gebhart/patrepeval huggingface dataset:
Novel Functions for a Fibrinolytic Pathway in Controlling the Stem Cell Niche. (2006)

Abstract Hematopoietic stem cells (HSCs) reside within specific niches, where they are maintained by self-renewal and can be mobilized into circulation, but the underlying mechanisms are still unknown. The hematopoietic niche comprises of a local network of stromal cells (like fibroblasts, endothelial cells), accessory cells (T lymphocytes, monocytes), their products (extracellular matrix (ECM) and cytokines, capable of influencing self-renewal, proliferation and differentiation of HSCs. One such ECM molecule is fibrin, which can be found along surfaces in the bone marrow. Its precursor fibrinogen can maintain hematopoiesis in long-term bone marrow liquid cultures and increase the colony size of bone marrow cells cultured in semisolid medium containing serum. Plasmin, a serine protease, proteolytically degrades fibrin and fibrinogen. Plasminogen (Plg), its inactive proenzyme is present in the plasma, interstitial fluid or adherent to ECM proteins and can be activated by tissue-type plasminogen activator (tPA), urokinase-type plasminogen activator (uPA) and other serine proteasesWe demonstrated previously that matrix metalloproteinase-9 (MMP-9) controls stem cell recruitment from the bone marrow niche. During fibrinolysis plasmin participates in the consecutive activation of MMPs. We initially wished to determine if this fibrinolytic cascade might be involved in regulating the stem cell niche. In this study we provide novel mechanistic data demonstrating that classical fibrinolytic factors-Plg/Plasmin are involved in recruitment of HSCs into the cell cycle following myelosuppression and their mobilization from the BM niche influencing cell differentiation, proliferation and migration by activating niche cells to secrete typical niche factors, including Kit-ligand and stromal cell-derived factor-1 (SDF-1, CXCL12). Deletion of Plg in mice prevented hematopoietic stem cells from entering the cell cycle and undergoing differentiation after myelosuppression, leading to the death of the mice. By Plg-dependent and Plg-independent pathways, tissue-type plasminogen activator activated matrix metalloproteinases and released Kit ligand and stromal cell-derived factor-1 from niche cells, thereby promoting stem cell recruitment and proliferation. We conclude that the fibrinolytic cascade plays a critical role in controlling the exit from the stem cell niche and that this represents a general stem cell regulatory axis.
A pathogen effector FOLD diversified in symbiotic fungi (2022)

Abstract Pathogenic fungi use secreted effector proteins to suppress immunity and support their infection, but effectors have also been reported from fungi that engage in nutritional symbioses with plants. Sequence based effector comparisons between pathogens and symbiotic arbuscular mycorrhizal (AM) fungi are hampered by the huge diversity of effector sequences even within closely related microbes. Here we used a systematic protein structure modelling approach to classify the secretome of the AM fungus Rhizophagus irregularis . We identified secreted proteins with high structural similarity to Fusarium oxysporum f. sp. lycopersici dual domain (FOLD) effectors, which occur in low numbers in fungal pathogen genomes. Contrastingly, genes encoding FOLD proteins from AM fungi (MycFOLDs) are found in enlarged and diversified gene families. Our structure-model comparison suggests that MycFOLDs are similar to carbohydrate binding motifs. Different MycFOLD genes are expressed during colonisation of different hosts and MycFOLD-17 transcripts accumulate in plant intracellular arbuscules. The exclusive presence of MycFOLDs across unrelated plant-colonising fungi, their inducible expression, lineage specific sequence diversification, and transcripts in arbuscules support the hypothesis that FOLD proteins act as effectors during plant colonisation by symbiotic and pathogenic fungi.
Bioactive Nutrient Fortified Fertilizer: A Novel Hybrid Approach for the Enrichment of Wheat Grains With Zinc (2021)

Zinc (Zn) is a critical micronutrient that synergizes nutrient use efficiency, and improves plant growth and human health. Low Zn bioavailability in soils affects produce quality and agricultural productivity worldwide ultimately inducing deficiency in humans and animals. Zn deficiency is a leading cause of malnutrition in underdeveloped countries where a widespread population depends upon staple cereals for daily intake of calories. Modern cereal cultivars are inherently low in Zn, eventually, plants need to be enriched with soil application of ZnSO<sub>4</sub>, but due to higher fixation losses, it becomes an inefficient source. Rhizosphere microbiome contains Zn-solubilizing bacteria (ZSB) that improve Zn bioavailability, thus increase the root function, Zn uptake, and plant growth. Niha Corp developed a hybrid process of bioactive nutrient fortified fertilizer (BNFF), which has been used to formulate Zabardast Urea (ZU) by coating bioactive Zn (BAZ) and ZSB on urea. Data obtained for 15 wheat varieties from 119 farmer field demonstration plots and eight replicated trials on 42 locations across multi-environment conditions conclude that ZU significantly improved the plant biomass and yield by 12% over non-Zn control and produced grains with 57 μg/g Zn contents, which can meet a major part of the recommended dietary allowance (RDA) of humans. The study recommends that this microbe-mediated hybrid invention (ZU) is a feasible approach to boost Zn bioavailability and Zn use efficiency, with enhanced yield and quality that may contribute to improve human health. To the best of our knowledge, this is the first wide-scale field testing of Zn enrichment in the grains of bread wheat using an innovative BNFF Urea Z technology.
ActiveMoCap: Optimized Viewpoint Selection for Active Human Motion Capture (2019)

The accuracy of monocular 3D human pose estimation depends on the viewpoint from which the image is captured. While freely moving cameras, such as on drones, provide control over this viewpoint, automatically positioning them at the location which will yield the highest accuracy remains an open problem. This is the problem that we address in this paper. Specifically, given a short video sequence, we introduce an algorithm that predicts which viewpoints should be chosen to capture future frames so as to maximize 3D human pose estimation accuracy. The key idea underlying our approach is a method to estimate the uncertainty of the 3D body pose estimates. We integrate several sources of uncertainty, originating from deep learning based regressors and temporal smoothness. Our motion planner yields improved 3D body pose estimates and outperforms or matches existing ones that are based on person following and orbiting.
Integration of porous low-kdielectrics using post porosity pore protection (2016)

Post porosity pore protection is studied as a means for low damage integration of porous low-k dielectrics. Homogeneous low-k densification is achieved using poly(methyl methacrylate) (PMMA) as a sacrificial filler. The improvement in plasma-induced damage is investigated on a plasma-enhanced chemical vapor deposition 2.0 porous organo-silicate glass, including damage from radicals and vacuum ultraviolet photons. Open pores are sealed upon polymer protection; therefore the penetration of metal species during deposition of a metal diffusion barrier is avoided. Various solutions for post metallization polymer removal are investigated, such as hydrogen remote plasma and an ultraviolet cure. The PMMA removal process is studied in order to avoid Cu wire degradation. Finally, low-k damage and barrier continuity are investigated on patterned wafers with functional circuits. By means of transmission electron microscopy inspection and electrical measurement, effective integrated k-values are extracted, giving a value k eff ~ 2.5–2.6 for the post metallization polymer removal option.
SuperSpec: development towards a full-scale filter bank (2016)

SuperSpec is a new spectrometer-on-a-chip technology for submm/mm-wave spectroscopy. SuperSpec stands out from other direct-detection submm spectrometer technologies in that the detectors are coupled to a series of resonant filters along a single microwave feedline instead of using dispersive optics. SuperSpec makes use of kinetic inductance detectors (KIDs) to detect radiation in this filter bank. The small profile of this design makes SuperSpec a natural choice to produce a multi-object spectrometer for tomographic mapping or galaxy redshift surveys. We have recently fabricated a device that is a 50 channel subset of a full 280 channel filter bank, which would cover the 190 - 310 GHz range at R = 275. Analysis of the data from this device informs us of the potential design modifications to enable a high-yield background-limited SuperSpec spectrometer. The results indicate that this subset filter bank can scale up to a full filter bank with only a few collisions in readout space and less than 20% variation in responsivity for the detectors. Additionally, the characterization of this and other prototype devices suggests that the noise performance is limited by generation-recombination noise. Finally, we find that the detectors are sufficiently sensitive for ground-based spectroscopy at R = 100, appropriate for tomographic mapping experiments. Further modifications are required to reach the background limit for R = 400, ideal for spectroscopy of individual galaxies.
Atrial fibrillation following autologous stem cell transplantation in patients with multiple myeloma: incidence and risk factors (2012)

AF is very frequent in patients with multiple myeloma when they receive ASCT. The presence of abnormal renal function, left ventricular systolic dysfunction, dilated left atrium, or hypertension at baseline identifies patients at high risk of developing AF following ASCT.
Poly(3-hexylthiophene)−CdSe Quantum Dot Bulk Heterojunction Solar Cells: Influence of the Functional End-Group of the Polymer (2009)

The synthesis of H/thiol terminated P3HT from Br/allyl-terminated P3HT precursor was analyzed. The photovoltaic response of blends were prepared of H/thiol terminated P3HT with spherical CdSe quantum dots(QD) and compares the results with regioregular H/Br and Br/aryl-terminated P3HT. Phase segregation was carried by mixing relatively polar pyridine treated CdSe QD with nonpolar P3HT. The experiment revealed that a high loading of CdSe is necessary for an efficient charge transport and different loading ratios of CdSe has been investigated to correlate the photovoltaic response as a function of ration between donor H/thiol-P3ht polymer and acceptor Cdse QD. The results show that H/Br-P3HT, H/thiol- and Br/allyl-terminated P3HT exhibits better performance and Cdse quantum dots were used to obtain results.
Full Utilization of Lithium Trivandate (Li1.1V3O8) in Thick Porous Electrodes with High Rate Capacity upon Extended Cycling Elucidated Via Operando Energy Dispersive X-Ray Diffraction (2021)

Newer, more demanding energy storage systems require high energy density along with high power and fast charge rates. Conventional battery electrode fabrication techniques are often limited by how much active material they can hold in the case of slurry-cast electrodes and how much of the electrode can be utilized in the case of dense pelletized electrodes. Thick porous electrode fabrication techniques have been developed as a way to obtain a higher active mass loading and an architecture which enables ionic and electronic transport. The homogeneity of the phase distribution of lithiated LVO in thick (∼500 μm) porous electrodes (TPEs) designed to facilitate both ion and electron transport was determined using synchrotron-based operando energy dispersive X-ray diffraction (EDXRD). Probing 3 positions in the TPE while cycling at a fast rate of 1C revealed a homogeneous phase transition across the thickness of the electrode at the 1 st and 95 th cycles. Continuum modelling indicated homogenous lithiation across the electrode upon discharge at 1C consistent with the EDXRD results and ascribed decreasing accessible active material to be the cause of loss in delivered capacity between the 1 st and 95 th cycles. The model was supported by the observation of significant particle fracture by SEM consistent with loss of electrical contact. The absence of the beta phase peaks in the EDXRD over extended cycling are consistent with electrochemical accessibility of only part of the active material. Overall, the combination of operando EDXRD, continuum modeling, and ex situ measurements enabled a deeper understanding of lithium vanadium oxide transport properties under high rate extended cycling within a thick highly porous electrode architecture.
Use of reactive gases with broad-beam radio frequency ion sources for industrial applications (2004)

Broad-beam ion sources are used for a number of important industrial etching and deposition applications, and the use of inductively coupled plasmas has greatly increased the feasibility of using beams of reactive gases, especially of chlorine and oxygen, but also of CO, CO2, CF4, CHF3, SF6, etc. In order to gain more understanding of the factors that affect the composition of beams of these gases, we have used a Hiden energy-dispersive quadrupole mass spectrometer to analyze the flux of ions and energetic particles produced by an Oxford Instruments 15 cm rf ion source. For all of the above gases, we have analyzed the effects of changing the operating conditions on the composition of the ion beam, and the fractional production of multiply charged ions; on the plasma potential (and the consequential divergence of the ion beam) and on the spread in energy of the ion beam. We discuss how these factors influence the correct use of the ion source in etching applications with these gases. It is important that the design of the ion source should be optimized for the process gases that are used. The source was originally optimized for use on argon. We discuss the effect of the design on the source’s performance with the different gases, and we consider whether design changes would be appropriate for optimum performance on different gases.
Terahertz absorption in non-polar rotator crystals (2010)

We characterize the phase behavior of linear n-alkanes with n &gt; 22, using terahertz spectroscopy. We observe enhanced absorption in the quasi-ordered rotator phase, the first report of disorder-induced THz absorption in a rotator crystal.
Nanoarrays of Single Virus Particles (2005)

A mosaic pattern: Single virus particle nanoarrays can be made through the positioning and orientation of viral particles on nanotemplate surfaces generated by dip-pen nanolithography. Viral immobilization was characterized with antibody–virus recognition and infrared spectroscopy (an example array of particles is shown in the AFM image). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z501978_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Fabrication of micro pore arrays in free standing COC membranes and their application for in vitro barrier tissue models (2013)

This paper reports a low-cost fabrication method for mass production of free standing cyclic olefin copolymer (COC) membranes embedded with micro pore arrays. We show that the method creates suspended membranes with thickness of 2μm and micro pores having diameter ranging from 3-5μm. We integrated the membrane in a microfluidic system designed to mimic the endothelial barrier in bone marrow sinusoids. The device was tested with HUVEC and supported their attachment and proliferation on the membrane.
The Effects of Nitrous Oxide After Exposure During Middle and Late Gestation (1986)

Recent evidence has indicated that the anesthetic gas nitrous oxide (N2O) is teratogenic to rats if exposed during the organogenesis phase of gestation. Little is known, however, of the anatomical or functional consequences of exposures occurring later in gestation when the brain is developing. Timed pregnant Sprague-Dawley rats were exposed to 75% N2O/25% O2 using one of the following protocols: 24 hr exposures on gestational days 11-15 or 16-20; or 8 hr exposures on gestational days 9-13, 11-15, 14-15 or day 15 only. Both 24 hr exposure protocols significantly reduced fetal and maternal body weight, an effect not observed after the 8 hr exposures. No N2O exposure resulted in gross morphological or skeletal changes. Likewise, no significant effects on total protein and DNA levels in fetal liver and brain tissues could be found subsequent to 24 hr exposures on days 16-20; or on one, three or six days following an 8 hr exposure on day 15. Evaluations of postnatal growth and neurological development in pups prenatally exposed for 8 hr on days 14 and 15 revealed two noteworthy effects. Their rate of growth in body weight was greater with respect to controls between the ages of 14 and 21 days, especially in the males. Also, reflex suspension was reduced, significantly so in the females. In conclusion, unlike 24 hr exposures, multiple 8 hr exposures to nitrous oxide during the middle to late stages of gestation did not produce effects detectable with standard teratological measures. Subtle differences in growth rate and reflex suspension, however, indicated that normal development had been interrupted, but its clear distinction as a lasting effect requires additional measures of function.
Biosynthesis of Firefly Luciferin in Adult Lantern: Decarboxylation of ʟ-Cysteine is a Key Step for Benzothiazole Ring Formation in Firefly Luciferin Synthesis (2013)

We demonstrated for the first time that D- and L-firefly luciferins are biosynthesized in the lantern of the adult firefly from two L-cysteine molecules with p-benzoquinone/1,4-hydroquinone, accompanied by the decarboxylation of L-cysteine.
Probing Predictions on OOD Images via Nearest Categories (2020)

We study out-of-distribution (OOD) prediction behavior of neural networks when they classify images from unseen classes or corrupted images. To probe the OOD behavior, we introduce a new measure, nearest category generalization (NCG), where we compute the fraction of OOD inputs that are classified with the same label as their nearest neighbor in the training set. Our motivation stems from understanding the prediction patterns of adversarially robust networks, since previous work has identified unexpected consequences of training to be robust to norm-bounded perturbations. We find that robust networks have consistently higher NCG accuracy than natural training, even when the OOD data is much farther away than the robustness radius. This implies that the local regularization of robust training has a significant impact on the network's decision regions. We replicate our findings using many datasets, comparing new and existing training methods. Overall, adversarially robust networks resemble a nearest neighbor classifier when it comes to OOD data. Code available at https://github.com/yangarbiter/nearest-category-generalization.
Characteristics of the Interfacial Wave Velocity on the Liquid Film of Annular Flow for Gas-Oil-Water Three-Phase Flow in a Horizontal Pipe (2011)

The experiments were conducted in a horizontal multiphase flow test loop (50mm inner diameter, 40m long) and the cross-correlation technology was used for the study of the characteristics of the interfacial wave velocity about two types of annular flow regimes (AN║DO/W and AN║DW/O) for gas-oil-water three-phase flow. The results show that the interfacial wave velocity on the liquid film of AN║DO/W flow pattern and AN║DW/O flow pattern all increases with the increase of gas superficial velocity and liquid superficial velocity on the condition of fixed ratio of oil and water flow rates, but the difference is that the increase is a linear monotonic increase for AN║DO/W flow pattern and a non-linear increase for AN║DW/O flow pattern, and the liquid superficial velocity makes a larger contribution than the gas superficial velocity. The interfacial wave velocity also increases with the increase of input water cut in liquid at different gas superficial velocities under the conditions of liquid superficial velocity fixed.
Biological effects of conjugated linoleic acids supplementation (2012)

Conjugated linoleic acids (CLA) are a group of polyunsaturated fatty acids (PUFA) with a single pair of conjugated double bonds. The major natural CLA isomer is 18:2 cis-9, trans-11 (c9, t11) linoleic acid, or rumenic acid (RA). Chemically synthesized CLA is also available, mostly as a mixture of RA and 18:2 trans-10, cis-12 (t10, c12) isomers in equal amounts (50:50). Consumption of ruminant meat (beef and lamb) and dairy products (milk and cheese) is the main source of dietary exposure to CLA. Despite numerous studies on animal and human models (tumorigenesis, obesity, immune response) it has not been established whether additional supplementation of CLA is of benefit. Moreover, some studies, conducted both in animals and in humans, reveal that CLA isomers may induce insulin resistance. Presently, balanced diet rich in CLA from natural sources is recommended. The purpose of this review was to sum up the results available in the literature.
HIGH DENSITY INFRARED PROCESSING OF WC/Ni–11P COMPOSITE COATINGS (2002)

A new high density infrared based coating process has been developed to produce wear resistant coatings on AISI 4340 steel substrates that are of commercial interest. The process combines infrared heating, with power densities up to 35 MW m -2 , with room temperature precursor spray deposition processes to rapidly form wear resistant coatings. Here, the process is demonstrated using a 20 vol.-%WC reinforced coating in a Ni-11 wt-%P binder on a AISI 4340 steel substrate, to produce a smooth, high density, 10 μm thick coating with minimal degradation of the WC reinforcement or base steel and a hardness seven times greater than that of the substrate.
Nonlinear microscopy of localized field enhancements in fractal shaped periodic metal nanostructures (2008)

Fractal shaped periodic nanostructures formed with a 100 nm period square lattice of gold nanoparticles placed on a gold film are characterized using far-field nonlinear scanning optical microscopy, in which two-photon photoluminescence (TPL) excited with a strongly focused femtosecond laser beam (in the wavelength range of 730-790 nm) is detected. TPL images obtained for all wavelengths in the laser range feature diffraction-limited (~0.6 μm) bright spots corresponding to intensity enhancements of up to ~170, whose positions are dictated by the incident light wavelength and polarization. We relate the observed TPL enhancements to constructive interference of surface plasmon polaritons partially reflected inside the structure boundaries and support the analysis with numerical simulations using the Green dyadic field propagator.