efficiency and sustainability of the production systems, changing consumer perception and behaviour and changing agricultural systems and practices. Many of these changes are expected to speed up the transition from a fossil-based to a bio-based economy and society.
Exploiting Excited-State Aromaticity To Design Highly Stable Singlet Fission Materials (2019)

Singlet fission, the process of forming two triplet excitons from one singlet exciton, is a characteristic reserved for only a handful of organic molecules due to the atypical energetic requirement for low energy excited triplet states. The predominant strategy for achieving such a trait is by increasing ground state diradical character; however, this greatly reduces ambient stability. Herein, we exploit Baird's rule of excited state aromaticity to manipulate the singlet-triplet energy gap and create novel singlet fission candidates. We achieve this through the inclusion of a [4n] 5-membered heterocycle, whose electronic resonance promotes aromaticity in the triplet state, stabilizing its energy relative to the singlet excited state. Using this theory, we design a family of derivatives of indolonaphthyridine thiophene (INDT) with highly tunable excited state energies. Not only do we access novel singlet fission materials, they also exhibit excellent ambient stability, imparted due to the delocalized nature of the triplet excited state. Spin-coated films retained up to 85% activity after several weeks of exposure to oxygen and light, while analogous films of TIPS-pentacene showed full degradation after 4 days, showcasing the excellent stability of this class of singlet fission scaffold. Extension of our theoretical analysis to almost ten thousand candidates reveals an unprecedented degree of tunability and several thousand potential fission-capable candidates, while clearly demonstrating the relationship between triplet aromaticity and singlet-triplet energy gap, confirming this novel strategy for manipulating the exchange energy in organic materials.
Reply to Comment on "Wide-field coherent anti-Stokes Raman scattering microscopy with non-phase-matching illumination" (2007)

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 D. Simanovskii, I. Toytman, and D. Palanker, "Reply to Comment on "Wide-field coherent anti-Stokes Raman scattering microscopy with non-phase-matching illumination"," Opt. Lett. 32, 3470-3470 (2007) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
The relation between preset distinguishing sequences and synchronizing sequences (2014)

Abstract We study the relation between synchronizing sequences and preset distinguishing sequences which are some special sequences used in finite state machine based testing. We show that the problems related to preset distinguishing sequences can be converted into related problems of synchronizing sequences. Using the results existing in the literature for synchronizing sequences, we offer several reflections of these results for preset distinguishing sequences. Although computing a preset distinguishing sequence is PSPACE-hard , we do identify a class of machines for which computing a preset distinguishing sequence can be performed in polynomial time and argue that this class is practically relevant. We also present an experimental study to compare the performance of exponential brute-force and polynomial heuristic algorithms to compute a preset distinguishing sequence.
On‐Chip Generation of Structured Light Based on Metasurface Optoelectronic Integration (2021)

Abstract Metasurfaces offer complete control of optical wavefront at the subwavelength scale, advancing a new class of artificial planar optics, including lenses, waveplates, and holograms, with unprecedented merits over conventional optical components. In particular, the ultrathin, flat, and compact characteristics of metasurfaces facilitate their integration with semiconductor devices for the development of miniaturized and multifunctional optoelectronic systems. In this work, generation of structured light is implemented at an ultracompact wafer‐level through the monolithic integration of metasurface with standard vertical cavity surface‐emitting lasers (VCSELs). This work opens new perspectives for the design of structured light systems with compactness, lightweight, and scalability. Ultracompact beam structured laser chips with versatile functionalities are experimentally demonstrated, including multichannel beams array generation, on‐chip large‐angle beam steering up to 60°, and wafer‐level holographic beam shaping with a wide field of view (about 124°). The results will promote the development of compact light structuring systems with great potential in 3D imaging, displays, robotic vision, human–computer interaction, and augmented/virtual reality.
NSABP B-38: Definitive analysis of a randomized adjuvant trial comparing dose-dense (DD) AC→paclitaxel (P) plus gemcitabine (G) with DD AC→P and with docetaxel, doxorubicin, and cyclophosphamide (TAC) in women with operable, node-positive breast cancer. (2012)

LBA1000 Background: The primary aims were to determine whether adjuvant DD AC→PG will be superior to DD AC→P as well as to TAC in DFS and to compare the relative DFS of TAC and DD AC→P. Secondary endpoints include survival and toxicity. Methods: From Nov 3, 2004 to May 3, 2007, 4894 women were randomized; 1630 to TAC (docetaxel [T] 75 mg/m 2 , doxorubicin [A] 50 mg/m 2 , cyclophosphamide [C] 500 mg/m 2 q3 wks x 6), 1634 to DD AC→P (A 60 mg/m 2 and C 600 mg/m 2 q2 wks x 4 followed by P 175 mg/m 2 q2 wks x 4), and 1630 to DD AC→PG (A 60 mg/m 2 and C 600 mg/m 2 q2 wks x 4 → P 175 mg/m 2 + G 2000 mg/m 2 q2 wks x 4). Primary G-CSF support was required and erythropoiesis-stimulating agents (ESA) were used at investigator discretion. 52% were postmenopausal, 65% had 1 - 3 positive nodes, and 80% had HR+ breast cancer. Log-rank tests were used for pair-wise comparisons of the primary (DFS) and secondary (OS) endpoints among the three treatment arms. Results: With 64 months median follow-up, 5-year DFS in DD AC→PG group was 80.6% compared with 82.2% in DD AC→P group (HR=1.1; p=0.27) and 80.1 % (HR=0.97; p=0.71) in TAC group. 5-year OS was 90.8% in DD AC→PG group as compared with 89.1% (HR=.89; p=0.25) in DD AC→P group and 89.6 % (HR=0.90; p=0.32) in TAC group. HR for DFS and OS of DD AC→P vs. TAC were 0.89 (p=0.14) and 1.01 (p=0.92) respectively. Toxicities for TAC, DD AC→P, DD AC→PG, respectively: febrile neutropenia (Gr 3/4: 9%, 4%, 4% [p&lt;0.001]), sensory neuropathy (Gr 3/4: &lt;1%, 7%, 6% [p&lt;0.001]), diarrhea (Gr 3/4: 8 %, 2%, 2% [p&lt;0.001]). Hgb was &lt;10 in 12%, 26%, 33% with ESA use in 35.2%, 47%, 51.6% and transfusions in 3.7%, 6.3%, 9.4%. Deaths on treatment: N=13, 5, 7 (p=0.2). AML/MDS: N=5, 8, 11. All cycles completed in 91% for TAC and 88% for DD regimens. Conclusions: Addition of G to DD AC→P did not improve outcomes. No significant differences in efficacy endpoints were identified between DD AC→P and TAC, though toxicity profiles differed. Funding: NCI PHS U10-CA-37377, -69974, -12027, -69651 and NCCTG U10-CA25224, with additional funding from Eli Lilly &amp; Company, and Amgen, Inc.
An Efficient Co(II) Catalyzed Auto Oxidation of 1,4‐Dihydropyridines. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Management of Occult Contralateral Inguinal Hernia: Diagnosis and Treatment With Laparoscopic Totally Extra Peritoneal Repair (2020)

As it is noninvasive, easily accessible and has high sensitivity, USG is recommended in diagnosis. In the case of occult contralateral inguinal hernia, bilateral TEP is considered as a safe procedure. Thus, the need for a second operation and related complications can be prevented. We recommend routine USG to detect whether contralateral occult inguinal hernia is present.
A Barcode Shape Descriptor for Curve Point Cloud Data (2004)

In this paper, we present a complete computational pipeline for extracting a compact shape descriptor for curve point cloud data. Our shape descriptor, called a barcode, is based on a blend of techniques from differential geometry and algebraic topology.We also provide a metric over the space of barcodes, enabling fast comparison of PCDs for shape recognition and clustering. To demonstrate the feasibility of our approach, we have implemented it and provide experimental evidence in shape classification and parametrization.
An image model and segmentation algorithm for reflectance confocal images of in vivo cervical tissue (2005)

The automatic segmentation of nuclei in confocal reflectance images of cervical tissue is an important goal toward developing less expensive cervical precancer detection methods. Since in vivo confocal reflectance microscopy is an emerging technology for cancer detection, no prior work has been reported on the automatic segmentation of in vivo confocal reflectance images. However, prior work has shown that nuclear size and nuclear-to-cytoplasmic ratio can determine the presence or extent of cervical precancer. Thus, segmenting nuclei in confocal images will aid in cervical precancer detection. Successful segmentation of images of any type can be significantly enhanced by the introduction of accurate image models. To enable a deeper understanding of confocal reflectance microscopy images of cervical tissue, and to supply a basis for parameter selection in a classification algorithm, we have developed a model that accounts for the properties of the imaging system and of the tissues. Using our model in conjunction with a powerful image enhancement tool (anisotropic median-diffusion), appropriate statistical image modeling of spatial interactions (Gaussian Markov random fields), and a Bayesian framework for classification-segmentation, we have developed an effective algorithm for automatically segmenting nuclei in confocal images of cervical tissue. We have applied our algorithm to an extensive set of cervical images and have found that it detects 90% of hand-segmented nuclei with an average of 6 false positives per frame.
The levels of mature glycosylated nicastrin are regulated and correlate with γ‐secretase processing of amyloid β‐precursor protein (2002)

Nicastrin, a type-I transmembrane glycoprotein, is a necessary component of the high molecular weight presenilin (PS) complexes that mediate intramembranous cleavage of beta-amyloid precursor protein (betaAPP) and Notch. Nicastrin undergoes trafficking-dependent glycosylation maturation, and PS1 interacts preferentially with these maturely glycosylated forms of nicastrin. We investigated the effects of differing levels of the immature and mature endoglycosidase-H-resistant forms of nicastrin on Abeta40- and Abeta42-peptide secretion in several cell lines stably expressing a mutant nicastrin (D336A/Y337A) that increases Abeta secretion. There was no correlation between Abeta secretion and the level of over-expression of the immature forms of nicastrin. The total level of mature nicastrin remained constant, but mutant nicastrin replaced endogenous mature nicastrin in varying degrees. Differences in the levels of mature mutant nicastrin positively correlated with Abeta secretion, but did not influence either betaAPP trafficking or processing by alpha- and beta-secretases. Proper trafficking and terminal maturation of nicastrin is therefore a necessary event for the regulated intramembranous proteolysis of betaAPP.
Automatic endotracheal tube position confirmation system based on image classification – A preliminary assessment (2011)

Endotracheal intubation is a complex medical procedure in which a ventilating tube is inserted into the human trachea. Improper positioning carries potentially fatal consequences and therefore confirmation of correct positioning is mandatory. This paper introduces a novel system for endotracheal tube position confirmation. The proposed system comprises a miniature complementary metal oxide silicon sensor (CMOS) attached to the tip of a semi rigid stylet and connected to a digital signal processor (DSP) with an integrated video acquisition component. Video signals are acquired and processed by a confirmation algorithm implemented on the processor. The confirmation approach is based on video image classification, i.e., identifying desired expected anatomical structures (upper trachea and main bifurcation of the trachea) and undesired structures (esophagus). The desired and undesired images are indicators of correct or incorrect endotracheal tube positioning. The proposed methodology is comprised of a continuous and probabilistic image representation scheme using Gaussian mixture models (GMMs), estimated using a greedy algorithm. A multi-dimensional feature space, which consists of several textural-based features, is utilized to represent the images. The performance of the proposed algorithm was evaluated using two datasets: a dataset of 1600 images extracted from 10 videos recorded during intubations on dead cows, and a dataset of 358 images extracted from 8 videos recorded during intubations performed on human subjects. Each one of the video images was classified by a medical expert into one of three categories: upper tracheal intubation, correct (carina) intubation and esophageal intubation. The results, obtained using a leave-one-case-out method, show that the system correctly classified 1530 out of 1600 (95.6%) of the cow intubations images, and 351 out of the 358 human images (98.0%). Misclassification of an image of the esophagus as carina or upper-trachea, which is potentially fatal, was extremely rare (only one case when in the animal dataset and no cases when in the human intubation dataset). The classification results of the cow intubations dataset compare favorably with a state-of-the-art classification method tested on the same dataset.
Building an active semantic data warehouse for precision dairy farming (2018)

Digitalization of agricultural technology has led to the emergence of precision dairy farming, which strives for the simultaneous improvement of productivity as well as animal well-being in dairy farming through advanced use of technology such as movement sensors and milking parlors to monitor, control, and improve dairy production processes. The data warehouse serves as the appropriate technology for effective and efficient data management, which is paramount to the success of precision dairy farming. This paper presents a joint effort between industry and academia on the experimental development of an active semantic data warehouse to support business intelligence and business analytics in precision dairy farming. The research follows an action research approach, deriving lessons for theory and practice from a set of actions taken in the course of the project. Among these actions are the development of a loading stage to facilitate data integration, the definition of an analysis view as well as the introduction of semantic OLAP patterns to facilitate analysis, and analysis rules to automate periodic analyses. The large volumes of generated sensor data in precision dairy farming required careful decision-making concerning the appropriate level of detail of the data stored in the data warehouse. Semantic technologies played a key role in rendering analysis accessible to end users.
Disease phenotype of a ferret CFTR-knockout model of cystic fibrosis (2010)

Cystic fibrosis (CF) is a recessive disease that affects multiple organs. It is caused by mutations in CFTR. Animal modeling of this disease has been challenging, with species- and strain-specific differences in organ biology and CFTR function influencing the emergence of disease pathology. Here, we report the phenotype of a CFTR-knockout ferret model of CF. Neonatal CFTR-knockout ferrets demonstrated many of the characteristics of human CF disease, including defective airway chloride transport and submucosal gland fluid secretion; variably penetrant meconium ileus (MI); pancreatic, liver, and vas deferens disease; and a predisposition to lung infection in the early postnatal period. Severe malabsorption by the gastrointestinal (GI) tract was the primary cause of death in CFTR-knockout kits that escaped MI. Elevated liver function tests in CFTR-knockout kits were corrected by oral administration of ursodeoxycholic acid, and the addition of an oral proton-pump inhibitor improved weight gain and survival. To overcome the limitations imposed by the severe intestinal phenotype, we cloned 4 gut-corrected transgenic CFTR-knockout kits that expressed ferret CFTR specifically in the intestine. One clone passed feces normally and demonstrated no detectable ferret CFTR expression in the lung or liver. The animals described in this study are likely to be useful tools for dissecting CF disease pathogenesis and developing treatments.
Venoms, venomics, antivenomics (2009)

Venoms comprise mixtures of peptides and proteins tailored by Natural Selection to act on vital systems of the prey or victim. Here we review our proteomic protocols for uncoiling the composition, immunological profile, and evolution of snake venoms. Our long-term goal is to gain a deep insight of all viperid venom proteomes. Knowledge of the inter- and intraspecies ontogenetic, individual, and geographic venom variability has applied importance for the design of immunization protocols aimed at producing more effective polyspecific antivenoms. A practical consequence of assessing the cross-reactivity of heterologous antivenoms is the possibility of circumventing the restricted availability of species-specific antivenoms in some regions. Further, the high degree of target specificity makes toxins valuable scaffolds for drug development.
Real-space investigation of initial growth process of hydrogenated amorphous silicon on a graphite substrate (1996)

Initial growth of hydrogenated amorphous silicon (a-Si:H) from silane plasma on a cleaved surface of highly oriented pyrolytic graphite (HOPG) has been investigated by means of in situ x-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). At a substrate temperature of 110 \ifmmode^\circ\else\textdegree\fi{}C, island nuclei were formed on atomically flat terraces as well as along the steps of the HOPG surface. At an increased substrate temperature of 230 \ifmmode^\circ\else\textdegree\fi{}C, the nucleation occurred only along the steps. Hydrogen plasma treatment of the HOPG surface prior to the a-Si:H deposition drastically changed the growth mode to a homogeneous coverage of the surface from the beginning of film deposition at both temperatures. In order to understand and analyze these results, we propose a mechanism, from analogy to epitaxial film growth, that consists of the adsorption, migration, and fixation (pinning) of precursors on the surface and of subsequent nucleation and growth of film. \textcopyright{} 1996 The American Physical Society.
Effects of CNS Demyelination and Myelin Recovery on Urinary Physiology (2020)

Abstract Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system (CNS). Of note, over 80% of MS patients have urinary symptoms as one of their earliest symptoms. Since MS patients often live into older age, urinary incontinence and retention are significant problems for which few if any effective preventive or therapeutic options are available. The mechanisms by which MS contributes to urinary dysfunction are not well understood. We propose to elucidate the impact of demyelination on urinary performance using the cuprizone model, a model used to study the effects of CNS demyelination and spontaneous remyelination. We hypothesize that CNS demyelination in the cuprizone model will result in aberrant changes in urinary function, and that after remyelination occurs this dysfunction will be alleviated. C57Bl/6 mice were treated with cuprizone (0.2% w/w) for four weeks to induce demyelination. One group was allowed four additional weeks to recover from demyelination, while the other continued cuprizone treatment. Following this eight-week treatment, pressure/flow cystometry, electromyography, and molecular studies were performed to assess demyelination-induced differences in urinary performance. Cuprizone-recovery mice displayed improvements in cystometric function compared to their demyelinated littermates, as seen through improved volume sensitivity and voiding efficiency. Pharmacologic studies showed no significant changes in contractile responsiveness. Thus, we conclude that CNS demyelination results in aging-like phenotype and urinary dysfunction consistent with that observed in clinical disease. Therapeutics aimed at increasing the remyelination potential of the CNS neurons offer the possibility of alleviating urinary dysfunction associated with MS.
Improved Arrhythmia Detection in Implantable Loop Recorders (2008)

The new sensing and detection scheme is expected to substantially reduce the occurrence of inappropriately detected episodes, relative to that of the original ILR.
Real-Time Rendering of Real World Environments (1999)

One of the most important goals of interactive computer graphics is to allow a user to freely walk around a virtual recreation of a real environment that looks as real as the world around us. But hand-modeling such a virtual environment is inherently limited and acquiring the scene model using devices also presents challenges. Interactively rendering such a detailed model is beyond the limits of current graphics hardware, but image-based approaches can significantly improve the status quo. We present an end-to-end system for acquiring highly detailed scans of large real world spaces, consisting of forty to eighty million range and color samples, using a digital camera and laser rangefinder. We explain successful techniques to represent these large data sets as image-based models and present contributions to image-based rendering that allow these models to be rendered in real time on existing graphics hardware without sacrificing the high resolution at which the data sets were acquired.
An experimental platform for large-scale research facing FI-IoT scenarios (2011)

Providing experimental facilities for the Internet of Things (IoT) world is of paramount importance to materialise the Future Internet (FI) vision. The level of maturity achieved at the networking level in Sensor and Actuator networks (SAN) justifies the increasing demand on the research community to shift IoT testbed facilities from the network to the service and information management areas. In this paper we present an Experimental Platform fulfilling these needs by: integrating heterogeneous SAN infrastructures in a homogeneous way; providing mechanisms to handle information, and facilitating the development of experimental services. It has already been used to deploy applications in three different field trials: smart metering, smart places and environmental monitoring and it will be one of the components over which the SmartSantander project, that targets a large-scale IoT experimental facility, will rely on.