gebhart/patrepeval huggingface dataset:
EVALUATION OF<i>MONKEYPOX VIRUS</i>INFECTION OF BLACK-TAILED PRAIRIE DOGS (<i>CYNOMYS LUDOVICIANUS</i>) USING IN VIVO BIOLUMINESCENT IMAGING (2014)

Monkeypox (MPX) is a re-emerging zoonotic disease that is endemic in Central and West Africa, where it can cause a smallpox-like disease in humans. Despite many epidemiologic and field investigations of MPX, no definitive reservoir species has been identified. Using recombinant viruses expressing the firefly luciferase (luc) gene, we previously demonstrated the suitability of in vivo bioluminescent imaging (BLI) to study the pathogenesis of MPX in animal models. Here, we evaluated BLI as a novel approach for tracking MPX virus infection in black-tailed prairie dogs (Cynomys ludovicianus). Prairie dogs were affected during a multistate outbreak of MPX in the US in 2003 and have since been used as an animal model of this disease. Our BLI results were compared with PCR and virus isolation from tissues collected postmortem. Virus was easily detected and quantified in skin and superficial tissues by BLI before and during clinical phases, as well as in subclinical secondary cases, but was not reliably detected in deep tissues such as the lung. Although there are limitations to viral detection in larger wild rodent species, BLI can enhance the use of prairie dogs as an animal model of MPX and can be used for the study of infection, disease progression, and transmission in potential wild rodent reservoirs.
Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2 (2021)

Abstract Cells respond to perturbations like inflammation by sensing changes in metabolite levels. Especially prominent is arginine, which has known connections to the inflammatory response. Here, we found that depletion of arginine during inflammation decreased levels of a nuclear form of arginyl-tRNA synthetase (ArgRS). Surprisingly, we found that nuclear ArgRS interacts with serine/arginine repetitive matrix protein 2 (SRRM2), a spliceosomal protein and nuclear speckle component and that arginine depletion impacted both condensate-like nuclear trafficking of SRRM2 and splice-site usage in certain genes. These splice-site usage changes cumulated in synthesis of different protein isoforms that altered cellular metabolism and peptide presentation to immune cells. Our findings uncover a novel mechanism whereby a tRNA synthetase cognate to a key amino acid that is metabolically controlled during inflammation modulates the splicing machinery.
Intercomparision of Monte Carlo Radiation Transport Codes MCNPX, GEANT4, and FLUKA for Simulating Proton Radiotherapy of the Eye (2009)

Monte Carlo simulations of an ocular treatment beam-line consisting of a nozzle and a water phantom were carried out using MCNPX, GEANT4, and FLUKA to compare the dosimetric accuracy and the simulation efficiency of the codes. Simulated central axis percent depth-dose profiles and cross-field dose profiles were compared with experimentally measured data for the comparison. Simulation speed was evaluated by comparing the number of proton histories simulated per second using each code. The results indicate that all the Monte Carlo transport codes calculate sufficiently accurate proton dose distributions in the eye and that the FLUKA transport code has the highest simulation efficiency.
Development of active optics for thin meniscus mirrors in 1-meter-class telescopes (2022)

This paper presents the ongoing project of implementing an active optics system in an 1-meter telescope to build a lightweight, cost-effective system with high imaging quality. A systematic design methodology for meniscus mirrors based on thin plate theory and finite element analysis enables target-oriented engineering of a support system that takes the application-dependent optical mirror requirements into account. The actuators for the lateral and axial system are based on stepper motors and designed in a modular manner, adjustable for a wide range of nominal force values. The axial actuators integrate an optical force measurement to achieve a compact design. Laser triangulation sensors placed in the mirror cell measure the lateral mirror position in 3 degrees of freedom with respect to its cell, providing position data that is used in a feedback control to compensate for finite stiffness of the support structure and thermal disturbances. Tests of the lateral system’s performance show maximum displacements of 1.4 μm in both lateral directions, keeping the according wavefront RMS error below 5 nm.
Physiological and behavioural responses of moose to hunting with dogs (2020)

Optimal management of hunted species requires an understanding of the impacts of hunting on both individual animal and population levels. Recent technological advancements in biologging enable us to obtain increasingly detailed information from free-ranging animals, covering longer periods of time, and providing the data needed to assess such impacts. In Sweden, more than 80 000 moose are harvested annually, mostly hunted with the use of baying dogs. The effects of this hunting method on animal welfare and stress are understudied. Here, we evaluated 6 real and 17 experimental hunting approaches with baying dogs [wearing global positioning system (GPS) collars] on 8 adult female moose equipped with ruminal temperature loggers, subcutaneous heart rate (HR) loggers and GPS collars with accelerometers. The obtained data were used to analyse the behavioural and physiological responses of moose to hunting with dogs. Successful experimental approaches (moose and dog were within 240 m for >10 min) resulted in higher maximum body temperature (T<sub>b,</sub> 0.88°C higher) and a mean increase in HR of 24 bpm in moose at the day of the approach compared to the day after. The moose rested on average >90 min longer the day after the approach compared to the day of the approach. The moose travelled on average 4.2 km longer and had a 1.3 m/s higher maximum speed the day of the approach compared to the day after. Our results demonstrate that hunting with dogs increase moose energy expenditure and resting time (and consequently decrease time available for foraging) on an individual level. This could possibly affect body condition and reproduction rates if the hunting disturbances occur frequently.
Greedy Hardware Optimization For Linear Digital Systems Using Number Splitting And Repeated Factorization (2005)

Most of the current state-of-the-art behavioral synthesis tools perform a direct translation of the high-level descriptions to circuit structures in which multiplier constants are implemented as given. Some systems perform a limited amount of transformation to optimize speed and area. In this paper we propose a new optimization technique based on successive gradient method (greedy approach) to minimize the area of linear digital systems using a combination of common subexpression elimination and modification of multiplier coefficients. Since the amount of logic required by a coefficient multiplier is dependent on the value of coefficient, the given system is transformed, using splitting of coefficients, in such a way that the new set of multiplier coefficients require less logic and area. The new synthesis scheme generates functionally equivalent but structurally different circuits with a 15% to 40% reduction in area, over conventional methods, for a set of benchmark circuits.
Minimally-verbal children with autism show deficits in theta and gamma oscillations during processing of semantically-related visual information (2019)

To acquire language, children must build phonemic representations of their native language, learn to associate auditory words to visual objects and assemble a lexicon. It is not clear however, whether the limited linguistic ability seen in minimally-verbal (MV) children with Autism Spectrum Disorder (ASD) relates to deficits in cortical representation of an object and/or in linking an object to its semantic information. This EEG-based study investigated neural mechanisms underlying visual processing of common objects in MV-ASD and control children. Ten MV-ASD children, 4- to 7- years-old and 15 age/gender-matched controls, were presented with a picture-word matching paradigm. Time-frequency analyses were conducted at the sources generating the event-related responses at both early and late visual processing. Permutation testing identified spectral power and phase coherence clusters that significantly differed between the groups. As compared to controls, MV-ASD children exhibited smaller amplitudes and longer source latencies; decreased gamma and theta power with less theta phase coherence in occipital regions, and reduced frontal gamma power. Our results confirm that visual processing is altered in MV-ASD children and suggest that some of the linguistic differences observed in these children arise from impaired object/label cortical representations and reduced allocation of attention, which would impact lexical acquisition.
437 The Leptomeninges as a New and Critical Organ: 1st ScR of “Arachnoiditis,” With 62 Other Names for the Same Pathology (2022)

INTRODUCTION: The goal of this prospective PRISMA-based Systematic Scoping Review with modified e-Delphi [ScR] is to synthesize all available information about a reportedly iatrogenic disease typically called “arachnoiditis” [arcs]. Past literature describes a rare, iatrogenic disease of the arachnoid membrane, with no known treatment. By 2021, nothing materially new had been added to the literature. The present ScR aims to clarify the clinical view of arcs. Grey data from legal documents, government proceedings, government and manufacturer device adverse events [AE] tracking, and investigative reporting was included. Although excluded from the data charting, we were surprised by multiple articles about the biology of the subarachnoid space [SAS] and the critical role it plays in protecting and maintaining the central nervous system [CNS]. METHODS: The entire ScR is published at https://arcsology.org/about-arcsology/scoping-systematic-review-of-arachnoiditis-official-protocol/. Data charting was standardized through an iterative process involving = 2 independent clinicians. Data synthesis was performed in R. RESULTS: A total of 46,646 sources were screened. Data from 887 sources are synthesized, finding 63 names used for pathology of the leptomeninges [LM]. “Arachnoiditis” is a misnomer. Leptomeningeal diseases are not rare and can cause a range of neurologic symptoms. Spinal versus brain presentations are similar, although the two categories differ substantially. Many causes were identified. In high-income countries, &gt;50% of cases are caused by non-communicable diseases, with spinal surgery as the largest single contributor. In underdeveloped countries, communicable diseases and trauma predominate. In sum: irritants in or around the LM can trigger an inflammatory and/or fibrotic cascade within the subarachnoid space. Prognosis is variable and continuous progression does not occur in most patients. CONCLUSION: These results impact all health care practitioners. Consistent and correct terminology is critical going forward. The WHO-ICD11 team is currently reviewing our proposal for name and hierarchical changes. The LM meet criteria for a newly recognized organ with a unique and critical structure, function, and cellular components. Integration of in vitro and animal models will be helpful for future directions.
Detuning Dependence of Losses in Bragg Gratings (2011)

Optical losses vary with detuning from Bragg resonance due to variation of stored optical power inside the grating. Additional modulation of the absorption coefficient will cause asymmetry in detuning dependence of losses. Experiments confirm analytic theory.
A new symbol synchronizer with reduced timing jitter for QAM systems (2002)

A new and simple symbol synchronizer for QAM systems with reduced timing jitter is proposed. In the symbol synchronization loop, the timing error detection algorithm proposed by Gardner (1986) is used and a first order PLL is used for tracking optimal sampling instants. In a common first order PLL used in a symbol synchronizer, the loop filter gain is a constant, while in the reduced timing jitter symbol synchronizer, the loop filter gain is adaptively changed so that the timing jitter is greatly decreased. The scheme is also suitable for the case where burst transmissions take place. Furthermore, the mechanism of changing the loop filter gain is quite simple. The paper describes the new scheme and gives simulation results when the scheme is applied to a 16 QAM system. The simulation results show that the timing jitter is much smaller than when a constant loop filter gain is used.
Prenatal murine skeletogenesis partially recovers from absent skeletal muscle as development progresses (2022)

Abstract Skeletal muscle contractions are critical for normal growth and morphogenesis of the skeleton, but it is unclear how the detrimental effects of absent muscle on the bones and joints change over time. Joint size, shape and cavitation, and rudiment length and mineralisation were assessed in multiple rudiments at two developmental stages (Theiler Stage (TS)24 and TS27) in the splotch-delayed “muscleless limb” mouse model and littermate controls. As development progressed, the effects of absent muscle on all parameters except for cavitation become less severe. All major joints in muscleless limbs were qualitatively and quantitatively abnormal in shape at TS24, while, by TS27, most muscleless joint shapes were normal, or nearly normal. In contrast, any joints which were fused at TS24 did not cavitate by TS27. Therefore, recovery in joint shape over development occurred despite absent cavitation. Mineralisation showed the most pronounced changes between TS24 and TS27 in the muscleless limbs. At TS24, all muscleless rudiments studied had less mineralisation than the controls, while at TS27, muscleless limb rudiments had either the same or significantly more mineralisation than controls of the same age. We conclude that the effects of absent muscle on prenatal murine skeletogenesis are most pronounced in early skeletal development and reduce in severity prior to birth. Understanding how mammalian bones and joints continue to develop in an environment without muscle contractions, but with mechanical stimulation due to the movement of the mother, provides important insights into conditions affecting human babies such as developmental dysplasia of the hip and arthrogryposis.
Metrics Development for Minimal Invasive Unilateral Laminotomy for Bilateral Decompression of Lumbar Spinal Stenosis With and Without Spondylolisthesis by an International Expert Panel (2020)

Surgical procedures can be broken down into elemental tasks necessary for the safe and effective completion of a reference approach to a specified surgical procedure. Spinal experts from 16 countries reached consensus on performance metrics for the procedure. This metric-based characterization can be used in a training curriculum and also for assessment of training and performance in clinical practice.
Layer Stack Design of High Density Read-Only-Memory Discs for Near-Field Systems using a Solid Immersion Lens (2009)

For high numerical aperture (NA) near-field systems using a solid immersion lens, layer stack types of first-surface read-only-memory (ROM) discs have been investigated. Complicated interactions of high-NA incident and diffracted waves with surface waves occur in multilayer-stacked subwavelength structures on the discs. Therefore, vector diffraction simulation in consideration of these effects is indispensable for the optimization of the disc structures. We used rigorous coupled wave analysis to numerically calculate readout signals from the discs. On the basis of the simulation results, we actually fabricated high-density ROM media. Consequently, a significantly low jitter of 6.8% was obtained for 100 Gbyte ROM media with a designed structure in an NA 2.0 system.
Hybrid graphene nanoribbon-nanopore devices for biomolecule detection and DNA sequencing (2014)

We present a study of hybrid graphene nanoribbons-nanopore devices [1] for biomolecule detection and ultimately DNA sequencing. When a graphene nanoribbon is constricted to nm sizes, the variation of the potential created by the different bases of the DNA strand passing through the adjacent nanopore will create a variation of the ribbon conductivity, enabling an electrical discrimination between DNA bases. We realized devices (Figure 1) comprised of nanopores with diameters in the range of 2−10 nm at the edge or in the center of graphene nanoribbons (GNRs), with widths between 5nm and 200 nm, on 40 nm thick silicon nitride (SiNx) membranes. We discuss the challenges encountered in the manufacturing of these nanoconstrictions (by lithograph or by electron beam sculpting) and the irradiation effects of the electron beam during the nanopore formation. GNR conductance is monitored in situ during electron irradiation-induced nanopore formation inside a transmission electron microscope (TEM) operating at 200 kV. We identify and study a linear and a supralinear regime for the increase of GNR resistance with the electron dose(Figure 2a), and correlate with the decrease by a factor of ten or more in mobility(Figure 3b) when GNRs are imaged at relatively high magnification with a broad beam prior to making a nanopore. Based on our findings we devise a scanning TEM procedure in which the position of the converged electron beam can be controlled with high spatial precision via automated feedback and we are able to quantify GNR electron induced damage (Figure 2b). This method minimizes the exposure of the GNRs to the beam before and during nanopore formation. A statistic of the resistances of the GNR-NP devices obtained by the TEM and STEM method(Figure 3a) shows that the TEM method severely damage the ribbons (increase in resistance on average 15 times), while the resistance of the STEM drilled ribbons remains virtually unchanged during the process. The resulting STEM GNRs can sustain microampere currents at low voltages (∼50 mV) in buffered electrolyte solution and exhibit high sensitivity and mobility, similar to pristine GNRs without nanopores(figure 3b). We finally present the operation of this sensor for biomolecule detection and DNA sequencing, correlating the electric signal measured in the GNR to the ionic current measured through the nanopore. The higher current(~uA) which can be driven through a GNR compared to the ionic current(~nA)[2] enable us to obtain a hundredfold increase in the measuring speed, making possible DNA sequencing without slowing the molecules, for a projected 10 minutes gull genome sequencing.
Staphylococcal Disease in Africa: Another Neglected ‘Tropical‘ Disease (2012)

The term 'neglected tropical diseases' predominantly refers to single-entity, mostly parasitic diseases. However, a considerable morbidity and mortality burden is carried by patients infected with Gram-positive cocci and Gram-negative bacilli that are prevalent all over the world, yet have impact in tropical and developing countries, particularly in children, with much higher incidence rates than those reported from developed countries. Staphylococcus aureus is among these pathogens. The African-German StaphNet consortium uses microbiological characterization of African S. aureus isolates, including identification of virulence factors, alongside the gathering of epidemiological and clinical data in an innovative research network between a European country (Germany) and several African partners. By creating an accessible strain repository and by implementing personnel training and capacity building, this network aims to put staphylococcal disease on the international agenda as a truly neglected condition with a major global impact on public health.
Impact of transition on quality of life in patients with congenital adrenal hyperplasia diagnosed during childhood (2017)

Regular medical follow-up in adulthood is associated with the transition between pediatric and adult care and with better QoL in adults with CAH.
Valorization of Aloe barbadensis Miller. (Aloe vera) Processing Waste (2022)

Aloe vera plant is known worldwide for its medicinal properties and application in gel-based products such as shampoo, soap, and sunscreen. However, the demand for these gel-based products has led to a surplus production of Aloe vera processing waste. An Aloe vera gel processing facility could generate up to 4000 kg of Aloe vera waste per month. Currently the Aloe vera waste is being disposed to the landfill or used as fertilizer. A sustainable management system for the Aloe vera processing waste should be considered, due to the negative societal and environmental impacts of the currents waste disposal methods. Therefore, this review focuses on various approaches that can be used to valorize Aloe vera waste into value-added products, such as animal and aquaculture feeds, biosorbents, biofuel and natural polymers. Researchers have reported Aloe vera waste for environmental applications biosorbents used for wastewater treatment of various pollutants. Several studies have also reported on the valorization of Aloe vera waste for production of biofuels such as bioethanol, mixed alcohol fuels, biogas and syngas. Aloe vera waste could also be valorized through isolation and synthesis of natural polymers for application in wound dressing, tissue engineering and drug delivery systems. Aloe vera waste valorization was also reviewed through extraction of value-added bioactive compounds such as aloe-emodin, aloin and aloeresin. These value-added bioactive compounds have various applications in the cosmetics (non-steroidal anti-inflammatory, tyrosinase inhibitors) and pharmaceutical (anticancer agent and COVID 19 inhibitors) industry.
NeuralPower: Predict and Deploy Energy-Efficient Convolutional Neural Networks (2017)

How much energy is consumed for an inference made by a convolutional neural network (CNN)? With the increased popularity of CNNs deployed on the wide-spectrum of platforms (from mobile devices to workstations), the answer to this question has drawn significant attention. From lengthening battery life of mobile devices to reducing the energy bill of a datacenter, it is important to understand the energy efficiency of CNNs during serving for making an inference, before actually training the model. In this work, we propose NeuralPower: a layer-wise predictive framework based on sparse polynomial regression, for predicting the serving energy consumption of a CNN deployed on any GPU platform. Given the architecture of a CNN, NeuralPower provides an accurate prediction and breakdown for power and runtime across all layers in the whole network, helping machine learners quickly identify the power, runtime, or energy bottlenecks. We also propose the energy-precision ratio (EPR) metric to guide machine learners in selecting an energy-efficient CNN architecture that better trades off the energy consumption and prediction accuracy. The experimental results show that the prediction accuracy of the proposed NeuralPower outperforms the best published model to date, yielding an improvement in accuracy of up to 68.5%. We also assess the accuracy of predictions at the network level, by predicting the runtime, power, and energy of state-of-the-art CNN architectures, achieving an average accuracy of 88.24% in runtime, 88.34% in power, and 97.21% in energy. We comprehensively corroborate the effectiveness of NeuralPower as a powerful framework for machine learners by testing it on different GPU platforms and Deep Learning software tools.