Miracle-dz/UniFAR-FTUs huggingface dataset:
Interferon-Gamma Promotes Infection of Astrocytes by Trypanosoma cruzi

The inflammatory cytokine interferon-gamma (IFNγ) is crucial for immunity against intracellular pathogens such as the protozoan parasite Trypanosoma cruzi, the causative agent of Chagas disease (CD). IFNγ is a pleiotropic cytokine which regulates activation of immune and non-immune cells; however, the effect of IFNγ in the central nervous system (CNS) and astrocytes during CD is unknown. Here we show that parasite persists in the CNS of C3H/He mice chronically infected with the Colombian T. cruzi strain despite the increased expression of IFNγ mRNA. Furthermore, most of the T. cruzi-bearing cells were astrocytes located near IFNγ+ cells. Surprisingly, in vitro experiments revealed that pretreatment with IFNγ promoted the infection of astrocytes by T. cruzi increasing uptake and proliferation of intracellular forms, despite inducing increased production of nitric oxide (NO). Importantly, the effect of IFNγ on T. cruzi uptake and growth is completely blocked by the anti-tumor necrosis factor (TNF) antibody Infliximab and partially blocked by the inhibitor of nitric oxide synthesis L-NAME. These data support that IFNγ fuels astrocyte infection by T. cruzi and critically implicate IFNγ-stimulated T. cruzi-infected astrocytes as sources of TNF and NO, which may contribute to parasite persistence and CNS pathology in CD.
Wave-domain adaptive filtering for acoustic human-machine interfaces based onwavefield analysis and synthesis

Wave field synthesis and wave field analysis are attractive techniques for high-quality sound-field auralization and recording using loudspeaker arrays and microphone arrays. However, to utilize these techniques in multichannel acoustic interfaces, several challenges in signal processing have to be overcome in this new context, e.g., acoustic echo cancellation (AEC) to avoid acoustic feedback in full-duplex systems, interference cancellation on the recording side, and room compensation on the reproduction side. In traditional setups, these problems are tackled using adaptive filtering techniques in the time-frequency domain. In this paper, we present a novel and highly efficient framework for adaptive filtering in the wave domain by reconciling the flexibility of adaptive filtering and the underlying physics described by the acoustic wave equation. The new framework explicitly takes into account the spatial dimensions of the closely spaced loudspeakers and the microphone arrays. Experimental results with a 32-channel AEC verify the concept for both, simulated and actually measured room acoustics.
Accuracy of Vessel-Encoded Pseudocontinuous Arterial Spin-Labeling in Identification of Feeding Arteries in Patients with Intracranial Arteriovenous Malformations

BACKGROUND AND PURPOSE: Identifying feeding arteries of intracranial AVMs is very important for preoperative evaluation. DSA remains the reference standard for diagnosis but is invasive. Our aim was to evaluate the diagnostic accuracy of vessel-encoded pseudocontinuous arterial spin-labeling in identifying feeding arteries of intracranial AVMs by using DSA as the criterion standard. MATERIALS AND METHODS: Eighteen patients with AVMs were examined with vessel-encoded pseudocontinuous arterial spin-labeling and DSA. Three postlabeling delays (postlabeling delay = 1, 1.3, and 1.6 seconds) were applied in 6 patients, and a single postlabeling delay (1 second) was applied in the remainder. Perfusion-weighted images were decoded into individual vascular territories with standard and relative tagging efficiencies, respectively. The supply fraction of each feeding artery to the AVM was calculated. The within-subject ANOVA was applied to compare supply fractions acquired across 3 postlabeling delays. Receiver operating characteristic analysis curves were calculated to evaluate the diagnostic accuracy of vessel-encoded pseudocontinuous arterial spin-labeling for identifying the feeding arteries of AVMs. RESULTS: There were no significant differences in supply fractions of the 3 major arteries to AVMs acquired with 3 postlabeling delays (P > .05). For vessel-encoded pseudocontinuous arterial spin-labeling with standard labeling efficiencies, the area under the receiver operating characteristic analysis curve was 0.942. The optimal cutoff of the supply fraction for identifying feeding arteries was 15.17%, and the resulting sensitivity and specificity were 84.62% and 93.33%, respectively. For vessel-encoded pseudocontinuous arterial spin-labeling with relative labeling efficiencies, the area under the receiver operating characteristic analysis curve was 0.957. The optimal cutoff of the supply fraction was 11.73%, which yielded an 89.74% sensitivity and 93.33% specificity. CONCLUSIONS: The contribution fraction of each feeding artery of the AVM can be reliably estimated by using vessel-encoded pseudocontinuous arterial spin-labeling. Vessel-encoded pseudocontinuous arterial spin-labeling with either standard or relative labeling efficiencies offers a high level of diagnostic accuracy compared with DSA for identifying feeding arteries.
Unexpected effects of the MIP‐CreER transgene and tamoxifen on β‐cell growth in C57Bl6/J male mice

Transgenic mouse models have been fundamental in the discovery of factors that regulate β‐cell development, mass, and function. Several groups have recently shown that some of these models display previously uncharacterized phenotypes due to the transgenic system itself. These include impaired islet function and increased β‐cell mass due to the presence of a human growth hormone (hGH) minigene as well as impaired β‐cell proliferation in response to tamoxifen (TM) administration. We aimed to determine how these systems impact β‐cell mass and proliferation during high fat diet (HFD). To this end, we utilized C57Bl6/J male MIP‐CreER mice, which are known to express hGH, or wild‐type (WT) mice treated with vehicle corn oil or TM. In the absence of TM, MIP‐CreER mice fed a chow diet have increased β‐cell mass due to hypertrophy, whereas replication is unchanged. Similarly, after 1 week on HFD, MIP‐CreER mice have increased β‐cell mass compared to WT, and this is due to hypertrophy rather than increased proliferation. To assess the impact of TM on β‐cell proliferation and mass, WT mice were treated with vehicle corn oil or TM and then fed a chow diet or HFD for 3 days. We observed that TM‐treated mice have improved glucose homeostasis on chow diet but impaired β‐cell proliferation in response to 3 days HFD feeding. These results unveil additional complications associated with commonly used pancreas‐specific mouse models.
In Situ Seeded Growth of High-Quality PbS/CdS Quantum Dots for Highly Efficient Photovoltaics

Panchromatic solar cells are of great prospects in virtue of the sufficient utilization of solar energy. The narrow bandgap semiconductors such as PbS can serve as promising candidates for light harvesting. In this paper, we report an in situ seeded growth of PbS quantum dots (QDs) onto TiO2 films for the construction of high-performance PbS/CdS QD-sensitized solar cells. Careful morphologic, optical, and electrical examinations were performed to probe into the superiority of such an approach. The predeposited PbSO3 seeds are used as nucleation sites for monodisperse PbS QDs with the particle size of ∼3.5 nm, which ensures favorable electron injection from PbS into TiO2. Meanwhile, the CdS passivation layer is synchronously loaded along with in situ seeded PbS, resulting in effective passivation of defect states at the PbS surface. Eventually, benefitted from improved carrier manipulation (i.e., electron injection and charge transport), the in situ seeded device yields a power conversion efficiency of 2.13%, exhibiting considerably enhanced photovoltaic performance in contrast to the identical PbS/CdS scheme processed by the conventional two-step successive ionic layer adsorption and reaction.
Do We Need Dereverberation for Hand-Held Telephony?

The necessity of dereverberation algorithms in hand-held speech communication systems is discussed in this contribution. The study is based on a new measurement campaign with artificial head and a two-microphone mock-up phone in realistic acoustical environments like an office, corridor and stairway. Based on objective speech quality measures as well as a listening test, we show that room reverberation can lead to a decrease in intelligibility even for hand-held telephony under certain conditions. Hence, the far-end listener can benefit from dereverberation algorithms in the sending device. All measured room impulse responses are available online as part of the Aachen Impulse Response (AIR) database.
Considerations for Achieving Cross-Platform Point Cloud Data Fusion across Different Dryland Ecosystem Structural States

Remotely sensing recent growth, herbivory, or disturbance of herbaceous and woody vegetation in dryland ecosystems requires high spatial resolution and multi-temporal depth. Three dimensional (3D) remote sensing technologies like lidar, and techniques like structure from motion (SfM) photogrammetry, each have strengths and weaknesses at detecting vegetation volume and extent, given the instrument's ground sample distance and ease of acquisition. Yet, a combination of platforms and techniques might provide solutions that overcome the weakness of a single platform. To explore the potential for combining platforms, we compared detection bias amongst two 3D remote sensing techniques (lidar and SfM) using three different platforms [ground-based, small unmanned aerial systems (sUAS), and manned aircraft]. We found aerial lidar to be more accurate for characterizing the bare earth (ground) in dense herbaceous vegetation than either terrestrial lidar or aerial SfM photogrammetry. Conversely, the manned aerial lidar did not detect grass and fine woody vegetation while the terrestrial lidar and high resolution near-distance (ground and sUAS) SfM photogrammetry detected these and were accurate. UAS SfM photogrammetry at lower spatial resolution under-estimated maximum heights in grass and shrubs. UAS and handheld SfM photogrammetry in near-distance high resolution collections had similar accuracy to terrestrial lidar for vegetation, but difficulty at measuring bare earth elevation beneath dense herbaceous cover. Combining point cloud data and derivatives (i.e., meshes and rasters) from two or more platforms allowed for more accurate measurement of herbaceous and woody vegetation (height and canopy cover) than any single technique alone. Availability and costs of manned aircraft lidar collection preclude high frequency repeatability but this is less limiting for terrestrial lidar, sUAS and handheld SfM. The post-processing of SfM photogrammetry data became the limiting factor at larger spatial scale and temporal repetition. Despite the utility of sUAS and handheld SfM for monitoring vegetation phenology and structure, their spatial extents are small relative to manned aircraft.
Training general practitioners in mental health skills

Changes need to be made to the way in which both undergraduates and vocational trainees are taught about mental disorders, so that teaching emphasises the psychological syndromes that general practitioners are likely to meet in their everyday work. Training packages need to be developed for primary care staff in the detection and management of mental disorders.
Functional MRI of Awake Behaving Macaques Using Standard Equipment

Functional magnetic resonance imaging (fMRI) is perhaps the most important development in the measurement of human brain function in recent neuroscience history. The technique allows for noninvasive whole-volume measurements of brain function in humans and repeatable non-invasive measurement of activity over the whole brain, providing a correlate of neural activity without use of tracers or electrodes. Well-developed commercial MRI systems with built-in support for functional imaging are widely available, as are a plethora of tools, both free and commercial, for the analysis of human functional brain images. The combination of non-invasiveness and the broad availability of equipment and tools to perform fMRI have made this technique popular and broadly adopted.
Molecular analysis of respiratory syncytial virus reinfections in infants from coastal Kenya.

BACKGROUND Individuals are reinfected with respiratory syncytial virus (RSV) repeatedly. The nature of reinfection, in relation to RSV genetic and antigenic diversity, is ill defined and has implications for persistence and vaccine control. METHODS We examined the molecular relatedness of RSV causing primary and repeat infections, by phylogenetic analysis of the attachment (G) gene in 12 infants from a birth cohort in rural Kenya, using nasal wash samples collected during a 16-month period in 2002-2003, which spanned 2 successive epidemics. RESULTS Six infants were infected during both epidemics, 4 with RSV-A in the first epidemic followed by RSV-B during the second epidemic and 2 with RSV-A during both epidemics, with no significant G gene sequence variability between samples. Two infants were infected and reinfected with different RSV-A strains during the same epidemic. Possible viral persistence was suspected in the remaining 4 infants, although reinfection with the same variant cannot be excluded. CONCLUSIONS These are the first data that specifically address strain-specific reinfections in infancy in relation to the primary infecting variant. The data strongly suggest that, following primary infection, some infants lose strain-specific immunity within 7-9 months (between epidemics) and group-specific immunity within 2-4 months (during an epidemic period).
Split and Rephrase

We propose a new sentence simplification task (Split-and-Rephrase) where the aim is to split a complex sentence into a meaning preserving sequence of shorter sentences. Like sentence simplification, splitting-and-rephrasing has the potential of benefiting both natural language processing and societal applications. Because shorter sentences are generally better processed by NLP systems, it could be used as a preprocessing step which facilitates and improves the performance of parsers, semantic role labellers and machine translation systems. It should also be of use for people with reading disabilities because it allows the conversion of longer sentences into shorter ones. This paper makes two contributions towards this new task. First, we create and make available a benchmark consisting of 1,066,115 tuples mapping a single complex sentence to a sequence of sentences expressing the same meaning. Second, we propose five models (vanilla sequence-to-sequence to semantically-motivated models) to understand the difficulty of the proposed task.
BFCO: A BPSO-Based Fine-Grained Communication Optimization Method for MPSoC

Fine-grained multithreaded models can provide more opportunities for system performance improvements, but they face large amount of communication overhead. To reduce the communication overhead to improve performance, message aggregation and communication pipeline have been proposed and their advantages have been discussed in previous works. However, when exploiting them in real-life applications, it is challenging to maximize their advantages due to their unrevealed problems. This paper investigates the two communication optimization techniques from the view of their problems to fulfill the studies. We have found that when applying the techniques, message aggregation may have the deadlock problem and latency problem, and communication pipeline may face the ineffective problem and prolog and epilog problem. Based on the basic requirement of allocating the two techniques on an initial schedule, we then present general solutions to avoid or handle the problems. To obtain a minimum schedule length for an initial schedule, we further develop a binary particle swarm optimization-based fine-grained communication optimization method to allocate message aggregation and communication pipeline for best performance. The method is also integrated into light and efficient simulink compiler for embedded application multithreaded code generator to generate high quality codes. Experimental results on both synthetic and real-life applications demonstrate the efficiency of the proposed method.
Edinburgh Research Explorer Genome sequence survey identifies unique sequences and key virulence genes with unusual rates of amino Acid substitution in bovine Staphylococcus aureus

Staphylococcus aureus is a major cause of mastitis in bovine and other ruminant species. We here present the results of a comparative genomic analysis between a bovine mastitis-associated clone, RF122, and the recently sequenced human-associated clones, Mu50 and N315, of Staphylococcus aureus . A shotgun sequence survey of (cid:2) 10% of the RF122 genome identiﬁed numerous unique sequences and those with elevated rates of nonsynonymous substitution. Taken together, these analyses show that there are notable differences in the genomes of bovine mastitis-associated and human clones of S. aureus and provide a framework for the identiﬁcation of speciﬁc factors associated with host speciﬁcity in this major human and animal pathogen. Staphylococcus aureus is a widely distributed animal and human pathogen. Phenotypic analyses of S. aureus strains iso-lated from human and bovine hosts have revealed important differences between the two populations of isolates, but the underlying genetic basis for the variation among S. aureus
A 3-month Safety Assessment of Human Bone Marrow Derived Mesenchymal Stromal Cells Administered Once by the Intramuscular Route to Immunodeficient Mice

Critical limb ischemia (CLI) represents the severest manifestation of peripheral arterial disease and is a major unmet medical need. This disease occurs when the arterial blood supply within the limb fails to meet the metabolic demands of the resting muscle or tissue, resulting in chronic ischemic rest pain and/or tissue necrosis. Human mesenchymal stromal cells, termed hMSCs, represent an exciting therapeutic modality for the treatment of this disease due to their immunomodulatory and tissue reparative functions. The aim of the study was to assess the preclinical toxicity profile of human bone marrow–derived MSCs in support of their use as a treatment for CLI. A 3-month toxicity study was carried out under good laboratory practices in immunodeficient mice who received, intramuscularly, a single dose of 3 × 105 (approximately 15 × 106 cells/kg) hMSCs manufactured under good manufacturing practices. No significant changes in body weight, food consumption, clinical signs, or histopathological changes were observed in the hMSC-treated mice in comparison to the controls. These results highlight that the administration of hMSCs during the 3-month study period was well tolerated and not associated with any test item–related tumors. This data set supported the initiation of a phase 1b first in human study in “no option” for revascularization patients with CLI.
High-Mass-Measurement Accu racy and 100 % Sequence Coverage of Enzymatically Digested Bovine Serum Albumin from an ESI-FTICR Mass Spectrum

Int. Cl. " . C07C 331/16; G01N 33/68 U.S. Cl. 436/173; 436/86; 436/89; 436/120; 436/161; 436/165; 436/166; 436/167; 436/168; 436/171; 436/173; 436/174; 436/175; 436/177; 530/350; 530/812; 530/391.5 Field of Search . 435/4, 7.1, 7.92, 435/24, 188, 6, 7.5, 23, 177,964; 436/168, 175, 165, 86, 89, 18, 120, 161, 166, 171, 167, 174, 173, 178,518, 538,523-535, 539, 541, 824, 825; 530/367,812, 391.5, 391.9, 807, 871
Cross-Layer Design of Wireless Multihop Networks Over Stochastic Channels With Time-Varying Statistics

Network utility maximization is often applied for the cross-layer design of wireless networks considering known wireless channels. However, realistic wireless channel capacities are stochastic bearing time-varying statistics, necessitating the redesign and solution of NUM problems to capture such effects. Based on NUM theory we develop a framework for scheduling, routing, congestion control and power control in wireless multihop networks that considers stochastic long or short term fading wireless channels. Specifically, the wireless channel is modeled via stochastic differential equations alleviating several assumptions that exist in state-of-the-art channel modeling within the NUM framework such as the finite number of states or the stationarity. Our consideration of wireless channel modeling leads to a NUM problem formulation that accommodates non-convex and time-varying utilities. We consider both cases of non orthogonal and orthogonal access of users to the medium. In the first case, scheduling is performed via power control, while the latter separates scheduling and power control and the role of power control is to further increase users' optimal utility by exploiting random reductions of the stochastic channel power loss while also considering energy efficiency. Finally, numerical results evaluate the performance and operation of the proposed approach and study the impact of several involved parameters on convergence.
Does replacing coal with wood lower CO2 emissions? Dynamic lifecycle analysis of wood bioenergy

Bioenergy is booming as nations seek to cut their greenhouse gas emissions. The European Union declared biofuels to be carbon-neutral, triggering a surge in wood use. But do biofuels actually reduce emissions? A molecule of CO2 emitted today has the same impact on radiative forcing whether it comes from coal or biomass. Biofuels can only reduce atmospheric CO2 over time through post-harvest increases in net primary production (NPP). The climate impact of biofuels therefore depends on CO2 emissions from combustion of biofuels versus fossil fuels, the fate of the harvested land and dynamics of NPP. Here we develop a model for dynamic bioenergy lifecycle analysis. The model tracks carbon stocks and fluxes among the atmosphere, biomass, and soils, is extensible to multiple land types and regions, and runs in ≈1s, enabling rapid, interactive policy design and sensitivity testing. We simulate substitution of wood for coal in power generation, estimating the parameters governing NPP and other fluxes using data for forests in the eastern US and using published estimates for supply chain emissions. Because combustion and processing efficiencies for wood are less than coal, the immediate impact of substituting wood for coal is an increase in atmospheric CO2 relative to coal. The payback time for this carbon debt ranges from 44–104 years after clearcut, depending on forest type—assuming the land remains forest. Surprisingly, replanting hardwood forests with fast-growing pine plantations raises the CO2 impact of wood because the equilibrium carbon density of plantations is lower than natural forests. Further, projected growth in wood harvest for bioenergy would increase atmospheric CO2 for at least a century because new carbon debt continuously exceeds NPP. Assuming biofuels are carbon neutral may worsen irreversible impacts of climate change before benefits accrue. Instead, explicit dynamic models should be used to assess the climate impacts of biofuels.