gebhart/patrepeval huggingface dataset:
The protein phosphatases involved in cellular regulation. Comparison of native and reconstituted Mg-ATP-dependent protein phosphatases from rabbit skeletal muscle (1984)

The 'native' Mg-ATP-dependent protein phosphatase was isolated from rabbit skeletal muscle by a procedure that avoided the use of organic solvents or heating at 90-100 degrees C. The purified enzyme was composed of two major proteins (molecular mass 37 kDa and 31 kDa) that were present in a 1:1 molar ratio, and accounted for 70-80% of the material. The 37-kDa component comigrated with the catalytic subunit of protein phosphatase-1, and its identity with this protein was established by peptide mapping, and by its cleavage to the characteristic 34-kDa and 33-kDa fragments following incubation with chymotrypsin. The 31-kDa protein comigrated with inhibitor-2, and its identity with this protein was established by its heat stability, ability to inhibit protein phosphatase-1 at nanomolar concentrations, and its phosphorylation on a threonine residue by glycogen synthase kinase 3. It is therefore concluded that the 'native' Mg-ATP-dependent protein phosphatase is composed of the catalytic subunit of protein phosphatase-1 (37 kDa) and inhibitor-2 (31 kDa) in a 1:1 molar ratio. The 'native' Mg-ATP-dependent protein phosphatase had virtually identical properties to the enzyme reconstituted from inhibitor-2 and the 37-kDa catalytic subunit of protein phosphatase-1. Each preparation had a similar specific activity and was inhibited by identical concentrations of inhibitor-1. Both enzymes could be activated by incubation with glycogen synthase kinase-3 and Mg-ATP, or by Mn2+ and trypsin (or chymotrypsin). However, Mn2+ alone, or proteinase digestion in the absence of Mn2+, failed to activate either preparation. Incubation with glycogen synthase kinase-3 and Mg-ATP did not dissociate the 'native' or 'reconstituted' enzymes, whereas treatment with Mn2+ and trypsin decreased their apparent molecular masses from 70 kDa to 35 kDa. Incubation with chymotrypsin converted the 'native' and 'reconstituted' enzymes to forms that required preincubation with glycogen synthase kinase-3, Mg-ATP and inhibitor-2, in order to exhibit catalytic activity. The Mg-ATP-dependent protein phosphatase reconstituted from the 'nicked' 33-kDa catalytic subunit dissociated upon activation, in contrast to the enzyme reconstituted from the undegraded 37-kDa catalytic subunit. The results suggest that a 3-4-kDa fragment at one end of the polypeptide is involved in strengthening interaction between the undegraded 37-kDa catalytic subunit and the phosphorylated form of inhibitor-2.
Maintenance of gene silencing by the coordinate action of the H3K9 methyltransferase G9a/KMT1C and the H3K4 demethylase Jarid1a/KDM5A (2012)

Chromatin remodeling is essential for controlling the expression of genes during development. The histone-modifying enzyme G9a/KMT1C can act both as a coactivator and a corepressor of transcription. Here, we show that the dual function of G9a as a coactivator vs. a corepressor entails its association within two distinct protein complexes, one containing the coactivator Mediator and one containing the corepressor Jarid1a/KDM5A. Functionally, G9a is important in stabilizing the Mediator complex for gene activation, whereas its repressive function entails a coordinate action with the histone H3 lysine 4 (H3K4) demethylase Jarid1a for the maintenance of gene repression. The essential nature of cross-talk between the histone methyltransferase G9a and the demethylase Jarid1a is demonstrated on the embryonic E(y)-globin gene, where the concurrent introduction of repressive histone marks (dimethylated H3K9 and dimethylated H3K27) and removal of activating histone mark (trimethylated H3K4) is required for maintenance of gene silencing. Taken together with our previous demonstration of cross-talk between UTX and MLL2 to mediate activation of the adult β(maj)-globin gene, these data suggest a model where "active" and "repressive" cross-talk between histone-modifying enzymes coexist on the same multigene locus and play a crucial role in the precise control of developmentally regulated gene expression.
Electromagnetic pulse excitation of finite- and infinitely-long lossy conductors over a lossy ground plane (2017)

This paper details a model for the response of a finite- or an infinite-length wire interacting with a conducting ground to an electromagnetic pulse excitation. We develop a frequency–domain method based on transmission line theory that we name ATLOG – Analytic Transmission Line Over Ground. This method is developed as an alternative to full-wave methods, as it delivers a fast and reliable solution. It allows for the treatment of finite or infinite lossy, coated wires, and lossy grounds. The cases of wire above ground, as well as resting on the ground and buried beneath the ground are treated. The reported method is general and the time response of the induced current is obtained using an inverse Fourier transform of the current in the frequency domain. The focus is on the characteristics and propagation of the transmission line mode. Comparisons with full-wave simulations strengthen the validity of the proposed method.
Optimizing test approaches for the detection of exposed metal surfaces within a chromatographic flow path (2022)

It is critical to the success of any chromatography-based assay that the performance of the LC instrument be checked for its readiness and ability to perform the intended analysis. This includes gaging the suitability of a system to fulfill the purpose of different types of methods. One type of analysis that requires special consideration is the analysis of compounds which are prone to a particular form of non-specific binding, namely metal adsorption, where analytes interact and potentially adsorb to metal contained within the chromatographic flow path. For an analysis of compounds which are susceptible to metal adsorption, ideally a system suitability test would be performed to ensure there will not be any sample loss or detrimental peak shape effects resulting from potential analyte-to-metal interactions. To help chromatographers assess system inertness concerns like this, we have developed a method of testing LC systems for metal interactions using adenosine 5'-(α,β-methylene)diphosphate (AMPcP). This nucleotide analog has been confirmed to have a propensity to adsorb to titanium and stainless-steel frits and is resistant to hydrolysis and stable to long-term storage and repeat use (as is befitting of any reagent proposed for system suitability testing). AMPcP has been used in a flow injection test (no column in-line) to monitor for losses in recovery and peak shape perturbations that can potentially be present in any chromatography system manufactured with one or more metal based components. In this approach, sequential injections of AMPcP were made without a column and various peak attributes were monitored and ultimately correlated to the amount of metal surface area in the flow path. The ability of this method to discriminate between inert chromatographic surfaces versus exposed metal surfaces was verified by comparing peak areas, peak shapes, and injection repeatability for AMPcP using a UHPLC equipped with MP35N metal alloy components versus an equivalent UHPLC equipped with an ethylene bridged hybrid organic-inorganic surface (or so-called hybrid surface technology). Injections of caffeine were also explored to establish a negative control for this system suitability measurement. Caffeine does not interact with metal surfaces and can therefore give an instrument specific representation of peak shape and dispersion as well as an indication of overall mechanical system performance. Additionally, replicate injections of AMPcP and caffeine onto a UHPLC partially configured with hybrid surface technology (HST) readily identified exposed metal surfaces through an increased peak area relative standard deviation as well as a reduction in absolute recovery. Finally, a novel visualization tool was developed to provide an alternative method of determining system inertness without having to perform chromatographic calculations but instead a graphical peak shape comparison between a negative control, caffeine, and the metal sensitive AMPcP test probe.
Passivation and process engineering approaches of halide perovskite films for high efficiency and stability perovskite solar cells (2021)

Recent advances on passivation and morphology engineering approaches adopted to obtain high efficiency and stability in perovskite solar cells are thoroughly reviewed.
3000V, 25A pulse power asymmetrical highly interdigitated SiC Thyristors (2010)

A 3000 V, 25 A asymmetrical Silicon Carbide (SiC) Thyristor for pulse power applications is described here. It was fabricated on ultra low micropipe density 4H-SiC wafers. The device design, fabrication, wafer testing, packaging, static and dynamic characteristics are presented. The devices' chip area is 4 mm × 4 mm, the yield after screening for blocking voltage, leakage current, forward drop, and latching is over 80%, a very high yield by the standards of SiC power devices. The chips are packaged in a 200°C capable, low profile, surface mount package with a low junction to case thermal resistance. The chips were tested both on-wafer and as packaged parts and exhibit very low leakage current (less than 1 ¿A at 3000 V and 25°C, less than 10 ¿A at 3000 V and 150°C), low forward drop at 25 A (4.55 V at 25A). Several devices were packaged and subsequently tested over several days under high current with no forward voltage degradation observed. While the devices were designed for 3 kV blocking voltage, the actual packaged parts had a breakdown voltage >3.5 kV. Pulse tests were performed to determine the devices' maximum pulse current, di/dt, and dv/dt performance.
P4) Technologies for Reading and Writing Omes. (2012)

Lowering the cost of technologies for reading and writing DNA (and biological systems) by a million-fold since 2004 means a 5-fold faster exponential than Moore's law. This enables radical engineering of biofuels, chemicals, materials, foods, multi-virus resistance, and atomically precise smart materials. It has also lead to the only fully open-access human Genome+Environment=Trait (GET) data (& interpretation tools: Evidence.PersonalGenomes.org). This impacts not only inherited genomes, but also day-to-day genomic variation -- immune, stem cell proliferation, microbes, allergens, vaccines, & subcellular-resolution epigenomics. The latest technologies include Fluorescent In Situ Sequencing (FISSEQ) and human genome engineering for personal functional diagnostics, personal synthetic tissues, microbiome & immunome transplantation therapies.
Antigen spacing on protein nanoparticles influences antibody responses to vaccination (2023)

Immunogen design approaches aim to control the specificity and quality of antibody responses to enable the creation of next-generation vaccines with improved potency and breadth. However, our understanding of the relationship between immunogen structure and immunogenicity is limited. Here we use computational protein design to generate a self-assembling nanoparticle vaccine platform based on the head domain of influenza hemagglutinin (HA) that enables precise control of antigen conformation, flexibility, and spacing on the nanoparticle exterior. Domain-based HA head antigens were presented either as monomers or in a native-like closed trimeric conformation that prevents exposure of trimer interface epitopes. These antigens were connected to the underlying nanoparticle by a rigid linker that was modularly extended to precisely control antigen spacing. We found that nanoparticle immunogens with decreased spacing between closed trimeric head antigens elicited antibodies with improved hemagglutination inhibition (HAI) and neutralization potency as well as binding breadth across diverse HAs within a subtype. Our "trihead" nanoparticle immunogen platform thus enables new insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used to generate next-generation vaccines against influenza and other viruses.
Effect of local heating of the rat testis on the levels in interstitial fluid of a putative paracrine regulator of the Leydig cells and its relationship to changes in Sertoli cell secretory function (1987)

Rat testes were exposed to heat (43 degrees C) for 15 or 30 min to induce moderate or severe disruption of spermatogenesis, respectively. Over 3-42 days after treatment, testicular morphology and weight, the serum concentrations of FSH and the concentrations in interstitial fluid of testosterone, androgen-binding protein (ABP) and a factor(s) capable of stimulating Leydig cell testosterone secretion were monitored. Moderate seminiferous tubule damage induced by 15 min heat exposure caused a small decrease (20%) in testicular weight, but did not affect the other measures, other than transiently. In contrast, after exposure of testes to heat for 30 min there was a major and progressive decline in testicular weight throughout the experimental period, reaching 39% of control values by 42 days. In these animals, the serum concentrations of FSH were significantly increased (P less than 0.01) throughout the period of study as also where the serum and interstitial fluid concentrations ABP (P less than 0.05-0.01) and levels of interstitial fluid factor (P less than 0.01). It is concluded that the activity of the interstitial fluid factor(s) can be increased by inducing severe but selective disruption of spermatogenesis, whereas moderate disruption has no effect. Moreover, as ABP secretion into interstitial fluid was increased after severe but not moderate disruption, this suggests that in such animals proportionately more ABP may be secreted via the base of the Sertoli cell. The parallel changes in activity of the interstitial fluid factor(s) and concentrations of ABP in interstitial fluid also provides further circumstantial evidence that these products may have a common (Sertoli cell) origin.
Interactions for two solitons in Raman-pumped fibers (1990)

The interactions between two neighboring solitons in a bidirectional Raman-pumped fiber system is considered. We choose two different separations between two adjacent solitons and three different pumping periods to illustrate this work. For the separation equal to 10 times the soliton pulse width, the interaction between solitons is negligible. With the BPM simulation, the longest acceptable pumping period is about 20 km.
Data from Combined Aurora Kinase A (AURKA) and WEE1 Inhibition Demonstrates Synergistic Antitumor Effect in Squamous Cell Carcinoma of the Head and Neck (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Human papillomavirus (HPV)-negative head and neck squamous cell carcinomas (HNSCC) commonly bear disruptive mutations in &lt;i&gt;TP53&lt;/i&gt;, resulting in treatment resistance. In these patients, direct targeting of p53 has not been successful, but synthetic lethal approaches have promise. Although Aurora A kinase (AURKA) is overexpressed and an oncogenic driver, its inhibition has only modest clinical effects in HPV-negative HNSCC. We explored a novel combination of AURKA and WEE1 inhibition to overcome intrinsic resistance to AURKA inhibition.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; AURKA protein expression was determined by fluorescence-based automated quantitative analysis of patient specimens and correlated with survival. We evaluated treatment with the AURKA inhibitor alisertib (MLN8237) and the WEE1 inhibitor adavosertib (AZD1775), alone or in combination, using &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; HNSCC models.&lt;/p&gt;Results:&lt;p&gt;Elevated nuclear AURKA correlated with worse survival among patients with p16(−) HNSCC. Alisertib caused spindle defects, G&lt;sub&gt;2&lt;/sub&gt;–M arrest and inhibitory CDK1 phosphorylation, and cytostasis in &lt;i&gt;TP53&lt;/i&gt; mutant HNSCC FaDu and UNC7 cells. Addition of adavosertib to alisertib instead triggered mitotic entry and mitotic catastrophe. Moreover, in FaDu and Detroit 562 xenografts, this combination demonstrated synergistic effects on tumor growth and extended overall survival compared with either vehicle or single-agent treatment.&lt;/p&gt;Conclusions:&lt;p&gt;Combinatorial treatment with adavosertib and alisertib leads to synergistic antitumor effects in &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; HNSCC models. These findings suggest a novel rational combination, providing a promising therapeutic avenue for &lt;i&gt;TP53-&lt;/i&gt;mutated cancers.&lt;/p&gt;&lt;/div&gt;
Tetrahedralization of Point Sets Using Expanding Spheres (2004)

The expanding sphere algorithm computes an alpha shape tetrahedralization of a point set. Starting with a seed tetrahedron, the circumscribing sphere is squeezed through each face until it either touches another point or exceeds a preset radius. If no point is found, that face of the tetrahedron is part of the surface of an object. If a point is found, a new tetrahedron is constructed. This process is iterated until all the faces of the tetrahedra have been processed and no more connected points can be found. If there are points left over, the process is iterated, creating additional objects. The algorithm generates a list of objects, with an alpha shape tetrahedralization and a surface triangulation for each. Any points that cannot be made part of a valid tetrahedron are also returned in the extra points list. The algorithm is efficient for uniformly distributed point sets, with a running time that is linear in the number of points for such sets. Since the operations are local, it is also robust.
Data from A Key Regulatory Role of the Transcription Factor NFATc2 in Bronchial Adenocarcinoma via CD8<sup>+</sup> T Lymphocytes (2023)

&lt;div&gt;Abstract&lt;p&gt;The Ca&lt;sup&gt;2+&lt;/sup&gt;-regulated calcineurin/nuclear factor of activated T cells (NFAT) cascade controls alternative pathways of T-cell activation and peripheral tolerance. Here, we describe reduction of NFATc2 mRNA expression in the lungs of patients with bronchial adenocarcinoma. In a murine model of bronchoalveolar adenocarcinoma, mice lacking NFATc2 developed more and larger solid tumors than wild-type littermates. The extent of central tumor necrosis was decreased in the tumors in NFATc2&lt;sup&gt;(−/−)&lt;/sup&gt; mice, and this finding was associated with reduced tumor necrosis factor-α and interleukin-2 (IL-2) production by CD8&lt;sup&gt;+&lt;/sup&gt; T cells. Adoptive transfer of CD8&lt;sup&gt;+&lt;/sup&gt; T cells of NFATc2&lt;sup&gt;(−/−)&lt;/sup&gt; mice induced transforming growth factor-β&lt;sub&gt;1&lt;/sub&gt; in the airways of recipient mice, thus supporting CD4&lt;sup&gt;+&lt;/sup&gt;CD25&lt;sup&gt;+&lt;/sup&gt;Foxp-3&lt;sup&gt;+&lt;/sup&gt;glucocorticoid-induced tumor necrosis factor receptor (GITR)&lt;sup&gt;+&lt;/sup&gt; regulatory T (T&lt;sub&gt;reg&lt;/sub&gt;) cell survival. Finally, engagement of GITR in NFATc2&lt;sup&gt;(−/−)&lt;/sup&gt; mice induced IFN-γ levels in the airways, reversed the suppression by T&lt;sub&gt;reg&lt;/sub&gt; cells, and costimulated effector CD4&lt;sup&gt;+&lt;/sup&gt;CD25&lt;sup&gt;+&lt;/sup&gt; (IL-2Rα) and memory CD4&lt;sup&gt;+&lt;/sup&gt;CD127&lt;sup&gt;+&lt;/sup&gt; (IL-7Rα) T cells, resulting in abrogation of carcinoma progression. Agonistic signaling through GITR, in the absence of NFATc2, thus emerges as a novel possible strategy for the treatment of human bronchial adenocarcinoma in the absence of NFATc2 by enhancing IL-2Rα&lt;sup&gt;+&lt;/sup&gt; effector and IL-7Rα&lt;sup&gt;+&lt;/sup&gt; memory-expressing T cells. [Cancer Res 2009;69(7):3069–76]&lt;/p&gt;&lt;/div&gt;
Single-Shot Vaccines against Bovine Respiratory Syncytial Virus (BRSV): Comparative Evaluation of Long-Term Protection after Immunization in the Presence of BRSV-Specific Maternal Antibodies (2021)

The induction of long-lasting clinical and virological protection is needed for a successful vaccination program against the bovine respiratory syncytial virus (BRSV). In this study, calves with BRSV-specific maternally derived antibodies were vaccinated once, either with (i) a BRSV pre-fusion protein (PreF) and Montanide<sup>TM</sup> ISA61 VG (ISA61, <i>n</i> = 6), (ii) BRSV lacking the SH gene (ΔSHrBRSV, <i>n</i> = 6), (iii) a commercial vaccine (CV, <i>n</i> = 6), or were injected with ISA61 alone (<i>n</i> = 6). All calves were challenged with BRSV 92 days later and were euthanized 13 days post-infection. Based on clinical, pathological, and proteomic data, all vaccines appeared safe. Compared to the controls, PreF induced the most significant clinical and virological protection post-challenge, followed by ΔSHrBRSV and CV, whereas the protection of PreF-vaccinated calves was correlated with BRSV-specific serum immunoglobulin (Ig)G antibody responses 84 days post-vaccination, and the IgG antibody titers of ΔSHrBRSV- and CV-vaccinated calves did not differ from the controls on this day. Nevertheless, strong anamnestic BRSV- and PreF-specific IgG responses occurred in calves vaccinated with either of the vaccines, following a BRSV challenge. In conclusion, PreF and ΔSHrBRSV are two efficient one-shot candidate vaccines. By inducing a protection for at least three months, they could potentially improve the control of BRSV in calves.
Banded Waveguides: Towards Physical Modeling of Bowed Bar Percussion Instruments (1999)

Efficient physical models of bar percussion instruments which preserve spatial sampling are not yet available. In this paper, banded waveguides are proposed as an efficient method for simulating the physics of bars including spatial sampling. In addition two other models are investigated. One is a generalization of the waveguide idea replacing unit delays by all-pass filters modeling the phase delay characteristics. The other extends on existing finite difference (FD) methods. According to this study all-pass filter chains show no advantages over FDs in terms of performance and physical realism. Finally, real bars were the target of experimental measurements.
Large local optical activity in fractal aggregates of nanoparticles (2001)

Large local optical activity in fractal aggregates of silver nanoparticles has been observed by means of photon scanning tunneling microscopy. The effect occurs because resonant plasmon modes in random fractals can have handedness in spatial distribution of their amplitudes. In agreement with experimental observations, numerical simulations show dramatic difference in dipole-moment distributions for right- and left-circularly polarized incident light when the cluster size is comparable with or larger than the wavelength. Variations in the local parameter describing the circular intensity difference of scattered light show that fractal aggregates are characterized by broad and random distributions of chiral plasmon modes.
A distributed channel probing scheme for wireless networks (2002)

This paper presents a distributed channel probing scheme for wireless networks. By transmitting a probing signal in a channel and measuring the signal-to-interference ratio (SIR), a wireless node can estimate channel admissibility and predict its required transmission power without fully powering up. The channel probing scheme can be used as part of a distributed channel allocation algorithm, and simulations have shown that it outperforms other schemes.
Systematic review and meta-analysis: islet autotransplantation after pancreatectomy for minimizing diabetes (2011)

IAT postpancreatectomy offers some patients a chance for insulin independence. Better data reporting are essential to establish the risks and benefits of IAT after pancreatic surgery.