gebhart/patrepeval huggingface dataset:
Microsystem strategies for sample preparation in biological detection. (2005)

The objective of this LDRD was to develop microdevice strategies for dealing with samples to be examined in biological detection systems. This includes three sub-components: namely, microdevice fabrication, sample delivery to the microdevice, and sample processing within the microdevice. The first component of this work focused on utilizing Sandia's surface micromachining technology to fabricate small volume (nanoliter) fluidic systems for processing small quantities of biological samples. The next component was to develop interfaces for the surface-micromachined silicon devices. We partnered with Micronics, a commercial company, to produce fluidic manifolds for sample delivery to our silicon devices. Pressure testing was completed to examine the strength of the bond between the pressure-sensitive adhesive layer and the silicon chip. We are also pursuing several other methods, both in house and external, to develop polymer-based fluidic manifolds for packaging silicon-based microfluidic devices. The second component, sample processing, is divided into two sub-tasks: cell collection and cell lysis. Cell collection was achieved using dielectrophoresis, which employs AC fields to collect cells at energized microelectrodes, while rejecting non-cellular particles. Both live and dead Staph. aureus bacteria have been collected using RF frequency dielectrophoresis. Bacteria have been separated from polystyrene microspheres using frequency-shifting dielectrophoresis. Computational modeling was performed to optimize device separation performance, and to predict particle response to the dielectrophoretic traps. Cell lysis is continuing to be pursued using microactuators to mechanically disrupt cell membranes. Novel thermal actuators, which can generate larger forces than previously tested electrostatic actuators, have been incorporated with and tested with cell lysis devices. Significant cell membrane distortion has been observed, but more experiments need to be conducted to determine the effects of the observed distortion on membrane integrity and cell viability. Finally, we are using a commercial PCR DNA amplification system to determine the limits of detectable sample size, and to examine the amplification of DNA bound to microspheres. Our objective is to use microspheres as capture-and-carry chaperones for small molecules such as DNA and proteins, enabling the capture and concentration of the small molecules using dielectrophoresis. Current tests demonstrated amplification of DNA bound to micron-sized polystyrene microspheres using 20-50 microliter volume size reactions.
Luminescent-Activated Transfected Killer Cells to Monitor Leukocyte Trafficking During Systemic Bacterial and Fungal Infection (2011)

ATAK cells accumulated in target organs with distinct profiles, depending on the microbial etiology of infection. Finally, generation of an anti-ATAK immune response may provide an important safety mechanism that helps clear the cells from the host as the marrow recovers.
ChemInform Abstract: Carbocyclic Carbene Ligands in Palladium‐Catalyzed C—N Coupling Reactions. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Analysis of retinal and choroidal images measured by laser Doppler holography (2019)

Laser Doppler holography (LDH) is a full-field imaging technique that was recently used in the human eye to reveal blood flow contrasts in the retinal and choroidal vasculature non-invasively, and with high temporal resolution. We here demonstrate that the ability of LDH to perform quantitative flow measurements with high temporal resolution enables arteriovenous differentiation in the retina and choroid. In the retina, arteries and veins can be differentiated on the basis of their respective power Doppler waveforms. Choroidal arteries and veins can instead be discriminated by computing low and high frequency power Doppler images to reveal low and high blood flow images, respectively.
Towards Instance-level Image-to-Image Translation (2019)

Unpaired Image-to-image Translation is a new rising and challenging vision problem that aims to learn a mapping between unaligned image pairs in diverse domains. Recent advances in this field like MUNIT and DRIT mainly focus on disentangling content and style/attribute from a given image first, then directly adopting the global style to guide the model to synthesize new domain images. However, this kind of approaches severely incurs contradiction if the target domain images are content-rich with multiple discrepant objects. In this paper, we present a simple yet effective instance-aware image-to-image translation approach (INIT), which employs the fine-grained local (instance) and global styles to the target image spatially. The proposed INIT exhibits three import advantages: (1) the instance-level objective loss can help learn a more accurate reconstruction and incorporate diverse attributes of objects; (2) the styles used for target domain of local/global areas are from corresponding spatial regions in source domain, which intuitively is a more reasonable mapping; (3) the joint training process can benefit both fine and coarse granularity and incorporates instance information to improve the quality of global translation. We also collect a large-scale benchmark for the new instance-level translation task. We observe that our synthetic images can even benefit real-world vision tasks like generic object detection.
Anticoagulation (2009)

Abstract Chapter 17 discusses anticoagulation, including definitions and key terms, key areas for attention when administering an anticoagulant, and practical considerations for using heparin.
Mutilans arthropathy in systemic lupus erythematosus. (1990)

The rare association of resorptive arthropathy with systemic lupus erythematosus is described in a 37-year-old female patient in order to emphasize the occurrence of aggressive joint abnormalities of the disease. This patient developed mild articular manifestations at the onset of the disease and 8 years later we detected mutilans changes in the DIP joints. Other diseases in which similar articular findings have previously been noted, were ruled out through the follow-up.
p95HER2 Methionine 611 Carboxy-Terminal Fragment Is Predictive of Trastuzumab Adjuvant Treatment Benefit in the FinHer Trial (2018)

<b>Purpose:</b> Expression of p95HER2 (p95), a truncated form of the HER2 receptor, which lacks the trastuzumab binding site but retains kinase activity, has been reported as a prognostic biomarker for poor outcomes in patients with trastuzumab-treated HER2-positive metastatic breast cancer. The impact of p95 expression on trastuzumab treatment efficacy in early HER2-positive breast cancer is less clear. In the current study, p95 was tested as a predictive marker of trastuzumab treatment benefit in the HER2-positive subset of the FinHer adjuvant phase III trial.<b>Experimental Design:</b> In the FinHer trial, 232 patients with HER2-positive early breast cancer were randomized to receive chemotherapy plus 9 weeks of trastuzumab or no trastuzumab treatment. Quantitative p95 protein expression was measured in formalin-fixed paraffin-embedded samples using the p95 VeraTag assay (Monogram Biosciences), specific for the M611 form of p95. Quantitative HER2 protein expression was measured using the HERmark assay (Monogram Biosciences). Distant disease-free survival (DDFS) was used as the primary outcome measure.<b>Results:</b> In the arm receiving chemotherapy only, increasing log<sub>10</sub>(p95) correlated with shorter DDFS (HR, 2.0; <i>P</i> = 0.02). In the arm receiving chemotherapy plus trastuzumab (<i>N</i> = 95), increasing log<sub>10</sub>(p95) was not correlated with a shorter DDFS. In a combined analysis of both treatment arms, high breast tumor p95 content was significantly correlated with trastuzumab treatment benefit in multivariate models (interaction <i>P</i> = 0.01).<b>Conclusions:</b> A high p95HER2/HER2 ratio identified patients with metastatic breast cancer with poor outcomes on trastuzumab-based therapies. Further investigation of the p95HER2/HER2 ratio as a potential prognostic or predictive biomarker for HER2-targeted therapy is warranted. <i>Clin Cancer Res; 24(13); 3046-52. ©2018 AACR</i>.
ChemInform Abstract: Homogenous Asymmetric Hydrogenation: Recent Trends and Industrial Applications (2011)

Abstract Review: 99 refs.
Automated sample plan selection for OPC modeling (2014)

It is desired to reduce the time required to produce metrology data for calibration of Optical Proximity Correction (OPC) models and also maintain or improve the quality of the data collected with regard to how well that data represents the types of patterns that occur in real circuit designs. Previous work based on clustering in geometry and/or image parameter space has shown some benefit over strictly manual or intuitive selection, but leads to arbitrary pattern exclusion or selection which may not be the best representation of the product. Forming the pattern selection as an optimization problem, which co-optimizes a number of objective functions reflecting modelers’ insight and expertise, has shown to produce models with equivalent quality to the traditional plan of record (POR) set but in a less time.
Systematic Design of Large-Scale Multiport Decoupling Networks (2014)

In radio-frequency systems that drive coupled dissipative loads, the matching network between the amplifiers and their loads needs to account for the coupling. With N amplifiers driving N loads, a favorite choice is a “decoupling” network, which is a lossless reciprocal network that has N input ports connected to the sources and N output ports connected to the loads. The decoupling network transforms the coupled impedance of the loads into the uncoupled characteristic impedance of the sources. Any incident signal at the input ports of the network is transferred, without reflection, to the loads. Decoupling networks can be realized by generalized Π-networks of lumped and distributed impedances, depending on the design frequency. Although the impedance requirements of the network are unique, its realization is not, and networks that involve many impedances can be difficult to lay out on circuit boards. In this paper, we establish that a decoupling network requires a minimum of N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> +N impedances for N arbitrarily coupled loads, and provide a systematic method for realizing this lower bound. We also provide methods for selectively eliminating impedances. We give an example where only 4N impedances are needed for loads that have coupling symmetry. Applications of the methods are presented.
Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy (1999)

This study indicates that the viral population in the patient does not have to represent the fittest possible variants, and thus antiretroviral therapy may drive the viral population first through a lower fitness level and then to a higher fitness level.
Gavage of Fecal Samples From Patients With Colorectal Cancer Promotes Intestinal Carcinogenesis in Germ-Free and Conventional Mice (2017)

We fed stool samples from patients with CRC and heathy individuals to germ-free mice and conventional mice with azoxymethane. We found stool from patients with CRC to increase the numbers of polyps, levels of intestinal dysplasia and proliferation, markers of inflammation, and proportions of Th1 and Th17 cells in colon, compared with stool from individuals without CRC. This study provides evidence that the fecal microbiota from patients with CRC can promote tumorigenesis in germ-free mice and mice given a carcinogen.
Janus, or the Inevitable Battle Between Too Much and Too Little Oxygen (2022)

<b><i>Significance:</i></b> Oxygen levels are key regulators of virtually every living mammalian cell, under both physiological and pathological conditions. Starting from embryonic and fetal development, through the growth, onset, and progression of diseases, oxygen is a subtle, although pivotal, mediator of key processes such as differentiation, proliferation, autophagy, necrosis, and apoptosis. Hypoxia-driven modifications of cellular physiology are investigated in depth or for their clinical and translational relevance, especially in the ischemic scenario. <b><i>Recent Advances:</i></b> The mild or severe lack of oxygen is, undoubtedly, related to cell death, although abundant evidence points at oscillating oxygen levels, instead of permanent low pO<sub>2</sub>, as the most detrimental factor. Different cell types can consume oxygen at different rates and, most interestingly, some cells can shift from low to high consumption according to the metabolic demand. Hence, we can assume that, in the intracellular compartment, oxygen tension varies from low to high levels depending on both supply and consumption. <b><i>Critical Issues:</i></b> The positive balance between supply and consumption leads to a pro-oxidative environment, with some cell types facing hypoxia/hyperoxia cycles, whereas some others are under fairly constant oxygen tension. <b><i>Future Directions:</i></b> Within this frame, the alterations of oxygen levels (dysoxia) are critical in two paradigmatic organs, the heart and brain, under physiological and pathological conditions and the interactions of oxygen with other physiologically relevant gases, such as nitric oxide, can alternatively contribute to the worsening or protection of ischemic organs. Further, the effects of dysoxia are of pivotal importance for iron metabolism. <i>Antioxid. Redox Signal.</i> 37, 972-989.
Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing (2014)

Neurexins are evolutionarily conserved presynaptic cell-adhesion molecules that are essential for normal synapse formation and synaptic transmission. Indirect evidence has indicated that extensive alternative splicing of neurexin mRNAs may produce hundreds if not thousands of neurexin isoforms, but no direct evidence for such diversity has been available. Here we use unbiased long-read sequencing of full-length neurexin (Nrxn)1α, Nrxn1β, Nrxn2β, Nrxn3α, and Nrxn3β mRNAs to systematically assess how many sites of alternative splicing are used in neurexins with a significant frequency, and whether alternative splicing events at these sites are independent of each other. In sequencing more than 25,000 full-length mRNAs, we identified a novel, abundantly used alternatively spliced exon of Nrxn1α and Nrxn3α (referred to as alternatively spliced sequence 6) that encodes a 9-residue insertion in the flexible hinge region between the fifth LNS (laminin-α, neurexin, sex hormone-binding globulin) domain and the third EGF-like sequence. In addition, we observed several larger-scale events of alternative splicing that deleted multiple domains and were much less frequent than the canonical six sites of alternative splicing in neurexins. All of the six canonical events of alternative splicing appear to be independent of each other, suggesting that neurexins may exhibit an even larger isoform diversity than previously envisioned and comprise thousands of variants. Our data are consistent with the notion that α-neurexins represent extracellular protein-interaction scaffolds in which different LNS and EGF domains mediate distinct interactions that affect diverse functions and are independently regulated by independent events of alternative splicing.
360° Single Image Super Resolution via Distortion-Aware Network and Distorted Perspective Images (2021)

Effective 360° imaging requires a very high resolution because the field of view is extraordinarily high. Single-image super-resolution (SISR) applied to 360° imaging has the potential to solve the resolution/quality problem in this modality. In this paper, we exploit existing perspective SISR networks to address this problem by (1) introducing a distortion map as an additional input with the $360^{\circ}-$ distortion-aware loss function, and (2) augmenting the training 360° images by distorting the perspective images. We also present a new 360° image dataset from YouTube for training. Our extensive experiments show that how each component contributes to the better transfer from the perspective domain to the 360° domain and merging all the ideas leads to the best performance in quantitative and qualitative ways for the 360° SISR task.
Correction for Spatial Averaging Artifacts for Circularly-Symmetric Pressure Beams Measured with Membrane Hydrophones (2020)

This paper investigates experimental underestimation of pressure measurements due to spatial averaging across a hydrophone sensitive element. Empirical relationships are measured to enable correction for hydrophone spatial averaging errors in peak compressional pressure (<i>p</i> <sub><i>c</i></sub> ), peak rarefactional pressure (<i>p</i> <sub><i>r</i></sub> ), and pulse intensity integral (<i>pii</i>). The empirical relationships show, for example, that if a 3-MHz, F/2 transducer is driven to moderate nonlinear distortion and measured at the focal point with a 500-μm membrane hydrophone, then spatial averaging errors are approximately 16% (<i>p</i> <sub><i>c</i></sub> ), 12% (<i>p</i> <sub><i>r</i></sub> ), and 24% (<i>pii</i>).
Abstract 291: Targeting the stroma to hit the tumor: MMP11 as a novel target for cancer immunotherapy (2015)

Abstract Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that mediate a number of physiological and pathological processes, such as matrix degradation, tissue remodeling, inflammation and tumor metastasis. The objective of this study was to develop and characterize a vaccine targeting stromal antigens expressed by cancer associated fibroblasts (CAFs). We focused on MMP11 (or stromelysin 3, ST3), that has been detected primarily in CAFs and its expression correlates with aggressive clinical behavior and invasiveness of different types of carcinoma. We demonstrated that intramuscular injection of genetic vectors such as Adenovirus (Ad) and plasmid DNA encoding MMP11 engineered variants followed by in vivo electroporation (DNA-EP) resulted in breakage of immune tolerance and induction of both cell mediated and humoral immune response. Importantly, MMP11 vaccine was able to confer significant antitumoral protection in a chemically induced, MMP11 overexpressing colon cancer model both in prophylactic and therapeutic settings. To determine the mechanism of action of MMP11 vaccine, we have utilized IFNgamma- and μmicroMT-knock out mice, devoid of T- and B-cell immune response, respectively. Our results show that both arms of the immune response are important to confer the therapeutic effect. Moreover, MMP11 stromal vaccine showed synergic effects when combined with genetic vaccines targeting classic tumor associated antigens, such as telomerase reverse transcriptase (TERT) and carcinoembryonic antigen (CEA). Finally, to assess the immunogenicity and the safety of MMP11 vaccine in a large animal model, nonhuman primates have been vaccinated with Ad and DNA-EP. A strong immune response was measured with no detectable side effects. In addition, MMP11 detection and spontaneous immune responses in the blood of breast and prostate cancer patients further corroborate MMP11 as a valid target for immune intervention. Taken together, these data support the use of MMP11 as a potential candidate for cancer immunotherapy in human clinical trials. Citation Format: Laura Luberto, Rita Mancini, Arianna Di Napoli, Daniela Peruzzi, Federica Mori, Giuseppe Roscilli, Emanuele Marra, Manuela Cappelletti, Gennaro Ciliberto, Luigi Aurisicchio. Targeting the stroma to hit the tumor: MMP11 as a novel target for cancer immunotherapy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 291. doi:10.1158/1538-7445.AM2015-291
A Soft Casting Technique for Managing Pediatric Hand and Foot Burns (2018)

Hand and foot burns in children are difficult to dress. The authors have developed a soft casting technique to manage burns to these areas. The aim of this study is to report the outcomes using weekly dressing changes with a soft casting technique to manage pediatric hand and foot burns in the outpatient setting. A retrospective chart review was performed on children with burns to the hands or feet, who underwent dressing changes with a soft casting technique at the Children's Hospital Colorado Burn Center. Soft casting was performed by placing antibiotic ointment-impregnated nonadherent gauze over the burn wound(s), wrapping the extremity using rolled gauze, applying soft cast pad, plaster, soft cast tape, and an elastic bandage. This was changed weekly. Two hundred ninety-eight children with hand burns had a mean age of 16.8 ± 2 months. Two hundred forty-eight children had partial thickness burn injuries (83%), 50 had full thickness burn injuries (17%), and the mean total body surface area (TBSA) was 1 ± 2.4%. The mean time to heal was 10.1 ± 1.7 days for all subjects. Sixty-six children with foot burns were identified with a mean age of 24 ± 2.6 months. Forty-six children had partial thickness injuries (70%), 20 had full thickness burn injuries (30%), and the mean TBSA was 2.3 ± 2.9%. The mean time to heal was 14.1 ± 2.2 days for all subjects. Weekly dressing changes using a soft casting technique are effective for the outpatient management of pediatric hand and foot burns. This method avoids costly inpatient hospital care, reduces the number of painful dressing changes, and allows children to heal in their own environment.
Supramolekulare organisch‐anorganische Hybridaggregate mit variabler Partikelgröße: Zusammenspiel von drei nichtkovalenten Wechselwirkungen (2013)

Gegensätze ziehen sich an: Gold- oder CdS-Nanopartikel und ionische Farbstoffmoleküle können supramolekulare Aggregate mit einer definierten Größe zwischen 100 und 300 nm bilden, wenn man ein Makroion als Templat und Bindeglied verwendet. Das Bild zeigt das erhaltene Gold-Dendrimer-Farbstoff-Aggregat (blaue Kugeln: dendritisches Makroion, rote Kugeln: Gold, rote Balken: ionischer Farbstoff). As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.