gebhart/patrepeval huggingface dataset:
Modular Reporter Hairpin Ribozymes for Analyzing Molecular Interactions (2008)

Methods for the detection of biologically relevant interactions by highly precise catalytic control elements based on hairpin ribozymes, and their subsequent analysis are described. These include ribozyme design, catalytic performance in real time as a function of fluorescence signal amplification, and applications for sensing protein and nucleic acid interactions in high-throughput formats. Detailed instructions for two of our main reporter ribozyme formats that either follow repressible or inducible regulatory mechanisms are provided. We have shown that these techniques can be applied for detecting diverse target molecules including microRNAs, or protein-protein interactions. These reporter systems thus represent a general way to obtain signal-amplifying sensors for diverse applications in molecular profiling.
Persistence of Coxsackievirus B4 in Pancreatic β Cells Disturbs Insulin Maturation, Pattern of Cellular Proteins, and DNA Methylation (2021)

Coxsackievirus-B4 (CV-B4) can persist in pancreatic cell lines and impair the phenoytpe and/or gene expressions in these cells; however, the models used to study this phenomenon did not produce insulin. Therefore, we investigated CV-B4 persistence and its consequences in insulin-producing pancreatic β cells. The insulin-secreting rat β cell line, INS-1, was infected with CV-B4. After lysis of a large part of the cell layer, the culture was still maintained and no additional cytopathic effect was observed. The amount of insulin in supernatants of cell cultures persistently infected with CV-B4 was not affected by the infection; in fact, a larger quantity of proinsulin was found. The mRNA expression of pro-hormone convertase 2, an enzyme involved in the maturation of proinsulin into insulin and studied using real-time reverse transcription-polymerase chain reaction, was inhibited in infected cultures. Further, the pattern of 47 cell proteins analyzed using Shotgun mass spectrometry was significantly modified. The DNA of persistently infected cell cultures was hypermethylated unlike that of controls. The persistent infection of INS-1 cells with CV-B4 had a deep impact on these cells, especially on insulin metabolism. Cellular changes caused by persistent CV-B4 infection of β cells can play a role in type 1 diabetes pathogenesis.
Advax adjuvant formulations promote protective immunity against aerosol Mycobacterium tuberculosis in the absence of deleterious inflammation and reactogenicity (2020)

Abstract The development of safe and effective adjuvants is a critical goal of vaccine development programs. In this report, we defined the immunostimulatory profile and protective effect against aerosol Mycobacterium tuberculosis infection of vaccine formulations incorporating the semi-crystalline adjuvant δ-inulin (Advax). Advax formulated with CpG oligonucleotide and the QS-21 saponin (Advax CpQS ) was the most effective combination, demonstrated by the capacity of CysVac2/Advax CpQS to significantly reduce the bacterial burden in the lungs of M. tuberculosis -infected mice. CysVac2/Advax CpQS protection was associated with rapid influx of neutrophils, macrophages and monocytes to the site of vaccination and the induction of antigen-specific IFN-γ + /IL-2 + /TNF + polyfunctional CD4 + T cells in the lung. When compared to the highly potent adjuvant combination of monophosphoryl lipid A and dimethyldioctadecylammonium bromide (MPL/DDA), Advax CpQS imparted a similar level of protective efficacy yet without the profound stimulation of inflammatory cytokines and vaccination site ulceration observed with MPL/DDA. Addition of DDA to CysVac2/ Advax CpQS further improved the protective effect of the vaccine, which correlated with increased polyfunctional CD4 + T cells in the lung but with no increase in vaccine reactogenicity. The data demonstrate that Advax formulations can decouple protective tuberculosis immunity from reactogenicity, making them ideal candidates for human application. Highlights Advax adjuvant formulations improve pulmonary protection against aerosol Mycobacterium tuberculosis infection Different combinations of adjuvant components markedly influence the level of protection observed Protection is associated with the rapid influx of myeloid cells to the site of vaccination and the induction of antigen-specific polyfunctional CD4 + T cells in the lung. Advax formulations abrogate vaccine-site ulceration and inflammatory cytokine production
Localization-delocalization transition in metal-dielectric films (2004)

Anderson localization in random potential fields has been studied extensively for the last fifty years. It is commonly accepted that in 1D and 2D systems characterized by non-correlated random potential distributions, all states are exponentially localized. In this paper we investigate the eigen-problem for Surface Plasmons (SP) in random metal-dielectric films. We show that short-range correlations presented in the governing Kirchhoff's Hamiltonian (KH) result in delocalization of the eigenstates at the band center. The delocalization is shown to be manifested through power law singularities for the density of states and SP localization lengths. The study of the system size dependence of the nearest neighbor's level spacing distributions shows a gradual shift of the SP eigen-problem from a metallic phase for small system sizes into an insulating quantum phase for infinite systems. It reveals a genuine metal-insulator transition that takes place in the composite and is characterized by quantum percolation threshold P<sub>q</sub> which is higher than the corresponding geometrical critical concentration P<sub>c</sub>.
Reactions of SiCl groups in amorphous SiO2 with mobile interstitial chemical species: Formation of interstitial Cl2 and HCl molecules, and role of interstitial H2O molecules (2005)

Reactions of the network-bound chloride (SiCl) groups in amorphous SiO2 (a-SiO2 or SiO2 glass) with mobile interstitial oxygen (O2), water (H2O), and hydrogen (H2) molecules thermally loaded from ambient atmosphere and with mobile radicals created by exposure to F2 laser light (λ=157nm,hν=7.9eV) were investigated. Reactions of the SiCl groups with O2 and H2O produce interstitial chlorine (Cl2) and hydrogen chloride (HCl) molecules, respectively. An infrared-absorption band appearing at ∼2815cm−1 is assigned to the interstitial HCl. The SiCl groups do not react with H2 below 400°C. However, sequential gas loading first with O2, then with H2 leads to the production of interstitial H2O, which decomposes the SiCl groups into HCl. Furthermore, the formation of the interstitial HCl with exposure to F2 laser light, most likely due to the cracking of the Si–Cl bonds with photogenerated hydrogen atoms (H0), was demonstrated. These findings yield a general picture of the reactions of the chlorine-related species in a-SiO2 and demonstrate the significant influence of even minor amounts (&amp;lt;1018cm−3) of interstitial H2O on defect formation and annihilation processes.
Deep learning-based defect detection using large FOV SEM for 28 nm pitch BEOL layer patterned with 0.33NA single exposure EUV (2021)

As we strive toward smaller and smaller pitches and new 3D constructs to enable device scaling, thorough defect characterization at wafer scale is essential during the early phases of process optimization. Often CD (critical dimension) variations and roughness lead to high SEM (scanning electron microscope) inspection noise. It is important to suppress this noise and increase DOI (defect of interest) SNR (signal-to-noise ratio) for better detection efficiency while maintaining high speed for meaningful wafer coverage. In this work, we describe experiments and show characterization results for capturing EUV (extreme ultraviolet) stochastic defects across various test structures of 28nm pitch devices that have been patterned using single exposure 0.33NA EUV lithography. We have used KLA eSL10TM for SEM inspection and analysis. The tool can also be used for high resolution and high-speed metrology, providing quick feedback on observed defect signatures and further root cause analysis.
Bovine Bone Morphogenetic Protein (bBMP) Fraction-induced Repair of Craniotomy Defects in the Rhesus Monkey (Macaca speciosa) (1987)

Large cranial defects do not always heal spontaneously, especially in humans; often they have to be obturated with metallic or acrylic fillers. Bilateral cranial trephine defects, measuring 14-20 mm in diameter, were created in three Rhesus monkeys, providing a typical primate model system for investigations in comparative physiology of bone regeneration. Each skull had one control and one experimental trephine defect. Control defects were implanted with bovine serum albumin (BSA). Experimental defects were implanted with 100-200 mg of a partially purified fraction of bovine bone morphogenetic protein (bBMP) in two monkeys. In one monkey, the BMP was incorporated in a 1:1 poly(lactic) poly(glycollic) acid copolymer, high-viscosity formula. The animals were killed at eight weeks, ten weeks, and 16 weeks after implantation. The tissue responses were analyzed by computed histomorphometry and routine histologic examination. At each time interval, the BMP implanted defects produced more complete regeneration than the control implants. The morphogenetic response occurred in the following sequences: mesenchymal cell proliferation, chondrogenesis, and increased bone formation. BMP-induced osteogenesis may initiate the regenerative process. The copolymer releases BMP but may constitute a barrier to the end stages of replacement by new bone, and would be more useful in a low-viscosity rapidly biodegradable form.
Energy harvesting and implantable medical devices - first order selection criteria (2011)

Power density is the critical attribute of an APS for use in an IMD, and benchmark value of at least 0.01 mW/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> has been established in order for an APS to be volumetrically superior to existing primary and rechargeable battery technologies. The benchmark power density enables the use of simple, physics-based models to quickly evaluate the potential viability of proposed APS technologies.
Anticancer and immunomodulatory activities of novel 1,8-naphthyridine derivatives (2009)

A number of 1,8-naphthyridine derivatives (22-62) have been synthesized and screened for their in vitro cytotoxicity against eight tumors and two non-tumor cell lines. Halogen substituted 1,8-naphthyridine-3-caboxamide derivatives showed potent activity with compound 47 having IC(50) of 0.41 and 0.77 microM on MIAPaCa and K-562 cancer cell lines, respectively while, compound 36 had IC(50) of 1.19 microM on PA-1 cancer cell line. However, one of the unsubstituted 1,8-naphthyridine-C-3'-heteroaryl derivative 29 showed potent cytotoxicity with IC(50) of 0.41 and 1.4 microM on PA-1 and SW620 cancer cell lines, respectively. These compounds were also evaluated for anti-inflammatory activity as suggested by downregulation of proinflammaotory cytokines.
Selective Janus Kinase 2 (JAK2) Pseudokinase Ligands with a Diaminotriazole Core (2020)

Janus kinases (JAKs) are non-receptor tyrosine kinases that are essential components of the JAK-STAT signaling pathway. Associated aberrant signaling is responsible for many forms of cancer and disorders of the immune system. The present focus is on the discovery of molecules that may regulate the activity of JAK2 by selective binding to the JAK2 pseudokinase domain, JH2. Specifically, the Val617Phe mutation in JH2 stimulates the activity of the adjacent kinase domain (JH1) resulting in myeloproliferative disorders. Starting from a non-selective screening hit, we have achieved the goal of discovering molecules that preferentially bind to the ATP binding site in JH2 instead of JH1. We report the design and synthesis of the compounds and binding results for the JH1, JH2, and JH2 V617F domains, as well as five crystal structures for JH2 complexes. Testing with a selective and non-selective JH2 binder on the autophosphorylation of wild-type and V617F JAK2 is also contrasted.
Variational analysis of new shape length extensional mode quartz crystal resonator taking account of lateral motion (2002)

A new shape length extensional mode quartz crystal resonator with a resonant frequency of 500 kHz to 1.536 MHz is proposed. It is especially suitable for a surface mounting. The resonant frequency, the frequency temperature behavior and the electrical characteristics of the new shape resonator, taking lateral motion into account, are analyzed and examined. In the analysis procedure, an equation of motion of the new shape length extensional mode quartz crystal resonator consisting of a vibrational portion and supporting portions is derived from an energy method. From the obtained equation of motion, the frequency equation is easily calculated. The frequency characteristics, the frequency temperature behavior, and the electrical characteristics of the resonator are analyzed and compared with the measured values. It is shown that the results agree well.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Degradable/cytocompatible and pH responsive amphiphilic conetwork gels based on agarose-graft copolymers and polycaprolactone (2015)

Amphiphilic conetwork (APCN) gels have emerged as an important class of biomaterials due to their diverse applications. APCN gels based on biocompatible/biodegradable polymers are useful for controlled release and tissue engineering applications. Herein, we report a facile synthesis of APCN gel films by click type sequential nucleophilic substitution reaction between pendent tertiary amine groups of agarose-g-poly(methyl methacrylate)-b(co)-poly(2-dimethylamino)ethyl methacrylate [Agr-g-PMMA-b(co)-PDMA] copolymers and activated benzyl chloride groups of polychloromethyl styrene or benzyl methyl chloride terminated polycaprolactone. A linear triblock copolymer (PDMA-b-PMMA-b-PDMA) containing a central PMMA block and end PDMA blocks was also employed for the synthesis of APCN gels for comparison purposes. These APCN gels exhibit co-continuous nanophase morphology, pH responsive water swelling and pH triggered release of hydrophobic and hydrophilic drugs. These gels are biodegradable/cytocompatible as confirmed by MTT assay and hemolysis experiment. The degraded species undergo micellization in aqueous environment and display a low critical micelle concentration. Milled APCN gel particles are injectable through a hypodermic syringe. This synthesis approach is extremely useful for the preparation of a library of APCN gels of diverse architectures and compositions for biomedical applications.
Efficacy of metal nanoparticles as a control tool against adult mosquito vectors: A review (2022)

Presently, there is a need to develop effective and novel modes of control for mosquitoes, which remain a key driver of infectious disease transmission throughout the world. Control methods for these vectors have historically relied on a limited number of active ingredients (AIs) that have not experienced significant change in usage since the mid-20 th century. The resulting development of widespread insecticide resistance has consequently increased the risk for future vector-borne disease outbreaks. Recently, metal nanoparticles have been explored for potential use in mosquito control due to their demonstrated toxicity against mosquitoes at all life stages. However, the majority of studies to date have focused on the larvicidal efficacy of metal nanoparticles with few studies examining their adulticidal potential. In this review, we analyze the current literature on green synthesized metal nanoparticles and their effect on adult mosquitoes.
Biochemical Analysis of Plant Protection Afforded by a Nonpathogenic Endophytic Mutant of Colletotrichum magna1 (1999)

A nonpathogenic mutant of Colletotrichum magna (path-1) was previously shown to protect watermelon (Citrullus lanatus) and cucumber (Cucumis sativus) seedlings from anthracnose disease elicited by wild-type C. magna. Disease protection was observed in stems of path-1-colonized cucurbits but not in cotyledons, indicating that path-1 conferred tissue-specific and/or localized protection. Plant biochemical indicators of a localized and systemic (peroxidase, phenylalanine ammonia-lyase, lignin, and salicylic acid) "plant-defense" response were investigated in anthracnose-resistant and -susceptible cultivars of cucurbit seedlings exposed to four treatments: (1) water (control), (2) path-1 conidia, (3) wild-type conidia, and (4) challenge conditions (inoculation into path-1 conidia for 48 h and then exposure to wild-type conidia). Collectively, these analyses indicated that disease protection in path-1-colonized plants was correlated with the ability of these plants to mount a defense response more rapidly and to equal or greater levels than plants exposed to wild-type C. magna alone. Watermelon plants colonized with path-1 were also protected against disease caused by Colletotrichum orbiculare and Fusarium oxysporum. A model based on the kinetics of plant-defense activation is presented to explain the mechanism of path-1-conferred disease protection.
2mm catheter design for endoscopic optical coherence tomography (2006)

A biophotonics catheter was conceived with collimation optics, an axicon lens, and custom design imaging optics yielding a 360 degree scan aimed at imaging within concave structures such as arteries and lung lobes. The large depth of focus is necessary to image a long-depth-range sample with constant transverse resolution in optical coherence tomography (OCT). There are two approaches to achieving constant invariant resolution in OCT: Dynamic focusing or Bessel beam formation. This paper focuses on imaging with Bessel beams. The Bessel beams may be created with axicon optics which can be used instead of a conventional focusing lens in the sample arm of the OCT interferometer. In this paper we present the design of a 2mm catheter for optical coherence endoscopy with resolution of about 5 micron across a depth of focus of about 1.6mm. Importantly, we investigated the fabrication of a 800&#956;m diameter axicon lens and the associated lateral resolution obtained over a long depth range in our OCT system, compared to the same OCT system using a conventional lens.
Electronic properties of freestanding Ti3C2Tx MXene monolayers (2016)

We report on the electrical characterization of single MXene Ti3C2Tx flakes (where T is a surface termination) and demonstrate the metallic nature of their conductivities. We also show that the carrier density can be modulated by an external gate voltage. The density of free carriers is estimated to be 8 ± 3 × 1021 cm−3 while their mobility is estimated to be 0.7 ± 0.2 cm2/V s. Electrical measurements, in the presence of a magnetic field, show a small, but clearly discernable, quadratic increase in conductance at 2.5 K.
Electrophoresis and Blotting of DNA (2013)

Abstract Deoxyribonucleic acid (DNA) electrophoresis and blotting are techniques commonly used to visualise DNA. Both techniques use simple, inexpensive protocols that rely on fundamental properties of DNA, and these protocols have changed little since they were introduced. Electrophoresis relies on the negative electrical charge of DNA to draw these molecules through a gel, separating DNA molecules on the basis of size. Southern blotting makes use of sequence complementarity to identify specific DNA fragments on the basis of their sequences. Despite the introduction of more powerful methods such as polymerase chain reaction and DNA sequencing, electrophoresis and blotting techniques are still widely used to identify DNA fragments of interest, including the identification of unusual structures within DNA and the analysis of larger fragments which are not easily analysed by other methods. Key Concepts: DNA electrophoresis and blotting are fundamental methods of molecular biology. Basic physical and chemical properties of DNA are used to analyse unknown sequences. Gel electrophoresis uses an electrical current to separate DNA by size. Southern blotting locates a specific DNA sequence on a gel using a probe sequence that is its chemical match. Minor variations on these procedures can improve results for specific experiments. These techniques are still used to analyse unknown DNA molecules and identify DNA fragments of interest. The principles behind electrophoresis and blotting can also be seen in newer methods.
Data from Structural Alterations of MET Trigger Response to MET Kinase Inhibition in Lung Adenocarcinoma Patients (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; We sought to investigate the clinical response to MET inhibition in patients diagnosed with structural MET alterations and to characterize their functional relevance in cellular models.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Patients were selected for treatment with crizotinib upon results of hybrid capture–based next-generation sequencing. To confirm the clinical observations, we analyzed cellular models that express these MET kinase alterations.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Three individual patients were identified to harbor alterations within the MET receptor. Two patients showed genomic rearrangements, leading to a gene fusion of &lt;i&gt;KIF5B&lt;/i&gt; or &lt;i&gt;STARD3NL&lt;/i&gt; and &lt;i&gt;MET&lt;/i&gt;. One patient diagnosed with an EML4-ALK rearrangement developed a MET kinase domain duplication as a resistance mechanism to ceritinib. All 3 patients showed a partial response to crizotinib that effectively inhibits MET and ALK among other kinases. The results were further confirmed using orthogonal cellular models.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Crizotinib leads to a clinical response in patients with MET rearrangements. Our functional analyses together with the clinical data suggest that these structural alterations may represent actionable targets in lung cancer patients. &lt;i&gt;Clin Cancer Res; 24(6); 1337–43. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
UWB wireless channels - propagation aspects and interplay with system design (2004)

This paper will first present an overview of the current state of the art in the measurement and modeling of UWB propagation channels. We will point out the difference between the two main frequency band of interest (¡900MHz and 3.1-10.6 GHz), and describe the key channel parameters (attenuation, delay spread, arrival time statistics, amplitude statistics) in different environments. We will especially discuss the difference between ¨sparseänd ¨dense ¨models. We then analyze what channel parameters have the biggest influence on system performance. Various Rake receiver structures, OFDM cyclic prefix duration, and transmitted-reference structures exemplify the systems that show a clear dependence on channel parameters.