gebhart/patrepeval huggingface dataset:
Effect of Interstitial Velocity on the Adsorption of Bacteria onto Soil (2005)

The adsorption of bacteria onto soil is affected by the physical and chemical characteristics of the soil and water, the size and morphology of the bacterial cells, and the water-flow characteristics in the soil. The present study focuses on the latter factor by investigating the effect of the interstitial velocity on the adsorption of bacteria onto soil. Columns of 10 cm diameter and 130 cm height, respectively, were packed with a sandy soil. The columns were saturated with water containing nalidixic acid-resistant Escherichia coli as a bio-tracer at three different pH levels. The columns were maintained at 20°C for 24 h before connecting the column outlet to its inlet by a pump in a closed loop. Water containing the biotracer was re-circulated through the column for another 24 h at three different interstitial velocities. Water samples were taken from a sampling tap connected to the pump at 4-h intervals. These samples were analyzed to determine the biotracer concentration. The results show that more biotracer cells were retained in the soil at the lower interstitial velocity. The higher interstitial velocity resulted in higher shear forces which caused more desorption of the biotracer cells from the surfaces of the soil particles. Bacterial adsorption was higher at the acidic pH value. The survival of the biotracer cells in soil solution was also tested at three different pH levels. The results show that no decline in the biotracer concentration occurred during the test period.
Identification of susceptibility genes for experimental autoimmune encephalomyelitis that overcome the effect of protective alleles at the eae2 locus (2002)

We have previously identified a locus on mouse chromosome 15 (eae2) that regulates susceptibility to experimental autoimmune encephalomyelitis in a cross between the susceptible strain B10.RIII and the resistant strain RIIIS/J. In an effort to verify the protective effect from having two RIIIS/J alleles at eae2, the resistant locus was bred into the susceptible strain in homozygous form. However, the expected effect was not as clear as in the original study. This might be due to an epistatic effect conferred by several unidentified genes in the genome of the resistant strain or due to the environment by genotype interactions, possibly overcoming the effect of protective alleles at eae2. To further the genetic understanding in this disease, a genome-wide linkage screening approach was employed on an F(2) intercross that carried the protective allele at eae2in homozygous form while the rest of the genome segregated between the B10.RIII and RIIIS/J strains as in the original investigation. In the present study we find one region on chromosome 7, not previously identified in this strain combination, that affects the disease at significant logarithm of the odds score and six regions showing suggestive evidence for linkage to disease phenotypes.
Control and Maintenance of Plant Regeneration in Sugarcane Callus Cultures (1988)

Chen, W. H., Davey, M. R., Power, J. B. and Cocking, E. C 1988. Control and maintenance of plant regeneration in sugarcane callus cultures.—J. exp. Bot. 39: 251–261. Sugarcane cultures produced three morphologically distinct types of callus: a white compact callus capable of plant regeneration, a friable non-morphogenic callus and a mucilaginous nodular callus which could revert to these other two types depending on the concentration of 2, 4-D in the culture medium. Leaf explants formed morphogenic callus more readily than excised stem apices, with most prolific callus formation in the dark. Variation was observed in the response of leaf explants, from different sugarcane species, varieties and commercial cultivars, to callus induction. Visual selection of suitable callus at each subculture combined with incubation in the dark and the use of alternating high-low 2, 4-D concentrations in the culture medium, were essential in maintaining the morphogenic callus. Using such a scheme, the capacity for plant regeneration was maintained for over 30 months after callus induction. Morphogenic callus younger than 12 months from induction formed somatic embryos and/or shoot meristems when transferred to a medium with activated charcoal. However, only organogenesis occurred in older cultures. Somatic embryos and/or shoot meristeras produced plants on auxin-free medium, which rooted on medium with 7% w/v sucrose. Over 90% of potted plants were grown to maturity in the glasshouse.
Modulating Photochemical Properties to Enhance the Stability of Electronically Dimmable Eye Protection Devices<sup>†</sup> (2023)

The study evaluates compatibility of stabilizers with dye doped liquid crystal (LC) scaffolds that are used in electronically dimmable materials. The photodegradation of the materials was investigated and suitable stabilizers were evaluated to slow the degradation process. Various types of benzotriazole-based stabilizers were evaluated for stabilizing the liquid crystals. Based on spin trapping experiments, radicals generated upon UV exposure is likely responsible for the degradation of the system. The radical generation is competitively inhibited by the addition of stabilizers.
Throughput and latency of finite-buffer wireless erasure networks with backpressure routing (2012)

We consider the problem of estimating throughput and average latency in wireless erasure networks with nodes having finite buffers. In these networks, packets are either lost due to link erasures or dropped because of full buffers. Further, a finite-buffer adaptation of backpressure routing policy is used. The exact Markov chain modeling of such networks for the sake of performance analysis turns out to be an extremely difficult problem in general due to the large number of states and their complicated transitions. In this paper, we propose a novel iterative method that estimates the performance parameters of such networks with much less complexity comparing to the exact analysis. The proposed framework leads to an accurate estimate of the steady-state probability distribution of buffer occupancies using which analytical expressions are obtained for throughput and average packet delay in the network. Finally, these analytical results are validated via simulations.
Simultaneous Observation of 3-Dimensional Magnetic Stray Field and Surface Structure Using New Force Microscope (1992)

A 3-dimensional (3-D) magnetic stray field and the surface structure have been observed using an atomic and magnetic force microscope (A/MFM) with an optical-beam-deflection force detector. Measurement is carried out by operating the microscope as a surface structure observer in constant repulsive force AFM mode. The 3-D magnetic stray field measurement is done in force gradient MFM mode with probe position control above the surface. Initial results have demonstrated that the 3-D magnetic stray field and surface structure of magneto-optical disk can be imaged simultaneously.
Supplementary Figure 3 from Proapoptotic Activity of Bortezomib in Gastrointestinal Stromal Tumor Cells (2023)

Supplementary Figure 3 from Proapoptotic Activity of Bortezomib in Gastrointestinal Stromal Tumor Cells
ChemInform Abstract: An Anomalous Metalation of a Trimethylsilyl Group. (1987)

Abstract The carbamate (I) is silylated to form the trimethylsilyl derivative (III) which reacts with sBuLi and DMF to give the silanol (IV).
Theoretical Study of Work Function Modification by Organic Molecule-Derived Linear Nanostructure on H−Silicon(100)-2 × 1 (2008)

Tuning of the electronic properties of semiconductors can be achieved by surface modification with organic molecules. In this work, we study, by periodic density functional theory, the change in work function that occurs upon the modification of nominally hydrogen-terminated Si(100)-2 × 1 by chemisorption of substituted styrene molecules. Our results show that monolayers derived from 4-X-styrene molecules, with X being electron donating groups or hydrogen, decrease the work function of the system. Conversely, monolayers derived from 4-X-styrene molecules, with X being electron withdrawing groups, increase the work function of the system. For the molecules used in the modeling, the calculations indicate that the work function can be substantially modified from −1.4 eV (XN(CH3)2) to +1.9 (XNO2) eV relative to H−Si(100)-2 × 1. Because the direction and magnitude of charge transferred upon chemisorption is the same for all molecules, the work function changes are not the result of band bending. The work function modification comes exclusively from the inherent dipoles of the molecules chemisorbed on the surface. The computed dipoles for the monolayers range from −1.3 (XN(CH3)2) to +1.4 (XNO2) Debye. We conclude that substantial local control over some of the electronic properties of silicon can be achieved by the chemisorption of dipole-containing molecules.
Real-time imaging of the membrane cirarging of mamalian cells exposed to nanosecond pulsed electric fields (2004)

For real-time imaging of the transmembrane voltage of Jurkat cells, exposed to nanosecond pulsed electric fields, the cells were stained with a voltage sensitive membrane dye (VSD) and illuminated with a 4.8 ns long dye-laser pulse at various time during the electric field pulse. The stained cells were located in a 100 mum stainless steel electrode arrangement mounted at the stage of an inverted microscope. Due to the weak fluorescence response from the membrane an intensified CCD camera was used for image acquisition. The camera was operated in an open-shutter mode. ANNINE-6, a recently developed ultra-fast VSD, and Di-8-ANEPPS were used for transient membrane voltage monitoring. Best results could be achieved with the ANNINE-6 dye. First results indicate a clear response of the VSDs attached to the membrane in case of exposing the cells to a 60 ns long electric field pulse
Connexin hemichannels mediate glutathione transport and protect lens fiber cells from oxidative stress (2018)

Elevated oxidized stress contributes to lens cataracts, and gap junctions play important roles in maintaining lens transparency. As well as forming gap junctions, connexin (Cx) proteins also form hemichannels. Here, we report a new mechanism whereby hemichannels mediate transport of reductant glutathione into lens fiber cells and protect cells against oxidative stress. We found that Cx50 (also known as GJA8) hemichannels opened in response to H<sub>2</sub>O<sub>2</sub> in lens fiber cells but that transport through the channels was inhibited by two dominant-negative mutants in Cx50, Cx50P88S, which inhibits transport through both gap junctions and hemichannels, and Cx50H156N, which only inhibits transport through hemichannels and not gap junctions. Treatment with H<sub>2</sub>O<sub>2</sub> increased the number of fiber cells undergoing apoptosis, and this increase was augmented with dominant-negative mutants that disrupted both hemichannels formed from Cx46 (also known as GJA3) and Cx50, while Cx50E48K, which only impairs gap junctions, did not have such an effect. Moreover, hemichannels mediate uptake of glutathione, and this uptake protected lens fiber cells against oxidative stress, while hemichannels with impaired transport had less protective benefit from glutathione. Taken together, these results show that oxidative stress activates connexin hemichannels in the lens fiber cells and that hemichannels likely protect lens cell against oxidative damage through transporting extracellular reductants.
Applicability of the<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi mathvariant="bold">k</mml:mi><mml:mo>⋅</mml:mo><mml:mi mathvariant="bold">p</mml:mi></mml:mrow></mml:math>method to modeling of InAs/GaSb short-period superlattices (2009)

We investigate the long-standing controversy surrounding modeling of the electronic spectra of InAs/GaSb short-period superlattices (SPSLs). Most commonly, such modeling for semiconductor heterostructures is based on the $\mathbf{k}\ensuremath{\cdot}\mathbf{p}$ method. However, this method has so far failed to predict the band structure for type-II InAs/GaSb SPSLs. Instead, it has systematically overestimated the energy gap between the electron and heavy-hole minibands, which led to the suggestion that the $\mathbf{k}\ensuremath{\cdot}\mathbf{p}$ method is inadequate for these heterostructures. Our results show that the physical origin of the discrepancy between modeling and experimental results may be the graded and asymmetric InAs/GaSb interface profile. We have performed band-structure modeling within the $\mathbf{k}\ensuremath{\cdot}\mathbf{p}$ method using a realistic interface profile based on experimental observations. Our calculations show good agreement with experimental data, both from our own measurements and from the published literature.
Time evolution of thermodynamic entropy for conservative and dissipative chaotic maps (2000)

We consider several low--dimensional chaotic maps started in far-from-equilibrium initial conditions and we study the process of relaxation to equilibrium. In the case of conservative maps the Boltzmann-Gibbs entropy S(t) increases linearly in time with a slope equal to the Kolmogorov-Sinai entropy rate. The same result is obtained also for a simple case of dissipative system, the logistic map, when considered in the chaotic regime. A very interesting results is found at the chaos threshold. In this case, the usual Boltzmann-Gibbs is not appropriate and in order to have a linear increase, as for the chaotic case, we need to use the generalized q-dependent Tsallis entropy $S_q(t)$ with a particular value of a q different from 1 (when q=1 the generalized entropy reduces to the Boltzmann-Gibbs). The entropic index q appears to be characteristic of the dynamical system.
Design of high rotation frequency composite tubes (2004)

This work relates to the sizing of subcritical and supercritical laminated composite drive shafts. The hollows drive shafts are designed to transmit the torsional load and to minimize the dynamic effects due to rotation. To meet this need, these structures must combined strength, rigidity and lightness. New high modulus carbon fibres can be adapted to a progress in this field. This work presents sizing tools for optimisation of supercritical drive shafts mounted on viscoelastic suspensions. Two items are discussed: dynamic analysis (response to forces excitation; free motion; instability), strength (buckling of thin tubes; torsional strength). Supercritical drive shafts examples made of high modulus fibres or high-strength fibres are presented.
Hip Instability (2011)

Understanding of the etiology and pathology of hip instability has increased in recent years as new information has emerged regarding the disease processes of the hip. Hip instability, heretofore considered uncommon in clinical practice, is increasingly recognized as a pathologic entity. Instability may be classified as traumatic or atraumatic, and diagnosis is made based on patient history, physical examination, and imaging studies. Plain radiography, MRI, MRI arthrography, and hip instability tests (eg, posterior impingement, dial) can be used to confirm the presence of instability. Nonsurgical management options include physical therapy and protected weight bearing. Surgical intervention, whether arthroscopic or open, is required for large acetabular fractures and refractory instability. Knowledge of the etiology and evolving research of hip instability is essential to understand the spectrum of hip disease.
Abstract 3550: Curcumin suppresses growth of human mesothelioma cells in vitro and in vivo, in part, by stimulating apoptosis (2011)

Abstract Malignant Pleural Mesothelioma (MPM) is an aggressive, asbestos-related malignancy of the thoracic pleura. Although platinum-based agents are the first line of therapy, there is an urgent need for second-line therapies to treat the drug-resistant MPM. Cell cycle as well as apoptosis regulatory pathways are frequently altered in MPM and thus remain attractive targets for therapeutic intervention strategies. Curcumin, the major component in the spice turmeric, alone or in combination with other chemotherapeutics has been under investigation for a number of cancers. Here we investigated the biological and molecular responses of MPM cells to Curcumin treatments and the mechanisms involved. Flow-cytometric analyses coupled with western immunoblotting and gene-array analyses were conducted to determine mechanisms of Curcumin-dependent growth suppression of human (H2373, H2452, H2461, and H226) and murine (AB12) MPM cells. Curcumin inhibited MPM cell growth in a dose and time dependent manner while pretreatment of MPM cells with Curcumin enhanced Cisplatin efficacy. Curcumin activated stress-activated p38 kinase, caspases 9 and 3, caused elevated levels of proapoptotic proteins Bax, stimulated PARP cleavage, and apoptosis. In addition, Curcumin treatments stimulated expression of novel transducers of cell growth suppression such as CARP-1, XAF1, and SULF1 proteins. Oral administration of Curcumin inhibited growth of murine MPM cell-derived tumors in vivo in part by stimulating apoptosis. Thus, Curcumin targets cell cycle and promotes apoptosis to suppress MPM growth in vitro and in vivo. Our studies provide a proof-of-principle rationale for further in-depth analysis of MPM growth suppression mechanisms and their future exploitation in development of effective therapeutic treatment options against resistant MPM. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3550. doi:10.1158/1538-7445.AM2011-3550
Dispositifs nanophotoniques pour l'émission thermique (2018)

Abordez les avancées et développements accomplis sur les sources thermiques infrarouges. L’avènement de la nanophotonique a permis de donner un caractère cohérent à la fois spatialement et temporellement à un rayonnement thermique.
Epidermal galactose spurs chytrid virulence and predicts amphibian colonization (2021)

The chytrid fungal pathogens Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans cause the skin disease chytridiomycosis in amphibians, which is driving a substantial proportion of an entire vertebrate class to extinction. Mitigation of its impact is largely unsuccessful and requires a thorough understanding of the mechanisms underpinning the disease ecology. By identifying skin factors that mediate key events during the early interaction with B. salamandrivorans zoospores, we discovered a marker for host colonization. Amphibian skin associated beta-galactose mediated fungal chemotaxis and adhesion to the skin and initiated a virulent fungal response. Fungal colonization correlated with the skin glycosylation pattern, with cutaneous galactose content effectively predicting variation in host susceptibility to fungal colonization between amphibian species. Ontogenetic galactose patterns correlated with low level and asymptomatic infections in salamander larvae that were carried over through metamorphosis, resulting in juvenile mortality. Pronounced variation of galactose content within some, but not all species, may promote the selection for more colonization resistant host lineages, opening new avenues for disease mitigation.
Abstract 773: A heterochromatin gene signature unveils HP1α mediating neuroendocrine prostate cancer development and aggressiveness (2018)

Abstract Neuroendocrine prostate cancer (NEPC) is a lethal subtype of prostate cancer (PCa) arising mostly from adenocarcinoma via NE transdifferentiation following androgen deprivation therapy. However, mechanisms contributing to both NEPC development and its aggressiveness remain elusive. In light of the fact that hyperchromatic nuclei is a distinguishing histopathological feature of NEPC, we identified 36 heterochromatin-related genes that are significantly enriched in NEPC by transcriptomic analyses of our patient-derived xenograft (PDX) models, multiple clinical cohorts, and genetically engineered mouse models. Longitudinal analysis using our unique, first-in-field PDX model of adenocarcinoma-to-NEPC transdifferentiation revealed that, among those 36 heterochromatin-related genes, heterochromatin protein 1α (HP1α) expression is increased early and steadily during NEPC development and remain elevated in the developed NEPC tumor. Its elevated expression is further confirmed in multiple PDX and clinical NEPC samples. Functional studies showed that HP1α knockdown in the NCI-H660 NEPC cell line dramatically inhibits proliferation, completely ablates colony formation, and induces apoptotic cell death, ultimately leading to tumor growth arrest. Its ectopic expression significantly promotes NE transdifferentiation in adenocarcinoma cells subjected to androgen deprivation treatment. Mechanistically, HP1α reduces expression of androgen receptor (AR) and RE1 silencing transcription factor (REST), two crucial transcription factors silenced in NEPC, and enriches the repressive histone mark trimethylation of histone H3 at Lys9 (H3K9me3) on their respective gene promoters. These observations indicate a novel mechanism underlying NEPC development mediated by abnormally expressed heterochromatin genes, with HP1α as an early functional mediator and a potential therapeutic target for NEPC prevention and/or management. Citation Format: Xinpei Ci, Jun Hao, Xin Dong, Stephen Y. Choi, Hui Xue, Sifeng Qu, Ladan Fazli, Francesco Crea, Christopher Ong, Amina Zoubeidi, Housheng H. He, Martin E. Gleave, Colin C. Collins, Dong Lin, Yuzhuo Wang. A heterochromatin gene signature unveils HP1α mediating neuroendocrine prostate cancer development and aggressiveness [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 773.
An Information-Theoretic View of Mixed-Delay Traffic in 5G and 6G (2022)

Fifth generation mobile communication systems (5G) have to accommodate both Ultra-Reliable Low-Latency Communication (URLLC) and enhanced Mobile Broadband (eMBB) services. While eMBB applications support high data rates, URLLC services aim at guaranteeing low-latencies and high-reliabilities. eMBB and URLLC services are scheduled on the same frequency band, where the different latency requirements of the communications render their coexistence challenging. In this survey, we review, from an information theoretic perspective, coding schemes that simultaneously accommodate URLLC and eMBB transmissions and show that they outperform traditional scheduling approaches. Various communication scenarios are considered, including point-to-point channels, broadcast channels, interference networks, cellular models, and cloud radio access networks (C-RANs). The main focus is on the set of rate pairs that can simultaneously be achieved for URLLC and eMBB messages, which captures well the tension between the two types of communications. We also discuss finite-blocklength results where the measure of interest is the set of error probability pairs that can simultaneously be achieved in the two communication regimes.