gebhart/patrepeval huggingface dataset:
On the applicability of genetic algorithms to protein folding (2002)

Discusses the protein folding problem and suggests the use of genetic algorithms for protein folding simulations. The issues of protein energy functions, search algorithms, and folding pathways are discussed. The authors review the current approaches to the protein folding problem, point out the limitations of the approaches, and present the genetic algorithm method, which is based on viewing evolution as an optimization process. The schemata theorem is proved in the context of protein structure, showing that during a genetic algorithm search more and more attention will be given to favorable local structures while unfavorable local structures will be rapidly abandoned. It is shown that genetic algorithms are a suitable tool in protein structure predictions. A version of the genetic algorithm is presented that is suitable for protein structure prediction. The behavior of the algorithm is explored in a single model of folding, and it is shown that the algorithm behaves as expected and is able to find the correct conformation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Purification and Biochemical Characterization of Polygalacturonase Produced by Penicillium expansum During Postharvest Decay of ‘Anjou’ Pear (2009)

A polygalacturonase (PG) was extracted and purified from decayed tissue of 'Anjou' pear fruit inoculated with Penicillium expansum. Ammonium sulfate precipitation, gel filtration, and cation exchange chromatography were used to purify the enzyme. Both chromatographic methods revealed a single peak corresponding to PG activity. PG enzyme activity from healthy and wounded pear tissue was undetectable, which supports the claim that the purified PG is of fungal origin. The purified enzyme had a molecular mass of 41 kDa and a pI of 7.8. Activity of the PG was not associated with a glycosylated protein. The enzyme was active over a broad pH range from 3 to 6, with optimal activity at 4.5 in sodium citrate and sodium acetate buffers. The optimal temperature for activity was 37 degrees C but the enzyme was also active at 0, 5, 10, 20, and 50 degrees C. Thin-layer chromatographic analysis of PG hydrolysis products showed that the enzyme exhibits endo- and exo-activity. The purified enzyme macerated tissue in vitro causing approximately 30% reduction in mass of pear plugs compared with approximately 17% reduction for apple. Additionally, it produced 1.5-fold more soluble polyuronides on pear than apple tissue. This work shows for the first time the production of a PG by P. expansum during postharvest decay of pear fruit is different from the previously described PG produced in decayed apple fruit by the same pathogen.
Current-driven chaotic magnetization dynamics in microwave assisted switching of spin-valve elements (2011)

The switching process of a uniformly magnetized spin-valve is considered. The system is subject to external dc applied fields and injected radio-frequency (RF) spin-polarized currents. The possibility of using the RF power to obtain a reduced coercivity of the particle is related to the onset of chaotic magnetization dynamics for moderately low values of the RF current amplitude. Perturbation technique for the estimation of the reduced coercive field is developed and applied to the microwave assisted switching of the particle. Numerical simulations confirm the predictions of the theory.
Measuring Techniques for Soft-Nanotechnology (2009)

The soft-nanotechnology that treats softmatter in nanometer scale needs to develop proper and original techniques for analyzing and handling the softmatter. The surface analysis of solids under vacuum condition has made remarkable progress. However, softmatter samples in vacuum atmosphere change their original properties, and are easily damaged by high energy probe beams. Thus, it is not suitable to observe “raw state” of the softmatter samples by the conventional surface analysis techniques. Scanning probe microscopy (SPM) such as atomic force microscopy (AFM) can analyze softmatter samples in moderate condition in air and water. Optical probe technique such as infrared absorption spectroscopy (IRAS) is also nondestructive method to analyze the softmatter samples. Scanning near-filed optical microscopy (SNOM), combined SPM and optical spectroscopy, enables the simultaneous measurements of topography and optical information. Here, we briefly introduce outlines of AFM, MIR-IRAS (Multiple internal reflection IRAS), and SNOM and examples of their applications.
Novel method for fabrication of integrated resistors on bilayer Ag/YBa2Cu3O7 films using Ni implantation (1997)

A novel ion implantation method is described for fabricating low inductance integrated resistors on Ag/YBa2Cu3O7 (YBCO) bilayer thin films. Parallel high and low value resistors were simultaneously formed by patterning bilayer films into 10-μm-wide lines, then masking and implanting with Ni to selectively inhibit superconductivity in YBCO. Low value resistors (&amp;lt;1 Ω/sq) were formed at 77 K as the supercurrent bypassed the Ni-doped nonsuperconducting YBCO and was shunted through the overlying low resistivity Ag metal. High value resistors (20–140 Ω/sq) were formed by removing Ag from above the implanted YBCO forcing the current through the implanted YBCO region. The sheet resistance of both types of resistors was found to increase systematically with increasing Ni implant energy.
The Role of Dopamine Receptors in Regulating the Size of Axonal Arbors (2001)

Factors that regulate terminal arbor size of substantia nigra pars compacta (SNpc) neurons during development and after injury are not well understood. This study examined the role of dopamine receptors in regulating arbor size. Terminal arbors were examined in mice with targeted deletion of the D1 or D2 dopamine receptor [D1(-/-) and D2(-/-) mice, respectively]. Terminal trees were also examined after treatment with receptor blockers and after partial SNpc lesions. Immunohistochemistry was performed, and the number of SNpc neurons and dopaminergic terminals in the striatum was estimated. The number of dopaminergic SNpc neurons were reduced in D1(-/-) and D2(-/-) mice. Density of dopaminergic terminals was unchanged in D1(-/-) mice and increased in D2 (-/-) mice. Steady-state striatal DA and DOPAC levels revealed that dopamine activity was enhanced in D2(-/-) mice but reduced in D1(-/-) mice. Two months after partial SNpc lesions, striatal terminal density was normal in both wild-type and D1(-/-) mice but reduced in D2(-/-) mice. Administration of DA receptor antagonists resulted in larger terminal arbors in D1(-/-) and wild-type mice, whereas D2(-/-) mice showed no change in terminal density. Functional blockade of the D2R during development or in the adult brain results in increased axonal sprouting. Partial SNpc lesions resulted in compensatory sprouting, only in mice with functional D2R. These results suggest that individual dopaminergic axons in D2(-/-) mice have reached maximal arbor size. We conclude that the D2 receptor may play a role in modulating the extent of the terminal arbor of SNpc neurons.
Utilizing SmartPhones for Non-Invasive Activity Recognition (2013)

In order for activity recognition systems to be implemented in real world scenarios such as health and wellness monitoring, the activity sensing modality must unobtrusively fit the human environment rather than forcing humans to adhere to sensor specific conditions.
Wave energy in the Netherlands: Past, present and future perspectives (2019)

With the renewable targets of 2020 reaching ever closer, Europe is continuing its ambitious plans for 2030 of developing innovative projects that assist tackling climate change and increase renewable energy integration. The Netherlands are trying to develop their renewable energy portfolio, to create a viable long-term decarbonized sustainable society. So far majority of development has been focused on wind and solar, with offshore wind gaining significant traction over the past years. However, for the renewable energy transition to be fully realised, all indigenous resources must be evaluated and utilized. &lt;br/&gt;The Netherlands have a long history of dealing with water, and have an extensive industrial base in ocean engineering and water infrastructure. However, when it comes to the development of wave energy the sector is lacking significantly compared to other offshore renewables. This study discusses the past, present and future status of wave energy in the Netherlands. We discuss the various schemes and propose a hybrid support scheme for the development of wave energy. Furthermore, we also consider the unique spatial characteristics of the coastlines and suggest a multizonal scheme, that can act beneficially and support development of different wave converter concepts.&lt;br/&gt;Finally, based on the spatial and a techno-economic, we propose that by 2030 the policy focus should be to install up to 24 MW and by 2040 to 44 MW, with initial estimations on reductions per Unit Cost also discussed. With wave technologies in early stages of development in terms of technology and regional applications, there are numerous opportunities that can assist in “unlocking” the&lt;br/&gt;wave energy industry in the Netherlands.
Enhanced penetration of mitomycin C through hairless mouse and rat skin by enhancers with terpene moieties (1987)

The effects of four new percutaneous absorption enhancers containing an azacyclo ring and terpene chain (1-geranylazacycloheptan-2-one (GAH), 1-farnesylazacycloheptan-2-one (FAH), 1-geranylazacyclopentan-2,5-dione (GAPD), and 1-farnesylazacyclopentan-2-one (FAP] and 1-dodecylazacycloheptan-2-one (Azone) on the percutaneous penetration of mitomycin C (MMC) through hairless mouse and rat skin in-vitro has been investigated. GAH, FAH, FAP and Azone enhanced MMC penetration by 20 to 60 times that of the control (ethanol). During the early part of the experiments, when the sink condition was maintained, FAH was the most effective for hairless mouse skin, whereas Azone showed the highest effect in the rat skin. The enhancing effect of GAPD was only about half that of the other enhancers, suggesting the importance of the polar group of the ring moiety in these compounds. The penetration of MMC through rat skin was also increased by pretreatment with these compounds, suggesting that the enhancers had a direct effect on the skin.
Base-promoted Rearrangement of N-Tosyl-2,3-exo-aziridino[2,3]norbornane (2001)

The first experimental evidence of the generation of an imino carbene from the tittle compound is reported.Although the chemistry of oxiranyl anions has been extensively considered in the literature, 1 more limited work on the related aziridinyl anions has been published to date.1b The base-promoted α-abstraction of hydrogen in epoxides to give oxiranyl anions which rearrange to α-hydroxy carbenes is a well-known process which has been considered in the case of bicyclic systems providing intramolecular C-H insertion products (Scheme 1). 2 Scheme 1However, an analogous study in the case of bicyclic aziridines has not been, to the best of our knowledge, reported.Thus, the formation of an α-imino carbene (or carbenoid) generated from a nonstabilized αaziridinyl anion 3 has never been observed.In this communication we wish to account for the first direct observation of the formation of this intermediate by treatment of compound (1) 4, 5 with LDA (Scheme 2).Thus, reaction of 1 (1.0 equiv.)with 5 equiv. of LDA (Et 2 O, -78 o C, 2 h) 6 affords a mixture of norbornanone (2) and N-Tosyl nortricyclylamine(3). 7, The structure of compound (3) was determined by comparison with the previously described Nbenzenesulfonyl derivative .8The ratio 2/3 and the overall yield of the reaction have been fairly well reproduced in three independent experiments indicated in Scheme 2. Scheme 2 TsN TsHN 5 equiv.LDA -78 o C, Et 2 O O + 1 2 3 Isolated Yields (%) Run
The cartilage specific microRNA‐140 targets histone deacetylase 4 in mouse cells (2006)

MicroRNAs (miRNA) are short RNA molecules regulating the expression of specific mRNAs. We investigated the expression pattern and potential targets of mouse miR-140 and found that miR-140 is specifically expressed in cartilage tissues of mouse embryos during both long and flat bone development. MiR-140 expression was detected in the limbs of E11.5 embryos in the primorida of future bones both in the fore and hindlimb and across autopod, zeugopod and stylopod. All digits of E14.5 fore- and hindlimbs showed accumulation of miR-140, except the first digit of the hindlimb. MiR-140 expression was also detected in the cartilagenous base of E17.5 skulls and in the sternum, the proximal rib heads and the developing vertebral column of E15.5 embryos. A potential target of miR-140, histone deacetylase 4, was validated experimentally and the possible role of miR-140 in long bone development is discussed.
Formation of Buried SiC by High-Dose MeV Ion Implantation at High Temperature. (1993)

A buried layer of crystalline SiC in a silicon wafer is synthesized by 1.5 MeV C+ implantation with a dose of 1.5×1018 ions/cm2 at a high temperature of 880°C. The infrared absorption spectra of this sample shows formation of the SiC crystal, and its crystal structure is found to be of the 3C type (β-SiC) from the X-ray diffraction pattern. The rocking curve shows that crystallographic orientation of the SiC buried layer is aligned with the lattice of the Si substrate.
Slinging MUD: Manufacturer usage descriptions: How the network can protect things (2016)

Through the simplifying assumption that a Thing has a single use or a small number of intended uses, it is possible to reduce the threat surface of the device by constraining the communication paths needed for those uses. This is accomplished using a small number of extensions to IEEE 802.1AR, a YANG model, DHCP, and IEEE 802.1AB, where a manufacturer maintains an online presence that is used inter alia to retrieve recommended configuration for a given device. This recommended configuration is used to create an access control list on a network device.
Transient ischemic attack (TIA) (2007)

Transient neurological symptoms often present a difficult diagnostic dilemma. It is often difficult to tell if the transient symptoms were due to ischemia or due to something else (see Chapter 1). Usually, by the time the physician sees the patient, the neurological exam has returned to normal.
ChemInform Abstract: Intramolecular Coordination in Organotin Chemistry. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
[Percutaneous closure of mitral perivalvular leak]. (2009)

Paravalvular leak (PVL) is a complication observed in patients after prosthetic valve replacement. The incidence of PVL is estimated as 2-3%. The cause of PVL may be paravalvular infection, suture continuity disruption, damage of tissues around the annulus or limitation of disc mobility by thrombus or vegetation. The preferable method of treatment of PVL is surgery. Recently, percutaneous closure of PVL became an alternative method. We present a case of successfully completed percutaneous closure of PVL with the use of Amplatzer occluder device in a patient with mitral PVL.
Radiation effects in hydrogen-impregnated vitreous silica (1979)

γ irradiation of vitreous silica normally leads to the formation of a large number of optical defects and to an increase in density. Irradiation of hydrogen-impregnated vitreous silica suppresses the formation of these optical defects, but does result in the formation of large quantities of bound hydroxyl and hydride. This process is accompanied by the expansion (density decrease) of the glass. The rates of hydroxyl and hydride formation and the density decrease all are proportional to the square root of the applied dose. The mechanism responsible for these results is not clear at this time.
Spread-spectrum cognitive networking: Distributed channelization and routing (2011)

We study a framework that captures the interdependencies between spreading channelization and routing for a secondary multi-hop cognitive radio network that operates cognitively to coexist with primary users. We consider interactions between dynamic routing and code-division channelization functionalities for cognitive radio networks. With this respect, we study the effect of joint routing, spreading code and power allocation on the network throughput. A solution for joint routing and spread-spectrum channelization is proposed as a localized approximation of the throughput-maximizing problem. Specifically, power and spreading code are allocated to guarantee the quality of service of the on-going primary and secondary transmissions, while the routing algorithm dynamically selects relays based on the network traffic dynamics and on the achievable data rates on different secondary links.
Satellite Payloads Pay Off (2015)

Software-Defined Satellite Payloads Based on Microwave Photonics! Satellite communication offers a number of distinct features that are not readily available with other means of communication, such as seamless coverage of remote and sparsely populated areas, reliable data relay for deep-space exploration, inherent multicasting and broadcasting capabilities, and reliable performance in extreme conditions (e.g., war, earthquakes, and other adverse events) [1], [2]. In recent years, the steep rise in mobile multimedia applications and increased space exploration activity have created unprecedented opportunities for innovative satellite communication. According to a report provided by the Satellite Industry Association in September 2014, the global revenue of the satellite communication industry for 2013 reached US$189.2 billion-60% of global space revenue and 4% of global telecommunications revenue [3]. Apple, Google, Amazon, Facebook, and many other large technology companies are currently seeking to bolster their satellite communication systems in the next five to ten years, fostering a continuous increase of revenue in this area.
PTPN2 Regulates Inflammasome Activation and Controls Onset of Intestinal Inflammation and Colon Cancer (2018)

Variants in the gene locus encoding protein tyrosine phosphatase non-receptor type 2 (PTPN2) are associated with inflammatory disorders, including inflammatory bowel diseases, rheumatoid arthritis, and type 1 diabetes. The anti-inflammatory role of PTPN2 is highlighted by the fact that PTPN2-deficient mice die a few weeks after birth because of systemic inflammation and severe colitis. However, the tissues, cells, and molecular mechanisms that contribute to this phenotype remain unclear. Here, we demonstrate that myeloid cell-specific deletion of PTPN2 in mice (PTPN2-LysMCre) promotes intestinal inflammation but protects from colitis-associated tumor formation in an IL-1β-dependent manner. Elevated levels of mature IL-1β production in PTPN2-LysMCre mice are a consequence of increased inflammasome assembly due to elevated phosphorylation of the inflammasome adaptor molecule ASC. Thus, we have identified a dual role for myeloid PTPN2 in directly regulating inflammasome activation and IL-1β production to suppress pro-inflammatory responses during colitis but promote intestinal tumor development.
Estimation of Polymer Coating Scratch Tensile Strength by Nano-Indentation, Micro-Scratch Testing, and Finite Element Modeling (2005)

In a previous paper, polymer coating viscoelastic/plastic properties were determined using nanoindentation and the finite element method. In this work, the individual layers, once characterized, were assembled into a multi-layered structure and subject to micro-scratch tests. These tests determined a critical scratch indentation load for the layered structure, as designated by the first appearance during scratching of visible surface layer tensile cracks. Scratch tests were carried out for three different conical scratch tip radii. The top-layer tensile strength of the layered structures was then estimated, utilizing the individual layer properties, the top layer friction coefficients, the micro-scratch test critical loads, and a finite element scratch model, for each scratch tip radius. The values of the top layer scratch tensile strengths were in good agreement for each of the three tip radii, as anticipated. The top-layer scratch tensile strengths may be utilized for further analysis and comparison of differences in gloss retention after gloss reduction experiments. The method may be used as a basis for coating selection, comparison, and performance testing in scratch-resistant polymer coating applications.
A Microporous Poly(arylene ether) Platform for Membrane-Based Gas Separation (2022)

Membrane-based gas separations are viewed as a critical component to accessing low-energy feedstocks and decarbonizing the chemical industry. However, it is exceedingly challenging to synthesize membrane materials that are high-performing, scalable, and processable. As a class of materials, microporous organic polymers (MOPs), which combine the gas sieving ability of microporous materials with the solution-processability of organic polymers, are highly desirable. Herein, we report the rational design and synthesis of linear microporous poly(arylene ether)s (PAEs) via Pd-catalyzed C-O polycondensation reaction. The scaffold of these microporous polymers consists of rigid three-dimensional triptycene and highly stereocontorted spirobifluorene, which endow these polymers with large internal free volume as well as high porosity with angstrom-sized pores. Unlike classic polymers of intrinsic microporosity (PIMs), this robust methodology for the synthesis of poly(arylene ether)s allows for the facile incorporation of functionalities and branched linkers for control of permeation and mechanical properties. CO2-philic groups, such as nitrile and tertiary amine groups, can be incorporated into this microporous polymeric scaffold for enhancing CO2 separation performance. In addition, a solution-processable branched polymer prepared using this synthetic strategy showed good gas separation performance and enhanced mechanical properties, which allowed for the formation of a submicron defect-free film with permeance-selectivity property sets that are comparable to high-performance ultrathin polymer membranes that have been optimized at industrial scale. In contrast with commercially available polymer membranes, the easily accessible PAE branching motif endows these materials with plasticization resistance. The structural tunability, high physical stability, and ease of processing suggest that this new platform of microporous polymers provides generalizable design strategies to address outstanding separation challenges for gas separation membranes.