gebhart/patrepeval huggingface dataset:
Dielectric metamaterial waveguide for optical interconnect and sensing (2019)

Silicon subwavelength grating metamaterial (SGM), formed by periodically interleaving two or more types of materials a pitch far less than the operating wavelength, has been attracting substantial interest in recent years. It provides an effective approach to tailor the optical properties of naturally existing materials and thereby develop integrated photonic devices with unprecedented applications. In this paper, we introduce silicon photonics SGM waveguide based devices for optical interconnect and sensing applications. Silicon provides high index contrast and thus device footprints can be made very small. However, high index contrast is a double-edged sword, which also leads to a few devastating limitations such as limited photon-matter interaction and high dispersion. SGM waveguide can potentially resolve these issues. For instance, silicon-organic hybrid SGM modulator demonstrates &lt; 44 GHz 6 dB bandwidth and estimated energy consumption of 2.55 <i>f</i>J/bit. SGM waveguide based refractive index sensors show eminent improvement on the sensitivity compared to conventional strip waveguide based resonators. In the meantime, unlike evanescent wave based sensors, the surface sensitivity of SGM sensors does not decrease as analytes accumulate on the waveguide surface. SGM waveguide based passive components demonstrate improved bandwidth due to the decrease of waveguide dispersion. Other potential applications of SGM waveguide will also be discussed.
Comment-to-Article Linking in the Online News Domain (2015)

Online commenting to news articles provides a communication channel between media professionals and readers offering a crucial tool for opinion exchange and freedom of expression. Currently, comments are detached from the news article and thus removed from the context that they were written for. In this work, we propose a method to connect readers' comments to the news article segments they refer to. We use similarity features to link comments to relevant article segments and evaluate both word-based and term-based vector spaces. Our results are comparable to state-of-theart topic modeling techniques when used for linking tasks. We demonstrate that article segments and comments representation are relevant to linking accuracy since we achieve better performances when similarity features are computed using similarity between terms rather than words.
Critical evaluation of the use of cell cultures for inclusion in clinical trials of patients affected by collagen VI myopathies (2011)

Collagen VI myopathies (Ullrich congenital muscular dystrophy (UCMD), Bethlem myopathy (BM), and myosclerosis myopathy) share a common pathogenesis, that is, mitochondrial dysfunction due to deregulation of the permeability transition pore (PTP). This effect was first identified in the Col6a1(-/-) mouse model and then in muscle cell cultures from UCMD and BM patients; the normalizing effect of cyclosporin A (CsA) confirmed the pathogenic role of PTP opening. In order to determine whether mitochondrial performance can be used as a criterion for inclusion in clinical trials and as an outcome measure of the patient response to therapy, it is mandatory to establish whether mitochondrial dysfunction is conserved in primary cell cultures from UCMD and BM patients. In this study we report evidence that mitochondrial dysfunction and the consequent increase of apoptotic rate can be detected not only, as previously reported, in muscle, but also in fibroblast cell cultures established from muscle biopsies of collagen VI-related myopathic patients. However, the mitochondrial phenotype is no longer maintained after nine passages in culture. These data demonstrate that the dire consequences of mitochondrial dysfunction are not limited to myogenic cells, and that this parameter can be used as a suitable diagnostic criterion, provided that the cell culture conditions are carefully established.
Investigation of the Wacker process in formamide microemulsions (1987)

I. Rico, F. Couderc, E. Perez, J. P. Laval and A. Lattes, J. Chem. Soc., Chem. Commun., 1987, 1205 DOI: 10.1039/C39870001205
Influence of the synthetic method on the properties of two-photon-sensitive mesoporous silica nanoparticles (2015)

Herein we report the modulation of the properties of mesoporous silica nanoparticles (NPs) via various synthetic approaches. Three types of elaborations were compared, one in aqueous media at 25 °C, and the other two at 80 °C in water or in a water-ethanol mixture. For all these methods, an alkoxysilylated two-photon photosensitizer (2PS) was co-condensed with tetraethylorthosilicate (TEOS) in the presence of cetyltrimethylammonium bromide (CTAB), leading to five two-photon-sensitive mesoporous silica (M2PS) NPs. The M2PS NP porous structure could be tuned from radial to worm-like and MCM-41 types of organization. Besides, the 2PS precursor spatial dispersion was found to be highly dependent on both the 2PS initial concentration and the elaboration process. As a result, two-photon properties were modulated by the choice of the synthesis, the best results being found in aqueous media at 25 or 80 °C. Finally, the M2PS NPs were used for in vitro two-photon imaging of cancer cells.
Stereo Vision and Scene Segmentation (2012)

This chapter focuses on how segmentation robustness can be improved by 3D scene geometry\nprovided by stereo vision systems, as they are simpler and relatively cheaper than most of\ncurrent range cameras. In fact, two inexpensive cameras arranged in a rig are often enough\nto obtain good results. Another noteworthy characteristic motivating the choice of stereo\nsystems is that they both provide 3D geometry and color information of the framed scene\nwithout requiring further hardware. Indeed, as it will be seen in following sections, 3D geometry\nextraction from a framed scene by a stereo system, also known as stereo reconstruction,\nmay be eased and improved by scene segmentation since the correspondence research can be\nrestricted within the same segment in the left and right images.
ATXN1L, CIC, and ETS Transcription Factors Modulate Sensitivity to MAPK Pathway Inhibition (2017)

Intrinsic resistance and RTK-RAS-MAPK pathway reactivation has limited the effectiveness of MEK and RAF inhibitors (MAPKi) in RAS- and RAF-mutant cancers. To identify genes that modulate sensitivity to MAPKi, we performed genome-scale CRISPR-Cas9 loss-of-function screens in two KRAS mutant pancreatic cancer cell lines treated with the MEK1/2 inhibitor trametinib. Loss of CIC, a transcriptional repressor of ETV1, ETV4, and ETV5, promoted survival in the setting of MAPKi in cancer cells derived from several lineages. ATXN1L deletion, which reduces CIC protein, or ectopic expression of ETV1, ETV4, or ETV5 also modulated sensitivity to trametinib. ATXN1L expression inversely correlates with response to MAPKi inhibition in clinical studies. These observations identify the ATXN1L-CIC-ETS transcription factor axis as a mediator of resistance to MAPKi.
Dissection of c&hyphen;Mpl and Thrombopoietin Function: Studies of Knockout Mice and Receptor Signal Transduction (1996)

The physiological roles and mechanisms of action of thrombopoietin (TPO) and its receptor c-Mpl have been studied through the analysis of mice genetically deficient in these molecules, as well as through the dissection of signaling events utilizing chimeric receptors. The evidence clearly demonstrates that the TPO/c-Mpl system provides dominant control in the regulation of megakaryocytopoiesis. The signaling mechanisms that underlie this process appear to be similar to those noted with other members of the hematopoietic cytokine and cytokine receptor families.
Chemistry and solar energy (2011)

Item consists of a digitized copy of a video recording of a Cecil and Ida Green lecture delivered at the Vancouver Institute by Harry B. Gray on March 21, 1992. Original video recording available in the University Archives (UBC VT 264).
The Quorum-Quenching Lactonase from Bacillus thuringiensis Is a Metalloprotein (2005)

Lactonases from Bacillus species hydrolyze the N-acylhomoserine lactone (AHL) signaling molecules used in quorum-sensing pathways of many Gram-negative bacteria, including Pseudomonas aeruginosa and Erwinia carotovora, both significant pathogens. Because of sequence similarity, these AHL lactonases have been assigned to the metallo-beta-lactamase superfamily of proteins, which includes metalloenzymes of diverse activity, mechanism, and metal content. However, a recent study claims that AHL lactonase from Bacillus sp. 240B1 is not a metalloprotein [Wang, L. H., et al. (2004) J. Biol. Chem. 279, 13645]. Here, the gene for an AHL lactonase from Bacillus thuringiensis is cloned, and the protein is expressed, purified, and found to bind 2 equiv of zinc. The metal-bound form of AHL lactonase catalyzes the hydrolysis of N-hexanoyl-(S)-homoserine lactone but not the (R) enantiomer. Removal of both zinc ions results in loss of activity, and reconstitution with zinc restores activity, indicating the importance of metal ions for catalytic activity. Metal content, sequence alignments, and X-ray absorption spectroscopy of the zinc-containing lactonase all support a proposed dinuclear zinc binding site similar to that found in glyoxalase II.
DNA-Decorated Carbon Nanotubes as Sensitive Layer for AlN Contour-Mode Resonant-MEMS Gravimetric Sensor (2009)

In this work a nano-enabled gravimetric chemical sensor prototype based on single-stranded DNA (ss-DNA) decorated single-walled carbon nanotubes (SWNT) as nano-functionalization layer for Aluminun Nitride (AIN) contour-mode resonant-MEMS gravimetric sensors has been demonstrated. Two resonators fabricated on the same silicon chip and operating at different resonance frequencies, 287 and 450 MHz, were functionalized with this novel bio-coating layer to experimentally prove the capability of two distinct single strands of DNA bound to SWNT to enhance differently the adsorption of volatile organic compounds such as dinitroluene (DNT, simulant for explosive vapor) and dymethyl-methylphosphonate (DMMP, a simulant for nerve agent sarin). The introduction of this bio-coating layer addresses the major drawbacks of recovery time (50% recovery in less than 29 seconds has been achieved) and lack of selectivity associated with gas sensor based on polymers and pristine carbon nanotube functionalization layers.
Convergence of Web 2.0 and Semantic Web: A Semantic Tagging and Searching System for Creating and Searching Blogs (2007)

During the last several years, the volume of user-generated content on the web has skyrocketed. Today, the major Internet players such as MySpace, Wordpress, and YouTube all provide a variety of Web 2.0 based applications that allow users to post photos, share video, and manage blogs with multimedia content. Keyword-based tags are used to classify the submitted content and to conduct searches for retrieval. Use of simple keyword-based tags provide less than optimal classification leading to poor search results. This work examines several proposed solutions to this problem and proposes a solution based on semantic tagging of online contents. These proposed semantic tags are intended to be “understandable” to both machines and humans; additionally we allow the user to specify a context for each tag. The combination of these measures permits searches based on inferences and synonyms in addition to simple keyword matches. Initial tests demonstrate that use of the proposed scheme leads to more accurate content classification and search results with a greater number of hits and higher relevancy. We describe the design and, implementation of a prototype system as proof of concept of our proposed solution. The prototype has been implemented with extensive use of open source software such as Jena, jBoss, the Spring framework, PostgreSQL database, and other freely available resources such as Wordnet.
Carbon−Carbon Bond Activation of R−CN (R = Me, Ar, iPr, tBu) Using a Cationic Rh(III) Complex (2002)

Addition of 1.0 equiv of Ph3SiH to [Cp*(PMe3)Rh(Me)(CH2Cl2)]+BAr'4- (1) resulted in release of methane and quantitative formation of [Cp*(PMe3)Rh(SiPh3)(CH2Cl2)]+BAr'4- (2). Subsequent addition of 1.0 equiv of MeCN to 2 caused immediate displacement of dichloromethane to form the eta1-nitrile adduct [Cp*(PMe3)Rh(SiPh3)(NCMe)]+BAr'4- (3). Upon standing at room-temperature overnight, complex 3 converted quantitatively to another product which has been characterized as the C-C activation product, [Cp*(PMe3)Rh(Me)(CNSiPh3)]+BAr'4- (5). Addition of other nitrile substrates (R-CN, R = Ph, (4-CF3)Ph, (4-MeO)Ph, iPr, tBu) to 2 also resulted in C-C activation of the R-CN bond to form [Cp*(PMe3)Rh(R)(CNSiPh3)]+BAr'4-. Evidence for an eta2-iminoacyl intermediate complex, [Cp*(PMe3)Rh(eta2-C(R)=N(SiPh3)]+BAr'4-, is also presented.
Flash-enabled database storage (2010)

Flash memory has emerged as a high-performing and viable storage alternative to magnetic disks for data-intensive applications. In our work we study how the storage layer of a database system can benefit from the presence of a flash disk. Due to the varying price and I/O characteristics of flash disks the optimal design decisions vary widely across different setups. We study how the system can take advantage of the random read efficiency of inexpensive flash disks by using the latter at the same level of memory hierarchy as magnetic disks in a hybrid setup; our algorithms provide efficient and adaptive data placement that leads to substantial performance improvement. We propose techniques to accurately predict the main memory cache behavior for systems consisting of heterogeneous storage media and selectively allocate memory buffers to devices; thereby, the I/O cost of the system drops significantly, even offsetting wrong data placement decisions. We also explore the design space for a system that uses flash memory as a cache to the underlying storage and propose techniques towards high performance. The experimental results, we believe, exhibit both the potential and necessity of our techniques in future database systems.
Facile Preparation Route for Nanostructured Composites: Surface-Initiated Ring-Opening Polymerization of ε-Caprolactone from High-Surface-Area Nanopaper (2012)

In this work, highly porous nanopaper, i.e., sheets of papers made from non-aggregated nanofibrillated cellulose (NFC), have been surface-grafted with poly(ε-caprolactone) (PCL) by surface-initiated ring-opening polymerization (SI-ROP). The nanopaper has exceptionally high surface area (∼300 m2/g). The “grafting from” of the nanopapers was compared to “grafting from” of cellulose in the form of filter paper, and in both cases either titanium n-butoxide (Ti(On-Bu)4) or tin octoate (Sn(Oct)2) was utilized as a catalyst. It was found that a high surface area leads to significantly higher amount of grafted PCL in the substrates when Sn(Oct)2 was utilized as a catalyst. Up to 79 wt % PCL was successfully grafted onto the nanopapers as compared to filter paper where only 2–3 wt % PCL was grafted. However, utilizing Ti(On-Bu)4 this effect was not seen and the grafted amount was essentially similar, irrespectively of surface area. The mechanical properties of the grafted nanopaper proved to be superior to those of pure PCL films, especially at elevated temperatures. The present bottom-up preparation route of NFC-based composites allows high NFC content and provides excellent nanostructural control. This is an important advantage compared with some existing preparation routes where dispersion of the filler in the matrix is challenging.
Development of microwave/millimeter wave integral passives for multi-layer organic MCMs (2002)

We present the design and development of the high-density multi-layer organic based MCMs at microwave/millimeter wave frequencies. Ta/sub 2/N thin-film resistors have been developed and directly integrated onto Kapton and benzocyclobutene (BCB) flex that increases the packaging density and improves manufacturability. The experimental results demonstrate that the integral 50-/spl Omega/ termination on multi-layer Kapton/BCB flex achieves a return loss of less than 20-dB up to 50 GHz.
Colonization factors among enterotoxigenic Escherichia coli isolates from children with moderate-to-severe diarrhea and from matched controls in the Global Enteric Multicenter Study (GEMS) (2019)

Major CF-based efficacious ETEC vaccines could potentially prevent up to 66% of pediatric MSD cases due to ST-encoding ETEC in developing countries; adding CS14 extends coverage to ~77%.
Limitations of incremental signal-tracing for FPGA debug (2012)

Developing state-of-the-art custom silicon can be a prohibitively expensive and risky undertaking, due in no small part to the need to perform thorough design verification. Field-Programmable Gate-Arrays offer a flexible platform for constructing prototypes to aid in their verification, but unlike software simulation, observability into these prototypes is a major challenge. Designers can choose to insert trace-instrumentation to enhance on-chip observability, but doing so often requires re-compiling the entire design for each new trace configuration. This work presents two contributions: to explore the limitations of incremental-synthesis for trace-buffer insertion, and to propose CAD optimizations exclusive to this application for improving runtime and routability. We find that 99.4% of all used cluster outputs (driving both combinational and sequential circuit signals) can be incrementally-traced to 75% of the free memory-capacity on an FPGA, an order of magnitude quicker than the original compilation and with a nominal impact on circuit delay, for a 20% minimum channel width (10% area) increase.
Resolution of psoriasis upon blockade of IL-15 biological activity in a xenograft mouse model (2003)

Psoriasis is a chronic inflammatory disease of the skin characterized by epidermal hyperplasia, dermal angiogenesis, infiltration of activated T cells, and increased cytokine levels. One of these cytokines, IL-15, triggers inflammatory cell recruitment, angiogenesis, and production of other inflammatory cytokines, including IFN-gamma, TNF-alpha, and IL-17, which are all upregulated in psoriatic lesions. To investigate the role of IL-15 in psoriasis, we generated mAb's using human immunoglobulin-transgenic mice. One of the IL-15-specific antibodies we generated, 146B7, did not compete with IL-15 for binding to its receptor but potently interfered with the assembly of the IL-15 receptor alpha, beta, gamma complex. This antibody effectively blocked IL-15-induced T cell proliferation and monocyte TNF-alpha release in vitro. In a human psoriasis xenograft model, antibody 146B7 reduced the severity of psoriasis, as measured by epidermal thickness, grade of parakeratosis, and numbers of inflammatory cells and cycling keratinocytes. These results obtained with this IL-15-specific mAb support an important role for IL-15 in the pathogenesis of psoriasis.
Framework for 3D histologic reconstruction and fusion with in vivo MRI: Preliminary results of characterizing pulmonary inflammation in a mouse model (2015)

The authors' 3D histology reconstruction and multimodal registration framework were successfully employed to reconstruct the histology volume of the lung and fuse it with in vivo MRI to create a ground truth map for inflammation on in vivo MRI. The analytic platform presented here lays the framework for a rigorous validation of the identified imaging features for chronic lung inflammation on MRI in a large prospective cohort.
Substrate Specificity in the Highly Heterogeneous M4 Peptidase Family Is Determined by a Small Subset of Amino Acids (2000)

The members of the M4 peptidase family are involved in processes as diverse as pathogenicity and industrial applications. For the first time a number of M4 family members, also known as thermolysin-like proteases, has been characterized with an identical substrate set and a uniform set of assay conditions. Characterization with peptide substrates as well as high performance liquid chromatography analysis of beta-casein digests shows that the M4 family is a homogeneous family in terms of catalysis, even though there is a significant degree of amino acid sequence variation. The results of this study show that differences in substrate specificity within the M4 family do not correlate with overall sequence differences but depend on a small number of identifiable amino acids. Indeed, molecular modeling followed by site-directed mutagenesis of one of the substrate binding pocket residues of the thermolysin-like proteases of Bacillus stearothermophilus converted the catalytic characteristics of this variant into that of thermolysin.
Smart Electrochemical sensing platform for pesticide residue analysis in soil run-off (2021)

There is a major requirement at present to address environmental sustainability in ecological and agricultural practices as highlighted by the United Nations’ “2030 Agenda for sustainable development” [1]. As a result of this proposition- there has been an influx in studies to develop biosensor technologies meant for green living and monitoring different areas in environmental and agri-food sectors. Despite these efforts, one particular vital component of the environment has been probed comparatively much more sparsely-namely, the soil ecosystem that directly and indirectly affects the agricultural health and throughput as well as ecosystem balance [2]. One specific problem is the application of pesticides in crops and other plants often finds its way seeping into soil in a large manner and there exists a leaching effect at the soil and ground water sources. The potential for a sensor system that detects in-field: the levels of pesticide residue in soil run-off is immense and would be beneficial to understand the negative effect of soil contaminants on food security and food safety by inhibiting soil microbial activity and therefore impacting crop throughput and food quality. This field deployable sensor probe would help promote responsible agricultural practices and curb overapplication of harmful agents to the soil [3]. Electrochemistry proves to be a viable choice of application for such a sensor to track pesticides in soil samples due to its feasibility for in-situ analysis used as well as solving for the ASSURED criteria as given by the World Health Organization (WHO), wherein it denotes- Affordable, Sensitive, Specific, User-friendly, Rapid, and robust, Equipment-free and Deliverable to end-users [4]. The proposed system would have to utilize minimally complex sensor modification/functionalization and no pre-processing of samples. Hence citing all these factors and requirements, in this work- we present a highly intuitive electroanalytical sensor approach towards rapid, on-demand screening of 2 commonly used pesticides in this proof-of-feasibility study- Glyphosate [5] and Atrazine [6] in soil run-off which have a half-life of 47 days and 60-75 days respectively. By studying the levels of soil contaminant residues at the field site-the sensor acts as a screening instrument for soil pollution levels.  The proposed sensor functions based on affinity biosensing mechanism driven via thiol-crosslinker and antibody receptors that holistically behaves as a recognition immunoassay stack (fig.1A) that is specific and sensitive to track test pesticide analytes in the parts per billion (ppb) range for glyphosate and parts per trillion (ppt) range for atrazine. Then, this developed sensor is integrated further to create a pesticide sensing ecosystem by means of a front-end field-deployable smart device (fig.1B) and thereby, a universal pesticide screening analytical device is designed and fabricated for pesticide assessment in real soil run-off samples.