gebhart/patrepeval huggingface dataset:
Molecular Organization in the Native State of Wood Cell Walls: Studies of Nanoscale Structure and its Development (2001)

With respect to cell wall biogenesis we have developed a theory concerning the formation of lignin in which the regulation of structure is attributed to the hemicelluloses; they are viewed as templates for the assembly of lignin. The key supporting evidence is derived from the symmetry of annual rings in trees free of reaction wood. This symmetry is interpreted to point to genetic encoding as the dominant factor in the pattern of interunit linkages in lignin. More recently, we have explored further the implications of annual ring symmetries within the contexts of systems and information theory and theories of organization of hierarchic structures. This has led us to proposed a unifying model for cell wall biogenesis that comprehends cell wall polysaccharides as well as lignin. The model is based on examining the implications of symmetries and of hierarchic relationships between different levels of structure, with respect to synchrony and coordination of the stages of formation of the individual constituents.
20-Hydroxyeicosatetraenoic acid is formed in response to EGF and is a mitogen in rat proximal tubule (1995)

Hydroxyeicosatetraenoic acid (20-HETE) is a major cytochrome P-450-arachidonic acid metabolite in the rat kidney, and its synthesis along the nephron is specifically localized to the proximal tubule, where receptor density for epidermal growth factor (EGF) is the highest. EGF stimulated endogenous 20-HETE formation in a concentration and time-dependent manner, i.e., from 1.6 to 2.6 +/- 0.3 and 3.0 +/- 0.6 pmol 20-HETE.mg-1.min-1 at 10(-8) and 10(-7) M EGF, respectively. The effect of 20-HETE on proximal tubular cell proliferation was examined using primary cultures of rat proximal tubular cells and proximal tubular-derived cell lines, LLC-PK1 and opossum kidney OK. In both cell lines, 20-HETE increased thymidine incorporation into DNA with maximal effect at 10(-9) M. Addition of 20-HETE to serum-deprived LLC-PK1 or OK cells for 48 h caused a concentration-dependent increase in cell number with maximal effect at 10(-9) M. This effect was specific, as structurally similar eicosanoids such as 20-COOH-arachidonic acid, 19(R)-HETE, and 19(S)-HETE did not increase cell number. In 4-day primary cultures of proximal tubular cells, EGF (10(-9) M) and 20-HETE (10(-9) M) increased bromodeoxyuridine (BrdU) incorporation by 40 and 28%, respectively. Addition of both resulted in a twofold increase in BrdU incorporation. Although 20-HETE synthesis in cultured cells is greatly diminished with time, significant picomolar concentrations can be obtained in 4-day cultures. Addition of 17-octadecynoic acid (17-ODYA), an inhibitor of 20-HETE synthesis, significantly inhibited EGF-stimulated BrdU incorporation. The demonstrations that EGF stimulates proximal tubular 20-HETE production and that the latter is a potent mitogen to these cells suggests that 20-HETE may act as a mediator of the EGF effect on cellular growth in the proximal tubule.
A high current focused electron ring-beam column design (2019)

There are many applications in electron microscopy, electron spectroscopy, as well as accelerator physics that require the combination of minimizing a focused electron beam’s probe size while maximizing its beam current. This paper describes how this can be done through the use of annular focused electron beam column designs, where an electron beam is propagated and focused in the form of a ring beam. For probe semi-angles of [Formula: see text] radians, a column consisting of two identical electric sectors and two identical focusing lenses functioning with odd symmetry will be presented, together with a wide-angle cold field emission gun design. The column is designed to cancel energy dispersion while limiting geometric aberrations to the third order at the point of final focus. This design is predicted to have over two orders of magnitude higher beam current than the corresponding conventional on-axis focused electron beam columns for the same final probe size. For a 1.2 keV annular electron beam, simulation results predict a spot radius of 4.8 nm at a working distance of 3.4 mm, final beam angle of [Formula: see text] mrad, and energy spread of [Formula: see text] eV.
Screening of Fungi for Removal of Wood Extractives (2004)

Eucalyptus camaldulensis logs were harvested from forest sites in central Taiwan, and fungi of the Ophiostoma genus were screened and 28 strains were obtained. These were inoculated on wood chips to evaluate their effects on weight losses of wood and the amounts of acetone extractive degraded. At the same time, GC-MS was engaged. By using internal standards and database of GC-MS ionic fragments, changes in lipophilic compounds were analysed. Among these fatty acid, hydrocarbon, sterol compounds, sterol ester and triglycerides were noted. After 2wks of fungal treatment, we found that 6 of the strains were capable of reducing the lipophilic fractions by more than 60% in a 2-wk treatment.
Cost‐ and Income‐based Measures of Human Capital (2003)

Human capital is increasingly believed to play an important role in the growth process, however, adequately measuring its stock remains controversial. In this paper three general approaches to measurement are identified; cost‐based, income‐based and educational stock‐based. This survey focuses on the first two approaches and provides a critical review of the theories and their applications to data from a range of countries. Particular emphasis is placed upon the work of Jorgenson and Fraumeni (1989, 1992) and some new results for New Zealand based upon their approach are also presented.
Influence of cooperative-controlled driving in the traffic flow (2018)

This paper presents some preliminary results on the influence of vehicles equipped with cooperative adaptive cruise control algorithms to the traffic flow. The design of the controller consists in regulating a policy distance that depends on the longitudinal speed of the vehicle and, when available, the velocity of precedent vehicles. The behaviour of the proposed algorithms are tested in numerical simulations. Additionally, the influence of cooperative driving to traffic properties in heterogenous roads, i.e., with a variable (and randomly) presence of controlled-vehicles is analysed using a standard traffic simulator.
Functional and Structural Characterization of a Thermostable Phospholipase A2 from a Sparidae Fish (Diplodus annularis) (2017)

Novel phospholipase (PLA<sub>2</sub>) genes from the Sparidae family were cloned. The sequenced PLA<sub>2</sub> revealed an identity with pancreatic PLA<sub>2</sub> group IB. To better understand the structure/function relationships of these enzymes and their evolution, the Diplodus annularis PLA<sub>2</sub> (DaPLA<sub>2</sub>) was overexpressed in E. coli. The refolded enzyme was purified by Ni-affinity chromatography and has a molecular mass of 15 kDa as determined by MALDI-TOF spectrometry. Interestingly, unlike the pancreatic type, the DaPLA<sub>2</sub> was active and stable at higher temperatures, which suggests its great potential in biotechnological applications. The 3D structure of DaPLA<sub>2</sub> was constructed to gain insights into the functional properties of sparidae PLA<sub>2</sub>. Molecular docking and dynamic simulations were performed to explain the higher thermal stability and the substrate specificity of DaPLA<sub>2</sub>. Using the monolayer technique, the purified DaPLA<sub>2</sub> was found to be active on various phospholipids ranging from 10 to 20 mN·m<sup>-1</sup>, which explained the absence of the hemolytic activity for DaPLA<sub>2</sub>.
Emissions from thermally modified beech wood, their reduction by solvent extraction and fungicidal effect of the organic solvent extracts (2009)

Abstract The characterization and removal of odorous substances caused by thermal treatment of wood were investigated using chromatographic and spectroscopic methods. Emissions of pentanal and hexanal, probably formed by oxidation of unsaturated fatty acids, were the prevailing aldehydes in untreated wood samples. Their amount decreased during thermal treatment, while furfural and 5-methylfurfural (degradation products of hemicelluloses) accounted for almost 100% of the aldehyde fraction. Furthermore, it can be assumed that odorous emissions of thermally modified wood can be strongly reduced by solvent extraction. An ethanol–cyclohexane mixture that produces wood samples without significant odour emissions obtained good results. Certain organic solvent extractives from thermally modified beech have fungicidal properties. Methanol extracts, resolubilized in propanone, caused a retardation of fungal growth on native beech specimens. Beech specimens impregnated with these extractives could be assigned to durability class 4 (not permanent). The analysis of methanol extracts using gas chromatography coupled with mass spectrometry showed an increased share of phenolic compounds known to cause resistance effects. Their presence in organic extracts of thermally modified wood may explain the improved resistance of the impregnated specimen.
Longitudinal and temporal distribution of freshwater ascomycetes and dematiaceous hyphomycetes on submerged wood in the Lam Tsuen River, Hong Kong (2001)

Longitudinal and temporal distribution patterns of freshwater ascomycetes and dematiaceous hyphomycetes on submerged wood were investigated at 3 sites along the Lam Tsuen River in Hong Kong. Two-hundred-and-six species were recorded. Ascomycete genera were dominated by Annulatascaceae, Halosphaeriaceae, Lasiosphaeriaceae, Lophiostomataceae, and Magnaporthaceae; the most common taxa were Aniptodera chesapeakensis, Aquaticola ellipsoidea, Helicosporium griseum, Massarina purpurascens, M. thalassioidea, Ophioceras commune, and Sporoschisma uniseptatum. There were no significant differences (ANOVA, p > 0.05) in total number of species among the sites. However, the number of species of Halosphaeriaceae (p < 0.01) and Lasiosphaeriaceae (p < 0.05) was significantly higher at Site 3, and Annulatascaceae was dominant at Sites 1 and 2 (p < 0.05). Downstream changes in species composition were strongly correlated with elevated concentrations of NO3-N (r2 = 0.66), NH3-N (r2 = 0.66), and PO4-P (r2 = 0.73) resulting from human disturbance. The variation in species composition was also weakly correlated with other physico-chemical variables such as conductivity (r2 = 0.16) and aluminum (r2 = 0.11). Species diversity fluctuated temporally but did not change (ANOVA, p > 0.05) between dry and wet seasons. Species composition shifted and the frequency of occurrence of certain dominant taxa declined after heavy rainfall associated with El Niño, possibly because increased discharge washed away well-colonized woody substrata.
Design of an Electron Optics System for 220GHz Traveling Wave Tube (2019)

Electron optics system (EOS) which includes Electron gun and focusing system is a key part of Traveling wave tube (TWT). In the meantime, focusing system uses periodic permanent magnet (PPM) to reduce the weight and volume of the vacuum electron device. The results show that the passing rate of electron beam is high and its ripple is low. The optimum parameters of EOS are listed as follows: the current emitted from the surface of cathode is about 25mA when the operating voltage is 15kV, the length and diameter of drift tube are 65mm and 0.2mm, respectively.
Face adaptation: Changing stable representations of familiar faces within minutes? (2005)

Three experiments are reported showing that the perception and the assessment of veridicality of familiar faces are highly adaptive to new visual information. Subjects were asked to discriminate between real photographs and altered versions of celebrities. Exposing participants to extremely deviated versions changed the usually stable representations of the famous faces within a very short time. In Experiment 1, expo-sure to an extreme face version resulted in identity decisions shifted towards the exposed one. Experiment 2 revealed that the effects are not short lasting. In Experiment 3, we showed that the effect also generalizes to different pictures of the same famous person. Together the experiments seem to indicate that the brain permanently adapts to new perceptual information and integrates new data within already elaborated representations in a fast way.
Predictive Value of Cytokines During Acute Severe Pancreatitis (2000)

Copyright © by 2000 by the Society of Critical Care Medicine and Wolters Kluwer Health, Inc. All Rights Reserved.
Sliding-Mode-Observer-Based Adaptive Control for Servo Actuator With Friction (2007)

In this paper, a novel sliding-mode-observer-based adaptive controller is developed for the servo actuators with friction. The LuGre dynamic friction model is adopted for adaptive friction compensation. A sliding-mode observer is proposed to estimate the internal friction state of LuGre model. Based on the estimated friction state, adaptation laws are designed to compensate the unknown friction and load torque. The stability of the adaptive controller with sliding-mode observer is analyzed. The position tracking performance has been verified through both simulation and experimental results
Mammary Response to Exogenous Prolactin or Frequent Milking During Early Lactation in Dairy Cows (2006)

Frequent milking of dairy cows during early lactation results in a persistent increase in milk yield; however, the mechanism underlying this effect is unknown. We hypothesized that increased exposure of the mammary gland to prolactin (PRL) mediates the milk yield response. Fifteen multiparous Holstein cows were assigned to 3 treatments for the first 3 wk of lactation: twice daily milking with (2x + PRL) or without (2x) supplemental exogenous PRL, or 4 times daily milking (4x). Mammary biopsies were obtained at 7 DIM, and rates of [(3)H]thymidine incorporation into DNA in vitro were determined. Mammary expression of suppressors of cytokine signaling (SOCS)-1, -2, and -3; the long form of PRL-receptor; and alpha-lactalbumin mRNA was measured by real-time reverse-transcription PCR. Incorporation of [(3)H]thymidine into DNA was not affected by frequent milking or PRL treatment; however, analysis of autoradiograms revealed that stromal cell proliferation was greater in 4x cows. Mammary expression of SOCS-1 was not affected by milking frequency or PRL treatment. Expression of SOCS-2 mRNA was increased with frequent milking or PRL treatment, whereas expression of SOCS-3 mRNA was reduced by frequent milking or exogenous PRL. Abundance of PRL-receptor mRNA was reduced, whereas alpha-lactalbumin mRNA was increased with PRL treatment. These results demonstrate that the bovine mammary gland is responsive to exogenous PRL during early lactation. In addition, differences in the response to frequent milking or exogenous PRL during early lactation indicate distinct effects of PRL and milk removal on the mammary function of dairy cows.
Code design for binary energy harvesting channel (2017)

We consider a binary energy harvesting communication system with a finite battery transmitter over a noisy channel, and design explicit and implementable codes based on concatenation of a nonlinear trellis code (NLTC) with an outer low density parity check (LDPC) code. We propose two different decoding methods where the simplified one ignores the memory in the battery state while the more sophisticated one utilizes the memory. Numerical results demonstrate that the designed codes outperform other reference schemes. The results also show the superiority of the improved decoding approach over the naive solution.
Investigation of Retained Strains and Microstructures for a Hot Deformed Stainless Steel (2008)

For the investigation of retained strains during hot forming, which are related to the dislocation structure, single and double hit compression tests were carried out at different temperatures and strain rates for a stainless steel. Using microhardness measurements the retained strains after the first and second pass were investigated as a function of the amount of deformation, temperatures as well as strain rates and dwell durations. In general, the retained strain decreases with increasing dwell durations in both the deformed and recrystallized grains, respectively. At a given total amount of deformation in a double hit compression, the retained strains for the as deformed unrecrystallized grains are reduced for a lower deformation in the first hit. For the recrystallized grains the retained strain increases, when comparing double hit with single hit compression.
Adaptive evolution in the toxicity of a spider’s venom enzymes (2015)

The evolution of Sphingomyelinase D has been driven by natural selection toward an increase in noxiousness, and this might help explain the toxic variation between classes.
AC Impedance-based Online State-of-charge Estimation for Li-ion Batteries (2018)

The accurate estimation of state-of-charge (SOC) is one of the most important core functions of a battery management system (BMS), which provides the essential information needed for battery management, monitoring, and status analysis. This paper presents an online SOC estimation method based on AC impedance. A circuit for sensing the voltage and current of the battery is also proposed. The sensed values can be utilized to calculate the AC impedance and then accurately estimate the SOC of a Li-ion battery. First, a 1 kHz sinusoidal ripple is injected into an 18650 Li-ion battery and the AC impedance values are measured from 0 to 100% charging status in 10% increments. The correlations between SOC and AC impedance are then determined by linear regression. In terms of practical application, we simply use the sensing circuit to measure the battery AC voltage and current and calculate the AC impedance. This AC impedance allows a fairly accurate estimation of the battery SOC. To validate the accuracy of the proposed method, a power analyzer was used to actually measure SOC. The average error in estimating SOC is within 4%. This encouraging result shows that the proposed method can provide a simple and practical solution for online estimation of the SOC of Li-ion batteries.
SNAP-Tag Technology: A Powerful Tool for Site Specific Conjugation of Therapeutic and Imaging Agents (2013)

In the past two decades, immense advances have been achieved in the engineering, production and purifying of recombinant proteins. These proteins are being widely utilized in many fields of biology, biotechnology and medicine, including diagnostic and therapeutic applications. These applications often require the modification or conjugation of these proteins with other molecules. Researchers are spending many efforts to develop and improve the methods of protein modifications. A main challenge they face is derivatizing proteins without affecting their structure and biological function. The conjugation methods available today include random and specific chemical modifications on endogenous amino acids or carbohydrate of the protein of interest. Other methods utilize self-labeling tags as fusion partners to the original protein enabling site-specific conjugation. SNAP-tag is one of the most promising self-labeling tags, which reacts specifically, rapidly and covalently with benzylguanine (BG) derivatives. SNAP-tag fusion proteins have been successfully used for imaging living cells. Recently, several studies have utilized the SNAP technology for generating antibody-based diagnostic and therapeutic tools. We here review these approaches and their possible impact on improving cancer targeting.
Faculty Opinions recommendation of Identification of the PTEN-ARID4B-PI3K pathway reveals the dependency on ARID4B by PTEN-deficient prostate cancer. (2020)

PTEN is frequently mutated in prostate cancer. The tumor suppressor function of PTEN is attributed to its lipid phosphatase activity that counters PI3K action. Here, we report a PTEN-ARID4B-PI3K axis in which PTEN inhibits expression of ARID4B, while ARID4B is a transcriptional activator of the PI3K subunit genes PIK3CA and PIK3R2 that are crucial for activation of the PI3K/AKT pathway. Reciprocal binding of ARID4B and histone H1 to the PIK3CA and PIK3R2 promoters modulates chromatin condensation, suggesting a mechanism by which ARID4B activates these promoters. Functional analyses reveals that ARID4B is required for prostate tumorigenesis when PTEN is deficient. The biological significance is further substantiated by the existence of a PTEN/ARID4B/PIK3CA three-gene signature that improves the predictive power for prostate cancer recurrence in patients. In summary, we identify ARID4B as a master regulator in the PTEN-PI3K pathway, thus providing a potential therapeutic target for prostate cancer carrying PTEN mutations. PMID: 31551414 Funding information This work was supported by: NCI NIH HHS, United States Grant ID: R21 CA187857 NCI NIH HHS, United States Grant ID: R01 CA188471
Tick-Borne Langat/Mosquito-Borne Dengue Flavivirus Chimera, a Candidate Live Attenuated Vaccine for Protection against Disease Caused by Members of the Tick-Borne Encephalitis Virus Complex: Evaluation in Rhesus Monkeys and in Mosquitoes (2001)

Langat virus (LGT), strain TP21, a naturally avirulent tick-borne flavivirus, was used to construct a chimeric candidate virus vaccine which contained LGT genes for premembrane (preM) and envelope (E) glycoprotein and all other sequences derived from dengue type 4 virus (DEN4). The live virus vaccine was developed to provide resistance to the highly virulent, closely related tick-borne flaviviruses that share protective E epitopes among themselves and with LGT. Toward that end the chimera, initially recovered in mosquito cells, was adapted to grow to high titer in qualified simian Vero cells. When inoculated intraperitoneally (i.p.), the Vero cell-adapted LGT TP21/DEN4 chimera remained completely attenuated for SCID mice. Significantly, the chimera protected immunocompetent mice against the most virulent tick-borne encephalitis virus (TBEV). Subsequently, rhesus monkeys were immunized in groups of 4 with 10(5) or 10(7) PFU of LGT strain TP21, with 10(5) PFU of DEN4, or with 10(3), 10(5), or 10(7) PFU of the chimera. Each of the monkeys inoculated with DEN4 or LGT TP21 became viremic, and the duration of viremia ranged from 1 to 5 days. In contrast, viremia was detected in only 1 of 12 monkeys inoculated with the LGT TP21/DEN4 chimera; in this instance the level of viremia was at the limit of detection. All monkeys immunized with the chimera or LGT TP21 virus developed a moderate to high level of neutralizing antibodies against LGT TP21 as well as TBEV and were completely protected against subsequent LGT TP21 challenge, whereas monkeys previously immunized with DEN4 virus became viremic when challenged with LGT TP21. These observations suggest that the chimera is attenuated, immunogenic, and able to induce a protective immune response. Furthermore, passive transfer of serum from monkeys immunized with chimera conferred significant protection to mice subsequently challenged with 100 i.p. 50% lethal doses of the highly virulent TBEV. The issue of transmissibility of the chimera by mosquitoes was addressed by inoculating a nonhematophagous mosquito, Toxorhynchites splendens, intrathoracically with the chimera or its DEN4 or LGT parent. Neither the LGT TP21/DEN4 vaccine candidate nor the wild-type LGT TP21 virus was able to infect this mosquito species, which is highly permissive for dengue viruses. Certain properties of the chimera, notably its attenuation for monkeys, its immunogenicity, and its failure to infect a highly permissive mosquito host, make it a promising vaccine candidate for use in immunization against severe disease caused by many tick-borne flaviviruses.