gebhart/patrepeval huggingface dataset:
307. Rational Development of 12 Different AAV Serotypes as Scaffolds for Peptide Display (2015)

Recombinant AAV vectors are some of the most attractive vehicles for therapeutic gene delivery available today, for many reasons. One is that AAV capsids are highly amenable to genetic engineering, permitting the creation and identification of vectors with novel properties including target cell specificities. One potent strategy is to insert a randomized peptide library into an exposed AAV2 capsid region, followed by iterative selection on desired cells to enrich single peptides binding to cell-surface receptors and hence mediating AAV transduction. However, several problems hamper the use of AAV2 as scaffold for peptide display: (i) neutralizing anti-AAV2 antibodies that are prevalent in the human population may interfere with transduction of AAV2 peptide mutants, and (ii) if not fully ablated, the AAV2 tropism for its genuine receptors will dampen retargeting efficiencies. Here, we aimed to overcome both problems by developing 11 other AAV serotypes as templates for peptide display, AAV1, 3-9, rh.10, po.1 and 12. We first engineered their capsid genes to contain unique restriction sites and then exploited these for insertion of 18 different oligonucleotides encoding peptides which were pre-selected in AAV2 on various cells. The resulting >200 AAV variants were subsequently produced as YFP-expressing vectors and screened in over 80 human or murine cells, including primary hepatocytes or keratinocytes, as well as T-cells and stem/iPS cells. Strikingly, many capsid-peptide combinations vastly outperformed the AAV2 counterparts, especially those based on AAV serotypes 1, 7-9 and rh.10, and those carrying 7mer peptides with an NxxRxxx motif (x = any amino acid). In addition, we found that disruption of residue R585 in AAV2 boosted the potency of several peptide display mutants by up to two orders of magnitude, whereas the same mutation had no effect in the chimeric capsid AAV-DJ, despite a common region surrounding R585. Another puzzling notion was that some serotypes were inactivated by peptide display, tempting us to model all 12 capsids after insertion of a prototype peptide. This revealed that in contrast to our prediction from linear sequence alignments, the exact position of the displayed peptide differed by up to four residues between the 12 capsids. Indeed, once adjusted accordingly, AAV3 and AAV6 were also markedly enhanced upon peptide insertion. Collectively, our data imply an enormous potential of alternative AAV serotypes as scaffolds for peptide display and provide a set of vital guidelines for their further development as gene therapy vectors. To aid in this process, we also present a protocol for AAV spotting and drying in 96/384-well plates which permits their long-term storage and shipping, and thus facilitates their evaluation in other labs.
Examination of cross contamination risks between hospitals by external medical staff via cross-sectional intercept survey of hand hygiene (2014)

Exposure to the same environment may result in similar hand contamination patterns of IR when compared caregivers. This supports the concern that industry representatives can cause cross infection between hospitals and hygiene sensitive areas like operation room, intensive care unit and central sterilization units particularly. Further study is required to clarify whether pre-existing bacterial colonization is an influencing factor and how industry is taking care of this to create a safe working environment for their employees, the customers and ultimately the patients.
Finite Element Modeling of C4 Cracking in a Large Die Large Laminate Coreless Flip Chip Package (2016)

BGA substrates made of organic materials are now industry standard as they provide significant advantages over the ceramic dielectric-based predecessors in manufacturing cost and electrical performance. A typical organic laminate structure consists of one or more layers of build-up and copper on each side of a copper clad core. In recent years, the industry has also introduced the concept of organic build up laminate without a core layer, more commonly known as coreless laminates, to overcome the disadvantages of the plated through holes (PTH) in the core structures, which specifically drive restrictions in wiring capability and retard signal transmission speed. Although coreless laminates offer better opportunity for low cost and high speed transmission package designs, they are usually associated with high thermal warpage due to the lack of reinforcement provided by a rigid core layer. This becomes particularly challenging in large body size substrates. Furthermore, the composite coefficient of thermal expansion (CTE) of a coreless laminate is significantly higher than cored alternatives, which leads to higher chip package interaction (CPI) stresses. This paper focuses on the reliability issues of C4 bump cracking in a large die large laminate (LDLL) coreless flip chip package. C4 solder bumps are subjected to shear strains and fatigue degradation during thermal cycling and power cycling in field operation. Such shear strain is normally proportional to the DNP (distance from neutral point). Therefore solder fatigue often occurs at the corner C4's first. To further increase the reliability concern, the composite CTE's of coreless organic laminates are higher than cored laminates, which impose additional shear strain to the C4 interconnect bumps. Two coreless flip chip packages, with pad defined C4 bumps and solder mask opening defined C4 bumps, will be examined in this paper. Comparison of fail counts after 1000 cycles of deep thermal cycling (DTC) reveals that pad defined C4 bumps are more robust than solder mask opening defined C4's. Failure analysis of the cracked C4 bumps will be illustrated. The thermal-mechanical modeling methodology will be outlined and verification of simulations with experimental results will be presented. Parametric studies on the effect of C4 bump geometry, laminate material properties and other form factors on C4 fatigue will be discussed. A predictive model for C4 solder joint fatigue in coreless flip chip packages will be proposed.
Hepatitis C virus infection and risk of liver-related and non-liver-related deaths: a population-based cohort study in Naples, southern Italy (2021)

These findings show the detrimental impact of HCV infection on all-cause mortality and, particularly, liver-related mortality. This effect emerged among individuals with chronic infection while those with cleared infection had the same risk of uninfected ones. These results underline the need to identify through screening all people with chronic HCV infection notably in areas with a high prevalence of HCV infection, and promptly provide them with DAAs treatment to achieve progressive HCV elimination and reduce HCV-related mortality.
The Unified Modeling Language User Guide (1999)

In The Unified Modeling Language User Guide, the original developers of the UML--Grady Booch, James Rumbaugh, and Ivar Jacobson--provide a tutorial to the core aspects of the language in a two-color format designed to facilitate learning. Starting with a conceptual model of the UML, the book progressively applies the UML to a series of increasingly complex modeling problems across a variety of application domains. This example-driven approach helps readers quickly understand and apply the UML. For more advanced developers, the book includes a learning track focused on applying the UML to advanced modeling problems.With The Unified Modeling Language User Guide, readers will:Understand what the UML is, what it is not, and why it is relevant to the development of software-intensive systemsMaster the vocabulary, rules, and idioms of the UML in order to speak the language effectivelyLearn how to apply the UML to a number of common modeling problemsSee illustrations of the UML's use interspersed with use cases for specific UML features, andGain insight into the UML from the original creators of the UML.
Patterned Illumination Wide-Field Two-Photon Microscopy for Enhanced Axial Resolution and Deep Imaging (2018)

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 J. K. Park, D. N. Wadduwage, and P. T. C. So, "Patterned Illumination Wide-Field Two-Photon Microscopy for Enhanced Axial Resolution and Deep Imaging," in Biophotonics Congress: Biomedical Optics Congress 2018 (Microscopy/Translational/Brain/OTS), OSA Technical Digest (Optica Publishing Group, 2018), paper MF2A.3. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Cascade R-CNN: High Quality Object Detection and Instance Segmentation (2019)

In object detection, the intersection over union (IoU) threshold is frequently used to define positives/negatives. The threshold used to train a detector defines its \textit{quality}. While the commonly used threshold of 0.5 leads to noisy (low-quality) detections, detection performance frequently degrades for larger thresholds. This paradox of high-quality detection has two causes: 1) overfitting, due to vanishing positive samples for large thresholds, and 2) inference-time quality mismatch between detector and test hypotheses. A multi-stage object detection architecture, the Cascade R-CNN, composed of a sequence of detectors trained with increasing IoU thresholds, is proposed to address these problems. The detectors are trained sequentially, using the output of a detector as training set for the next. This resampling progressively improves hypotheses quality, guaranteeing a positive training set of equivalent size for all detectors and minimizing overfitting. The same cascade is applied at inference, to eliminate quality mismatches between hypotheses and detectors. An implementation of the Cascade R-CNN without bells or whistles achieves state-of-the-art performance on the COCO dataset, and significantly improves high-quality detection on generic and specific object detection datasets, including VOC, KITTI, CityPerson, and WiderFace. Finally, the Cascade R-CNN is generalized to instance segmentation, with nontrivial improvements over the Mask R-CNN. To facilitate future research, two implementations are made available at \url{https://github.com/zhaoweicai/cascade-rcnn} (Caffe) and \url{https://github.com/zhaoweicai/Detectron-Cascade-RCNN} (Detectron).
Brown, Harry Gunnison (1880–1975) (2006)

Brown, Harry Gunnison Harry Gunnison Brown was born in Troy, New York, on May 7, 1880 to Milton Peers Brown and Elizabeth H. Gunnison. He died in March 1975 in Columbia, Missouri. He graduated from high school and worked for a year as a factory worker before a childhood illness (tuberculosis of the
Evaluation of Antimicrobial Properties of African Basil ( Ocimum gratissimum ) and Tassel Flower ( Emilia coccinea ) Leaf Extracts (2018)

The use of plant extracts and phytoconstituents with antimicrobial properties may provide therapeutic benefits and application in consumer products such lotions and soaps, and active food packaging. The objective of this study was to assess the efficacy of water, methanol, butanol and ethyl acetate extracts of Ocimum gratissimum leaf (OGL) in inhibiting the growth of selected bacteria (E. coli O157:H7 (ATCC 43894), Salmonella enterica serovar Typhimurium DT‐104 (CDC H3380), Aeromonas hydrophila K144, and Pseudomonas aeruginosa (ATCC 7700)). In a parallel study, water, methanol, and butanol extracts of Emilia coccinea leaf (ECL) and OGL were also tested against E. coli, Pseudomonas aeruginosa , and Staphylococcus aureus . To screen for antimicrobial activity, the susceptibility of these selected pathogens and non‐pathogenic bacteria was determined using the disk diffusion assay. Selected antibiotics such as tetracycline, streptomycin, ampicillin and kanamycin were used as positive control. Following incubation, zone of inhibition differed between control and extracts, with larger zone of inhibition in the OGL butanol extract than the water, methanol, and ethyl acetate extracts in all the four pathogens tested, and a smaller zone of inhibition for E. coli, Salmonella and Pseudomonas cultures. Aeromonas hydrophila K144 cultures were found to be susceptible to butanol extract showing 10 mm of clearance zone. Incubation of ampicillin with Aeromonas hydrophila K144, Salmonella enterica serovar Typhimurium DT‐104 (CDC H3380) and Pseudomonas aeruginosa (ATCC 7700) led to minor changes in the zone of inhibition of these antimicrobials. P. Aeruginosa and S. aureus were resistant and susceptible to all antibiotic controls tested, respectively. E. coli, P . aeruginosa , S. aureus were all susceptible to the methanol and butanol extracts of OGL and ECL. Butanol and methanol extracts of Ocimum gratissimum and Emilia coccinea leaf could be suitable alternative to some chemical antimicrobials, satisfying consumer demand for natural products. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Revision of the absolute stereochemistry of (+)-abscisic acid (1972)

G. Ryback, J. Chem. Soc., Chem. Commun., 1972, 1190 DOI: 10.1039/C39720001190
Hollow core large mode area fiber employing a zero contrast subwavelength grating reflector (2015)

We propose a hollow core large mode area fiber with a new type of guiding mechanism. The fiber is based on a zero contrast high refractive index subwavelength grating embedded on a silica cladding. The hollow core exhibits guided mode resonance for incident waves on a circular grating, thus acting as a highly reflective circular mirror. Finite element simulations are utilized to demonstrate low leakage loss near the guided mode resonances and to investigate the corresponding mode profiles and the reflectivity spectra. We also present alternative high-contrast self-suspended grating and compare the results.
Underwater techniques to characterize the near scattered acoustic vector field (2014)

In this study, we investigate the properties of the scattered acoustic vector fields generated by simple geometric objects, including the infinite rigid plate, disk, and sphere. Analytical solutions are derived from acoustic target strength scattering models in the near-field region. Of particular interest is the understanding of the characteristics of energy flow of the scattered acoustic vector field in the near- to far- field transition region. We utilize the time and space separable instantaneous active and reactive acoustic intensities to investigate the relative phase properties of the scattered field. Numerical results are presented for the near region scattered acoustic vector field of simple objects in both two and three dimensions. Previous in-air measurements are summarized, and an approach to taking water-borne measurements is offered.
Platelet Model for Halothane‐Induced Effects on Nucleotide Metabolism Applied to Malignant Hyperthermia (1984)

A relatively non-invasive screening technique using venous blood analyzed by high performance liquid chromatography (HPLC) was developed to assess the effects of halothane on platelet nucleotide metabolism. Platelets were selected for study because of their contractile characteristics and many metabolic similarities to voluntary muscle. Platelets of 22 patients who previously had a documented clinical episode of malignant hyperthermia demonstrated a significant change in their nucleotide profile due to halothane exposure compared to normal subjects and 10 patients with musculo-skeletal and metabolic disorders. These results showed 100% correlation with the skeletal muscle contracture test for malignant hyperthermia (PHB). The platelet-halothane bioassay is highly reproducible and specific for detecting malignant hyperthermia with a significant degree of expression at the time of venipuncture. The assay deserves further study as an aid to the diagnosis of the degree of malignant hyperthermia susceptibility.
Wireless Electrostimulation: A New Approach in Combating Infection? (2017)

Electrostimulation (ES), hitherto successfully employed in wound treatment, has shown potential in antimicrobial applications, suggesting its use as synergistic to or replacement of antibiotics. The differential susceptibility of pathogens and host tissue and organs to various ES modalities might allow selective use against specific infections. The use of ES is cheaper in terms of development/testing, routine application and environmental footprint. If extensive substitution of chemical compounds is achieved, the development of resistance might be reversed through negative selection. A promising setup of ES seems to be the noncontact current transfer, due to low amperage similar to innate bioelectricity, painlessness, simple logistics and low risk for treatment-caused infection.
Alternate protein kinase A activity identifies a unique population of stromal cells in adult bone (2010)

A population of stromal cells that retains osteogenic capacity in adult bone (adult bone stromal cells or aBSCs) exists and is under intense investigation. Mice heterozygous for a null allele of prkar1a (Prkar1a(+/-)), the primary receptor for cyclic adenosine monophosphate (cAMP) and regulator of protein kinase A (PKA) activity, developed bone lesions that were derived from cAMP-responsive osteogenic cells and resembled fibrous dysplasia (FD). Prkar1a(+/-) mice were crossed with mice that were heterozygous for catalytic subunit Calpha (Prkaca(+/-)), the main PKA activity-mediating molecule, to generate a mouse model with double heterozygosity for prkar1a and prkaca (Prkar1a(+/-)Prkaca(+/-)). Unexpectedly, Prkar1a(+/-)Prkaca(+/-) mice developed a greater number of osseous lesions starting at 3 months of age that varied from the rare chondromas in the long bones and the ubiquitous osteochondrodysplasia of vertebral bodies to the occasional sarcoma in older animals. Cells from these lesions originated from an area proximal to the growth plate, expressed osteogenic cell markers, and showed higher PKA activity that was mostly type II (PKA-II) mediated by an alternate pattern of catalytic subunit expression. Gene expression profiling confirmed a preosteoblastic nature for these cells but also showed a signature that was indicative of mesenchymal-to-epithelial transition and increased Wnt signaling. These studies show that a specific subpopulation of aBSCs can be stimulated in adult bone by alternate PKA and catalytic subunit activity; abnormal proliferation of these cells leads to skeletal lesions that have similarities to human FD and bone tumors.
Acoustic interaction between 3D fabricated cubic bubbles (2020)

ĂSpherical bubbles are notoriously difficult to hold in specific arrangements in water and tend to dissolve over time. Here, using stereolithographic printing, we built an assembly of millimetric cubic frames overcoming these limitations. Indeed, each of these open frames holds an air bubble when immersed into water, resulting in bubbles that are stable for long times and still able to oscillate acoustically. Several bubbles can be placed in any wanted spatial arrangement thanks to the fabrication process. We show that bubbles are coupled acoustically when disposed along lines, planes or 3D arrangement, and that their collective resonance frequency is shifted to much lower values, especially for 3D arrangements where bubbles have higher number of close neighbours. Considering that these cubic bubbles behave acoustically as spherical bubbles of the same volume, we develop a theory allowing to predict the acoustical emission of any arbitrary group of bubbles, in agreement with experiments.
Multimegabit Operation Multiplexer System (1973)

International Telemetering Conference Proceedings / October 09-11, 1973 / Sheraton Inn Northeast, Washington, D.C.
Guest Editorial Special Issue on Artificial Intelligence-Based Sensors for Next Generation IoT Applications (2021)

The path towards next-generation IoT is fundamentally characterized by artificial intelligence-based sensors. However, there are still some open issues, such as efficiency, accuracy, privacy, data trustworthiness, quality etc., that need to be addressed. Therefore, this special issue aims to solicit original papers to solve these issues. Finally, some excellent papers are selected in this special issue from about 160 submissions. Due to the limitation of the editorial space, only 3 papers will be introduced here.
Industrie 4.0 – Begriff, Stand der Umsetzung und kritische Würdigung (2013)

„Industrie 4.0“ ist die Bezeichnung fur eines der zehn Zukunftsprojekte der Bundesregierung im Rahmen ihrer 
Hightech-Strategie fur Deutschland (BMBF 2013; Kagermann et al. 2012, S. 4). Die Entstehung des Begriffes 
„Industrie 4.0“ basiert auf der Einschatzung, dass Wirtschaft und Gesellschaft – nach drei industriellen 
Revolutionen (siehe Abb. 1), ausgelost durch Dampfmaschine, Fliesband und Computer – derzeit am Beginn einer 
vierten industriellen Revolution stunden (ebd., S. 10).
Perforated Fairings for Bluff Body Noise Control (2007)

Landing gears of commercial aircraft make an important contribution to total aircraft noise in the approach conflguration. Using fairings to shield components from high speed impingement reduces noise. Furthermore, perforating these fairings has been conflrmed by ∞ight tests to further enable noise reduction. A fundamental study has been performed to investigate and optimize the beneflts of bleeding air through the fairing by application of perforations. Wind tunnel tests have been performed with a simplifled fairing-cylindrical strut combination to clarify in∞uence of perforations on ∞ow behaviour and acoustics. The results show that for this speciflc case, the fairing self noise is reduced signiflcantly by breakdown of the vortex shedding process. The perforated fairings, exhibiting difierent porosities between 33% and 55%, appear to be equally e‐cient in removing the spectral peak associated with the vortex shedding. A redistribution of the velocities is achieved depending on the applied porosity. Perforate selfnoise manifests itself at higher frequencies, although scaling of this phenomenon with oriflce diameter opens up the possibility to shift it above the upper limit of the audible range.
Creating Policy Frameworks for Public Health Genomics to Benefit Developing Countries (2014)

Unprecedented advances in life sciences, as exemplified by the revolution in genomics, are yet to translate into effective public health interventions to benefit the health of populations living in the developing world. The developing countries continue to bear the major burden of disease globally, both infectious and chronic diseases, and they could clearly benefit from genomics being harnessed and used to address the greatest public health problems in addition to benefits for the health of individuals. For this to happen, we need to understand what are the major challenges or bottlenecks to be overcome and, informed by these priorities, create an effective, inclusive, equitable and sustainable policy framework within which knowledge translation into improved health outcomes of underprivileged populations can take place.
X-ray standing waves in garnet crystals (1984)

Measurement of fluorescent radiation produced by x-ray standing waves is applied to site-occupancy determination in both thin layers and bulk garnet single crystals. The fluorescence yield for atoms in different crystallographic sites has been calculated for the (521) and (444) reflections in the case of gadolinium gallium garnet for both a thin layer and a bulk crystal. Primary extinction is discussed. We find that, although it may play a major role in determining the line shape of the fluorescence yield, the effect is not as dramatic in garnets as it is in silicon or germanium, so that different crystallographic sites give clearly distinctive fluorescence patterns even for bulk crystals. Finally, theoretical and experimental line shapes are compared.