gebhart/patrepeval huggingface dataset:
Modeling Infectious Diseases in Mice with a “Humanized” Immune System (2020)

Immunocompetent mice harbor several layers of immune defense that can promote rejection of cell and tissue xenografts; these include innate mechanisms (mediated by complement, macrophage, and neutrophils) as well as adaptive immune responses (T cell-mediated and antibody-mediated rejection). In addition, resident tissues in the mouse harbor self-renewing stem cells and their differentiated progeny, which can effectively compete with human cells for endogenous tissue resources (physical space, nutrients, growth factors, etc.) that may play a role in sustaining human xenografts. As such, the development of “humanized” mouse models (human immune system [HIS] mice) is closely associated with the history of mutant mouse strains that harbor defects in hematopoietic system development and function. In recent decades, knowledge of the molecular mechanisms that regulate innate and adaptive immunity has led to the development of mouse models with an ever-increasing capacity to engraft human cells and tissues (reviewed in references 1–4). With respect to engraftment of the human hematopoietic system, as the severity of the immune deficiency in the mouse host has increased, the efficiency and durability of human hematopoietic cell “take” have improved remarkably, and importantly, a diverse compartment comprising many unique human immune subsets (including not only lymphocytes but also myeloid cells) has been achieved (Fig. 1).
Development of wood-burning rocket cookstove with forced air-injection (2021)

Nearly 40% of the world's population still relies on biomass stoves as their primary cooking source. Indoor cooking with biomass stoves produces harmful emissions such as fine particulate matter (PM2.5) and can result in significant cardiovascular and respiratory disease. Air injection technology, in the forms of over-fire, under-fire, and staged (a combination of under- and over-fire), has been used for decades to reduce emissions in small-scale industrial biomass burners. Recently, researchers have begun integrating air-injection into biomass cookstoves, but the number of studies is limited, and improper air-injection can result in worsening stove performance. In this paper, we develop and analyze three wood-burning biomass rocket stove air-injection strategies using computational fluid dynamics and experiments. We consider over-fire and under-fire air-injection independently, and then develop a staged air-injection system that combines the optimal jet characteristics from the purely over-fire and under-fire systems. Results show that significant performance gains, both in terms of reduced emissions and increased burn-rate are achievable with forced air-injection. For a radial over-fire air injection system, jet momentum flux is found to control fuel and air mixing and is the driving metric for reducing particulate emissions. For the under-fire system, excess air ratio was found to control both the emissions rate and firepower. In a comparison of all three air-injection strategies, over-fire air injection was found to have the largest reduction in emissions, under-fire air injection had the largest increase in firepower and reduction in boiling times, and the staged air injection method achieved both improved emissions and burn-rate. Additionally, the combustion start-up phase was observed to account for the majority of emissions in all forced-draft stoves, and is most sensitive to under-fire injection, remaining an area ripe for improvement.
Boosted Convolutional Neural Networks (2016)

In this work, we propose a new algorithm for boosting Deep Convolutional Neural Networks (BoostCNN) to combine the merits of boosting and these networks. To learn this new model, we propose a novel algorithm to incorporate boosting weights into the deep learning architecture based on least square objective function. We also show that it is possible to use networks of different structures within the proposed boosting framework and BoostCNN is able to select the best network structure in each iteration. This not only results in superior performance but also reduces the required manual effort for finding the right network structure. Experiments show that the proposed method is able to achieve state-of-the-art performance on several fine-grained classification tasks such as bird, car, and aircraft classification.
Two-Dimensionalπ-Conjugated Covalent-Organic Frameworks as Quantum Anomalous Hall Topological Insulators (2016)

The quantum anomalous Hall (QAH) insulator is a novel topological state of matter characterized by a nonzero quantized Hall conductivity without an external magnetic field. Using first-principles calculations, we predict the QAH state in monolayers of covalent-organic frameworks based on the newly synthesized X_{3}(C_{18}H_{12}N_{6})_{2} structure where X represents 5d transition metal elements Ta, Re, and Ir. The π conjugation between X d_{xz} and d_{yz} orbitals, mediated by N p_{z} and C p_{z} orbitals, gives rise to a massive Dirac spectrum in momentum space with a band gap of up to 24 meV due to strong spin-orbit coupling. We show that the QAH state can appear by chemically engineering the exchange field and the Fermi level in the monolayer structure, resulting in nonzero Chern numbers. Our results suggest a reliable pathway toward the realization of a QAH phase at temperatures between 100 K and room temperature in covalent-organic frameworks.
Diphenylphosphinoyl-mediated synthesis of ketones (2006)

alpha-Diphenylphosphinoyl ketones are selectively and sequentially alkylated at the alpha-position. Double lithiation and selective alkylation occurs at the less stabilised gamma-position. Dephosphinoylation of the alkylation products gives ketones. Mono-alkylation is selective, highly crystalline intermediates are formed and a one-pot strategy is possible. The method is ideally suited for the preparation of acid-sensitive ketones.
Current State of the Opioid Epidemic as it Pertains to Pediatric Orthopaedics From the Advocacy Committee of the Pediatric Orthopaedic Society of North America (2018)

The magnitude of this problem is overwhelming. Education of care providers, patients and families, standardization of narcotic prescribing practices which incorporate patient characteristics, and appropriate plans for disposal of unused narcotics are immediate concepts to consider in correcting this problem. Long-term issues to tackle will be changing patient a family expectations, legislation, and obtaining additional resources directed towards this issue.
Computer Vision Techniques for Inspection of Pipes (2000)

Closed Circuit Television (CCTV) surveys are used widely in North America to assess the structural integrity of underground pipes. The video images are examined visually, and classified into grades according to degrees of damage. The human eye is extremely effective at recognition and classification, but it is not suitable for assessing pipe defects in thousands of miles of pipeline images due to fatigue, subjectivity, time and cost. The paper presents a system for the application of computer vision techniques to the automatic assessment of the structural condition of underground pipes from scanned images. Automatic recognition of various pipe defects is of considerable interest since it solves problems of fatigue, subjectivity, and ambiguity, leading to economic benefits. The proposed system could overcome many of the limitations of the current CCTV surveys, and can provide a more accurate assessment of underground pipe conditions.
Frontostriatal and Dopamine Markers of Individual Differences in Reinforcement Learning: A Multi-modal Investigation (2017)

Prior studies have shown that dopamine (DA) functioning in frontostriatal circuits supports reinforcement learning (RL), as phasic DA activity in ventral striatum signals unexpected reward and may drive coordinated activity of striatal and orbitofrontal regions that support updating of action plans. However, the nature of DA functioning in RL is complex, in particular regarding the role of DA clearance in RL behavior. Here, in a multi-modal neuroimaging study with healthy adults, we took an individual differences approach to the examination of RL behavior and DA clearance mechanisms in frontostriatal learning networks. We predicted that better RL would be associated with decreased striatal DA transporter (DAT) availability and increased intrinsic functional connectivity among DA-rich frontostriatal regions. In support of these predictions, individual differences in RL behavior were related to DAT binding potential in ventral striatum and resting-state functional connectivity between ventral striatum and orbitofrontal cortex. Critically, DAT binding potential had an indirect effect on reinforcement learning behavior through frontostriatal connectivity, suggesting potential causal relationships across levels of neurocognitive functioning. These data suggest that individual differences in DA clearance and frontostriatal coordination may serve as markers for RL, and suggest directions for research on psychopathologies characterized by altered RL.
"Predictive Model for Permeability Reduction by Small Wetting Phase Saturations" (2006)

Field experience in unconventional gas reservoirs indicates that well deliverability can vary dramatically, even between closely spaced wells. A possible explanation lies in laboratory experiments which show that a small increase in water saturation can decrease the gas phase permeability significantly. Conversely, drying out the water saturation during gas cycling in reservoirs or during injection of CO2 into deep saline aquifers affects petrophysical properties such as absolute permeability and capillary pressure. The precipitation of salts from the evaporating brine is one contributor to these effects. In this paper we quantify the effect of small saturations of the wetting phase on nonwetting phase relative permeability. We also show how certain porosity-reducing processes magnify this effect. To compute phase geometry and permeability we use a physically representative network model. The network is extracted from a model rock, built from a dense random packing of spheres modified geometrically to simulate various rock-forming processes. At small saturations (near the drainage endpoint) the wetting phase exists largely in the form of pendular rings held at grain contacts. Pore throats correspond to the constriction between groups of three grains, each pair of which can be in contact. Thus the existence of these pendular rings decreases the void area available for flowing non-wetting phase. Because the hydraulic conductance of the throat varies with the square of the void area, the effect on permeability is disproportionate to the volume occupied by the rings. The same approach quantifies the reduction in permeability by salt precipitation during drying. Convention holds that connate water has little effect on oil or gas permeability because it occupies the smaller pores. Comparing predictions for unconsolidated model rocks with those for cemented model rocks allows one to reconcile this view with the sensitivity reported in the field and the laboratory. We validate the model against experiments, and show that models that do not explicitly account for the phase geometry, such as the Kozeny-Carman equation, cannot capture the observed behavior.
Peripheral arterial disease in diabetes—a review (2009)

Diabetic patients are at high risk for peripheral arterial disease (PAD) characterized by symptoms of intermittent claudication or critical limb ischaemia. Given the inconsistencies of clinical findings in the diagnosis of PAD in the diabetic patient, measurement of ankle-brachial pressure index (ABI) has emerged as the relatively simple, non-invasive and inexpensive diagnostic tool of choice. An ABI < 0.9 is not only diagnostic of PAD even in the asymptomatic patient, but is also an independent marker of increased morbidity and mortality from cardiovascular diseases. With better understanding of the process of atherosclerosis, avenues for treatment have increased. Modification of lifestyle and effective management of the established risk factors such as smoking, dyslipidaemia, hyperglycaemia and hypertension retard the progression of the disease and reduce cardiovascular events in these patients. Newer risk factors such as insulin resistance, hyperfibrinogenaemia, hyperhomocysteinaemia and low-grade inflammation have been identified, but the advantages of modifying them in patients with PAD are yet to be proven. Therapeutic angiogenesis, on the other hand, represents a promising therapeutic adjunct in the management of PAD in these patients. Outcomes after revascularization procedures, such as percutaneous transluminal angioplasty and surgical bypasses in diabetic patients, are poorer, with increased perioperative morbidity and mortality compared with that in non-diabetic patients. Amputation rates are higher due to the distal nature of the disease. Efforts towards increasing awareness and intensive treatment of the risk factors will help to reduce morbidity and mortality in diabetic patients with PAD.
Multiwalled carbon nanotubes for stray light suppression in space flight instruments (2010)

Observations of the Earth are extremely challenging; its large angular extent floods scientific instruments with high flux within and adjacent to the desired field of view. This bright light diffracts from instrument structures, rattles around and invariably contaminates measurements. Astrophysical observations also are impacted by stray light that obscures very dim objects and degrades signal to noise in spectroscopic measurements. Stray light is controlled by utilizing low reflectance structural surface treatments and by using baffles and stops to limit this background noise. In 2007 GSFC researchers discovered that Multiwalled Carbon Nanotubes (MWCNTs) are exceptionally good absorbers, with potential to provide order-of-magnitude improvement over current surface treatments and a resulting factor of 10,000 reduction in stray light when applied to an entire optical train. Development of this technology will provide numerous benefits including: a.) simplification of instrument stray light controls to achieve equivalent performance, b.) increasing observational efficiencies by recovering currently unusable scenes in high contrast regions, and c.) enabling low-noise observations that are beyond current capabilities. Our objective was to develop and apply MWCNTs to instrument components to realize these benefits. We have addressed the technical challenges to advance the technology by tuning the MWCNT geometry using a variety of methods to provide a factor of 10 improvement over current surface treatments used in space flight hardware. Techniques are being developed to apply the optimized geometry to typical instrument components such as spiders, baffles and tubes. Application of the nanostructures to alternate materials (or by contact transfer) is also being investigated. In addition, candidate geometries have been tested and optimized for robustness to survive integration, testing, launch and operations associated with space flight hardware. The benefits of this technology extend to space science where observations of extremely dim objects require suppression of stray light.
Functional Characterization of FTDP-17 tau Gene Mutations through Their Effects on Xenopus Oocyte Maturation (2002)

tau gene mutations cause frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17). Here we have used Xenopus oocyte maturation as an indicator of microtubule function. We show that wild-type four-repeat Tau protein inhibits maturation in a concentration-dependent manner, whereas three-repeat Tau has no effect. Of the seven four-repeat Tau proteins with FTDP-17 mutations tested, five (G272V, DeltaK280, P301L, P301S, and V337M) failed to interfere significantly with oocyte maturation, demonstrating a greatly reduced ability to interact with microtubules. One mutant protein (R406W) almost behaved like wild-type Tau, and one (S305N) inhibited maturation more strongly than wild-type Tau. With the exception of R406W, wild-type Tau and all the mutants studied were similarly phosphorylated during the Xenopus oocyte maturation, and this was independent of their effects on this process. Data obtained with R406W and S305N may be related to charge changes (phosphorylation and basic amino acids). Our results demonstrate variable effects of FTDP-17 mutations on microtubules in an intact cell situation. Those findings establish Xenopus oocyte maturation as a system allowing the study of the functional effects of tau gene mutations in a quantitative manner.
Differences in Gene Transcriptomic Pattern of Plasmodium falciparum in Children with Cerebral Malaria and Asymptomatic Carriers (2014)

The mechanisms underlying the heterogeneity of clinical malaria remain largely unknown. We hypothesized that differential gene expression contributes to phenotypic variation of parasites which results in a specific interaction with the host, leading to different clinical features of malaria. In this study, we analyzed the transcriptomes of isolates obtained from asymptomatic carriers and patients with uncomplicated or cerebral malaria. We also investigated the transcriptomes of 3D7 clone and 3D7-Lib that expresses severe malaria associated-variant surface antigen. Our findings revealed a specific up-regulation of genes involved in pathogenesis, adhesion to host cell, and erythrocyte aggregation in parasites from patients with cerebral malaria and 3D7-Lib, compared to parasites from asymptomatic carriers and 3D7, respectively. However, we did not find any significant difference between the transcriptomes of parasites from cerebral malaria and uncomplicated malaria, suggesting similar transcriptomic pattern in these two parasite populations. The difference between isolates from asymptomatic children and cerebral malaria concerned genes coding for exported proteins, Maurer's cleft proteins, transcriptional factor proteins, proteins implicated in protein transport, as well as Plasmodium conserved and hypothetical proteins. Interestingly, UPs A1, A2, A3 and UPs B1 of var genes were predominantly found in cerebral malaria-associated isolates and those containing architectural domains of DC4, DC5, DC13 and their neighboring rif genes in 3D7-lib. Therefore, more investigations are needed to analyze the effective role of these genes during malaria infection to provide with new knowledge on malaria pathology. In addition, concomitant regulation of genes within the chromosomal neighborhood suggests a common mechanism of gene regulation in P. falciparum.
Navigation in total-knee arthroplastyCT-based implantation compared with the conventional technique (2004)

Background Exact axial limb alignment in total-knee arthroplasty (TKA) is important for a successful outcome. We evaluated the efficiency of computer-assisted implantation in TKA and compared it with the classical surgeon-controlled technique. Patients and methods We implanted 100 TKA using either the computer-assisted technique (50) or the conventional approach (50). There were no significant differences between the groups regarding the preoperative leg deformity. Accuracy of implantation was determined in postoperative long-leg coronal and lateral radiographs. Results A postoperative leg axis between 3 degrees varus and 3 degrees valgus was achieved in 46 patients in the group with computer-assisted implantation and 36 patients in the control group (p=0.01). A significant difference was also seen for the femoral component alignment in frontal plane. No complications influencing the clinical outcome were observed. Interpretation A CT-based navigation system improves the accuracy of TKA, but higher costs and time-consuming planning will mean that its usage is limited to special cases. Additional tools such as ligament balancing, which are presently only available with the CT-free software module, require to be added to the CT-based system.
Characterisation of thermally treated and untreated polyethylene–polypropylene blends using DSC, TGA and IR techniques (2009)

The thermal characteristics of thermally treated and untreated very low density polyethylene, isotactic polypropylene and their blends were investigated. Injection moulded blends containing five different weight percentages of VLDPE/iPP were prepared and thermally treated at 100°C for 2, 4, 7 and 14 days. Differential scanning calorimetry, thermogravimetry and infrared spectral analysis techniques were used to study the effect of thermal treatment and blending ratio on the thermal and chemical stability. The addition of PE had caused the T m, heat of fusion and percentage crystallinity of PP main melting peak to decrease, indicating that both polymers are partially miscible. T m has been found to increase with aging time, however, the heat of fusion is not significantly affected. The initial and final decomposition temperatures, maximum decomposition rate temperature, order of decomposition reaction, activation energy and activation enthalpy were calculated, in a dynamic nitrogen atmosphere, and discussed in terms of blending ratios and aging times. The IR spectra of all blends at different aging times do not show any degradation products.
Fatigue Behavior in Filled Natural Rubber: Study of the Mechanical Damage Dynamics (2011)

Rupture dynamics in reinforced elastomers is a much more complex process than in pure elastomers due to the intrinsic heterogeneous mixture of a rubber matrix with filler particles at submicronic scale. In the case of natural rubber, an additional source of heterogeneity is the strain-crystallization effect. How rupture dynamics and crack path are affected by filler particles and strain-crystallization is still a matter of debate. Actually, understanding how rupture dynamics and crack path are correlated to each other is probably an important key in order to improve long time resistance of reinforced rubbers.
Electronic structure, photoemission, and magnetism inGd2Co andEr2Co glasses (1987)

The electronic and magnetic structures of amorphous ${\mathrm{Gd}}_{2}$Co and ${\mathrm{Er}}_{2}$Co are studied by ultraviolet and x-ray photoemission measurements and band calculations. The spectra for both glasses show a band of Co 3d levels centered at a binding energy ${E}_{B}$ of about -1.0 eV and peaks arising from 4f levels at ${E}_{B}$=-8.4 eV and ${E}_{B}$apeq2-5--9 eV for Gd and Er, respectively. Magnetization data have shown that a-${\mathrm{Gd}}_{2}$Co possesses a ferrimagnetic structure with a small Co moment. The linear-muffin-tin-orbital method is used to perform self-consistent, spin-polarized calculations in the semirelativistic approximation for ${\mathrm{Gd}}_{2}$Co. Because of the complexity of the glassy structure, the calculations are performed for body-centered-tetragonal and cubic fluorite structures, and the sensitivity to local environment effects studied. The calculations are in a good overall agreement with the photoemission and magnetic-moment results.
Circulating Levels of FGF-21 in Obese Youth: Associations With Liver Fat Content and Markers of Liver Damage (2013)

Plasma FGF-21 levels are increased in obese adolescents, particularly in those with fatty liver. FGF-21 concentrations significantly and independently correlate with hepatic fat content and markers of hepatic apoptosis in obese youths.