cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Comparison and Evaluation of Semantic Search Engines
Publisher: name: Iranian Research Institute for Information Science and Technology (IranDoc)
Year: 2015

description: In this study, we evaluate the performance of five semantic search engines that are available on the web, using 45 criteria, in the form of a researcher-made checklist. Criteria provided in the checklist included both common and semantic features. Common criteria or features are those applicable to all search engines and semantic ones are those only applicable to semantic search engines. Findings show that the selected search engines do not have suitable performance and expected efficiency. DuckDuckGo, has the most points, considering regular features. Cluuz is in the second place with 20 points and Hakia with 18 points was in the third place. Lexxe and Factbites, with scores of 15 and 10 were placed in the next categories in order of their points. In semantic features, DuckDuckGo, with 10/65 points was in the first place. Hakia with 9/99 points was in the second place, and then the search engines Cluuz with 8/66 Points, Lexxe with 8/65 points and Factbites with 7/32 points were allocated to the next levels. The research results also indicated that on the whole, considering ordinary and semantic features, DuckDuckGo with 31/65 points, Cluuz with 28/66, Hakia with 27/99 points, Lexxe with 23/65 points and Factbites with 17/32 points, got the highest scores out of it.
روش شناسیِ خودمردم نگاری به مثابه روشی در خودبازاندیشی و رشد حرفه ای معلمان: پژوهشی)فرا-( خودمردم نگارانه
Publisher: name: دانشگاه کردستان
Year: 2022

description: با آنکه پژوهش ­های بسیاری به بررسی رابطۀ میانِ بازاندیشیِ معلمان و عملکرد حرفه ­ای آن ها پرداخته است، رویکردهای معدودی بسترِ خودبازاندیشی را برای معلمان فراهم کرده است. با توجه به این ضرورت، پژوهشِ حاضر بر آن است تا به معرفیِ روشِ «خودمردم­نگاری» به مثابه یک روشِ پژوهشِ کیفی در خود­باز­اندیشیِ معلمان و تأثیر آن در زندگیِ حرفه­ ای و شخصیِ آن ها بپردازد. در این پژوهش، تجربۀ نویسندۀ اول از روش خودمردم ­نگاری با نگاهی «فرا-خودمردم ­نگارانه» مورد بررسی قرار گرفته است. آموخته­ هایِ محقق از روایتِ تجربه­ ها و یافتنِ معنا در انبوهی از داده­ ها، نگارش داستان­ گونه، رعایتِ اخلاق و تغییرِ نگاه او نسبت به معیارهایِ ارزیابیِ کیفیت خودمردم­ نگاری تشریح شده است. یافته های پژوهش حاکی از تأثیر عمیقِ خودمردم ­نگاری بر تحولاتِ درونی و بیرونی محقق است که از آن جمله می توان به تغییراتِی در رویکرد او نسبت به کارِگروهی و تلاش او در به ­کارگیری و آموزشِ آن در کلاس، چرخش نگرش او از اثبات ­گرایانه به پسامدرنیته و تأثیر آن بر زندگی او اشاره کرد. به اشتراک­ گذاری تجربه ­های یک معلم خودمرد م­نگار می­تواند معلمانِ دیگر را با کارکردِ خودمردم ­نگاری در جهتِ رشد و تعالی خود آشنا نماید. همچنین، تشریحِ فهمِ یک معلم از خودمردم­ نگاری می­تواند در جهتِ تعمیمِ این روشِ پژوهشی در حیطۀ آموزش مؤثر واقع شود
The Solar Neighborhood XXXV: Distances to 1404 M Dwarf Systems Within 25 pc in the Southern Sky
Creators: name: Winters, Jennifer G.
name: Henry, Todd J.
name: Lurie, John C.
name: Hambly, Nigel C.
name: Jao, Wei-Chun
name: Bartlett, Jennifer L.
name: Boyd, Mark R.
name: Dieterich, Sergio B.
name: Finch, Charlie T.
name: Hosey, Altonio D.
name: Ianna, Philip A.
name: Riedel, Adric R.
name: Slatten, Kenneth J.
name: Subasavage, John P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present trigonometric, photometric, and photographic distances to 1748 southern ($δ\leq$0$^\circ$) M dwarf systems with $μ\ge$ 0\farcs18 yr$^{-1}$, of which 1404 are believed to lie within 25 parsecs of the Sun. The stars have 6.67 $\leq$ $V_J$ $\leq$ 21.38 and 3.50 $\leq$ ($V_J-K_s$) $\leq$ 9.27, covering the entire M dwarf spectral sequence from M0.0V through M9.5V. This sample therefore provides a comprehensive snapshot of our current knowledge of the southern sky for the nearest M dwarfs that dominate the stellar population of the Galaxy. Roughly one-third of the 1748 systems, each of which has an M dwarf primary, have published high quality parallaxes, including 179 from the RECONS astrometry program. For the remaining systems, we offer photometric distance estimates that have well-calibrated errors. The bulk of these ($\sim$700) are based on new $V_JR_{KC}I_{KC}$ photometry acquired at the CTIO/SMARTS 0.9m telescope, while the remaining 500 primaries have photographic plate distance estimates calculated using SuperCOSMOS $B_JR_{59F}I_{IVN}$ photometry. Confirmed and candidate subdwarfs in the sample have been identified, and a census of companions is included.
description: accepted by The Astronomical Journal on 25 July, 2014; 75 pages of tables, 11 figures
Immune plexins and semaphorins: old proteins, new immune functions
Creators: name: Holl, Eda
name: Ting, Jenny
name: Roney, Kelly
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Plexins and semaphorins are a large family of proteins that are involved in cell movement and response. The importance of plexins and semaphorins has been emphasized by their discovery in many organ systems including the nervous (Nkyimbeng-Takwi and Chapoval, 2011; McCormick and Leipzig, 2012; Yaron and Sprinzak, 2012), epithelial (Miao et al., 1999; Fujii et al., 2002), and immune systems (Takamatsu and Kumanogoh, 2012) as well as diverse cell processes including angiogenesis (Serini et al., 2009; Sakurai et al., 2012), embryogenesis (Perala et al., 2012), and cancer (Potiron et al., 2009; Micucci et al., 2010). Plexins and semaphorins are transmembrane proteins that share a conserved extracellular semaphorin domain (Hota and Buck, 2012). The plexins and semaphorins are divided into four and eight subfamilies respectively based on their structural homology. Semaphorins are relatively small proteins containing the extracellular semaphorin domain and short intra-cellular tails. Plexins contain the semaphorin domain and long intracellular tails (Hota and Buck, 2012). The majority of plexin and semaphorin research has focused on the nervous system, particularly the developing nervous system, where these proteins are found to mediate many common neuronal cell processes including cell movement, cytoskeletal rearrangement, and signal transduction (Choi et al., 2008; Takamatsu et al., 2010). Their roles in the immune system are the focus of this review.
Dark Matter Freeze-In with a Heavy Mediator: Beyond the EFT Approach
Creators: name: Frangipane, Evan
name: Gori, Stefania
name: Shakya, Bibhushan
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We study dark matter freeze-in scenarios where the mass of the mediator particle that couples dark matter to the Standard Model is larger than the reheat temperature, TRH, in the early Universe. In such setups, the standard approach is to work with an effective field theory (EFT) where the mediator is integrated out. We examine the validity of this approach in various generic s- and t-channel mediator frameworks. We find that the EFT approach breaks down when the mediator mass is between one to two orders of magnitude larger than TRH due to various effects such as s-channel resonance, a small thermally-suppressed abundance of the mediator, or decays of Standard Model particles through loops induced by the mediator. This highlights the necessity of including these contributions in such dark matter freeze-in studies. We also discuss the collider phenomenology of the heavy mediators, which is qualitatively different from standard freeze-in scenarios. We highlight that, due to the low TRH, the Standard Model-dark matter coupling in these scenarios can be relatively larger than in standard freeze-in scenarios, improving the testability prospects of these setups.
description: 39 pages, 11 figures
DSSylation, a novel protein modification targets proteins induced by oxidative stress, and facilitates their degradation in cells
Creators: name: Wei, Sung-Jen
name: Junco, Jacob J.
name: Ding, Xiang
name: He, Rongqiao
name: Slaga, Thomas J.
name: Chang, Fang-Mei
name: Kim, Dae Joon
name: Yang, Fuquan
name: Huang, Jianjun
name: Zhang, Yinghao
name: Maffi, Shivani K.
name: Pridgen, Hannah I.
name: Dang, Hong
name: Catano, Gabriel
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Timely removal of oxidatively damaged proteins is critical for cells exposed to oxidative stresses; however, cellular mechanism for clearing oxidized proteins is not clear. Our study reveals a novel type of protein modification that may play a role in targeting oxidized proteins and remove them. In this process, DSS1 (deleted in split hand/split foot 1), an evolutionally conserved small protein, is conjugated to proteins induced by oxidative stresses in vitro and in vivo, implying oxidized proteins are DSS1 clients. A subsequent ubiquitination targeting DSS1-protein adducts has been observed, suggesting the client proteins are degraded through the ubiquitin-proteasome pathway. The DSS1 attachment to its clients is evidenced to be an enzymatic process modulated by an unidentified ATPase. We name this novel protein modification as DSSylation, in which DSS1 plays as a modifier, whose attachment may render target proteins a signature leading to their subsequent ubiquitination, thereby recruits proteasome to degrade them.Electronic supplementary materialThe online version of this article (doi:10.1007/s13238-013-0018-8) contains supplementary material, which is available to authorized users.
Ambiguities in Direction-of-Arrival Estimation with Linear Arrays
Creators: name: Matter, Frederic
name: Fischer, Tobias
name: Pesavento, Marius
name: Pfetsch, Marc E.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Signal Processing (eess.SP)
subject: Information Theory (cs.IT)
subject: Optimization and Control (math.OC)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: In this paper, we present a novel approach to compute ambiguities in thinned uniform linear arrays, i.e., sparse non-uniform linear arrays, via a mixed-integer program. Ambiguities arise when there exists a set of distinct directions-of-arrival, for which the corresponding steering matrix is rank-deficient and are associated with nonunique parameter estimation. Our approach uses Young tableaux for which a submatrix of the steering matrix has a vanishing determinant, which can be expressed through vanishing sums of unit roots. Each of these vanishing sums then corresponds to an ambiguous set of directions-of-arrival. We derive a method to enumerate such ambiguous sets using a mixed-integer program and present results on several examples.
A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins
Creators: name: Jacak, R.
name: Choi, E. J.
name: Kuhlman, B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: We have developed a protocol for identifying proteins that are predisposed to bind linear epitopes on target proteins of interest. The protocol searches through the protein database for proteins (scaffolds) that are bound to peptides with sequences similar to accessible, linear epitopes on the target protein. The sequence match is considered more significant if residues calculated to be important in the scaffold–peptide interaction are present in the target epitope. The crystal structure of the scaffold–peptide complex is then used as a template for creating a model of the scaffold bound to the target epitope. This model can then be used in conjunction with sequence optimization algorithms or directed evolution methods to search for scaffold mutations that further increase affinity for the target protein. To test the applicability of this approach we targeted three disease-causing proteins: a tuberculosis virulence factor (TVF), the apical membrane antigen (AMA) from malaria, and hemagglutinin from influenza. In each case the best scoring scaffold was tested, and binders with Kds equal to 37 μM and 50 nM for TVF and AMA, respectively, were identified. A web server (http://rosettadesign.med.unc.edu/scaffold/) has been created for performing the scaffold search process with user-defined target sequences.
Effects of turbulence and rotation on protostar formation as a precursor to seed black holes
Creators: name: Van Borm, C.
name: Bovino, S.
name: Latif, M. A.
name: Schleicher, D. R. G.
name: Spaans, M.
name: Grassi, T.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Context. The seeds of the first supermassive black holes may have resulted from the direct collapse of hot primordial gas in $\gtrsim 10^4$ K haloes, forming a supermassive or quasistar as an intermediate stage. Aims. We explore the formation of a protostar resulting from the collapse of primordial gas in the presence of a strong Lyman-Werner radiation background. Particularly, we investigate the impact of turbulence and rotation on the fragmentation behaviour of the gas cloud. We accomplish this goal by varying the initial turbulent and rotational velocities. Methods. We performed 3D adaptive mesh refinement simulations with a resolution of 64 cells per Jeans length using the ENZO code, simulating the formation of a protostar up to unprecedentedly high central densities of $10^{21}$ cm$^{-3}$, and spatial scales of a few solar radii. To achieve this goal, we employed the KROME package to improve modelling of the chemical and thermal processes. Results. We find that the physical properties of the simulated gas clouds become similar on small scales, irrespective of the initial amount of turbulence and rotation. After the highest level of refinement was reached, the simulations have been evolved for an additional ~5 freefall times. A single bound clump with a radius of $2 \times 10^{-2}$ AU and a mass of ~$7 \times 10^{-2}$ M$_{\odot}$ is formed at the end of each simulation, marking the onset of protostar formation. No strong fragmentation is observed by the end of the simulations, regardless of the initial amount of turbulence or rotation, and high accretion rates of a few solar masses per year are found. Conclusions. Given such high accretion rates, a quasistar of $10^5$ M$_{\odot}$ is expected to form within $10^5$ years.
description: 18 pages, 7 figures, fixed typos, added references and clarified some details; accepted for publication in A&A
Coupled-channel description for mirror mass-11 nuclei compared to shell-model structures
Creators: name: Amos, K.
name: Karataglidis, S.
name: Canton, L.
name: Fraser, P. R.
name: Murulane, K.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The spectra of mass-11 nuclei are unusual, and so pose a challenge for theoretical models of their structure. The set of isobars range from being well bound to nucleon emission (11B,11C) through weakly bound (11Li, 11Be), with the former taking the form of a two neutron halo, to being proton unstable (11N,11O). A self-consistent approach to understand this set of nuclei is especially important as the mirror pair 11Be-11N exhibit a parity-inverted ground state compared to their neighbouring nuclei. Herein the Multi-Channel Algebraic Scattering (MCAS) method has been used to describe the low excitation spectra of those isobars in terms of nucleon-nucleus clusters. A collective model description of the low-excitation states of the mass-10 core nuclei has been used to form the coupled-channel interactions required in the method. For comparison, and to understand the underlying configurations, a shell model approach has been used to obtain those spectra with no-core (0+2+4)hw and (0+2)hw shell-model spaces for the mass 10 and mass 11 nuclei respectively.The results of the calculations suggest the need of a strong coupling in the collective coupled-channel vibrational model. In particular, the strong coupling of the collective 2+_1 state of 10Be to the valence neutron plays a decisive role in forming the positive parity ground state in11Be.
description: 23 pages, 8 figures
Engineering a genetically encoded competitive inhibitor of the KEAP1–NRF2 interaction via structure-based design and phage display
Creators: name: Lewis, Steven M.
name: Guntas, Gurkan
name: Kuhlman, Brian
name: Lane, Thomas R.
name: Tripathy, Ashutosh
name: Mulvaney, Kathleen M.
name: Cloer, Erica W.
name: Major, Michael B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: In its basal state, KEAP1 binds the transcription factor NRF2 (Kd = 5 nM) and promotes its degradation by ubiquitylation. Changes in the redox environment lead to modification of key cysteines within KEAP1, resulting in NRF2 protein accumulation and the transcription of genes important for restoring the cellular redox state. Using phage display and a computational loop grafting protocol, we engineered a monobody (R1) that is a potent competitive inhibitor of the KEAP1–NRF2 interaction. R1 bound to KEAP1 with a Kd of 300 pM and in human cells freed NRF2 from KEAP1 resulting in activation of the NRF2 promoter. Unlike cysteine-reactive small molecules that lack protein specificity, R1 is a genetically encoded, reversible inhibitor designed specifically for KEAP1. R1 should prove useful for studying the role of the KEAP1–NRF2 interaction in several disease states. The structure-based phage display strategy employed here is a general approach for engineering high-affinity binders that compete with naturally occurring interactions.
بررسی رابطه استفاده از تکنولوژی آموزشی با خلاقیت و نوآوری دانشجویان (مورد مطالعه: دانشجویان رشته علوم تربیتی دانشگاه کردستان)
Publisher: name: دانشگاه کردستان
Year: 2022

description: امروزه در نظام های آموزشی، تکنولوژی به مثابه عنصر بنیادین برای بهبود فرآیند آموزش و یادگیری دانشجویان پنداشته می شود. به نحوی که استفاده از فناوری های آموزشی منجر به پیامدهای مثبت گوناگون برای یادگیرندگان می شود. هدف تحقیق حاضر بررسی رابطه استفاده از تکنولوژی آموزشی بر خلاقیت و نوآوری دانشجویان رشته علوم تربیتی دانشگاه کردستان است. روش تحقیق حاضر از لحاظ هدف، کاربردی و از نظر ماهیت و روش، توصیفی - پیمایشی است. جامعه آماری، شامل دانشجویان رشته علوم تربیتی در دانشگاه کردستان اعم از دانشجویان کلیه مقاطع کارشناسی، کارشناسی ارشد و دکتری در سال تحصیلی 1401-1400  بود و با حجم 620 نفر و نمونه­ ای به حجم 235 نفر با استفاده از فرمول کوکران و به روش نمونه گیری تصادفی ساده انتخاب گردید. گردآوری اطلاعات از طریق پرسشنامه انجام گرفت. روایی همگرایی و پایایی ابزار پژوهش نیز با استفاده از مدل اندازه گیری مدل معادلات ساختاری پی.ال.اس 3 تأیید گردید. تجزیه وتحلیل داده ها با استفاده از نرم افزار اس.پی.اس.اس 26 صورت گرفت و جهت برازش مدل اندازه گیری از مدل معادلات ساختاری اسمارت پی.ال.اس 3 استفاده شد. نتایج پژوهش نشان داد بین استفاده از تکنولوژی آموزشی با خلاقیت و نوآوری دانشجویان رشته علوم تربیتی دانشگاه کردستان رابطه مثبت و معنا داری وجود دارد. همچنین نتایج حاصل از مدل نشان داد که متغیر تکنولوژی آموزشی توانسته  (%57) از تغییرات خلاقیت و نوآوری را تبیین نماید. منابع آموزشی با بیشترین ضریب استاندارد شده بتا (911/0) در رتبه اول قرار دارد. همچنین رتبه دوم مربوط به متغیر شرایط آموزشی با ضریب استاندارد شده بتا (904/0) است. چنانکه بهتر است که پژوهشگران آینده برای درک عمیق تر از موضوع، چنین پژوهش هایی را بر روی دانشجویان رشته تکنولوژی آموزشی انجام داده و میزان تأثیر آن را با سایر رشته ها مقایسه کنند. بر اساس این نتایج این نکته کلیدی استخراج گشت که هر کدام از مؤلفه های تکنولوژی آموزشی به روشی خاص اذهان یادگیرندگان را در جهت مسیرهای متناسب با رویکرد های خلاقانه و نوآورانه سوق داد
Refolding and kinetic characterization of the phosphodiesterase-8A catalytic domain
Creators: name: Ke, Hengming
name: Cai, Jiwen
name: Wang, Huanchen
name: Yan, Zier
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Cyclic nucleotide phosphodiesterase-8 (PDE8) hydrolyzes the second messenger cAMP and is involved in many biological processes such as testosterone production. Although the bacterial and mammalian expression systems have been extensively tried, production of large quantity of soluble and active PDE8 remains to be a major hurdle for pharmacological and structural studies. Reported here is a detailed protocol of refolding and purification of large quantity of the PDE8A1 catalytic domain (residues 480–820) and kinetic characterization of the refolded protein. This protocol yielded about 8 mg of the PDE8A catalytic domain from 2 liter E. coli culture, which has at least 40-fold higher activity than those reported in literature. The PDE8A1 catalytic domain has kcat of 4.0 s−1 for Mn2+ and 2.9 s−1 for Mg2+, and the KM values of 1–1.8 μM. In addition, the PDE8A1 (205–820) fragment that contains both PAS and catalytic domains was expressed in E. coli and refolded. This PDE8A1 (205–820) fragment has kcat of 1.1 s−1 and KM of 0.28 μM, but aggregated at high concentration. The KM of PDE8A1 (205–820) is 2- to 7-fold higher than the KM values of 40–150 nM for the full-length PDE8s in literature, but about 6-fold lower than that of the catalytic domain. Thus, the KM difference likely implies an allosteric regulation of the PDE8A activity by its PAS domain.
تأثیر قصه گویی دیجیتال بر خودکارآمدی و تفکر انتقادی دانش آموزان دوم ابتدایی
Publisher: name: دانشگاه کردستان
Year: 2022

description: هدف : این پژوهش با هدف بررسی تأثیر قصه گویی دیجیتال بر خودکارآمدی و تفکر انتقادی دانش آموزان\nپایه دوم ابتدایی در سامانه شاد به انجام رسیده است\nروش: این پژوهش یک مطالعه شبه آزمایشی با طرح پیش آزمون – پس آزمون با گروه گواه بود. جامعه آماری\nشامل کلیه دانش آموزان دختر پایه دوم ابتدایی شهرستان گنبدکاووس در سال تحصیلی 3411 -3111 بود\nکه دانش آموزان پایه دوم دبستان کودکان ایران زمین روستای قزلجه ماتی انتخاب گردید. تعداد اعضای هر\nیک از گروه های کنترل و آزمایش 31 نفر بوده؛ که به صورت جایگزینی تصادفی در دو گروه کنترل و آزمایشی\nقرار گرفتند. مداخله قصه گویی دیجیتال برای گروه آزمایش انجام شد، درصورتی که گروه کنترل قصه گویی به\nروش سنتی بود. قبل و بعد از اجرای آزمایش پیش آزمون و پسآزمون برای دو گروه آزمایش و گواه صورت\nگرفت. برای گردآوری داده ها از پرسشنامه تفکر انتقادی ای. (سی.تی.دی)و پرسشنامه استاندارد خودکارآمدی\nکودکان و نوجوانان(اس.ای.کیو-سی) استفاده شد\nیافته ها: روشهای آماری به کار رفته این پژوهش شامل روش های آمار توصیفی)میانگین، انحراف معیار و\nروش های آمار استنباطی)آزمون کوواریانس چند متغیره( بوده است. با توجه به نتایج تحلیل کوواریانس و)\nمیانگین های تعدیل شده و با در نظر گرفتن محدودیت های پژوهش میتوان گفت قصه گویی دیجیتال بر\nافزایش خودکارآمدی و تفکر انتقادی دانش آموزان دوم ابتدایی در محیط برخط شاد مؤثر بوده است
The spin-spin problem in Celestial Mechanics
Creators: name: Celletti, Alessandra
name: Gimeno, Joan
name: Misquero, Mauricio
Publisher: name: arXiv
Year: 2021
Subjects: subject: Dynamical Systems (math.DS)
subject: Mathematical Physics (math-ph)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: We study the dynamics of two homogeneous rigid ellipsoids subject to their mutual gravitational influence. We assume that the spin axis of each ellipsoid coincides with its shortest physical axis and is perpendicular to the orbital plane. Due to such assumptions, the problem is planar and depends on particular parameters of the ellipsoids, most notably, the equatorial oblateness and the flattening with respect to the shortest physical axes. We consider two models for such configuration: while in the full model, there is a coupling between the orbital and rotational motions, in the Keplerian model, the centers of mass of the bodies are constrained to move on coplanar Keplerian ellipses. The Keplerian case, in the approximation that includes the coupling between the spins of the two ellipsoids, is what we call spin-spin problem, that is a generalization of the classical spin-orbit problem. In this paper we continue the investigations of [Mis21] on the spin-spin problem by comparing it with the spin-orbit problem and also with the full model. Beside detailing the models associated to the spin-orbit and spin-spin problems, we introduce the notions of standard and balanced resonances, which lead us to investigate the existence of periodic and quasi-periodic solutions. We also give a qualitative description of the phase space and provide results on the linear stability of solutions for the spin-orbit and spin-spin problems. We conclude by providing a comparison between the full and the Keplerian models with particular reference to the interaction between the rotational and orbital motions.
D1.1 - BBioNets FAN Operational Framework - Draft
Creators: name: Rosa Álvarez, Paula
Publisher: name: Zenodo
Year: 2024
Subjects: multi-actor
multiactor
framework
thematic
network
thematic network
EIP-AGRI
Operational Group
BBioNets
Forest
Agriculture
Networks
FANs
Bio-Based Technologies
Protocol
Identification
Guidelines
Member
Engaging

description: This document titled “D1.1: BBioNets FAN Operational Framework”, has been elaborated as a deliverable of BBioNets describing the approach followed for the development of BBioNets multi-actor framework. In response to the increasing need for grassroots and knowledge sharing to address major challenges such as climate resilience and increased mitigation of GHG emissions, while supporting zero waste and circular economy with biomass reuse, BBioNets have constituted a thematic network that rely on, promote, and further advance the work carried out by EIP AGRI Operational Groups (OGs) with respect to management and/or processing of agricultural and forest biomass with Bio-Based Technologies (BBTs), being BBTs those technologies or practices that use either non-food feedstock or circularity principles -or both- for delivering diverse products.

Applying the quintuple helix model and a multi-actor approach both within the consortium itself and on the ground activities, BBioNets constituted 6 regional Forest and Agriculture Networks – FANs (Ireland, Spain, Italy, Greece, Poland, Czech Republic) that have ensured a balanced representation of all kinds of stakeholders. Fans compromised of stakeholders covering a broad range of stakeholders from the forest and agricultural sector who will be engaged in key project activities throughout the project.

To successfully establish and operate its multi-actor framework, BBioNets has elaborated a tailored methodology to ensure comparable but well-adjusted to local contexts results from regional FANs. The mission of the FANs, as well as the expected structure and expected contribution of their members, have been defined to set the foundation of our methodology. A common protocol for the identification, selection of the FANs has been set to be used as a guide for consortium partners leading a FAN to efficiently establish these structures, as well as guidelines for inviting members and managing their inclusion as well as potential conflicts of interest that may arise during project activities. The rights and duties of members, their expected role and terms of participation have been developed to promote clear communication among partners and stakeholders.

With our multi-actor approach framework in place, our target is to directly engage a minimum of 60 actors in the FANs. At the moment of writing of this report, over 39 stakeholders have confirmed their acceptance to participate in the project’s FANs. The recruitment process is well under way and multi-actor structures will be open for new members throughout the project.
Error-correcting neural networks for semi-Lagrangian advection in the level-set method
Creators: name: Larios-Cárdenas, Luis Ángel
name: Gibou, Frédéric
Publisher: name: arXiv
Year: 2021
Subjects: subject: Machine Learning (cs.LG)
subject: Numerical Analysis (math.NA)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: I.2.6; G.1.8
subject: 65D15, 65D18, 65N06, 65N50, 65Z05, 68T20

description: We present a machine learning framework that blends image super-resolution technologies with passive, scalar transport in the level-set method. Here, we investigate whether we can compute on-the-fly, data-driven corrections to minimize numerical viscosity in the coarse-mesh evolution of an interface. The proposed system's starting point is the semi-Lagrangian formulation. And, to reduce numerical dissipation, we introduce an error-quantifying multilayer perceptron. The role of this neural network is to improve the numerically estimated surface trajectory. To do so, it processes localized level-set, velocity, and positional data in a single time frame for select vertices near the moving front. Our main contribution is thus a novel machine-learning-augmented transport algorithm that operates alongside selective redistancing and alternates with conventional advection to keep the adjusted interface trajectory smooth. Consequently, our procedure is more efficient than full-scan convolutional-based applications because it concentrates computational effort only around the free boundary. Also, we show through various tests that our strategy is effective at counteracting both numerical diffusion and mass loss. In simple advection problems, for example, our method can achieve the same precision as the baseline scheme at twice the resolution but at a fraction of the cost. Similarly, our hybrid technique can produce feasible solidification fronts for crystallization processes. On the other hand, tangential shear flows and highly deforming simulations can precipitate bias artifacts and inference deterioration. Likewise, stringent design velocity constraints can limit our solver's application to problems involving rapid interface changes. In the latter cases, we have identified several opportunities to enhance robustness without forgoing our approach's basic concept.
Recombinant human sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDHS) is expressed at high yield as an active homotetramer in baculovirus-infected insect cells
Creators: name: Lamson, David R.
name: Sexton, Jonathan Z.
name: Yeh, Li-An
name: House, Alan J.
name: Williams, Kevin P.
name: O’Brien, Deborah A.
name: Sanyang, Khaddijatou
name: Danshina, Polina V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2011

description: The sperm-specific glyceraldehyde-3-phosphate dehydrogenase (GAPDHS) isoform is a promising contraceptive target because it is specific to male germ cells, essential for sperm motility and male fertility, and well suited to pharmacological inhibition. However, GAPDHS is difficult to isolate from native sources and recombinant expression frequently results in high production of insoluble enzyme. We chose to use the Bac-to-Bac baculovirus-insect cell system to express a His-tagged form of human GAPDHS (Hu his-GAPDHS) lacking the proline-rich N-terminal sequence. This recombinant Hu his-GAPDHS was successfully produced in Spodoptera frugiperda 9 (Sf9) cells by infection with recombinant virus as a soluble, enzymatically active form in high yield, >35mg/L culture. Biochemical characterization of the purified enzyme by mass spectrometry and size exclusion chromatography confirmed the presence of the tetrameric form. Further characterization by peptide ion matching mass spectrometry and Edman sequencing showed that unlike the mixed tetramer forms produced in bacterial expression systems, human his-GAPDHS expressed in baculovirus-infected insect cells is homotetrameric. The ability to express and purify active human GAPDHS as homotetramers in high amounts will greatly aid in drug discovery efforts targeting this enzyme for discovery of novel contraceptives and three compounds were identified as inhibitors of Hu his-GAPDHS from a pilot screen of 1120 FDA-approved compounds.
Investigation of using agarwood sawdust on growth and yield of the Bhutan oyster mushroom Cultivated
Creators: name: Chatmongkol Seeprasong
Publisher: name: Faculty of Science, Ubon Ratchathani University
Year: 2023
Subjects: Agarwood sawdust
Growth and yield
The Bhutan oyster mushroom

description: Journal of Science and Science Education, 6, 1, 31-39
Superluminous quasars and mesolensing
Creators: name: Raikov, Alexander
name: Lovyagin, Nikita
name: Yershov, Vladimir
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Observed magnitudes of many quasars with redshifts exceeding $z=5$ correspond to luminosities $L_{\rm bol} > 10^{14}\,L_\odot$. The standard mechanism of quasar energy release by accretion suggests that masses of superluminous quasars should exceed $10^{10}\,M_\odot$. On the other hand, the age of these objects in the standard cosmological model is below one billion years, which is too short to explain their formation in the early Universe. Many quasars are known to be gravitationally lensed; showing multiple images of the same object. In the case of remote quasars with no multiple images, it is still possible that they are also gravitationally lensed by foreground objects of intermediate masses, such as globular clusters or dwarf galaxies. Such mesolensing would result in essential amplification of quasar brightnesses, subject to geometrical configuration between the lens and the lensed object. Here we estimate the fraction of quasars whose brightness might have been amplified by gravitational lensing.
description: To be published in Proc. conf. VAK-2021, August 23-28, 2021, Sternberg Astronomical Institute, Moscow
GO_28, files from linear-scaling DFT and non-bonded parameters calculations
Creators: name: Pinto, Alexandre V.
Publisher: name: Zenodo
Year: 2022

description: Coordinates, topology, electron density cube file and files from Chargemol analysis for GO_28 obtained through Linear-Scaling Calculations in CP2K (check https://doi.org/10.1021/acs.jpcb.2c06037)
A First Test of the Framed Standard Model against Experiment
Creators: name: Bordes, J
name: Chan, HM
name: Tsou, ST
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The framed standard model (FSM) is obtained from the standard model by incorporating, as field variables, the frame vectors (vielbeins) in internal symmetry space. It gives the standard Higgs boson and 3 generations of quarks and leptons as immediate consequences. It gives moreover a fermion mass matrix of the form: $m = m_T αα^\dagger$, where $α$ is a vector in generation space independent of the fermion species and rotating with changing scale, which has already been shown to lead, generically, to up-down mixing, neutrino oscillations and mass hierarchy. In this paper, pushing the FSM further, one first derives to 1-loop order the RGE for the rotation of $α$, and then applies it to fit mass and mixing data as a first test of the model. With 7 real adjustable parameters, 18 measured quantities are fitted, most (12) to within experimental error or to better than 0.5 percent, and the rest (6) not far off. (A summary of this fit can be found in Table 2 in the text.) Two notable features, both generic to FSM, not just specific to the fit, are: (i) that a theta-angle of order unity in the instanton term in QCD would translate via rotation into a Kobayashi-Maskawa phase in the CKM matrix of about the observed magnitude ($J \sim 10^{-5}$), (ii) that it would come out correctly that $m_u
description: 45 pages, 7 figures
Thermal stability of purified and reconstituted CFTR in a locked open channel conformation
Creators: name: He, Lihua
name: Aleksandrov, Luba A.
name: Kousouros, Joseph N.
name: Cui, Liying
name: Aleksandrov, Andrei A.
name: Jensen, Timothy J.
name: Riordan, John R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: CFTR is unique among ABC transporters as the only one functioning as an ion channel and from a human health perspective because mutations in its gene cause cystic fibrosis. Although considerable advances have been made towards understanding CFTR’s mechanism of action and the impact of mutations, the lack of a high-resolution 3D structure has hindered progress. The large multi-domain membrane glycoprotein is normally present at low copy number and when over expressed at high levels it aggregates strongly, limiting the production of stable mono-disperse preparations. While the reasons for the strong self-association are not fully understood, its relatively low thermal stability seems likely to be one. The major CF causing mutation, ΔF508, renders the protein very thermally unstable and therefore a great deal of attention has been paid to this property of CFTR. Multiple second site mutations of CFTR in NBD1 where F508 normally resides and small molecule binders of the domain increase the thermal stability of the mutant. These manipulations also stabilize the wild-type protein. Here we have applied ΔF508-stabilizing changes and other modifications to generate wild-type constructs that express at much higher levels in scaled-up suspension cultures of mammalian cells. After purification and reconstitution into liposomes these proteins are active in a locked-open conformation at temperatures as high as 50°C and remain monodisperse at 4°C in detergent or lipid for at least a week. The availability of adequate amounts of these and related stable active preparations of homogeneous CFTR will enable stalled structural and ligand binding studies to proceed.
Amide proton exchange rates of oxidized and reduced saccharomyces cerevisiae iso-1-cytochrome c
Creators: name: Auld, Douglas S.
name: Doyle, Donald F.
name: Marmorino, Jennifer L.
name: Pielak, Gary J.
name: Betz, Stephen F.
name: Young, Gregory B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1993

description: Proton NMR spectroscopy was used to determine the rate constant, kobs, for exchange of labile protons in both oxidized (Fe(III)) and reduced (Fe(II)) iso-1-cytochrome c. We find that slowly exchanging backbone amide protons tend to lack solvent-accessible surface area, possess backbone hydrogen bonds, and are present in regions of regular secondary structure as well as in omega-loops. Furthermore, there is no correlation between kobs and the distance from a backbone amide nitrogen to the nearest solvent-accessible atom. These observations are consistent with the local unfolding model. Comparisons of the free energy change for denaturation, delta Gd, at 298 K to the free energy change for local unfolding, delta Gop, at 298 K for the oxidized protein suggest that certain conformations possessing higher free energy than the denatured state are detected at equilibrium. Reduction of the protein results in a general increase in delta Gop. Comparisons of delta Gd to delta Gop for the reduced protein show that the most open states of the reduced protein possess more structure than its chemically denatured form. This persistent structure in high-energy conformations of the reduced form appears to involve the axially coordinated heme.
Modelling the Magnetic Field Configuration of Neutron Stars
Creators: name: Ciolfi, Riccardo
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The properties of the extremely strong magnetic fields of neutron stars affect in a unique way their evolution and the associated phenomenology. Due to the lack of constraints from direct observations, our understanding of the magnetic field configuration in neutron star interiors depends on the progress in theoretical modelling. Here we discuss the effort in building models of magnetized neutron stars focussing on some of the recent results. In particular, we comment on the instability of purely poloidal and purely toroidal magnetic field configurations and on the evidence in favour of the so-called twisted-torus solutions. We conclude with an outlook on the present status of the field and future directions.
description: 6 pages, 2 figures. Proceedings of STARS2013 - 2nd Caribbean Symposium on Cosmology, Gravitation, Nuclear and Astroparticle Physics / SMFNS2013 - 3rd International Symposium on Strong Electromagnetic Fields and Neutron Stars
Probing weakly polar interactions in cytochrome c
Creators: name: Auld, Douglas S.
name: Young, Gregory B.
name: Saunders, Aleister J.
name: Pielak, Gary J.
name: Doyle, Donald F.
name: Betz, Stephen F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1993

description: Theoretical, statistical, and model studies suggest that proteins are stabilized by weakly polar attractions between sulfur atoms and properly oriented aromatic rings. The two sulfur-containing amino acids, methionine and cysteine, occur frequently among functional alleles in random mutant libraries of Saccharomyces cerevisiae iso-1-cytochrome c genes at positions that form a weakly polar aromatic-aromatic interaction, the wild-type protein. To determine if a weakly polar sulfur-aromatic interaction replaced the aromatic-aromatic interaction, the structure and stability of two variants were examined. Phenylalanine 10, which interacts with tyrosine 97, was replaced by methionine and cysteine. The cysteine was modified to form the methionine and cysteine analog, S-methyl cysteine (CysSMe). Proton NMR studies indicate that changing Phe 10 to Met or CysSMe affects only local structure and that the structures of sulfur-containing variants are nearly identical. Analysis of chemical shifts and nuclear Overhauser effect data indicates that both sulfur-containing side chains are in position to form a weakly polar interaction with Tyr 97. The F10M and F10CSMe variants are 2-3 kcal mol-1 less stable than iso-1-cytochrome c at 300 K. Comparison of the stabilities of the F10M and F10CSMe variants allows evaluation of the potential weakly polar interaction between the additional sulfur atom of F10CSMe and the aromatic moiety of Tyr 97. The F10CSMe;C102T variant is 0.7 +/- 0.3 kcal mol-1 more stable than the F10M;C102T protein. The increased stability is explained by the difference in hydrophobicity of the sulfur-containing side chains. We conclude that any weakly polar interaction between the additional sulfur and the aromatic ring is too weak to detect or is masked by destabilizing contributions to the free energy of denaturation.
Deuterium exchange of α-helices and β-sheets as monitored by electrospray ionization mass spectrometry
Creators: name: Anderegg, Robert J.
name: Melton, Laura G.
name: Erickson, Bruce W.
name: Yan, Yibing
name: Wagner, David S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1994

description: Deuterium exchange was monitored by electrospray ionization mass spectrometry (ESI-MS) to study the slowly exchanging (hydrogen bonded) peptide hydrogens of several alpha-helical peptides and beta-sheet proteins. Polypeptides were synthetically engineered to have mainly disordered, alpha-helical, or beta-sheet structure. For 3 isomeric 31-residue alpha-helical peptides, the number of slowly exchanging hydrogens as measured by ESI-MS in 50% CF3CD2OD (pD 9.5) provided estimates of their alpha-helicities (26%, 40%, 94%) that agreed well with the values (17%, 34%, 98%) measured by circular dichroic spectroscopy in the same nondeuterated solvent. For 3 betabellins containing a pair of beta-sheets and a related disordered peptide, their order of structural stability (12D > 12S > 14D > 14S) shown by their deuterium exchange rates in 10% CD3OD/0.5% CD3CO2D (pD 3.8) as measured by ESI-MS was the same as their order of structural stability to unfolding with increasing temperature or guanidinium chloride concentration as measured by circular dichroic spectroscopy in water. Compared to monitoring deuterium exchange by proton NMR spectrometry, monitoring deuterium exchange by ESI-MS requires much less sample (1-50 micrograms), much shorter analysis time (10-90 min), and no chemical quenching of the exchange reaction.
Strong lensing in UNIONS: Toward a pipeline from discovery to modeling
Creators: name: Savary, E.
name: Rojas, K.
name: Maus, M.
name: Clément, B.
name: Courbin, F.
name: Gavazzi, R.
name: Chan, J. H. H.
name: Lemon, C.
name: Vernardos, G.
name: Cañameras, R.
name: Schuldt, S.
name: Suyu, S. H.
name: Cuillandre, J. -C.
name: Fabbro, S.
name: Gwyn, S.
name: Hudson, M. J.
name: Kilbinger, M.
name: Scott, D.
name: Stone, C.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present a search for galaxy-scale strong gravitational lenses in the initial 2 500 square degrees of the Canada-France Imaging Survey (CFIS). We designed a convolutional neural network (CNN) committee that we applied to a selection of 2 344 002 exquisite-seeing $r$-band images of color-selected luminous red galaxies (LRGs). Our classification uses a realistic training set where the lensing galaxies and the lensed sources are both taken from real data, namely the CFIS $r$-band images themselves and the Hubble Space Telescope (HST). A total of 9 460 candidates obtain a score above 0.5 with the CNN committee. After a visual inspection of the candidates, we find a total of 133 lens candidates, of which 104 are completely new. The set of false positives mainly contains ring, spiral, and merger galaxies, and to a lesser extent galaxies with nearby companions. We classify 32 of the lens candidates as secure lenses and 101 as maybe lenses. For the 32 highest quality lenses, we also fit a singular isothermal ellipsoid mass profile with external shear along with an elliptical Sersic profile for the lens and source light. This automated modeling step provides distributions of properties for both sources and lenses that have Einstein radii in the range $0.5\arcsec<θ_E<2.5\arcsec$. Finally, we introduce a new lens and/or source single-band deblending algorithm based on auto-encoder representation of our candidates. This is the first time an end-to-end lens-finding and modeling pipeline is assembled together, in view of future lens searches in a single band, as will be possible with Euclid.
description: 29 pages, 21 figures, accepted by A&A, in press
Variations in Abundance Enhancements in Impulsive Solar Energetic-Particle Events and Related CMEs and Flares
Creators: name: Reames, Donald V.
name: Cliver, Edward W.
name: Kahler, Stephen W.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We study event-to-event variations in the abundance enhancements of the elements He through Pb for Fe-rich impulsive solar energetic-particle (SEP) events, and their relationship with properties of associated coronal mass ejections (CMEs) and solar flares. Using a least-squares procedure we fit the power-law enhancement of element abundances as a function of their mass-to-charge ratio A/Q to determine both the power and the coronal temperature (which determines Q) in each of 111 impulsive SEP events identified previously. Individual SEP events with the steepest element enhancements, e.g. ~(A/Q)^6, tend to be smaller, lower-fluence events with steeper energy spectra that are associated with B- and C-class X-ray flares, with cooler (~2.5 MK) coronal plasma, and with narrow (<100 deg), slower (<700 km/s) CMEs. On the other hand, higher-fluence SEP events have flatter energy spectra, less-dramatic heavy-element enhancements, e.g. ~(A/Q)^3, and come from somewhat hotter coronal plasma (~3.2 MK) associated with C-, M- and even X-class X-ray flares and with wider CMEs. Enhancements in 3He/4He are uncorrelated with those in heavy elements. However, events with 3He/4He > 0.1 are even more strongly associated with narrow, slow CMEs, with cooler coronal plasma, and with B- and C-class X-ray flares than are other Fe-rich impulsive SEP events with smaller enhancements of 3He.
description: 21 pages, 12 figures, Accepted for publication for Solar Physics