gebhart/patrepeval huggingface dataset:
PERSISTENT ANTIGENIC VARIATION OF INFLUENZA A VIRUSES AFTER INCOMPLETE NEUTRALIZATION IN OVO WITH HETEROLOGOUS IMMUNE SERUM (1950)

Antigenic variants of influenza A virus strains emerge on serial passage in ovo in the presence of immune serum against different but related strains. An old laboratory strain (PR8) which had been through hundreds of animal passages was as readily modified by this procedure as recently recovered strains. Such variants apparently can be obtained at will and show antigenic patterns which are reproducible and appear to be predictable in terms of the immune serum used for their selection. Variant strains retain their new antigenic patterns on serial passage in ovo in the absence of immune serum. Limited serial passage in ovo of strains in the absence of immune serum did not result in the emergence of antigenic variants. Similarly, serial passages of strains in ovo in the presence of immune serum against widely different strains, which failed to show significant cross-neutralization, did not lead to the appearance of antigenic variants.
Factors Affecting the Solubilities of Trace Metals in Soils (1981)

Trace metal equilibria in soils can be viewed in terms of reactions within aqueous solution, solid, and gaseous phases. With knowledge of the existence of various metastable and stable solid phases in soil systems, the kinetic factor can be introduced into a predictive scheme such as chemical modeling. Ion exchange-adsorption reactions play an important role in controlling trace metal concentrations in soil solution. This is particularly true in cases where trace metal concentrations are too low to initiate any precipitation reactions. In the chemical modeling of soil systems the existence of equilibrium with respect to trace metal speciation in solution and ion exchange-adsorption reactions can address adequately the reaction kinetics. The program GEOCHEM differs from REDEQL2 in that it includes thermodynamic data for hundreds of additional complexes and solids that are particularly relevant to trace metal equilibria in soils; it includes a model for cation exchange on constant charge surface.
Alpha-Synuclein Preserves Mitochondrial Fusion and Function in Neuronal Cells (2019)

Dysregulations of mitochondria with alterations in trafficking and morphology of these organelles have been related to Parkinson's disease (PD), a neurodegenerative disorder characterized by brain accumulation of Lewy bodies (LB), intraneuronal inclusions mainly composed of <i>α</i>-synuclein (<i>α</i>-syn) fibrils. Experimental evidence supports that <i>α</i>-syn pathological aggregation can negatively impinge on mitochondrial functions suggesting that this protein may be crucially involved in the control of mitochondrial homeostasis. The aim of this study was to assay this hypothesis by analyzing mitochondrial function and morphology in primary cortical neurons from C57BL/6JOlaHsd <i>α</i>-syn null and C57BL/6J wild-type (wt) mice. Primary cortical neurons from mice lacking <i>α</i>-syn showed decreased respiration capacity measured with a Seahorse XFe24 Extracellular Flux Analyzer. In addition, morphological Airyscan superresolution microscopy showed the presence of fragmented mitochondria while real-time PCR and western blot confirmed altered expression of proteins involved in mitochondrial shape modifications in the primary cortical neurons of <i>α</i>-syn null mice. Transmission electron microscopy (TEM) studies showed that <i>α</i>-syn null neurons exhibited impaired mitochondria-endoplasmic reticulum (ER) physical interaction. Specifically, we identified a decreased number of mitochondria-ER contacts (MERCs) paralleled by a significant increase in ER-mitochondria distance (i.e., MERC length). These findings support that <i>α</i>-syn physiologically preserves mitochondrial functions and homeostasis. Studying <i>α</i>-syn/mitochondria interplay in health and disease is thus pivotal for understanding their involvement in PD and other LB disorders.
Time resolved optical emission spectroscopy of an inductively coupled plasma in argon and oxygen (1998)

We present the space-time resolved excitation data for a single coil inductively coupled plasma (ICP) reactor operating in collision dominated regime in argon and oxygen at 13.56 MHz. Robot assisted scanning was used in order to obtain Abel inverted radial profiles of emission and subsequently of the net excitation rate as well as the number density of excited states. The net excitation rate in argon has modulation close to the walls due to the azimuthal field time dependence and a large bulk value independent of the time presumably due to low energy electron-metastable atom collisions. The time resolved profile in oxygen shows a much more pronounced modulation due to the azimuthal field and a much lower degree of excitation for the center of the tube. At low pressures a structure is observed in the temporal dependence of the net excitation rate that is consistent with two different mechanisms of electron acceleration with phase shift of $\ensuremath{\pi}/4$: (I) by azimuthal field and (II) due to the drift motion in crossed electric and magnetic fields that leads to a motion in the azimuthal or radial direction and consequently to energy gain.
Regulation of AKT Signaling in Mouse Uterus (2021)

17β-estradiol (E2) treatment of ovariectomized adult mice stimulates the uterine PI3K-AKT signaling pathway and epithelial proliferation through estrogen receptor 1 (ESR1). However, epithelial proliferation occurs independently of E2/ESR1 signaling in neonatal uteri. Similarly, estrogen-independent uterine epithelial proliferation is seen in adulthood in mice lacking Ezh2, critical for histone methylation, and in wild-type (WT) mice treated neonatally with estrogen. The role of AKT in estrogen-independent uterine epithelial proliferation was the focus of this study. Expression of the catalytically active phosphorylated form of AKT (p-AKT) and epithelial proliferation were high in estrogen receptor 1 knockout and WT mice at postnatal day 6, when E2 concentrations were low, indicating that neither ESR1 nor E2 are essential for p-AKT expression and epithelial proliferation in these mice. However, p-AKT levels and proliferation remained estrogen responsive in preweaning WT mice. Expression of p-AKT and proliferation were both high in uterine luminal epithelium of mice estrogenized neonatally and ovariectomized during adulthood. Increased expression of phosphorylated (inactive) EZH2 was also observed. Consistent with this, Ezh2 conditional knockout mice show ovary-independent uterine epithelial proliferation and high epithelial p-AKT. Thus, adult p-AKT expression is constitutive and E2/ESR1 independent in both model systems. Finally, E2-induced p-AKT expression and normal uterine proliferation did not occur in mice lacking membrane (m)ESR1, indicating a key role for membrane ESR1 in AKT activation. These findings emphasize the importance of AKT activation in promoting uterine epithelial proliferation even when that proliferation is not E2/ESR1 dependent and further indicate that p-AKT can be uncoupled from E2/ESR1 signaling in several experimental scenarios.
Partial model checking (2002)

A major obstacle in applying finite-state model checking to the verification of large systems is the combinatorial explosion of the state space arising when many loosely coupled parallel processes are considered. The problem also known as the state-explosion problem has been attacked from various sides. This paper presents a new approach based on partial model checking where parts of the concurrent system are gradually removed while transforming the specification accordingly. When the intermediate specifications constructed in this manner can be kept small, the state-explosion problem is avoided. Experimental results with a prototype implemented in Standard ML, shows that for Milner's Scheduler-an often used benchmark-this approach improves on the published results on binary decision diagrams and is comparable to results obtained using generalized decision diagrams. Specifications are expressed in a variant of the modal /spl mu/-calculus.
Preoperative molecular testing in thyroid nodules with Bethesda VI cytology: Clinical experience and review of the literature (2020)

Risk assessment is critical to determine the timing of elective surgeries and preserve valuable resources in time of pandemic. This study was undertaken to better understand the potential value of molecular testing to risk-stratify thyroid nodules with malignant cytology (Bethesda VI). Systematic review of the literature contributed 21 studies representing 2036 preoperative specimens. The BRAF p.V600E substitution was detected in 46% to 90% of cases with a pooled positivity rate of 70% (95% confidence intervals: 64%-76%). None of the studies used comprehensive oncogene panels. Retrospective analysis of 531 clinical specimens evaluated with the next-generation sequencing ThyGeNEXT Thyroid Oncogene Panel identified a total of 436 gene alterations. BRAF mutation rate was 64% in specimens tested as part of standard clinical care and 75% in specimens from cross-sectional research studies (P = .022). Testing for additional actionable gene alterations such as TERT promoter mutations or RET and NTRK gene rearrangements further increased the diagnostic yield to 78%-85% and up to 95% when including the ThyraMIR Thyroid miRNA Classifier. These data support the role of molecular cytopathology in surgical and therapeutic decision-making and warrant additional studies.
Supplementary Figure Legends 1-5 from Equilibrium between Host and Cancer Caused by Effector T Cells Killing Tumor Stroma (2023)

Supplementary Figure Legends 1-5 from Equilibrium between Host and Cancer Caused by Effector T Cells Killing Tumor Stroma
Selection of Low Ozone Depleting Oxygen System Cleaning Solvents (2007)

CFC113 (1,1,2-trichlorotrifluoroethane) was widely used in the military for removing dirt and lubricants from equipment. Users sought substitute “environmentally friendly” solvents due to banning of the ozone-depleting compounds. In this work, for wipe and liquid cleaning of liquid and gaseous oxygen systems, seven solvents, plus CFC113 as a baseline, were evaluated as CFC113 replacements. First, the cleaning ability was evaluated with common military lubricants and other common contaminants anticipated to be found on oxygen system components, MIL-PRF-7808 (ester-based gas turbine engine oil), MIL-PRF-83282 (hydraulic fluid), MIL-PRF-27617 (perfluoropolyalkylether-based PTFE thickened grease), MIL-PRF-27617 sprinkled with Arizona road dust, SAE 20W-50 tube bending oil, and 3M 250 tape residue. These solvents were also tested for compatibility with oxygen systems using the liquid oxygen mechanical impact test and by determining the autogenous ignition temperature in pure oxygen. Candidate solvents must also be compatible with elastomer seals. None of the solvents caused permanent damage to the seals. No single solvent performed as well as nor was as universal as CFC113 but several were close.
Inhibition of Werner Syndrome Helicase Activity by Benzo[a]pyrene Diol Epoxide Adducts Can Be Overcome by Replication Protein A (2005)

RecQ helicases are believed to function in repairing replication forks stalled by DNA damage and may also play a role in the intra-S-phase checkpoint, which delays the replication of damaged DNA, thus permitting repair to occur. Since little is known regarding the effects of DNA damage on RecQ helicases, and because the replication and recombination defects in Werner syndrome cells may reflect abnormal processing of damaged DNA associated with the replication fork, we examined the effects of specific bulky, covalent adducts at N(6) of deoxyadenosine (dA) or N(2) of deoxyguanosine (dG) on Werner (WRN) syndrome helicase activity. The adducts are derived from the optically active 7,8-diol 9,10-epoxide (DE) metabolites of the carcinogen benzo[a]pyrene (BaP). The results demonstrate that WRN helicase activity is inhibited in a strand-specific manner by BaP DE-dG adducts only when on the translocating strand. These adducts either occupy the minor groove without significant perturbation of DNA structure (trans adducts) or cause base displacement at the adduct site (cis adducts). In contrast, helicase activity is only mildly affected by intercalating BaP DE-dA adducts that locally perturb DNA double helical structure. This differs from our previous observation that intercalating dA adducts derived from benzo[c]phenanthrene (BcPh) DEs inhibit WRN activity in a strand- and stereospecific manner. Partial unwinding of the DNA helix at BaP DE-dA adduct sites may make such adducted DNAs more susceptible to the action of helicase than DNA containing the corresponding BcPh DE-dA adducts, which cause little or no destabilization of duplex DNA. The single-stranded DNA binding protein RPA, an auxiliary factor for WRN helicase, enabled the DNA unwinding enzyme to overcome inhibition by either the trans-R or cis-R BaP DE-dG adduct, suggesting that WRN and RPA may function together to unwind duplex DNA harboring specific covalent adducts that otherwise block WRN helicase acting alone.
Judicious use of redundant transmissions in multichannel ALOHA networks with deadlines (1999)

This paper shows how to improve the classic multichannel slotted ALOHA protocols by judiciously using redundant transmissions. The focus is on user-oriented requirements: a deadline along with a permissible probability of failing to meet it. Subject to satisfying those, maximization of capacity is the optimization goal. When there is no success/failure feedback prior to the deadline, the use of information dispersal with some redundancy provided by error-correcting codes for the data in conjunction with a replicated, separately transmitted synchronization preamble, is proposed. It is shown to sharply reduce the overhead resulting from the use of shorter packets and to significantly increase the capacity. When the deadline permits several transmission-feedback rounds, we propose a novel replication-based retransmission policy: all attempts except the final one entail the transmission of a single or very few copies, and a larger number of copies are transmitted in the final attempt. This sharply increases channel capacity, even with a single transmitter per station. The proposed approaches are particularly suitable for high-bandwidth satellites with on-board processing.
High data rate acoustic modem for underwater aplications (2014)

The development of an underwater wireless communication systems is becoming a research and a technological priority due to the increasing demand for exploring the potential of oceans in fields such as pharmaceutics, oil, minerals, environmental and biodiversity. However, underwater wireless communications still fail to ensure high data-rate connections which support real time applications. In this work a low power high data-rate acoustic modem is presented, based on a piezoelectric poly (vinylidene fluoride) polymer as a transducer and a Xilinx Field Programmable Gate Array (FPGA) that can be programmed to work with different types of modulations. The system has been validated by the implementation of a full duplex point-to-point communication at 1 Mbps using On-Off Keying (OOK) modulation with a 1 MHz single carrier and it represents a major advance in the state of the art and a breakthrough in underwater acoustic communications, being the first to show the possibility to achieve data rates up to 1Mbps. It was successfully tested with a 1 Mbps rate, achieving a 3×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> Bit Error Rate (BER) using just 1.4 μW of power consumption per bit.
Implementation and Sensorless Vector-Control Design and Tuning Strategy for SMPM Machines in Fan-Type Applications (2006)

This paper presents a complete design methodology for the sensorless vector control of permanent magnet synchronous machine (PMSM) motor drives in fan-type applications. The proposed strategy is built over a linear asymptotic state observer used to estimate the PMSM back-EMF, and a novel tracking controller based on a Phase-Locked Loop (PLL) system, which by synchronizing the estimated and actual d-q frames estimates the rotor speed and position. The paper presents the complete derivation of all associated control-loops, namely state observer, tracking controller, d-q axes current regulator, speed controller, an anti-saturation control loop—which provides inherent operation in the flux-weakening region, and all corresponding anti-windup loops. Detailed design rules are provided for each of these loops, respectively verified through time-domain simulations, frequency-response analysis, and experimental results using a 300 Vdc 3.5 kW PMSM PWM motor-drive, validating both the design methodology and the excellent performance attained by the proposed control strategy.
Steel Construction Evaluation by MLR‐Strategies (1985)

Improvements in design, achieved through a better understanding of fabrication costs, may cause an overall cost reduction for steel structures. Multiple Linear Regression (MLR) provides the mechanism for transformation of data collected by an information system to data which is used in the evaluation of structural steel fabrication costs. The integration of fabrication control and analysis provided by this system permits its implementation in existing fabrication environments, and presents a desperately needed technological gain for the fabrication process. Traditional design approaches which have relied heavily on experience can now be evaluated and improved in terms of cost competitiveness, prior to or during fabrication by the proposed MLR strategy.
Birefringence induced by bends and twists in single-mode optical fiber (1980)

Bend-induced retardation and twist-induced rotation in single-mode optical fibers are important variables in the design of optical fiber current measurement systems. Bend-induced retardation varies with the square of the curvature and is believed caused by a waveguide geometry effect. Twist-induced rotation varies with the angle through which the fiber is twisted and is produced by torsional strain in the fiber. Both effects were found highly reproducible and to have small temperature dependence. Neither effect should significantly limit the performance of optical measurement systems using single-mode fibers.
Intravesicular calcium transient during calcium release from sarcoplasmic reticulum (1991)

The time course of changes in the intravesicular Ca2+ concentration ([Ca2+]i) in terminal cisternal sarcoplasmic reticulum vesicles upon the induction of Ca2+ release was investigated by using tetramethylmurexide (TMX) as an intravesicular Ca2+ probe. Upon the addition of polylysine at the concentration that led to the maximum rate of Ca2+ release, [Ca2+]i decreased monotonically in parallel with Ca2+ release. Upon induction of Ca2+ release by lower concentrations of polylysine, [Ca2+]i first increased above the resting level, followed by a decrease well below it. The release triggers polylysine, and caffeine brought about dissociation of calcium that bound to a nonvesicular membrane segment consisting of the junctional face membrane and calsequestrin bound to it, as monitored with TMX. No Ca2+ dissociation from calsequestrin-free junctional face membranes or from the dissociated calsequestrin was produced by release triggers, but upon reassociation of the dissociated calsequestrin and the junctional face membrane, Ca2+ dissociation by triggers was restored. On the basis of these results, we propose that the release triggers elicit a signal in the junctional face membrane, presumably in the foot protein moiety, which is then transmitted to calsequestrin, leading to the dissociation of the bound calcium; and in SR vesicles, to the transient increase of [Ca2+]i, and subsequently release across the membrane.
Acoustic determination of polymer molecular weights and rotation times (2002)

Abstract An acoustic waveguide device was shown to be sensitive to the molecular weight of poly(ethylene glycol) in solution over a molecular weight range determined by the operating frequency of the device. The acoustic device used generates a shear wave with displacement in the plane of the device surface and normal to the direction of propagation. Liquid over the device exhibits viscous coupling to the oscillating surface, affecting propagation of the acoustic wave. The propagation loss was shown to be directly proportional to the weight percentage of the solute. For a given weight percent of polymer in solution, the loss increased with increasing molecular weight until a maximum loss value was reached; this may be due to the fact that rotational times for polymer molecules increase with molecular weight until they reach a point at which the rotation is limited by the oscillation time on the device surface. The molecular weight at which the maximum loss value was attained was 10,000 g/mol for a device operating at 104 MHz and 3350 g/mol for a device operating at 331 MHz, implying a rotational time of 1 ns for each 2200 increase in molecular weight. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 1490–1495, 2002
Organizing and sharing distributed personal web-service data (2008)

The migration from desktop applications to Web-based services is scattering personal data across a myriad of Web sites, such as Google, Flickr, YouTube, and Amazon S3. This dispersal poses new challenges for users, making it more difficult for them to: (1) organize, search, and archive their data, much of which is now hosted by Web sites; (2) create heterogeneous, multi-Web-service object collections and share them in a protected way; and (3) manipulate their data with standard applications or scripts.
Soft x-ray imager (SXI) onboard ASTRO-H (2012)

Soft X-ray Imager (SXI) is a CCD camera onboard the ASTRO-H satellite which is scheduled to be launched in 2014. The SXI camera contains four CCD chips, each with an imaging area of 31mm&times; 31 mm, arrayed in mosaic, which cover the whole FOV area of 38' &times; 38'. The SXI CCDs are a P-channel back-illuminated (BI) type with a depletion layer thickness of 200 &mu;m. High QE of 77% at 10 keV expected for this device is an advantage to cover an overlapping energy band with the Hard X-ray Imager (HXI) onboard ASTRO-H. Verification with engineering model of the SXI has been performed since 2011. Flight model design was fixed and its fabrication has started in 2012.