gebhart/patrepeval huggingface dataset:
Self-Adjuvanting Glycopeptide Conjugate Vaccine against Disseminated Candidiasis (2012)

Our research on pathogenesis of disseminated candidiasis led to the discovery that antibodies specific for Candida albicans cell surface β-1, 2-mannotriose [β-(Man)(3)] protect mice. A 14 mer peptide Fba, which derived from the N-terminal portion of the C. albicans cytosolic/cell surface protein fructose-bisphosphate aldolase, was used as the glycan carrier and resulted in a novel synthetic glycopeptide vaccine β-(Man)(3)-Fba. By a dendritic cell-based immunization approach, this conjugate induced protective antibody responses against both the glycan and peptide parts of the vaccine. In this report, we modified the β-(Man)(3)-Fba conjugate by coupling it to tetanus toxoid (TT) in order to improve immunogenicity and allow for use of an adjuvant suitable for human use. By new immunization procedures entirely compatible with human use, the modified β-(Man)(3)-Fba-TT was administered either alone or as a mixture made with alum or monophosphoryl lipid A (MPL) adjuvants and given to mice by a subcutaneous (s.c.) route. Mice vaccinated with or, surprisingly, without adjuvant responded well by making robust antibody responses. The immunized groups showed a high degree of protection against a lethal challenge with C. albicans as evidenced by increased survival times and reduced kidney fungal burden as compared to control groups that received only adjuvant or DPBS buffer prior to challenge. To confirm that induced antibodies were protective, sera from mice immunized against the β-(Man)(3)-Fba-TT conjugate transferred protection against disseminated candidiasis to naïve mice, whereas C. albicans-absorbed immune sera did not. Similar antibody responses and protection induced by the β-(Man)(3)-Fba-TT vaccine was observed in inbred BALB/c and outbred Swiss Webster mice. We conclude that addition of TT to the glycopeptide conjugate results in a self-adjuvanting vaccine that promotes robust antibody responses without the need for additional adjuvant, which is novel and represents a major step forward in vaccine design against disseminated candidiasis.
Ontology-driven requirements engineering with reference to the aerospace industry (2009)

This paper provides an overview regarding the application of an ontology-driven requirements engineering methodology, namely OntoREM, in the aerospace industry with the objective to assess the extent to which this approach has the potential to develop better quality requirements in less time and at less cost compared to traditional requirements engineering processes, taking the Airbus wing-engineering requirements as the case study. The OntoREM's Metamodel is briefly introduced, which embodies both the key process and task ontologies that guide the OntoREM related requirements engineering activities along with the supporting tooling environments, both existing and newly developed ones. Finally, the paper provides an overview of a small number of focused case studies in the aerospace context that are currently being undertaken and will help to further evolve and critically evaluate OntoREM with the objective to investigate the potential of a more knowledge-driven as opposed to process-driven approach to RE.
Catalysis of Protein Folding by Protein Disulfide Isomerase and Small-Molecule Mimics (2003)

Protein disulfide isomerase (PDI) catalyzes the formation of native disulfide pairings in secretory proteins. The ability of PDI to act as a disulfide isomerase makes it an essential enzyme in eukaryotes. PDI also fulfills other important roles. Recent studies have emphasized the importance of PDI as an oxidant in the endoplasmic reticulum. Intriguing questions remain regarding how PDI is able to catalyze both isomerization and oxidation in vivo. Studies of PDI and its homologues have led to the development of small-molecule folding catalysts that are able to accelerate disulfide isomerization in vitro and in vivo. PDI will continue to provide both an inspiration for the design of such artificial foldases and a benchmark with which to gauge the success of those designs. Here, we review current understanding of the chemistry and biology of PDI, its homologues, and small molecules that mimic its catalytic activity.
Molecular Structure and Spectroscopy of a Bacteriopurpurin. A New Class of Bacteriochlorin Photosensitizers (1999)

Bacteriochlorins mediate energy and electron transfer in vivo and serve as biomimetic models of bacterial photosynthesis. Recently, the same physicochemical properties of the chromophores have made them attractive as photosensitizers for photodynamic therapy, a medical treatment that combines light, porphyrins, and oxygen to attack and destroy malignant tissue. Despite this intense biophysical, chemical, and medicinal interest in bacteriochlorins, very few high precision structures of the chromophores exist to provide the basis for theoretical calculations that seek to predict their extensively studied physicochemical properties. We report here the synthesis, spectral characterization, and structural determination of a metal-free bacteriopurpurin 1, a paradigm for a new class of photosensitizers comprised of porphyrins at the saturation level of bacteriochlorins flanked by two annelated, exocyclic cyclopentenyl rings. The molecule exhibits a very red-shifted Qy transition at 843 nm and is readily oxidized (at 0.39V vs SCE) to a π cation radical with a distinctive EPR signal. The crystallographic results for 1 unambiguously identify the bacteriopurpurin, provide the first stereochemical parameters for this new class of expanded bacteriochlorins, extend the high resolution structural database for bacteriochlorins, and form the basis for theoretical calculations which correctly describe the optical features and electron density profile of 1 and its cation radical.
Supercritical Fluid Technology in Textile Processing:  An Overview (2000)

In light of environmental concerns, the textile industry has accelerated efforts to reduce or eliminate water consumption in all areas of yarn preparation, dyeing, and finishing. Supercritical fluid dyeing technology has the potential to accomplish this objective in many commercial textile applications around the world, both at present and in the future around the world. Increased interest in this technology has made a fundamental understanding of thermophysical (equilibrium solubility) and transport (kinetics) properties of such fluids and fluid mixtures necessary. Supercritical carbon dioxide (SC-CO2) is one of the most environmentally acceptable solvents in use today, and textile processes using it have many advantages when compared to conventional aqueous processes.1-4 Positive environmental effects range from drastically reduced water consumption to eliminating hazardous industrial effluent. Furthermore, economic benefits include increased productivity and energy savings. Successfully commercializing supercritical fluid CO2 processing will improve the economics of dyeing and other textile chemical processes by eliminating water usage and wastewater discharges and increasing productivity by reducing processing times as well as required chemicals and auxiliaries and reducing energy consumption and air emissions. As a result, SC-CO2 processing will be more rapid, more economical, and more environmentally friendly.1
Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography (2019)

Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Micro-CT optimized for cellular characterization (histotomography) allows brain nuclei to be computationally segmented and assigned to brain regions, and cell shapes and volumes to be computed for motor neurons and red blood cells. Striking individual phenotypic variation was apparent from color maps of computed densities of brain nuclei. Unlike histology, the histotomography also allows the study of 3-dimensional structures of millimeter scale that cross multiple tissue planes. We expect the computational and visual insights into 3D cell and tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
A statistical temperature sensor (2014)

The physical effect which is used in this type of temperature sensor is the temperature coefficient mismatch of transistors. The basic cell for evaluating the effect is a bi-stable cell. For instance this could be an SRAM cell. After powering up the circuit such a cell provides either a 1 or a 0 at its output. In the case that such a bi-stable cell is used as a temperature-sensor, a well-designed cell bases its decision on the mismatch of two NMOS transistors (N1 and N2). The threshold voltage of NMOS transistors is decreasing over temperature. The amount of change is mainly defined by the coefficient KT1 (see BSIM). It turns out that there is a mismatch on KT1 between the different transistors. Thus it may happen that the startup value (or initial value) may change over the temperature. If a huge number of cells is used an accurate value of the temperature can be given. Once a startup vector at a well-defined temperature is defined, the temperature difference can be derived by measuring the Hamming distance (HD) between the reference vector and the output at the actual temperature.
Polyurethane scaffold formation via a combination of salt leaching and thermally induced phase separation (2008)

Porous scaffolds have been made from two polyurethanes based on thermally induced phase separation of polymer dissolved in a DMSO/water mixture in combination with salt leaching. It is possible to obtain very porous foams with a very high interconnectivity. A major advantage of this method is that variables like porosity, pore size, and interconnectivity can be independently adjusted with the absence of toxic materials in the production process. The obtained compression moduli were between 200 kPa and 1 MPa with a variation in porosity between 76 and 84%. Currently the biological and medical aspects are under evaluation.
Class-B Microwave-Photonic Link Using Optical Frequency Modulation and Linear Frequency Discriminators (2007)

A class-B optical link is demonstrated as a means to provide high spur-free dynamic-range (110.4 dBmiddotHz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2/3</sup> ) with a minimum average received power associated with the optical carrier. The link uses optical frequency modulation, linear fiber-Bragg-grating frequency discriminators, and balanced detection to provide high linearity and maximum signal power. Shot and intensity noises are minimized by the low total average received photocurrent (0.88 mA) that results from class-B operation
Online Domain Adaptation for Multi-Object Tracking (2015)

Automatically detecting, labeling, and tracking objects in videos depends first and foremost on accurate category-level object detectors. These might, however, not always be available in practice, as acquiring high-quality large scale labeled training datasets is either too costly or impractical for all possible real-world application scenarios. A scalable solution consists in re-using object detectors pre-trained on generic datasets. This work is the first to investigate the problem of on-line domain adaptation of object detectors for causal multi-object tracking (MOT). We propose to alleviate the dataset bias by adapting detectors from category to instances, and back: (i) we jointly learn all target models by adapting them from the pre-trained one, and (ii) we also adapt the pre-trained model on-line. We introduce an on-line multi-task learning algorithm to efficiently share parameters and reduce drift, while gradually improving recall. Our approach is applicable to any linear object detector, and we evaluate both cheap "mini-Fisher Vectors" and expensive "off-the-shelf" ConvNet features. We quantitatively measure the benefit of our domain adaptation strategy on the KITTI tracking benchmark and on a new dataset (PASCAL-to-KITTI) we introduce to study the domain mismatch problem in MOT.
Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes (2015)

In metazoans, transition from fetal to adult heart is accompanied by a switch in energy metabolism-glycolysis to fatty acid oxidation. The molecular factors regulating this metabolic switch remain largely unexplored. We first demonstrate that the molecular signatures in 1-year (y) matured human embryonic stem cell-derived cardiomyocytes (hESC-CMs) are similar to those seen in in vivo-derived mature cardiac tissues, thus making them an excellent model to study human cardiac maturation. We further show that let-7 is the most highly up-regulated microRNA (miRNA) family during in vitro human cardiac maturation. Gain- and loss-of-function analyses of let-7g in hESC-CMs demonstrate it is both required and sufficient for maturation, but not for early differentiation of CMs. Overexpression of let-7 family members in hESC-CMs enhances cell size, sarcomere length, force of contraction, and respiratory capacity. Interestingly, large-scale expression data, target analysis, and metabolic flux assays suggest this let-7-driven CM maturation could be a result of down-regulation of the phosphoinositide 3 kinase (PI3K)/AKT protein kinase/insulin pathway and an up-regulation of fatty acid metabolism. These results indicate let-7 is an important mediator in augmenting metabolic energetics in maturing CMs. Promoting maturation of hESC-CMs with let-7 overexpression will be highly significant for basic and applied research.
Semaphorin 3F Is Critical for Development of Limbic System Circuitry and Is Required in Neurons for Selective CNS Axon Guidance Events (2003)

Little is known about the role of class 3 semaphorins in the development of CNS circuitry. Several class 3 semaphorins, including semaphorin 3F (Sema3F) bind to the receptor neuropilin-2 to confer chemorepulsive responses in vitro. To understand the role of Sema3F in the establishment of neural circuitry in vivo, we have generated sema3F null and sema3F conditional mutant mice. Inspection of the peripheral nervous system in sema3F null mice reveals that Sema3F is essential for the proper organization of specific cranial nerve projections. Analysis of the CNS in sema3F null mice reveals a crucial role for Sema3F in the rostral forebrain, midbrain, and hippocampus in establishing specific Npn-2 (neuropilin-2)-expressing limbic tracts. Furthermore, we identify Sema3F and Npn-2 as the first guidance cue-receptor pair shown to be essential for controlling the development of amygdaloid circuitry. In addition, we provide genetic evidence in vertebrates for a neuronal requirement of a soluble axon guidance cue in CNS axon guidance. Our data reveal a requirement for neuronal Sema3F in the normal development of the anterior commissure in the ventral forebrain and infrapyramidal tract in the hippocampus. Thus, our results show that Sema3F is the principal ligand for Npn-2-mediated axon guidance events in vivo and is a critical determinant of limbic and peripheral nervous system circuitry.
Optimizing a multifunctional microsphere scaffold to improve neural precursor cell transplantation for traumatic brain injury repair (2013)

Tissue engineering using stem cells is widely used to repair damaged tissues in diverse biological systems; however, this approach has met with less success in regenerating the central nervous system (CNS). In this study we optimized and characterized the surface chemistry of chitosan-based scaffolds for CNS repair. To maintain radial glial cell (RGC) character of primitive neural precursors, fibronectin was adsorbed to chitosan. The chitosan was further modified by covalently linking heparin using genipin, which then served as a linker to immobilize fibroblast growth factor-2 (FGF-2), creating a multifunctional film. Fetal rat neural precursors plated onto this multifunctional film proliferated and remained multipotent for at least 3 days without providing soluble FGF-2. Moreover, they remained less mature and more highly proliferative than cells maintained on fibronectin-coated substrates in culture medium supplemented with soluble FGF-2. To create a vehicle for cell transplantation, a 3% chitosan solution was electrosprayed into a coagulation bath to generate microspheres (range 30-100 µm, mean 64 µm) that were subsequently modified. Radial glial cells seeded onto these multifunctional microspheres proliferated for at least 7 days in culture and the microspheres containing cells were small enough to be injected, using 23 Gauge Hamilton syringes, into the brains of adult rats that had previously sustained cortical contusion injuries. When analysed 3 days later, the transplanted RGCs were positive for the stem cell/progenitor marker Nestin. These results demonstrate that this multifunctional scaffold can be used as a cellular and growth factor delivery vehicle for the use in developing cell transplantation therapies for traumatic brain injuries. Copyright © 2013 John Wiley & Sons, Ltd.
Generation of Bright Isolated Attosecond Soft X-Ray Pulses Driven by Multi-Cycle Mid-Infrared Lasers (2014)

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 M. -. Chen, C. Mancuso, C. Hernández-García, F. Dollar, B. Galloway, D. Popmintchev, P. -. Huang, B. C. Walker, L. Plaja, A. Jaron-Becker, A. Becker, M. M. Murnane, H. C. Kapteyn, and T. Popmintchev, "Generation of Bright Isolated Attosecond Soft X-Ray Pulses Driven by Multi-Cycle Mid-Infrared Lasers," in Frontiers in Optics 2014, OSA Technical Digest (online) (Optical Society of America, 2014), paper LW1H.1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Towards an MPI-Like Framework for the Azure Cloud Platform (2014)

Message Passing Interface (MPI) has been the predominant standardized system for writing parallel and distributed applications. However, while MPI has been the software system of choice for traditional parallel and distributed computing platforms such as large compute clusters and Grid, MPI is not the system of choice for cloud platforms. The primary reasons for this is the lack of low latency high bandwidth network capabilities of the cloud platforms and the inherent architectural differences from traditional compute clusters. Prior studies suggest that the message latency of cloud platforms could be as much as 35x slower than that of an infiniband-connected cluster [1] for popular MPI implementations. MPI-like environment on cloud platforms is desirable for a large class of applications that run for long time spans with varying computing needs, such as the modeling and analysis to predict swath of a hurricane. Such applications could benefit from cloud's resiliency and on-demand access for a robust and green solution. Interestingly, most of the cloud vendors provide APIs to access cloud resources in an efficient manner different than how an MPI implementation would avail of those resources. We have done extensive research to identify the pain-points for designing and implementing an MPI-like framework for cloud platforms. Our research has provided us with vital guidelines that we are sharing in this paper. We present the details of the key components required for such a framework along with our experience while implementing a preliminary MPI-like framework over Azure dubbed cloud MPI and evaluate its pros and cons. A large GIS application has been ported over cloud MPI to study its effectiveness and limitations.
Application of NIR Raman spectroscopy for detecting and characterizing early dental caries (2006)

Early dental caries detection facilitates implementation of non-surgical methods for arresting caries progression and promoting tooth remineralization. We present a method based on Raman spectroscopy with near-IR laser excitation to provide biochemical contrast for detecting and characterizing incipient carious lesions found in extracted human teeth. Changes in Raman spectra are observed in PO<sub>4</sub><sup>3-</sup> vibrations arising from hydroxyapatite of mineralized tooth tissue. Examination of various intensities of the PO<sub>4</sub><sup>3-</sup> ν2, ν3, ν4 vibrations showed consistent increased intensities in spectra of carious lesions compared to sound enamel. The spectral changes are attributed to demineralization-induced alterations of enamel crystallite morphology and/or orientation. This hypothesis is supported by reduced Raman polarization anisotropy derived from polarized Raman spectra of carious lesions. Polarized Raman spectral imaging of carious lesions found on whole (i.e. un-sectioned) tooth samples will also be presented.
A Readily Available, Highly Potent E-Selectin Antagonist (2001)

Eine Mischung aus Zufall, Spürsinn und rationalem Design führte zu 1, dem derzeit wirksamsten E-Selectin-Inhibitor. 1 wurde in einer zehnstufigen Synthese in einer Gesamtausbeute von >25 % erhalten. In einem statischen Assay war 1 hundertmal wirksamer als Sialyl-Lewisx. In einem noch aussagekräftigeren Fluss-Assay, der die dynamischen In-vivo-Bedingungen nachstellt, ergab sich ein IC50 von 1–2 μM, während Sialyl-Lewisx bei Konzentrationen bis 1000 μM keine inhibierende Wirkung zeigte.
A simple test for multistage MIMO detection (2005)

Maximum likelihood detection of multiple input multiple output (MIMO) signals requires computational capabilities that are challenging to obtain in most practical systems. Although many alternative schemes have been devised to reduce the operational burden, the complexity of algorithmic schemes remains much higher than that of equalizer-based techniques, which in turn provide poor performance in terms of error rate. In this paper, we derive a low-complexity test that allows to run a more efficient but complex detection scheme only on selected received symbols. The few symbols that are identified as erroneously detected by the low complexity method are the only ones to be reprocessed. The global complexity is hence reduced, typically by more than one order of magnitude, with very little loss in performance
Deletion of CD2-like gene from the genome of African swine fever virus strain Georgia does not attenuate virulence in swine (2020)

Abstract The CD2-like African swine fever virus (ASFV) gene 8DR, (also known as EP402R) encodes for a structural transmembrane glycoprotein that has been shown to mediate hemadsorption and be involved in host immunomodulation as well as the induction of protective immune response. In addition, several natural ASFV isolates showing decreased virulence in swine has been shown to be non-hemadsorbing suggesting an association between altered or deleted forms of 8DR and virus attenuation. Here we demonstrate that deletion of 8DR gene from the genome of ASFV Georgia2010 isolate (ASFV-G-Δ8DR) does not significantly alter the virulence of the virus. ASFV-G-Δ8DR inoculated intramuscularly or intranasally (in a range of 10 2 to 10 4 TCID 50 ) produced a clinical disease in domestic pigs indistinguishable from that induced by the same doses of the virulent parental ASFV Georgia2010 isolate. In addition, viremia values in ASFV-G-Δ8DR do not differ from those detected in animals infected with parental virus. Therefore, deletion of 8DR gene is not associated with a noticeable decrease in virulence of the ASFV Georgia isolate.