gebhart/patrepeval huggingface dataset:
Analysis of Phagosomal Antigen Degradation by Flow Organellocytometry (2016)

Professional phagocytes internalize self and non-self particles by phagocytosis to initiate innate immune responses. After internalization, the formed phagosome matures through fusion and fission events with endosomes and lysosomes to obtain a more acidic, oxidative and hydrolytic environment for the degradation of its cargo. Interestingly, phagosome maturation kinetics differ between cell types and cell activation states. This protocol allows to quantify phagosome maturation kinetics on a single organelle level in different types of phagocytes using flow cytometry. Here, ovalbumin (OVA)-coupled particles are used as phagocytosis model system in dendritic cells (DC), which are internalized by phagocytosis. After different time points, phagosome maturation parameters, such as phagosomal degradation of OVA and acquisition of lysosomal proteins (like LAMP-1), can be measured simultaneously in a highly quantitative manner by flow organellocytometry. These read-outs can be correlated to other phagosomal functions, for example antigen degradation, processing and loading in DC.
Phosphorylation of the Cardiac Ryanodine Receptor by cAMP-Dependent Protein Kinase1 (1989)

The phosphorylation of canine cardiac and skeletal muscle ryanodine receptors by the catalytic subunit of cAMP-dependent protein kinase has been studied. A high-molecular-weight protein (Mr 400,000) in cardiac microsomes was phosphorylated by the catalytic subunit of cAMP-dependent protein kinase. A monoclonal antibody against the cardiac ryanodine receptor immunoprecipitated this phosphoprotein. In contrast, high-molecular-weight proteins (Mr 400,000-450,000) in canine skeletal microsomes isolated from extensor carpi radialis (fast) or superficial digitalis flexor (slow) muscle fibers were not significantly phosphorylated. In agreement with these findings, the ryanodine receptor purified from cardiac microsomes was also phosphorylated by cAMP-dependent protein kinase. Phosphorylation of the cardiac ryanodine receptor in microsomal and purified preparations occurred at the ratio of about one mol per mol of ryanodine-binding site. Upon phosphorylation of the cardiac ryanodine receptor, the levels of [3H]ryanodine binding at saturating concentrations of this ligand increased by up to 30% in the presence of Ca2+ concentrations above 1 microM in both cardiac microsomes and the purified cardiac ryanodine receptor preparation. In contrast, the Ca2+ concentration dependence of [3H]ryanodine binding did not change significantly. These results suggest that phosphorylation of the ryanodine receptor by cAMP-dependent protein kinase may be an important regulatory mechanism for the calcium release channel function in the cardiac sarcoplasmic reticulum.
State of the art in Monte Carlo global illumination (2004)

Realistic image synthesis is increasingly important in areas such as entertainment (movies, special effects and games), design, architecture and more. A common trend in all these areas is the quest for more realistic images of increasingly complex models. Monte Carlo global illumination algorithms are the only methods that can handle this complexity. Recent advances in algorithms and compute power has made Monte Carlo algorithms very practical and a natural choice for most problems.The purpose of this course is to impart upon the attendees a thorough understanding of the principles of Monte Carlo path tracing methods, as well as a detailed overview of the most recently developed methods.Part 1 will cover the fundamentals of realistic image synthesis (radiometry, rendering equation). Part 2 focuses on the mathematical tools needed to compute integrals using Monte Carlo sampling. Parts 3 and 4 cover specific algorithms that have proven very useful in global illumination rendering.
Effect of Diseases on Soybean Yields in the United States and Ontario (1999 to 2002) (2003)

Soybean yields in the U.S. and Ontario have often been suppressed by diseases. The resulting losses are important to rural economies and to the economies of allied industries in urban areas. The authors compiled estimates of soybean yield losses due to diseases for each soybean producing state in the U.S. and Ontario from 1999 to 2002. The goal was to provide this information to help funding agencies and scientists prioritize research objectives and budgets. Accepted for publication 4 March 2003. Published 25 March 2003.
Isolation of Onosmins A and B, Lipoxygenase Inhibitors from Onosma hispida. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Establishment of the Minimum Biological Capacity for Nitrogen Excretion in Pigs (2001)

To determine the minimum biological capacity for nitrogen (N) excretion for pigs, dietary regimens were created and fed that were designed to eliminate fecal excretion of undigested feed N, minimize endogenous N secretions and minimize intakes of nitrogenous compounds (amino acids) above those of the pigs biological needs. Excretion of undigested fecal N was eliminated by feeding ingredients containing highly digestible (≈100%) sources of nitrogen and by eliminating compounds that bind N. Endogenous secretions were minimized by eliminating antinutritional factors from the diet and by minimizing enteric bacterial populations. Intakes of amino acids above the animal's needs were minimized by providing a pattern of amino acids that closely matched that needed by the pig. Furthermore, dietary amino acids were provided to the pigs in amounts above, at, and below their biological needs based on the amounts of urea N excreted in the urine and the amounts of N accrued in the body. From two-slope breakpoint analysis, apparent digestible N intake resulting in maximum N retention (2.58g⋅kg-1BW.75⋅d-1) was determined to be 3.66g⋅kg-1BW.75⋅d-1. When daily apparent digestible nitrogen intakes were below the pigs' determined need, the amount of digestible N (mg⋅kg-1BW.75⋅d-1) lost for body maintenance processes was estimated as .239 in urine and .080 in feces. The amount lost in urine as unusable for body N accretion was .206 g⋅kg-1BW.75⋅d-1 of each gram of digestible N consumed above body maintenance needs. When daily apparent digestible N intakes were above the pigs determined need, .900 g of each gram of additional N consumed above that needed for body N accretion was excreted. The minimum biological capacity for N excretion in pigs, defined as total (urinary plus fecal) obligatory losses of N, is estimated to be .287g⋅kg-1BW.75⋅d-1 to support pigs at N maintenance and 1.11 g⋅kg-1BW.75⋅d-1 for pigs at maximum body N accretion.\nUsing these estimates, the minimal biological capacity for N excretion can be calculated for pigs at various stages of growth. For example, in 60 kg pigs, minimum capacity for N excretion is estimated at .10 and .39 g/kg body weight/day in pigs in states of N maintenance and maximum body N accretion, respectively. These values are 12 and 44%, respectively, of N excretion relative to published standards (ASAE D384.1). Similarly, the N content of excreta from animals excreting N at their biological minimum was determined to be 2.57 g N/liter, or 18% of standard excreta N content (corrected for volatilization, ASAE D384.1). Based on these data, the minimum biological capacity for the excretion of N in pigs is substantially less than current estimates of N excretion and can be achieved by eliminating dietary factors that contribute to N excretion. Furthermore, dietary regimens that allow the minimum biological capacity for N excretion to be achieved are biologically capable of supporting maximum rates of body accretion (i.e., lean tissue growth) in pigs.
Highly rotationalC60dynamics inside single-walled carbon nanotubes: NMR observations (2008)

Rotational dynamics of ${\mathrm{C}}_{60}$ molecules composing a one-dimensional (1D) linear array inside single-walled carbon nanotubes have been investigated by $^{13}\mathrm{C}$ NMR in a temperature range from $4.2\phantom{\rule{0.3em}{0ex}}\text{to}\phantom{\rule{0.3em}{0ex}}300\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. The temperature dependence of the NMR lineshape and spin-lattice relaxation time $({T}_{1})$ indicate that the encapsulated ${\mathrm{C}}_{60}$ molecules exhibit a quasi-free-rotation with correlation times of $5--10\phantom{\rule{0.3em}{0ex}}\mathrm{ps}$ at $300\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. With decreasing temperature, the large amplitude molecular rotation continues to $30\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ with an activation energy of $467\phantom{\rule{0.3em}{0ex}}\mathrm{K}$. It is suggested that the ${\mathrm{C}}_{60}$ linear array does not undergo an orientational phase transition, which is associated with its 1D nature. Furthermore, no evidence for the polymerization of ${\mathrm{C}}_{60}$ molecules is found from the $^{13}\mathrm{C}$ NMR line shape analysis.
Efficient, Widely-Tunable Wavelength Conversion for Packets With In-Band Labels (2013)

We propose and demonstrate a tunable wavelength converter for optical packets with a 40 Gb/s non-return-to-zero differential phase shift keying payload and an in-band 1.25-Gb/s on-off keying label. To achieve wide wavelength coverage and integrability, we use a dual pump scheme exploiting four-wave mixing in semiconductor amplifiers. For flexibility and scalability, in-band labels are used. For phase stability, we use a quantum-dash mode-locked laser as a multi-wavelength source for the dual pumps with tunability provided by the output filter. The bit error rate (BER) performance is evaluated for both payload and label after wavelength conversion. We report error free conversion for both the converted payload and label over a range of 12 nm with power penalty.
RNA Editing of the Mitochondrial atpA/atp9 Co-Transcript of Triticale, Carrying the timopheevi Cytoplasmic Male Sterility Cytoplasm from Wheat (1995)

Subunits a and nine are components from two different portions of the mt H+-ATP synthase enzyme, namely the soluble catalytic (F,) and the membranous proton-conduction (F,-ATPase) complexes. In wheat and triticale the genes for both subunits are located adjacently in the mt genome, irrespective of whether these lines are carrying the aestivum, durum, or timopheevi cytoplasmic male sterility cytoplasm. However, in the timopheevi mt genome the atpA/ atp9 cistron is part of a large DNA repeat and thus present in two different genomic environments. The repeat comprises at least 9 kb that are delimited 941 bp downstream of the atp9 gene. The 2.7-kb triticale atpAlatp9 sequence shows 100% homology with a Triticum aestivum sequence
Unique Porous Structures Supported by Anodic Treatments in Liquid Ammonia (-50°C, Patm) (2022)

Since the first anodic porosification of semiconductors in the 1950s, numerous studies have reported a wide range of porous structures. The conditions used during the growth of pores can explain the shapes obtained but the growth mechanism and especially the influence of surface chemistry during the porosification still raise many questions. It is in this context that the contribution of liquid ammonia (-55°C, Patm) is significant. Indeed, this remarkable non-aqueous solvent allows, on the one hand, to obtain novel porous structures on III-Vsc, and on the other hand, it allows for the first time a specific and original interfacial chemistry, governed by the chemistry of nitrogen.
Data from Targeting UGCG Overcomes Resistance to Lysosomal Autophagy Inhibition (2023)

&lt;div&gt;Abstract&lt;p&gt;Lysosomal autophagy inhibition (LAI) with hydroxychloroquine or DC661 can enhance cancer therapy, but tumor regrowth is common. To elucidate LAI resistance, proteomics and immunoblotting demonstrated that LAI induced lipid metabolism enzymes in multiple cancer cell lines. Lipidomics showed that LAI increased cholesterol, sphingolipids, and glycosphingolipids. These changes were associated with striking levels of GM1&lt;sup&gt;+&lt;/sup&gt; membrane microdomains (GMM) in plasma membranes and lysosomes. Inhibition of cholesterol/sphingolipid metabolism proteins enhanced LAI cytotoxicity. Targeting UDP-glucose ceramide glucosyltransferase (UGCG) synergistically augmented LAI cytotoxicity. Although &lt;i&gt;UGCG&lt;/i&gt; inhibition decreased LAI-induced GMM and augmented cell death, &lt;i&gt;UGCG&lt;/i&gt; overexpression led to LAI resistance. Melanoma patients with high &lt;i&gt;UGCG&lt;/i&gt; expression had significantly shorter disease-specific survival. The FDA-approved UGCG inhibitor eliglustat combined with LAI significantly inhibited tumor growth and improved survival in syngeneic tumors and a therapy-resistant patient-derived xenograft. These findings nominate UGCG as a new cancer target, and clinical trials testing UGCG inhibition in combination with LAI are warranted.&lt;/p&gt;Significance:&lt;p&gt;We discovered UGCG-dependent lipid remodeling drives resistance to LAI. Targeting UGCG with a drug approved for a lysosomal storage disorder enhanced LAI antitumor activity without toxicity. LAI and UGCG inhibition could be tested clinically in multiple cancers.&lt;/p&gt;&lt;p&gt;&lt;i&gt;&lt;a href="https://aacrjournals.org/cancerdiscovery/article/doi/10.1158/2159-8290.CD-13-2-ITI" target="_blank"&gt;This article is highlighted in the In This Issue feature, p. 247&lt;/a&gt;&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
NRST: Non-rigid Surface Tracking from Monocular Video (2021)

We propose an efficient method for non-rigid surface tracking from monocular RGB videos. Given a video and a template mesh, our algorithm sequentially registers the template non-rigidly to each frame. We formulate the per-frame registration as an optimization problem that includes a novel texture term specifically tailored towards tracking objects with uniform texture but fine-scale structure, such as the regular micro-structural patterns of fabric. Our texture term exploits the orientation information in the micro-structures of the objects, e.g., the yarn patterns of fabrics. This enables us to accurately track uniformly colored materials that have these high frequency micro-structures, for which traditional photometric terms are usually less effective. The results demonstrate the effectiveness of our method on both general textured non-rigid objects and monochromatic fabrics.
Detecting visual texture patterns in binary sequences through pattern features (2023)

We measured human ability to detect texture patterns in a signal detection task. Observers viewed sequences of 20 blue or yellow tokens placed horizontally in a row. They attempted to discriminate sequences generated by a random generator ("a fair coin") from sequences produced by a disrupted Markov sequence (DMS) generator. The DMSs were generated in two stages: first a sequence was generated using a Markov chain with probability, pr = 0.9, that a token would be the same color as the token to its left. The Markov sequence was then disrupted by flipping each token from blue to yellow or vice versa with probability, pd-the probability of disruption. Disruption played the role of noise in signal detection terms. We can frame what observers are asked to do as detecting Markov texture patterns disrupted by noise. The experiment included three conditions differing in pd (0.1, 0.2, 0.3). Ninety-two observers participated, each in only one condition. Overall, human observers' sensitivities to texture patterns (d' values) were markedly less than those of an optimal Bayesian observer. We considered the possibility that observers based their judgments not on the entire texture sequence but on specific features of the sequences such as the length of the longest repeating subsequence. We compared human performance with that of multiple optimal Bayesian classifiers based on such features. We identify the single- and multiple-feature models that best match the performance of observers across conditions and develop a pattern feature pool model for the signal detection task considered.
TCP Performance Enhancement for UMTS Access Network (2008)

We aim at optimize the TCP performance over UMTS access network challenged by the large delay bandwidth product that is mainly caused by the latency from the link layer ARQ retransmissions and diversity technique at physical layer. We propose to place a split TCP proxy at GGSN nodes which is between UMTS access network and Internet. The split proxy divides the bandwidth delay product into two parts, resulting in two TCP connections with smaller bandwidth delay products. Simulation results show, the split TCP proxy can significantly improve the TCP performance under high bit rate DCH channel scenario (e.g.256 kbps). Besides, the split TCP proxy brings more performance gain for downloading large files than downloading small ones. Finally, an aggressive initial TCP congestion window size at proxy can brings even more performance gain for radio links with high data rates DCH channels with large delay bandwidth product.
Hyperthermia-driven aberrations of secreted microRNAs in breast cancer in vitro (2016)

Hyperthermia-dependent down-regulatory influence on three distinct BC-related microRNAs in vitro generates translational aspects for clinical BC treatment, since the identified microRNAs miR-10b, miR-15b and miR-139 are known to have oncogenic as well as tumour suppressor functions in BC. However, an evaluation regarding the potential impact of microRNA-related hyperthermia-dependent alterations for innovative BC treatment approaches demands further analysis including in vivo data.
Response of the jalpaite membrane copper(II) ion‐selective electrode in marine waters (1997)

Abstract The response of the Orion 94‐29 Cu II ion‐selective electrode (ISE) [employing a jalpaite membrane] in seawater has been related to levels of free Cu II yielding results for the Derwent River and San Diego Bay that are 2 to 3 orders of magnitude higher than those for the Pacific Ocean. Response data for the electrode in acidified seawater at pH 2 are internally consistent with total Cu II levels determined using differential pulse anodic stripping voltammetry (DPASV) and graphite furnace atomic absorption spectrometry (GFAAS). It has been found that, even in acidified seawater, the organic ligands influence the response of the electrode, and this effect can be compensated successfully by either analyzing UV‐photooxidized seawater and/or using a standard addition technique. The assigned ISE results for total Cu II in acidified seawater fall within ± (0.1–0.5) pCu unit of values determined using GFAAS. Electrode drift in seawater can be minimized by using a polished electrode that has been conditioned in seawater for 24 h. The improved response rate of a conditioned ISE minimizes electrode soaking times and sample contamination through membrane corrosion.
[P249] Two cases of pyogenic granuloma on a nail bed (2017)

Pyogenic granuloma(PG) is a rapidly developing vascular lesion, histopathologically a lobular capillary hemangioma. The lesion is a commonly reddish papule with a smooth surface, with or without crusts and erosion. Typical locations include the cheek, forehead or gingiva but virtually any body site including the mucous membranes may be affected. An 17-year-old woman presented with a partial defect of her left first proximal nail plate of 1 week in duration. She had no history of trauma but the nail plate dissolved spontaneously. Histopathologic examination of the lesion on the nail bed revealed lobular aggregates of proliferating capillaries with edema and numerous neutrophils, which was supportive for PG. The lesion of nail was improved after surgical excision and curettage of PG, and her nail showed normal growth. A 33-year-old woman presented with painful tiny splitting of a nail plate of right thumb of 2 week in duration. She had no history of trauma. Histopathologic examination of the lesion on the nail bed revealed proliferation of small vasculatures such as capillaries, which was supportive for PG. We are under close observation for her. There have been numerous reports about PG on the finger, lips, mouth, trunk, and toes. We report this two cases because it``s rare cases of PG involving a nail bed. Dermatologist should be aware that PG on the nail bed could often cause nail dystrophy.
Vision as an Energy-Driven Process (2020)

It is frequently assumed that the fundamental purpose of vision is to extract information from light and process it in the brain in order to gain knowledge about environmental objects. Treating vision as an information-driven process has been fruitful for many areas of vision science. But this approach has inherent limitations and may not be sufficient to explain at the most fundamental level why and how we see. Energy is a prime mover in the evolution and operation of all biological systems, including vision, and early researchers in physiological optics and experimental psychology regarded vision as an energy-driven process. Yet to date there has been little attempt to analyze the fundamentals of vision in energetic terms. This paper is a provisional attempt to sketch an account of the early stages of vision as an energy-driven process. On this account, vision is a form of biological work in which energy from the environment is absorbed and processed by neurobiological systems in order to guide behaviour. Evidence from the evolution and neurobiology of vision is presented in support of this approach. I conclude that treating vision as an energy-driven process can contribute to our understanding of its fundamental nature and operation.
An embedded systems course and course sequence (2005)

Recently, the University of Alabama Department of Electrical and Computer Engineering adopted curricular changes to incorporate embedded systems into its computer engineering core course sequence. One of the major changes implemented was the creation of a senior lecture/laboratory combination specifically dedicated to embedded systems. This paper describes the specific lecture and laboratory content of this senior-level course and how this course fits within the new curriculum a The University of Alabama.
[Evaluation of the effects of a complex of physical factors on the functional state of men doing mental work]. (1997)

The article evaluates influence of environmental, physical factors (noise, vibration, ambient temperature, illumination) on human functional state. The study involved 3 males performing mental tasks (following the object movements on monitor and correcting the track after variable interferences appearing in uneven time intervals) in specific microclimate chamber. The study revealed physiologic parameters more substantial for human functional state if influenced by environmental physical factors. For each parameter of human functional state and environmental physical factor a significance share was determined. If significant (r = 0.82, p < 0.001), correlations between parameters of human functional state and environmental physical factors became a material for integral equations. Method of cluster analyses defined 3 classes of human functional state and environmental status. Evaluation and regulation of those integral parameters became possible through a probability nomogram obtained.