gebhart/patrepeval huggingface dataset:
Rapid analysis of known and unknown pathogens using a pan-microbial detection microarray (2010)

Background: Rapid analysis of known, emerging and unknown viral and bacterial infections is critical for public health. Assays that can only identify a small handful of pathogens are not sufficient to deal with complex microbial infections. In this study, we report our development of a high-throughput microarray designed to detect known and discover unknown pathogens. Methods: We designed a pan-Microbial Detection Array (MDA) to detect all viruses, bacteria, and plasmids with 2195 viral species and 924 bacterial species represented. We took an approach balancing the goals of conservation and uniqueness for probe design, aiming for uniqueness relative to other families and kingdoms, and for conservation, to the extent possible, within a family. Long probes were selected to tolerate some sequence variation to enable detection of novel, divergent species with homology to sequenced organisms. We have used our arrays to identify pathogen infections from various clinical samples. We developed a novel statistical analysis method, maximum likelihood analysis method that enabled quantifiable predictions of likelihood for the presence of multiple organisms in a complex sample. Results: The MDA correctly identified multiple viral and bacterial infections in unknown fecal, sputum and nasopharyngeal samples that were later confirmed through independent highthroughput sequencing or PCR assays. Up to strain level identification can be achieved for fully sequenced pathogens in as little as a few hours. Family level identification was achieved for highly divergent viruses. The array is highly sensitive and able to achieve low-copy viral genome detection of spiked samples when coupled with whole genome random amplification. Conclusion: Our Microbial Detection Array is a fast, efficient and cost-effective tool to rapidly characterize known, emerging and unknown pathogens from clinical and environmental samples. The MDA has higher probe density and larger phylogenetic representation of viral and bacterial sequenced genomes than other available array designs. It can be applied to problems in viral and bacterial detection from pure or complex environmental or clinical samples. It will enable informed responses to novel biological threats and infectious agents and provide a complement to high-throughput sequencing data. Abstracts for SupplementInternational Journal of Infectious DiseasesVol. 14Preview Full-Text PDF Open Archive
Augmented Reality with HoloLens in Parotid Tumor Surgery: A prospective feasibility study (2020)

Objective Augmented Reality (AR) is an innovative way to improve planning and execution of complex surgical procedures. Head-mounted devices (HMD) such as the HoloLens from Microsoft seem to be particularly suitable to achieve these aims. The HoloLens is controlled by hand gestures. This enables contactless handling in a sterile environment. Unlike other surgical fields, so far, these systems have not found their way into head and neck surgery. The goal of this pilot study was to evaluate the feasibility of this HMD in parotid tumor surgery.
A Concentric Ring Electrode for a Wall‐jet Cell in a Microfluidic Device (2019)

Abstract A concentric ring array electrode that amplifies the current signal without redox cycling has been developed for highly sensitive electrochemical detection at a single potential in a microfluidic platform. Herein, the effect of ring‐electrode width on the current and current density was examined. A ring‐array electrode with widths that decrease from the inner to the outer ring was shown to exhibit the highest sensitivity. This electrode delivered a current density that was approximately 50 % higher than that of a conventionally used disc electrode. We used numerical simulations to further optimize this type of array electrode, which led to a limit of detection for catechol of 6.2 nmol/L. This ring array electrode has great potential for use in a variety of applications because it can be used to detect irreversible targets with a simple apparatus at a single potential and requires no electrode modification to achieve high sensitivity.
Block‐Selected Molecular Recognition and Formation of Polypseudorotaxanes between Poly(propylene oxide)‐Poly(ethylene oxide)‐Poly(propylene oxide) Triblock Copolymers and α‐Cyclodextrin (2004)

In der Zuschrift “Block-Selected Molecular Recognition and Formation of Polypseudorotaxanes between Poly(propylene oxide)-Poly(ethylene oxide)-Poly(propylene oxide) Triblock Copolymers and α-Cyclodextrin” von J. Li, X. Ni und K. Leong (1) haben es die Autoren versäumt, auf ihre thematisch verwandte Veröffentlichung in J. Am. Chem. Soc. 2003, 125, 1788–1795 von J. Li, X. Ni, Z. Zhou und K. Leong zu verweisen. In diesem Full Paper werden die Details der Synthese und Charakterisierung der Polypseudorotaxane beschrieben. Die Autoren bitten um Entschuldigung für dieses Versehen.
Enzymatic synthesis of l-fucose from l-fuculose using a fucose isomerase from Raoultella sp. and the biochemical and structural analyses of the enzyme (2019)

<i>Rd</i>FucI-catalyzed isomerization favored the reaction from l-fuculose to l-fucose. The biochemical and structural data of <i>Rd</i>FucI will be helpful for the better understanding of the molecular mechanism of l-FucIs and the industrial production of l-fucose.
Adaptive preview control for piecewise discrete-time systems using multiple models (2016)

In this paper, the problem of multi-model adaptive preview control is proposed for discrete-time systems with unknown piecewise constant coefficients. Following preview control theory, corresponding augmented error systems for piecewise discrete-time systems are constructed. By making use of the Heine–Borel covering theorem, a finite set of fixed augmented systems covering the range of the unknown parameters is established, and associated fixed preview controllers are derived. Based on the core idea of multi-model adaptive control, switching law of the controllers is designed, and eventually, an adaptive preview controller is obtained. The exponential asymptotic stability of closed-loop systems with large uncertainties is discussed in detail. Finally, simulation results are given to demonstrate the effectiveness of the theoretical results.
J0501-2-2 Effect of Stator on Rotating Stall Inception in Axial Flow Compressor Rotor (2010)

The effect of stators on the rotating stall inception in axial flow compressor rotors has not been well focused and therefore it has been investigated in the present works. To make the effect of stators clear, numerical analyses in two conditions were conducted: RSA (Rotor-Stator Analysis) and ROA (Rotor-Only Analysis). For RSA, the calculation domain includes stator upstream and downstream of the rotor. For ROA, the calculation domain has no stator. The rotating stall inception point of RSA shows good agreement with the experiment, however, the one of ROA is higher than the experimental inception point. In this paper, the difference between the flow fields for RSA and ROA is discussed and the effect of stators on the rotating stall inception has been elucidated.
New approach to silver halide photography using radical cation chemistry (2001)

Abstract A new mechanism for spectral sensitization of silver halide is described, which can potentially double the sensitivity of photographic emulsions. The photooxidized sensitizing dye is trapped using an organic donor molecule, which fragments to form a cation and a reducing radical, which injects an electron into the conduction band of the silver halide. In this way, two conduction-band electrons can be produced for each absorbed photon.
Supplementary Fig. S10 from <i>Salmonella</i>-Based Therapy Targeting Indoleamine 2,3-Dioxygenase Coupled with Enzymatic Depletion of Tumor Hyaluronan Induces Complete Regression of Aggressive Pancreatic Tumors (2023)

&lt;p&gt;Preliminary testing of PEGPH20/shIDO-ST in autochthonous KPC-Brca1 mouse model. PMN and DAPI immunofluorescence staining of an autochthonous tumor section from a KPC-Brca1 mouse treated with PEGPH20/shIDO-ST. Tumor was excised, flash frozen, sectioned, and stained 5 days following treatment. Central DAPI negative region of tumor with neutrophils (red) is depicted at 10X magnification with DAPI+ tumor cells (blue) at upper right (T).&lt;/p&gt;
<title>Switching and amplification in WDM systems</title> (1992)

In this paper we discuss several intriguing issues pertaining to wavelength-division-multiplexed optical systems. An indepth treatment is made of topics which include wavelength routing, packet contention resolution, and incorporating Erbium-doped fiber-optic amplifiers.
Cs2SnI6-Encapsulated Multidye-Sensitized All-Solid-State Solar Cells (2019)

The design of a dye-sensitized solar cell (DSSC) based on the simultaneous incorporation of multiple dyes is examined. By investigating the use of the porphyrin-based YD2-o-C8 and YDD6, and the organic chromophore TTAR, which can act as complementary absorbers, we are able to enhance the capture of incoming light across the solar spectrum. This is demonstrated first by using a conventional DSSC architecture with a liquid electrolyte and performed a power conversion efficiency (PCE) of 11.2%, representing an improvement over cells based on each of the independent dyes. Next, we used Cs<sub>2</sub>SnI<sub>6</sub> as an encapsulating layer over the sensitizing molecules to reduce charge leakage across the dye layers and also added to the absorption of longer wavelengths up to one micron. Finally, we fabricated a cell utilizing a Cs<sub>2</sub>SnI<sub>6</sub>/succinonitrile solid hole-transport electrolyte and achieved a PCE of ∼8.5%. It is expected that the all solid-state design will go a long way toward improving long-term device stability.
Directly modulated DBR lasers for long-haul transmission at 1.7 Gbit/s (1993)

Abstract We demonstrate 1.7 Gbit/s transmission through 257 km of conventional fiber using directly modulated distributed-Bragg reflector (DBR) lasers and fiber amplifiers. This experiment resulted in a record bit rate distance product of 437 km Gb/s for direct modulation at rates between 1 and 3 Gbit/s. This paper has been accepted for presentation at OFC '92.
Complete open-state testing of limitedly nondeterministic systems (2009)

An approach to the problem of complete testing is proposed. Testing is interpreted as the check of an implementation’s conformance to the given requirements described by a specification. The completeness means that a test suite finds all the possible implementation errors. In practice, testing must end in a finite amount of time. In the general case, the requirements of completeness and finiteness contradict each other. However, finite complete test suites can be constructed for certain classes of implementations and specifications provided that there are specific test capabilities. Test algorithms are proposed for finite specifications and finite implementations with limited nondeterminism for the case of open-state testing. The complexity of those algorithms is estimated.
Regulation of sialic acid transport and catabolism in Haemophilus influenzae (2007)

Virulence of nontypeable Haemophilus influenzae (NTHi) is dependent on the decoration of lipooligosaccharide with sialic acid. This sugar must be derived from the host, as NTHi cannot synthesize sialic acids. NTHi can also use sialic acid as a carbon source. The genes encoding the sialic acid transporter and the genes encoding the catabolic activities are localized to two divergently transcribed operons, the siaPT operon and the nan operon respectively. In this study, we identified SiaR as a repressor of sialic acid transport and catabolism in NTHi. Inactivation of siaR resulted in the unregulated expression of the genes in both operons. Unregulated catabolism of sialic acid in the siaR mutant resulted in the reduction of surface sialylation and an increase in serum sensitivity. In addition to SiaR-mediated repression, CRP, the cAMP receptor protein, was shown to activate expression of the siaPT operon but not the nan operon. We describe a model in which SiaR and CRP work to modulate intracellular sialic acid levels. Our results demonstrate the importance of SiaR-mediated regulation to balance the requirement of surface sialylation and the toxic accumulation of intracellular sialic acid.
EVI1-rearranged acute myeloid leukemias are characterized by distinct molecular alterations (2014)

The genetic and transcriptional signature of EVI1 (ecotropic viral integration site 1)-rearranged (EVI1-r) acute myeloid leukemias (AMLs) remains poorly defined. We performed RNA sequencing of 12 EVI1-r AMLs and compared the results with those of other AML subtypes (n = 139) and normal CD34(+) cells (n = 17). Results confirm high frequencies of RAS and other activated signaling mutations (10/12 AMLs) and identify new recurrent mutations in splicing factors (5/12 AMLs in SF3B1 and 2/12 AMLs in U2AF1), IKZF1 (3/12 AMLs), and TP53 (3/12 AMLs). Mutations in IKZF1, a gene located on chromosome 7, and monosomy 7 are mutually exclusive in this disease. Moreover IKZF1 expression is halved in monosomy 7 leukemias. EVI-r AMLs are also characterized by a unique transcriptional signature with high expression levels of MECOM, PREX2, VIP, MYCT1, and PAWR. Our results suggest that EVI1-r AMLs could be molecularly defined by specific transcriptomic anomalies and a hitherto unseen mutational pattern. Larger patient cohorts will better determine the frequency of these events.
Enhanced cytotoxic activity of ex vivo-differentiated human natural killer cells in the presence of HOXB4. (2014)

International audience
Channel allocation in SDMA cellular systems (2002)

Spatial division multiple access (SDMA) is recognized as a promising technique for improving capacity in future cellular systems, by exploiting the spatial filtering capability of adaptive antennas. In SDMA systems, in-cell users can share the same channel, making the channel allocation strategy play an important role in the system performance. In this paper, we analyze by simulation different strategies for channel allocation in cellular systems employing adaptive antennas and SDMA technique. Results show that high performance in SDMA systems is achieved by balancing channel reuse among cells with channel reuse within cells. Attempts to maximize channel reuse within cells may increase excessively cochannel interference, limiting capacity. Results also show that, while carried traffic is not severely affected by high level of user mobility, other performance parameters, such as the number of channel reassignment requests, are strongly affected by user mobility.
Arabidopsis vegetative actin isoforms, AtACT2 and AtACT7, generate distinct filament arrays in living plant cells (2018)

Flowering plants express multiple actin isoforms. Previous studies suggest that individual actin isoforms have specific functions; however, the subcellular localization of actin isoforms in plant cells remains obscure. Here, we transiently expressed and observed major Arabidopsis vegetative actin isoforms, AtACT2 and AtACT7, as fluorescent-fusion proteins. By optimizing the linker sequence between fluorescent protein and actin, we succeeded in observing filaments that contained these expressed actin isoforms fused with green fluorescent protein (GFP) in Arabidopsis protoplasts. Different colored fluorescent proteins fused with AtACT2 and AtACT7 and co-expressed in Nicotiana benthamiana mesophyll cells co-polymerized in a segregated manner along filaments. In epidermal cells, surprisingly, AtACT2 and AtACT7 tended to polymerize into different types of filaments. AtACT2 was incorporated into thinner filaments, whereas AtACT7 was incorporated into thick bundles. We conclude that different actin isoforms are capable of constructing unique filament arrays, depending on the cell type or tissue. Interestingly, staining patterns induced by two indirect actin filament probes, Lifeact and mTalin1, were different between filaments containing AtACT2 and those containing AtACT7. We suggest that filaments containing different actin isoforms bind specific actin-binding proteins in vivo, since the two probes comprise actin-binding domains from different actin-binding proteins.
The OpenRT-API (2005)

In the preceding course sections, all the basic constituents of a complete realtime ray tracing engine have been described: A highly efficient ray tracing kernel for modern CPUs, its efficient parallelization, and a simple yet efficient framework for handling dynamic scenes.
A RANDOMIZED DOUBLE-BLIND CONTROLLED EFFICACY STUDY, INTRADISCAL ELECTROTHERMAL THERAPY (IDET) VERSUS PLACEBO (2004)

Introduction: Intra-Discal Electrothermal Therapy (IDET) has been proposed as a treatment for chronic discogenic low back pain. Reports from prospective outcome studies demonstrate statistically significant improvements, but to date there are no published randomized controlled trials assessing efficacy versus a placebo group. Methods: Ethical committee approval was obtained prior to the study. Patients with chronic low back pain who failed to improve with conservative therapy were considered for the study. Inclusion criteria included the presence of one or two level symptomatic disc degeneration with posterior or posterolateral annular tears as determined by provocative CT/discography. Patients were excluded if there was > 50% loss of disc height or previous back surgery. Fifty-seven patients were randomized with a 2:1 (IDET: Placebo) ratio, 38 to the active IDET arm and 19 to the sham procedure (placebo). In all cases the IDET catheter was positioned under sedation to cover at least 70% of the annular tear defined by the CT/ discogram. An independent technician connected the catheter to the generator and either delivered electrothermal energy (active group) or did not (sham group). Both surgeon and patient were blinded to the treatment. Patients followed a standard post-procedural rehabilitation programme. Outcome Measures: Low Back Outcome Score (LBOS), Oswestry Disability Index (ODI), SF-36 questionnaire, Zung Depression Index (ZDI) and Modified Somatic Perceptions Questionnaire (MSPQ) were measured at baseline and 6 months. Successful outcome was defined as: No neurological deficit resulting from the procedure, improvement in LBOS of > 7 points, improvements in SF-36 subsets (pain / disability, physical functioning and bodily pain) Results: Two subjects withdrew from the study (both IDET). Baseline demographic data, employment and worker’s compensation status, sitting tolerance, initial LBOS, ODI, SF-36, ZDI and MSPQ were similar for both groups. No neurological deficits occurred as a result of either procedure. No subject in either treatment arm showed improvement of > 7 points in LBOS or specified domains of the SF-36. Mean ODI was 41.4 at baseline and 39.7 at 6 months for the IDET group compared to 40.7 at baseline and 41.5 at six months for the Placebo group. There was no significant change in ZDI or MSPQ scores for either group. Discussion: No subject in either treatment arm met criteria for successful outcome. Further analysis showed no significant change in outcome measures in either group at six months. This study demonstrates no significant benefit from IDET over placebo.
Prevention of Spread of Communicable Disease by Air Travel (2009)

Mathematical modeling suggests that travel restrictions are likely to have only a limited effect on minimizing the spread of disease. Nevertheless, medical screening of travelers remains an option to be considered in a risk-reduction strategy. Screening of departing and/or arriving travelers are possibilities, although the World Health Organization (WHO) favors the former as it is normally easier to geographically contain a disease prior to its transmission outside the outbreak area. Apart from airport screening, several other related issues require consideration, including: transmission of disease on board aircraft; transmission of disease in airport terminal buildings; and contact tracing. A major challenge is to ensure adequate resources are devoted to pandemic preparedness planning in the aviation sector, which may not be fully considered in a national preparedness plan. This is because the prevention of accidents occupies most of the attention of regulatory aviation authorities, and public health authorities do not always see aviation as a priority area. Chief medical officers of regulatory authorities may be in a position to facilitate collaboration between the many stakeholders involved in preparedness planning for aviation.
Anti-leukemia activity of alloreactive NK cells in KIR ligand-mismatched haploidentical HSCT for pediatric patients: evaluation of the functional role of activating KIR and redefinition of inhibitory KIR specificity (2008)

Abstract We analyzed 21 children with leukemia receiving haploidentical hematopoietic stem cell transplantation (haplo-HSCT) from killer immunoglobulin (Ig)–like receptors (KIR) ligand-mismatched donors. We showed that, in most transplantation patients, variable proportions of donor-derived alloreactive natural killer (NK) cells displaying anti-leukemia activity were generated and maintained even late after transplantation. This was assessed through analysis of donor KIR genotype, as well as through phenotypic and functional analyses of NK cells, both at the polyclonal and clonal level. Donor-derived KIR2DL1+ NK cells isolated from the recipient displayed the expected capability of selectively killing C1/C1 target cells, including patient leukemia blasts. Differently, KIR2DL2/3+ NK cells displayed poor alloreactivity against leukemia cells carrying human leukocyte antigen (HLA) alleles belonging to C2 group. Unexpectedly, this was due to recognition of C2 by KIR2DL2/3, as revealed by receptor blocking experiments and by binding assays of soluble KIR to HLA-C transfectants. Remarkably, however, C2/C2 leukemia blasts were killed by KIR2DL2/3+ (or by NKG2A+) NK cells that coexpressed KIR2DS1. This could be explained by the ability of KIR2DS1 to directly recognize C2 on leukemia cells. A role of the KIR2DS2 activating receptor in leukemia cell lysis could not be demonstrated. Altogether, these results may have important clinical implications for the selection of optimal donors for haplo-HSCT.
A New Controller for Bidirectional Wireless Power Transfer Systems (2017)

Wireless power transfer (WPT) is a promising technology for supplying power to various applications with no physical contacts. Recently, bidirectional WPT (BD-WPT) systems are gaining popularity for grid-to-vehicle and vehicle-to-grid applications which essentially require power transfer in both directions. However, BD-WPT systems are complex in nature, and require sophisticated control strategies to provide synchronization as well as to regulate the power flow between two sides. This paper proposes a new controller that uses measured active power (P) and reactive power (Q) at the resonant network of BD-WPT systems to regulate the power flow in both directions while providing synchronization between two sides without a dedicated communication interface for controlling power transfer. The controller, located on the pickup side, is applicable to BD-WPT systems with either single or multiple loads and ensures that the volt-ampere rating of the pickup converter is at lowest for battery charging, by keeping the reactive power at the resonant tank intake by the load side minimum. Experimental results obtained from a 1-kW prototype system show good agreement with simulated results, validating that the proposed controller can be used to regulate the power flow in BD-WPT systems.