gebhart/patrepeval huggingface dataset:
Abnormal cardiac inflow patterns during postnatal development in a mouse model of Holt-Oram syndrome (2005)

Tbx5(del/+) mice provide a model of human Holt-Oram syndrome. In this study, the cardiac functional phenotypes of this mouse model were investigated with 30-MHz ultrasound by comparing 12 Tbx5(del/+) mice with 12 wild-type littermates at 1, 2, 4, and 8 wk of age. Cardiac dimensions were measured with two-dimensional and M-mode imaging. The flow patterns in the left and right ventricular inflow channels were evaluated with Doppler flow sampling. Compared with wild-type littermates, Tbx5(del/+) mice showed significant changes in the mitral flow pattern, including decreased peak velocity of the left ventricular (LV) early filling wave (E wave), increased peak velocity of the late filling wave (A wave), and decreased or even reversed peak E-to-A ratio. The prolongation of LV isovolumic relaxation time was detected in Tbx5(del/+) neonates as early as 1 wk of age. In Tbx5(del/+) mice, LV wall thickness appeared normal but LV chamber dimension was significantly reduced. LV systolic function did not differ from that in wild-type littermates. In contrast, the Doppler flow spectrum in the enlarged tricuspid orifice of Tbx5(del/+) mice demonstrated increased peak velocities of both E and A waves and increased total time-velocity integral but unchanged peak E/A. In another 13 mice (7 Tbx5(del/+), 6 wild-type) at 2 wk of age, significant correlation was found between Tbx5 gene expression level in ventricular myocardium and LV filling parameters. In conclusion, the LV diastolic function of Tbx5(del/+) mice is significantly deteriorated, whereas the systolic function remains normal.
Quantitative phase analysis from neutron powder diffraction data using the Rietveld method (1987)

The weight of a phase in a mixture is proportional to the product of the scale factor, as derived in a multi-component Rietveld analysis of the powder diffraction pattern, with the mass and volume of the unit cell. If all phases are identified and crystalline, the weight fraction W of phase p is given by W_{p} = S_{p}(ZMV)_{p}/\sum_{i}S_{i}(ZMV)_{i},where S, Z, M and V are, respectively, the Rietveld scale factor, the number of formula units per unit cell, the mass of the formula unit and the unit-cell volume. This is the basis of a method providing accurate phase analyses without the need for standards or for laborious experimental calibration procedures. The method is demonstrated by measurements on binary mixtures of rutile, corundum, silicon and quartz.
Developing an abstraction layer for the visualization of HSMM-based predictive decision support (2009)

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2009.
β‐Ca<sub>3</sub>N<sub>2</sub>, a Metastable Nitride in the System Ca–N (2009)

The structural chemistry of calcium nitrides is represented by just two different intermediate phases: cubic Ca(3)N(2) (referred to as alpha-Ca(3)N(2), Mn(2)O(3) type structure) and Ca(2)N (CdCl(2) type structure). Other binary phases ("gamma-Ca(3)N(2)", "Ca(11)N(8)") have been proven to represent cyanamide nitrides, Ca(4)N(2)[CN(2)] and Ca(11)N(6)[CN(2)](2), respectively. The metastable nitride beta-Ca(3)N(2) is prepared either by reaction of freshly distilled calcium metal with nitrogen at 700 K, or by reaction of Ca(2)N with N(2) at 500 K. beta-Ca(3)N(2) transforms monotropically (T(trans) approximately 810 K) to cubic alpha-Ca(3)N(2). The crystal structure of beta-Ca(3)N(2) (rhombohedral R3c, no. 167, a=619.884(3) pm, c=1662.958(10) pm) is an isotype of the corundum structure (alpha-Al(2)O(3)) and comprises a network of NCa(6/4) octahedra that share common faces and edges. Magnetic susceptibility and electrical resistivity measurements confirm that beta-Ca(3)N(2) is a diamagnetic semiconductor.
Detection of viruses in nasal swab samples from horses with acute, febrile, respiratory disease using virus isolation, polymerase chain reaction and serology (2007)

By virus isolation and PCR, 17 viruses were identified in nasal swab samples from 12 of 20 horses that had acute febrile respiratory disease consistent with a diagnosis of virus infection. Initial PCR identification and subsequent virus isolation led to the isolation of ERBV2 for the first time in Australia and the second time anywhere of ERBV2.
Achieving Optimal Performance by Using the IEEE 802.11 MAC Protocol With Service Differentiation Enhancements (2007)

Wireless local area networks are currently evolving to support adequate degrees of service differentiation. Work is in progress to define an enhanced version of the IEEE 802.11 distributed coordination function, which is capable of supporting quality of service for multimedia traffic at the medium access control layer. In this paper, we aim at gaining insight into one mechanism to differentiate among traffic categories, i.e., differentiating the minimum contention window sizes according to the priority of different traffic categories. The contribution of this paper is the analysis of the optimal operation point where maximum throughput can be achieved. Through the analysis, we answer some fundamental questions about the existence and uniqueness of the optimal operation point, about the maximum system throughput, about the existence of simple rules to decide if the system operates under the optimal state or not, and about procedures to lead the system to the optimal operation point. The other contribution is the proposal of a simple adaptive scheme that makes the system operate under the optimal operation point and, at the same time, achieve target service differentiation between different traffic flows. The results that are obtained in this paper are relevant to both theoretical research and implementations of real systems
<title>Super-resolution MAP algorithms applied to fluorescence imaging</title> (1997)

We have developed efficient image restoration algorithms for restoration of images that are acquired by conventional and confocal fluorescence microscopy. Assuming additive Gaussian noise or Poisson noise in the image and Gaussian or entropy prior distributions, functionals are formulated that must be minimized to obtain maximum a posteriori (MAP) and maximum likelihood (ML) estimations. We propose computationally efficient algorithms to find the solutions. The quality of the MAP restorations is determined largely by the choice of the regularization parameter, which determines the tradeoff between fitting and smoothing the solution. We propose a normalization method to ease the interactive choice of the regularization parameter if the variance of the noise is known. The performance of the algorithms was tested using simulated fluorescence conventional microscopy and fluorescence confocal laser scanning microscopy. Several error measures and quantitative measurements were used to evaluate the quality of the restoration result. We have tested the super-resolution capabilities and have found that the algorithms are capable of recovering partially the frequencies that were lost. The performance of the algorithms was compared to two existing algorithms that are commonly used for fluorescence imaging: the accelerated EM algorithm of Holmes and the regularized algorithm of Carrington.
Associations of genetic polymorphisms of Siglecs with human diseases (2014)

Genetic polymorphism studies in humans provide unique opportunities to understand human biology and the mechanisms of diseases. Correlations between polymorphisms in the genes encoding human Siglecs and various diseases have been reported. Leading examples, such as the CD33 polymorphism associated with late-onset Alzheimer's disease, are well supported by genetic replication and mechanistic studies, while some others (such as SIGLEC8 polymorphism associated with bronchial asthma and SIGLEC14 polymorphism associated with exacerbation of chronic obstructive pulmonary disease) may benefit reinforcement by independent genetic replication or mechanistic studies. In a few cases, such as MAG polymorphism associated with psychological disorder and CD22 polymorphism associated with autoimmune disease, the phenotype associated with a genetic polymorphism of a Siglec gene and that of an enzyme gene involved in the biosynthesis of Siglec ligand show some overlap, providing indirect support for the observed genotype-phenotype association. Although studies using engineered mutant mice have provided invaluable insights into the biological functions and mechanisms of diseases, it is not always possible to develop appropriate mouse model to replicate human situations because of significant species-to-species differences, which can be a major obstacle in understanding the biology of some of human CD33/Siglec-3-related Siglecs. Further studies in genetic polymorphisms of human Siglecs, combined with appropriate functional studies, may reveal unexpected biological roles of human Siglecs, and identify possible targets for prevention and/or treatment of certain diseases.
Indoor microlocation with BLE beacons and incremental rule learning (2015)

Location is one of the most valuable and extensively used information in mobile context-aware systems. Its understanding may vary from geolocation that uses GPS infrastructure to locate objects on Earth, up to microlocation, which aims at locating users and objects inside closed areas. Although geolocation can be considered as a mature field, there is an ongoing research in the area of microlocation. Despite that, microlocation techniques do not offer satisfactory level of accuracy and implementation flexibility to be practically incorporated into commercial solutions. This is mainly because of high workload that needs to be done in terms of maps preparation and algorithms tuning. In this paper we present a method that can overcome this issue by providing incremental rule learning algorithm for automated discovery of user location on a room-level accuracy. We also show a method of augmenting semantic annotations on physical objects with a use of Bluetooth Low Energy beacons.
Atmospheric Measurements by Ultra-Light SpEctrometer (AMULSE) Dedicated to Vertical Profile in Situ Measurements of Carbon Dioxide (CO2) Under Weather Balloons: Instrumental Development and Field Application (2016)

The concentration of greenhouse gases in the atmosphere plays an important role in the radiative effects in the Earth's climate system. Therefore, it is crucial to increase the number of atmospheric observations in order to quantify the natural sinks and emission sources. We report in this paper the development of a new compact lightweight spectrometer (1.8 kg) called AMULSE based on near infrared laser technology at 2.04 µm coupled to a 6-m open-path multipass cell. The measurements were made using the Wavelength Modulation Spectroscopy (WMS) technique and the spectrometer is hence dedicated to in situ measuring the vertical profiles of the CO₂ at high precision levels (σ<sub>Allan</sub> = 0.96 ppm in 1 s integration time (1σ)) and with high temporal/spatial resolution (1 Hz/5 m) using meteorological balloons. The instrument is compact, robust, cost-effective, fully autonomous, has low-power consumption, a non-intrusive probe and is plug & play. It was first calibrated and validated in the laboratory and then used for 17 successful flights up to 10 km altitude in the region Champagne-Ardenne, France in 2014. A rate of 100% of instrument recovery was validated due to the pre-localization prediction of the Météo-France based on the flight simulation software.
Diverse driving forces underlie the invariant occurrence of the T42A, E139D, I282V and T468M SHP2 amino acid substitutions causing Noonan and LEOPARD syndromes (2008)

Missense PTPN11 mutations cause Noonan and LEOPARD syndromes (NS and LS), two developmental disorders with pleiomorphic phenotypes. PTPN11 encodes SHP2, an SH2 domain-containing protein tyrosine phosphatase functioning as a signal transducer. Generally, different substitutions of a particular amino acid residue are observed in these diseases, indicating that the crucial factor is the residue being replaced. For a few codons, only one substitution is observed, suggesting the possibility of specific roles for the residue introduced. We analyzed the biochemical behavior and ligand-binding properties of all possible substitutions arising from single-base changes affecting codons 42, 139, 279, 282 and 468 to investigate the mechanisms underlying the invariant occurrence of the T42A, E139D and I282V substitutions in NS and the Y279C and T468M changes in LS. Our data demonstrate that the isoleucine-to-valine change at codon 282 is the only substitution at that position perturbing the stability of SHP2's closed conformation without impairing catalysis, while the threonine-to-alanine change at codon 42, but not other substitutions of that residue, promotes increased phosphopeptide-binding affinity. The recognition specificity of the C-SH2 domain bearing the E139D substitution differed substantially from its wild-type counterpart acquiring binding properties similar to those observed for the N-SH2 domain, revealing a novel mechanism of SHP2's functional dysregulation. Finally, while functional selection does not seem to occur for the substitutions at codons 279 and 468, we point to deamination of the methylated cytosine at nucleotide 1403 as the driving factor leading to the high prevalence of the T468M change in LS.
Comparison of Hospitalwide Surveillance and Targeted Intensive Care Unit Surveillance of Healthcare-Associated Infections (2007)

Rates of HAIs were highest in the ICUs, intermediate in step-down units, and lowest in the wards. The rates of infections in the step-down units were more similar to those in the wards than to those in the ICUs. To prevent HAIs, more comprehensive surveillance may be indicated.
REVIEW: The functional organization of the intraparietal sulcus in humans and monkeys (2005)

In macaque monkeys, the posterior parietal cortex (PPC) is concerned with the integration of multimodal information for constructing a spatial representation of the external world (in relation to the macaque's body or parts thereof), and planning and executing object-centred movements. The areas within the intraparietal sulcus (IPS), in particular, serve as interfaces between the perceptive and motor systems for controlling arm and eye movements in space. We review here the latest evidence for the existence of the IPS areas AIP (anterior intraparietal area), VIP (ventral intraparietal area), MIP (medial intraparietal area), LIP (lateral intraparietal area) and CIP (caudal intraparietal area) in macaques, and discuss putative human equivalents as assessed with functional magnetic resonance imaging. The data suggest that anterior parts of the IPS comprising areas AIP and VIP are relatively well preserved across species. By contrast, posterior areas such as area LIP and CIP have been found more medially in humans, possibly reflecting differences in the evolution of the dorsal visual stream and the inferior parietal lobule. Despite interspecies differences in the precise functional anatomy of the IPS areas, the functional relevance of this sulcus for visuomotor tasks comprising target selections for arm and eye movements, object manipulation and visuospatial attention is similar in humans and macaques, as is also suggested by studies of neurological deficits (apraxia, neglect, Bálint's syndrome) resulting from lesions to this region.
Iron-dependent oxidation, ubiquitination, and degradation of iron regulatory protein 2: Implications for degradation of oxidized proteins (1998)

The ability of iron to catalyze formation of reactive oxygen species significantly contributes to its toxicity in cells and animals. Iron uptake and distribution is regulated tightly in mammalian cells, in part by iron regulatory protein 2 (IRP2), a protein that is degraded efficiently by the proteasome in iron-replete cells. Here, we demonstrate that IRP2 is oxidized and ubiquitinated in cells before degradation. Moreover, iron-dependent oxidation converts IRP2 into a substrate for ubiquitination in vitro . A regulatory pathway is described in which excess iron is sensed by its ability to catalyze site-specific oxidations in IRP2, oxidized IRP2 is ubiquitinated, and ubiquitinated IRP2 subsequently is degraded by the proteasome. Selective targeting and removal of oxidatively modified proteins may contribute to the turnover of many proteins that are degraded by the proteasome.
Effective Chikungunya Virus-like Particle Vaccine Produced in Insect Cells (2013)

The emerging arthritogenic, mosquito-borne chikungunya virus (CHIKV) causes severe disease in humans and represents a serious public health threat in countries where Aedes spp mosquitoes are present. This study describes for the first time the successful production of CHIKV virus-like particles (VLPs) in insect cells using recombinant baculoviruses. This well-established expression system is rapidly scalable to volumes required for epidemic responses and proved well suited for processing of CHIKV glycoproteins and production of enveloped VLPs. Herein we show that a single immunization with 1 µg of non-adjuvanted CHIKV VLPs induced high titer neutralizing antibody responses and provided complete protection against viraemia and joint inflammation upon challenge with the Réunion Island CHIKV strain in an adult wild-type mouse model of CHIKV disease. CHIKV VLPs produced in insect cells using recombinant baculoviruses thus represents as a new, safe, non-replicating and effective vaccine candidate against CHIKV infections.
Genomics‐based selection and functional characterization of triterpene glycosyltransferases from the model legume <i>Medicago truncatula</i> (2005)

The biosynthesis of triterpene saponins is poorly characterized in spite of the importance of these glycosylated secondary metabolites for plant defense and animal health. The model legume Medicago truncatula synthesizes more than 30 different saponins based on at least five triterpene aglycones; soyasapogenols B and E, medicagenic acid, hederagenin and bayogenin. We have employed an inducible cell culture system, DNA array-based and in silico transcript profiling, and targeted metabolite profiling, to identify triterpene glycosyltransferases (GTs) from among the more than 300 GTs expressed in M. truncatula. Two uridine diphosphate glucosyltransferases were functionally characterized; UGT73K1 with specificity for hederagenin and soyasapogenols B and E, and UGT71G1 with specificity for medicagenic acid. The latter enzyme also glycosylated certain isoflavones and the flavonol quercetin with higher efficiency than triterpenes; however, integrated transcript and metabolite profiling supported a function for UGT71G1 in terpenoid but not (iso)flavonoid biosynthesis in the elicited cell cultures.
Macrophage A2A Adenosinergic Receptor Modulates Oxygen-Induced Augmentation of Murine Lung Injury (2013)

Acute respiratory distress syndrome (ARDS) causes significant morbidity and mortality. Exacerbating factors increasing the risk of ARDS remain unknown. Supplemental oxygen is often necessary in both mild and severe lung disease. The potential effects of supplemental oxygen may include augmentation of lung inflammation by inhibiting anti-inflammatory pathways in alveolar macrophages. We sought to determine oxygen-derived effects on the anti-inflammatory A2A adenosinergic (ADORA2A) receptor in macrophages, and the role of the ADORA2A receptor in lung injury. Wild-type (WT) and ADORA2A(-/-) mice received intratracheal lipopolysaccharide (IT LPS), followed 12 hours later by continuous exposure to 21% oxygen (control mice) or 60% oxygen for 1 to 3 days. We measured the phenotypic endpoints of lung injury and the alveolar macrophage inflammatory state. We tested an ADORA2A-specific agonist, CGS-21680 hydrochloride, in LPS plus oxygen-exposed WT and ADORA2A(-/-) mice. We determined the specific effects of myeloid ADORA2A, using chimera experiments. Compared with WT mice, ADORA2A(-/-) mice exposed to IT LPS and 60% oxygen demonstrated significantly more histologic lung injury, alveolar neutrophils, and protein. Macrophages from ADORA2A(-/-) mice exposed to LPS plus oxygen expressed higher concentrations of proinflammatory cytokines and cosignaling molecules. CGS-21680 prevented the oxygen-induced augmentation of lung injury after LPS only in WT mice. Chimera experiments demonstrated that the transfer of WT but not ADORA2A(-/-) bone marrow cells into irradiated ADORA2A(-/-) mice reduced lung injury after LPS plus oxygen, demonstrating myeloid ADORA2A protection. ADORA2A is protective against lung injury after LPS and oxygen. Oxygen after LPS increases macrophage activation to augment lung injury by inhibiting the ADORA2A pathway.
Ultrafast spectroscopic investigation of the artificial photosynthetic activity of CuAlS<sub>2</sub>/ZnS quantum dots (2021)

Abstract CuAlS 2 /ZnS Quantum dots (QDs) are known to directly convert aqueous solutions of bicarbonate ions to oxygen and organic molecules such as formate with a remarkable efficiency even under sunlight. In cases, fairly complicated organic reaction products such as acetate and methanol have been observed when reactions are allowed to continue for longer periods of time. Here, we investigate the electron dynamics that occurs within CuAlS 2 /ZnS QDs and show that it is essentially dominated by ultrafast electron transfer (560 fs for 0.4 excitons per dot) to the surface. The electron dwell time in the conduction band increases exponentially (for example 872 fs for 1.4 excitons per dot) with the excitation fluence. This is reverse of the auger limited response of conventional QDs and is hypothesized to exhibit strong charge separation that lies at the root of the remarkable photocatalytic activity. We further investigate this system through multi‐pump experiments. We find that the system response to prior excitation changes over the period of nanoseconds, consistent with the charge reorganization in the system, well after the initial electron transfer. The results of these experiments are summarized in terms of a coulomb‐well interpretation.
Ontology alignment in geographical hard-soft information fusion systems (2010)

Information fusion exists over many forms of hard data (e.g. from physical sensors) and soft data (e.g. from human reports) to interpret observations of real-world objects. As demonstrated from the Geographical Information Systems (GIS) community, there is a growing need for the linking and alignment of both (1) exploited physical imagery products and (2) derived ontological textual labels (semantic markup). Semantic markup can be done on both exploited data (e.g. automated image segmentation), as well as user reports (e.g. weather forecasts). Since the derived information is collected, stored, and displayed into distinct ontological structures by different agencies; ontological alignment is thus required whenever the semantic information is paired with distinct real-world imagery observations. In this paper, we explore issues of fusing hard and soft data as related to ontology alignment. A maritime domain situational awareness example with geographical imagery and textural ontologies is shown to demonstrate the need for ontology alignment to assist users for pragmatic surveillance.