cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories
Creators: name: Reinhardt, Manuel
name: Tkačik, Gašper
name: Wolde, Pieter Rein ten
Publisher: name: arXiv
Year: 2022
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Information Theory (cs.IT)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals, requires the mutual information between the input and output signals as a function of time, i.e. between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called Path Weight Sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory, and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While Direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and Thermodynamic Integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient, but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger.
description: 19 pages (+ 14 pages appendix), 9 figures
On the Consistency of Approximate Quantum Dynamics Simulation Methods for Vibrational Spectra in the Condensed Phase
Creators: name: Rossi, Mariana
name: Liu, Hanchao
name: Paesani, Francesco
name: Bowman, Joel
name: Ceriotti, Michele
Publisher: name: arXiv
Year: 2014
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these limitations can be traced down to two approaches: methods that treat a small subset of the degrees of freedom with rigorous quantum mechanics, considering the rest of the system as a static or classical environment, and methods that treat the whole system quantum mechanically, but using approximate dynamics. Here we perform a systematic comparison between these two philosophies for the description of quantum effects in vibrational spectroscopy, taking the Embedded Local Monomer (LMon) model and a mixed quantum-classical (MQC) model as representatives of the first family of methods, and centroid molecular dynamics (CMD) and thermostatted ring polymer molecular dynamics (TRPMD) as examples of the latter. We use as benchmarks D$_2$O doped with HOD and pure H$_2$O at three distinct thermodynamic state points (ice Ih at 150K, and the liquid at 300K and 600K), modeled with the simple q-TIP4P/F potential energy and dipole moment surfaces. With few exceptions the different techniques yield IR absorption frequencies that are consistent with one another within a few tens of cm$^{-1}$. Comparison with classical molecular dynamics demonstrates the importance of nuclear quantum effects up to the highest temperature, and a detailed discussion of the discrepancies between the various methods let us draw some (circumstantial) conclusions about the impact of the very different approximations that underlie them. Such cross validation between radically different approaches could indicate a way forward to further improve the state of the art in simulations of condensed-phase quantum dynamics.
description: Bundled together with the Supporting Materials
ПАТРИОТИЧЕСКИЕ НАСТРОЕНИЯ МОЛОДЕЖИ: СОЦИАЛЬНОФИЛОСОФСКИЙ АНАЛИЗ
Creators: name: Журавлева Л.А.
name: Зарубина Е.В.
name: Кохановский А.А.
name: Симачкова Н.Н.
name: Чупина И.П.
Publisher: name: Образование и право
Year: 2022
Subjects: молодежь
социологическое исследование
отношение к своей стране
отношение к СВО
геополитика
патриотизм
патриотические настроения
патриотическое воспитание
программа патриотического воспитания
методы и приемы патриотического воспитания.

description: В статье представлены результаты второго этапа социологического исследования «Мировоззрение современной молодежи», который был проведен осенью 2022 года. В исследовании приняли участие 128 представителей поколения Z, в основном студентов Уральского государственного аграрного университета и других вузов г. Екатеринбурга. 71% респондентов составили женщины, 29% мужчины. Методологической основой исследования стала социологическая теория поколений Нейла Хоу и Уильяма Штрауса. Исследование проводилось с помощью таких качественных методов социологии, как анализ личных документов, серии интервью и работы с респондентами в фокус-группах. Респонденты письменно отвечали на вопросы о мировоззрении молодежи по ряду позиций, в том числе об отношении к своей стране, а также об их отношении к специальной военной операции, которую Россия проводит на Украине с 24 февраля 2022 года. В статье представлен анализ патриотических настроений респондентов на основе интерпретации их ответов на вопрос об отношении к своей стране и на вопрос об отношении к специальной военной операции России на Украине. Проведенное исследование позволило выявить ярко выраженные патриотические настроения большей части современной молодежи к своей стране. Около двух третей участников проведенного исследования считают себя патриотами, а также умеют обосновать свою позицию. Авторы анализируют причины формирования мировоззрение небольшой части «не патриотов», предлагают дифференцированный подход патриотическому воспитанию молодых людей. В заключение статьи предложены рекомендации по составлению программы патриотического воспитания молодежи, метода и формам ее проведения.
Additional file 3 of Teachers as multipliers of knowledge about schistosomiasis: a possible approach for health education programmes
Creators: name: Murta, Felipe Leão Gomes
name: Massara, Cristiano Lara
name: Rodrigues, Maria Gabriela
name: Beck, Lilian Christina Nóbrega Holsbach
name: Favre, Tereza Cristina
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 3. Focus group discussion guide. https://doi.org/10.6084/m9.figshare.19990883.v1 .
Characterization of species-specific genes regulated by E2-2 in human plasmacytoid dendritic cells
Creators: name: Du, Peishuang
name: Yu, Haisheng
name: Zhang, Xuyuan
name: Cheng, Menglan
name: Plumas, Joël
name: Zhang, Liguo
name: Chaperot, Laurance
name: Su, Lishan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Dendritic cells (DCs) are sentinels of the immune system and comprise two distinct subsets: conventional DCs (cDCs) and plasmacytoid DCs (pDCs). Human pDCs are distinguished from mouse pDCs phenotypically and functionally. Basic helix-loop-helix protein E2-2 is defined as an essential transcription factor for mouse pDC development, cell fate maintenance and gene programe. It is unknown whether E2-2 regulation contributes to this species-specific difference. Here we investigated the function of E2-2 in human pDCs and screened human-specific genes regulated by E2-2. Reduced E2-2 expression in human pDC cell line GEN2.2 resulted in diminished IFN-α production in response to CpG but elevated antigen presentation capacity. Gene expression profiling showed that E2-2 silence down-regulated pDC signature genes but up-regulated cDC signature genes. Thirty human-specific genes regulated by E2-2 knockdown were identified. Among these genes, we confirmed that expression of Siglec-6 was inhibited by E2-2. Further more, Siglec-6 was expressed at a higher level on a human pDC subset with drastically lower expression of E2-2. Collectively, these results highlight that E2-2 modulates pDC function in a species-specific manner, which may provide insights for pDC development and functions.
Additional file 10 of Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study
Creators: name: Carda-Diéguez, Miguel
name: Moazzez, Rebecca
name: Mira, Alex
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 10: Additional Figure 9. Changes in bacterial communities’ gene content and activity after Fluoride + Arginine treatment. Each dot represents a gene that was significantly under- or over-represented in the metagenomics (MTG) or metatranscriptomic (MTT) datasets after 6-month use of Fl+Arg dentifrice. The abundance/expression level in the MTG/MTT (expressed as the number of reads normalized per gene length per Mpb of sequencing coverage) and the fold change (RLM before/RLM after) are shown for each gene. Dots corresponding to genes over-represented after fluoride treatment are labeled in orange and those in green correspond to genes over-represented after Fl+Arg treatment. Genes differentially represented in Caries-Active sites (CA) and Caries-Free individuals (CF) are shown at the top and lower panels, respectively. AgDS, agmatine deiminase system; ADS, arginine deiminase system; NQR, NADH:quinone oxidoreductase; Na+ATPase, V/A-type H+/Na+-transporting ATPase; PTS, phosphotransferase system.
ПОВЫШЕНИЕ КВАЛИФИКАЦИИ ПРОКУРОРСКИХ РАБОТНИКОВ КАК ПРИОРИТЕТНОЕ НАПРАВЛЕНИЕ КАДРОВОГО ОБЕСПЕЧЕНИЯ ПРОКУРАТУРЫ РОССИИ: ПРАКТИКА ПРОКУРАТУРЫ Г. САНКТ-ПЕТЕРБУРГА
Creators: name: Алексеева Ю.Б.
Publisher: name: Образование и право
Year: 2022
Subjects: повышение квалификации
прокуратура
переподготовка
надзор
профессионализм
цифровизация.

description: В статье отражена практика прокуратуры г. Санкт-Петербурга по повышению квалификации, как важного направления кадрового обеспечения органов прокуратуры с реализацией Комплексной программы профессиональной подготовки вновь принятых прокурорских работников. Рассмотрены инновационные способы применения компьютерных технологий в системе обучения и воспитания молодых специалистов прокуратуры г. Санкт-Петербурга.
Additional file 4 of Teachers as multipliers of knowledge about schistosomiasis: a possible approach for health education programmes
Creators: name: Murta, Felipe Leão Gomes
name: Massara, Cristiano Lara
name: Rodrigues, Maria Gabriela
name: Beck, Lilian Christina Nóbrega Holsbach
name: Favre, Tereza Cristina
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 4. Consolidated criteria for reporting qualitative research (COREQ). https://doi.org/10.6084/m9.figshare.19990865.v1 .
ПОЗНАВАЯ МЕТОДОЛОГИЮ МУСУЛЬМАНСКОГО ПРАВА
Creators: name: Рамазанов А.Х.
name: Халилова А.М.
Publisher: name: Образование и право
Year: 2022
Subjects: методология права
мусульманское право
формационный подход
цивилизационный подход
метафизика права.

description: Познанию всегда сопутствуют контекст цивилизации и эпохи, они придают свои смыслы и символы; одно и то же слово, познание понимаются и осмысляются по-разному в плоскости времени и пространства. В современной правовой науке господствует позитивизм, право представляется материалистической конструкцией, не воплощающей в себе сокровенного знания; если мы обратим взор в прошлое, то увидим, как право внутренними связами скреплено с духовностью и духом человека. Нам представляется важным исследовать усуль аль-фикх, методологию мусульманского права через подходы разных методологий (формационной, цивилизационной и метафизической).
$2^{1296}$ Exponentially Complex Quantum Many-Body Simulation via Scalable Deep Learning Method
Creators: name: Liang, Xiao
name: Li, Mingfan
name: Xiao, Qian
name: An, Hong
name: He, Lixin
name: Zhao, Xuncheng
name: Chen, Junshi
name: Yang, Chao
name: Wang, Fei
name: Qian, Hong
name: Shen, Li
name: Jia, Dongning
name: Gu, Yongjian
name: Liu, Xin
name: Wei, Zhiqiang
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: For decades, people are developing efficient numerical methods for solving the challenging quantum many-body problem, whose Hilbert space grows exponentially with the size of the problem. However, this journey is far from over, as previous methods all have serious limitations. The recently developed deep learning methods provide a very promising new route to solve the long-standing quantum many-body problems. We report that a deep learning based simulation protocol can achieve the solution with state-of-the-art precision in the Hilbert space as large as $2^{1296}$ for spin system and $3^{144}$ for fermion system , using a HPC-AI hybrid framework on the new Sunway supercomputer. With highly scalability up to 40 million heterogeneous cores, our applications have measured 94% weak scaling efficiency and 72% strong scaling efficiency. The accomplishment of this work opens the door to simulate spin models and Fermion models on unprecedented lattice size with extreme high precision.
description: Massive ground state optimizations of CNN-based wave-functions for $J1$-$J2$ model and $t$-$J$ model carried out on a heterogeneous cores supercomputer
ПОНЯТИЕ ГОСУДАРСТВЕННОГО ФИНАНСОВОГО КОНТРОЛЯ
Creators: name: Примак В.В.
Publisher: name: Образование и право
Year: 2022
Subjects: финансовое право
финансовый контроль
государственный финансовый контроль
понятие государственного финансового контроля
признаки финансового контроля.

description: Авторами данной работы была поставлена цель проанализировать одно из наиболее важных и фундаментальных понятий финансового права – государственный финансовый контроль. На сегодняшний день законодателем не представлено универсального и конкретного понятия государственного финансового контроля. Следствием этого стало появление в доктрине множества различных точек зрения. Авторы данной работы выявили признаки данного понятия на основании множества трудов отечественных авторов и на основе исследованных материалов предложили свое видение на данный законодательный пробел.
Enhancement of muonium emission rate from silica aerogel with a laser ablated surface
Creators: name: Beer, G. A.
name: Fujiwara, Y.
name: Hirota, S.
name: Ishida, K.
name: Iwasaki, M.
name: Kanda, S.
name: Kawai, H.
name: Kawamura, N.
name: Kitamura, R.
name: Lee, S.
name: Marshall, W. Lee G. M.
name: Mibe, T.
name: Miyake, Y.
name: Okada, S.
name: Olchanski, K.
name: Olin, A.
name: Oishi, Y.
name: Onishi, H.
name: Otani, M.
name: Saito, N.
name: Shimomura, K.
name: Strasser, P.
name: Tabata, M.
name: Tomono, D.
name: Ueno, K.
name: Yokoyama, K.
name: Won, E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: Emission of muonium ($μ^+e^-$) atoms from a laser-processed aerogel surface into vacuum was studied for the first time. Laser ablation was used to create hole-like regions with diameter of about 270$~μ$m in a triangular pattern with hole separation in the range of 300--500$~μ$m. The emission probability for the laser-processed aerogel sample is at least eight times higher than for a uniform one.
ПРАВОВАЯ ПРИРОДА СТЕЙКИНГА В ИНВЕСТИЦИОННОМ АСПЕКТЕ
Creators: name: Иванов К.О.
Publisher: name: Образование и право
Year: 2022
Subjects: стейкинг
блокчейн
криптовалюта
инвестиции
предпринимательская деятельность
инвестиционная деятельность.

description: Инвестиции становятся всё более популярными, в связи с чем инвесторы ищут новые инструменты для своей деятельности. Одним из них является стейкинг. Данный феномен не имеет регулирования в современном российском законодательстве (как частноправовом, так и публичноправовом), в связи с чем возникает проблема правовой неопределённости со всеми вытекающими из неё негативными последствиями. В исследовании автор предполагает, что для регулирования стейкинга – принципиально нового инвестиционного инструмента – не требуется радикальное изменение текущего законодательства. В обоснование гипотезы автор изучает и описывает технический механизм работы стейкинга, определяет его правовую природу, сравнивает с уже существующими правовыми институтами, пытается найти место стейкинга в современной парадигме гражданского права. В исследовании применяются метод аналогии, аналитический, сравнительно-правовой, системный методы. Автор приходит к выводу о том, что стейкинг с позиции современного частного права можно охарактеризовать как одновременно разновидность предпринимательской и инвестиционной деятельности, хотя не любая разновидность стейкинга подпадает под эту дефиницию.
Additional file 11 of Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study
Creators: name: Carda-Diéguez, Miguel
name: Moazzez, Rebecca
name: Mira, Alex
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 11: Additional Figure 10. Effect of genome-size normalization on taxonomic composition. The abundance of the top-15 genera for the MTG dataset was normalized considering not only the size of the dataset but also by the corresponding genome size (Mbp).
Cortical actin networks induce spatio-temporal confinement of phospholipids in the plasma membrane – a minimally invasive investigation by STED-FCS
Creators: name: Mueller, Veronika
name: Lagerholm, B. Christoffer
name: Clausen, Mathias P.
name: Andrade, Débora M.
name: Eggeling, Christian
name: Hell, Stefan W.
name: Keller, Jan
name: Wu, Congying
name: Bear, James E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Important discoveries in the last decades have changed our view of the plasma membrane organisation. Specifically, the cortical cytoskeleton has emerged as a key modulator of the lateral diffusion of membrane proteins. Cytoskeleton-dependent compartmentalised lipid diffusion has been proposed, but this concept remains controversial because this phenomenon has thus far only been observed with artefact-prone probes in combination with a single technique: single particle tracking. In this paper, we report the first direct observation of compartmentalised phospholipid diffusion in the plasma membrane of living cells using a minimally invasive, fluorescent dye labelled lipid analogue. These observations were made using optical STED nanoscopy in combination with fluorescence correlation spectroscopy (STED-FCS), a technique which allows the study of membrane dynamics on a sub-millisecond time-scale and with a spatial resolution of down to 40 nm. Specifically, we find that compartmentalised phospholipid diffusion depends on the cortical actin cytoskeleton, and that this constrained diffusion is directly dependent on the F-actin branching nucleator Arp2/3. These findings provide solid evidence that the Arp2/3-dependent cortical actin cytoskeleton plays a pivotal role in the dynamic organisation of the plasma membrane, potentially regulating fundamental cellular processes.
Economic development and coastal ecosystem change in China
Creators: name: Bai, Junhong
name: Bruno, John F.
name: Ehrlich, Paul R.
name: Liu, Jianguo
name: Chen, Guoqian
name: He, Qiang
name: Bertness, Mark D.
name: Cui, Baoshan
name: Sun, Tao
name: Coverdale, Tyler C.
name: Li, Bo
name: Altieri, Andrew H.
name: Pennings, Steven C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Despite their value, coastal ecosystems are globally threatened by anthropogenic impacts, yet how these impacts are driven by economic development is not well understood. We compiled a multifaceted dataset to quantify coastal trends and examine the role of economic growth in China's coastal degradation since the 1950s. Although China's coastal population growth did not change following the 1978 economic reforms, its coastal economy increased by orders of magnitude. All 15 coastal human impacts examined increased over time, especially after the reforms. Econometric analysis revealed positive relationships between most impacts and GDP across temporal and spatial scales, often lacking dropping thresholds. These relationships generally held when influences of population growth were addressed by analyzing per capita impacts, and when population density was included as explanatory variables. Historical trends in physical and biotic indicators showed that China's coastal ecosystems changed little or slowly between the 1950s and 1978, but have degraded at accelerated rates since 1978. Thus economic growth has been the cause of accelerating human damage to China's coastal ecosystems. China's GDP per capita remains very low. Without strict conservation efforts, continuing economic growth will further degrade China's coastal ecosystems.
The impact of super-survey modes on cosmological constraints from cosmic shear fields
Creators: name: Carron, Julien
name: Szapudi, István
Publisher: name: arXiv
Year: 2014
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Applications (stat.AP)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Owing to the mass-sheet degeneracy, cosmic shear maps do not probe directly the Fourier modes of the underlying mass distribution on scales comparable to the survey size and larger. To assess the corresponding effect on attainable cosmological parameter constraints, we quantify the information on super-survey modes in a lognormal model and, when interpreted as nuisance parameters, their degeneracies to cosmological parameters. Our analytical and numerical calculations clarify the central role of super-sample covariance (SSC) in shaping the statistical power of cosmological observables. Reconstructing the background modes from their non-Gaussian statistical dependence to small scales modes yields the renormalized convergence. This diagonalizes the spectrum covariance matrix, and the information content of the corresponding power spectrum is increased by a factor of two over standard methods. Unfortunately, careful calculation of the Cramer-Rao bound shows that the information recovery can never be made complete, any observable built from shear fields, including optimal sufficient statistics, are subject to severe information loss, typically $80\%$ to $90\%$ below $\ell \sim 3000$ for generic cosmological parameters. The lost information can only be recovered from additional, non-shear based data. Our predictions hold just as well for a tomographic analysis, and/or full sky surveys.
description: 11 pages, 4 figures, matches version accepted for publication in MNRAS
Supplementary Data Collection and Analysis Methods from Navigating polycrisis: long-run socio-cultural factors shape response to changing climate
Creators: name: Hoyer, Daniel
name: Bennett, James S.
name: Reddish, Jenny
name: Holder, Samantha
name: Howard, Robert
name: Benam, Majid
name: Levine, Jill
name: Ludlow, Francis
name: Feinman, Gary
name: Turchin, Peter
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Environmental Science

description: Supplementary Data Methods
Efficient genetic manipulation of the NOD-Rag1-/-IL2RgammaC-null mouse by combining in vitro fertilization and CRISPR/Cas9 technology
Creators: name: Zhang, Liguo
name: Banner, Debra
name: Cowley, Dale O.
name: Li, Feng
name: Su, Lishan
name: Holle, Eric
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Humanized mouse models have become increasingly important and widely used in modeling human diseases in biomedical research. Immunodeficient mice such as NOD-Rag1-/-IL2RgammaC-null (NRG) or NOD-SCID-IL2RgammaC-null (NSG) mice are critical for efficient engraftment of human cells or tissues. However, their genetic modification remains challenging due to a lack of embryonic stem cells and difficulty in the collection of timed embryos after superovulation. Here, we report the generation of gene knockout NRG mice by combining in vitro fertilization (IVF) and CRISPR/Cas9 technology. Sufficient numbers of fertilized embryos were produced through IVF, and a high rate of Fah gene targeting was achieved with microinjection of Cas9 mRNA, gRNA and single strand oligonucleotide DNA (ssDNA) into the embryos. The technology paves the way to construct NRG or NSG mutant mice to facilitate new humanized mouse models. The technology can also be readily adapted to introduce mutations in other species such as swine and non-human primates.
Sign Problem in Quantum Monte Carlo Simulation
Creators: name: Pan, Gaopei
name: Meng, Zi Yang
Publisher: name: arXiv
Year: 2022
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Sign problem in quantum Monte Carlo (QMC) simulation appears to be an extremely hard yet interesting problem. In this article, we present a pedagogical overview on the origin of the sign problem in various quantum Monte Carlo simulation techniques, ranging from the world-line and stochastic series expansion Monte Carlo for boson and spin systems to the determinant and momentum-space quantum Monte Carlo for interacting fermions. We point out the basis dependency of the sign problem and summarize the progresses to cure, ease and even make use of the sign problem over the years, such as symmetry analysis of the underlying Hamiltonian, basis optimization in writting down the partition functions and many others. Moreover, we state that although traditional lore saying that in case of sign problem, the average sign in QMC simulation approaches zero exponentially fast with the space-time volume of the configurational space, there are recent breakthroughs showing this is not always the case and based on the properties of the partition function for finite size systems, one could distinguish when the average sign has the usual exponential scaling and when it is bestowed with an algebraic scaling at the low temperature limit. Fermionic QMC simulations with such algebraic sign problems have been successfully carried out for extended Hubbard-type and quantum Moiré lattice models.
description: Book chapter for Elsevier Encyclopedia of Condensed Matter Physics. Comments and missing references are welcome
Additional file 5 of Teachers as multipliers of knowledge about schistosomiasis: a possible approach for health education programmes
Creators: name: Murta, Felipe Leão Gomes
name: Massara, Cristiano Lara
name: Rodrigues, Maria Gabriela
name: Beck, Lilian Christina Nóbrega Holsbach
name: Favre, Tereza Cristina
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 5. Schistosomiasis questionnaire applied to students. https://doi.org/10.6084/m9.figshare.20201246.v1 .
ПРАВА ДЕТЕЙ С ОГРАНИЧЕННЫМИ ВОЗМОЖНОСТЯМИ ЗДОРОВЬЯ НА ОБРАЗОВАНИЕ
Creators: name: Дибраев А.Д.
name: Аскерова Я.Н.
name: Кадиева Ф.А.
Publisher: name: Образование и право
Year: 2022
Subjects: ребенок-инвалид
права детей с ограниченными возможностями здоровья на образование
проблемы детей с ограниченными возможностями здоровья в плане социализации.

description: Для работы была выбрана тема «Права детей с ограниченными возможностями на образование» . Данная тема актуальна во всем своем многообразии, затрагивает сферу правовых знаний, социологии, психологии и других дисциплин, так как рассматривает проблему приспособленности детей-инвалидов к окружающему их миру, проблему адаптации их к нормальной и полноценной жизни в обществе. Проанализированы проблемы нахождения детей-инвалидов в обществе, рассмотрела вопросы обучения, развития и творчества детей с ограниченными возможностями.
Additional file 12 of Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study
Creators: name: Carda-Diéguez, Miguel
name: Moazzez, Rebecca
name: Mira, Alex
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 12. Additional Material and Methods.
ПРАВОВОЕ РЕГУЛИРОВАНИЕ МЕЖДУНАРОДНОГО СТРОИТЕЛЬНОГО ПОДРЯДА В СТРАНАХ ЕАЭС
Creators: name: Аносов Я.А.
Publisher: name: Образование и право
Year: 2022
Subjects: договор строительного подряда
зарубежное законодательство
заказчик
подрядчик.

description: В статье содержится обзор зарубежных источников правового регулирования отношений, возникающих из международного строительного подряда. Отмечаются тенденции в правовой регламентации выполнения строительных работ, выражающиеся в сочетании законодательного регулирования с условиями типовых контрактов.
Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation
Creators: name: Yokomori, Kyoko
name: Hahn, Klaus M.
name: Gaus, Katharina
name: Hinde, Elizabeth
name: Gratton, Enrico
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Here we describe a fluctuation-based method to quantify how protein oligomerisation modulates signalling activity of a multifunctional protein. By recording fluorescence lifetime imaging microscopy (FLIM) data of a FRET biosensor in a format that enables concomitant phasor and cross Number and Brightness (cN&B) analysis, we measure the nuclear dynamics of a Rac1 FRET biosensor and assess how Rac1 homo-oligomers (N&B) regulate Rac1 activity (hetero-oligomerisation with the biosensor affinity reagent, PBD, by FLIM-FRET) or interaction with an unknown binding partner (cN&B). The high spatiotemporal resolution of this method allowed us to discover that upon DNA damage monomeric and active Rac1 in the nucleus is segregated from dimeric and inactive Rac1 in the cytoplasm. This reorganisation requires Rac1 GTPase activity and is associated with an importin-α2 redistribution. Only with this multiplexed approach can we assess the oligomeric state a molecular complex must form in order to regulate a complex signalling network.
ПРАВОВОЕ РЕГУЛИРОВАНИЕ ЭКОЛОГИЧЕСКОЙ БЕЗОПАСНОСТИ
Creators: name: Арутюнян Р.Э.
name: Карапетян М.Г.
Publisher: name: Образование и право
Year: 2022
Subjects: экологическая безопасность
экологическое право
нормативные акты
окружающая среда
экологизация
экологический контроль
экологическая экспертиза.

description: Статья посвящена рассмотрению правового обеспечения экологической безопасности РФ, также рассматриваются правовые, нормативные акты, механизмы регулирования защиты окружающей среды, ответственность за нарушение экологического законодательства, экологический контроль, описываются нормативы качества природной окружающей среды, а также экономический механизм охраны окружающей среды. Важнейшей характеристикой состояния экономики и качества жизни является безопасность человека и среды его обитания. Существуют различные виды безопасности, главным из которых является экологическая безопасность.
Collective Coordinates Theory for Discrete Soliton Ratchets in the sine-Gordon Model
Creators: name: Sánchez-Rey, B.
name: Quintero, N. R.
name: Cuevas-Maraver, J.
name: Alejo, M. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: A collective coordinate theory is develop for soliton ratchets in the damped discrete sine-Gordon model driven by a biharmonic force. An ansatz with two collective coordinates, namely the center and the width of the soliton, is assumed as an approximated solution of the discrete non-linear equation. The evolution of these two collective coordinates, obtained by means of the Generalized Travelling Wave Method, explains the mechanism underlying the soliton ratchet and captures qualitatively all the main features of this phenomenon. The theory accounts for the existence of a non-zero depinning threshold, the non-sinusoidal behaviour of the average velocity as a function of the difference phase between the harmonics of the driver, the non-monotonic dependence of the average velocity on the damping and the existence of non-transporting regimes beyond the depinning threshold. In particular it provides a good description of the intriguing and complex pattern of subspaces corresponding to different dynamical regimes in parameter space.
ПРАВОВОЙ ПРОГНОЗ ИЛИ ПРОГНОЗ РЕЦИДИВА В УГОЛОВНО-ИСПОЛНИТЕЛЬНОЙ ПРАКТИКЕ ГЕРМАНИИ
Creators: name: Шишигина С.Н.
Publisher: name: Образование и право
Year: 2022
Subjects: осужденный
правовой прогноз
риск рецидива
условно-досрочное освобождение
пенитенциарная система
безопасность
исправление
терапия.

description: Правовой прогноз или прогноз рецидива имеет решающее значение для вопроса о необходимости назначения или продолжения содержания осужденного в исправительном учреждении. Основой для создания правового прогноза является точное исследование испытуемого. Для этой цели существует ряд инструментов прогнозирования. Прогноз рецидива также составляет врач-психиатр по запросу суда, в том числе в качестве основы для принятия таких решений как помещение в учреждение, освобождение из исправительного учреждения, при послаблениях режима, а также условно-досрочном освобождение из-под стражи. В статье рассматривается правовой прогноз или прогноз рецидива осужденного как один из критериев определения готовности его к назначению послаблений режима исполнения наказания и к условно-досрочному освобождению из пенитенциарных учреждений Германии, в том числе от пожизненного лишения свободы.
Gene expression in breastmilk cells is associated with maternal and infant characteristics
Creators: name: Tat Lai, Ching
name: Blancafort, Pilar
name: Geddes, Donna T.
name: Twigger, Alecia-Jane
name: Stuebe, Alison M.
name: Hartmann, Peter E.
name: Hepworth, Anna R.
name: Chetwynd, Ellen
name: Kakulas, Foteini
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Breastmilk is a rich source of cells with a heterogeneous composition comprising early-stage stem cells, progenitors and more differentiated cells. The gene expression profiles of these cells and their associations with characteristics of the breastfeeding mother and infant are poorly understood. This study investigated factors associated with the cellular dynamics of breastmilk and explored variations amongst women. Genes representing different breastmilk cell populations including mammary epithelial and myoepithelial cells, progenitors, and multi-lineage stem cells showed great variation in expression. Stem cell markers ESRRB and CK5, myoepithelial marker CK14, and lactocyte marker α-lactalbumin were amongst the genes most highly expressed across all samples tested. Genes exerting similar functions, such as either stem cell regulation or milk production, were found to be closely associated. Infant gestational age at delivery and changes in maternal bra cup size between pre-pregnancy and postpartum lactation were associated with expression of genes controlling stemness as well as milk synthesis. Additional correlations were found between genes and dyad characteristics, which may explain abnormalities related to low breastmilk supply or preterm birth. Our findings highlight the heterogeneity of breastmilk cell content and its changes associated with characteristics of the breastfeeding dyad that may reflect changing infant needs.
Additional file 2 of The usefulness of the total metabolic tumor volume for predicting the postoperative recurrence of thoracic esophageal squamous cell carcinoma
Creators: name: Kaida, Hayato
name: Yasuda, Takushi
name: Shiraishi, Osamu
name: Kato, Hiroaki
name: Kimura, Yutaka
name: Hanaoka, Kohei
name: Yamada, Minoru
name: Matsukubo, Yuko
name: Tsurusaki, Masakatsu
name: Kitajima, Kazuhiro
name: Hattori, Satoshi
name: Ishii, Kazunari
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer

description: Additional file 2.
Vertical shear instability in accretion disc models with radiation transport
Creators: name: Stoll, Moritz H. R.
name: Kley, Wilhelm
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The origin of turbulence in accretion discs is still not fully understood. While the magneto-rotational instability is considered to operate in sufficiently ionized discs, its role in the poorly ionized protoplanetary disc is questionable. Recently, the vertical shear instability (VSI) has been suggested as a possible alternative. Our goal is to study the characteristics of this instability and the efficiency of angular momentum transport, in extended discs, under the influence of radiative transport and irradiation from the central star. We use multi-dimensional hydrodynamic simulations to model a larger section of an accretion disc. First we study inviscid and weakly viscous discs using a fixed radial temperature profile in two and three spatial dimensions. The simulations are then extended to include radiative transport and irradiation from the central star. In agreement with previous studies we find for the isothermal disc a sustained unstable state with a weak positive angular momentum transport of the order of $α\approx 10^{-4}$. Under the inclusion of radiative transport the disc cools off and the turbulence terminates. For discs irradiated from the central star we find again a persistent instability with a similar $α$ value as for the isothermal case. We find that the VSI can indeed generate sustained turbulence in discs albeit at a relatively low level with $α$ about few times $10^{-4}$
description: 12 pages, 24 figures, accepted for publication in Astronomy & Astrophysics
GSAASeqSP: A Toolset for Gene Set Association Analysis of RNA-Seq Data
Creators: name: Xiong, Qing
name: Furey, Terrence S.
name: Mukherjee, Sayan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: RNA-Seq is quickly becoming the preferred method for comprehensively characterizing whole transcriptome activity, and the analysis of count data from RNA-Seq requires new computational tools. We developed GSAASeqSP, a novel toolset for genome-wide gene set association analysis of sequence count data. This toolset offers a variety of statistical procedures via combinations of multiple gene-level and gene set-level statistics, each having their own strengths under different sample and experimental conditions. These methods can be employed independently, or results generated from multiple or all methods can be integrated to determine more robust profiles of significantly altered biological pathways. Using simulations, we demonstrate the ability of these methods to identify association signals and to measure the strength of the association. We show that GSAASeqSP analyses of RNA-Seq data from diverse tissue samples provide meaningful insights into the biological mechanisms that differentiate these samples. GSAASeqSP is a powerful platform for investigating molecular underpinnings of complex traits and diseases arising from differential activity within the biological pathways. GSAASeqSP is available at http://gsaa.unc.edu.
Realization Theory Of Recurrent Neural ODEs Using Polynomial System Embeddings
Creators: name: Gonzalez, Martin
name: Defourneau, Thibault
name: Hajri, Hatem
name: Petreczky, Mihaly
Publisher: name: arXiv
Year: 2022
Subjects: subject: Optimization and Control (math.OC)
subject: Machine Learning (cs.LG)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: In this paper we show that neural ODE analogs of recurrent (ODE-RNN) and Long Short-Term Memory (ODE-LSTM) networks can be algorithmically embeddeded into the class of polynomial systems. This embedding preserves input-output behavior and can suitably be extended to other neural DE architectures. We then use realization theory of polynomial systems to provide necessary conditions for an input-output map to be realizable by an ODE-LSTM and sufficient conditions for minimality of such systems. These results represent the first steps towards realization theory of recurrent neural ODE architectures, which is is expected be useful for model reduction and learning algorithm analysis of recurrent neural ODEs.
description: 10 pages. Corrected typos and added references
Guanine- 5-carboxylcytosine base pairs mimic mismatches during DNA replication
Creators: name: Toda, Mariko
name: Collins, Leonard B.
name: Iwai, Shigenori
name: Shibata, Marika
name: Urabe, Miho
name: Swenberg, James A.
name: Shibutani, Toshihiro
name: Koseki, Haruhiko
name: Masuda, Yuji
name: Ito, Shinsuke
name: Kuraoka, Isao
name: Masutani, Chikahide
name: Hanaoka, Fumio
name: Kanao, Rie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The genetic information encoded in genomes must be faithfully replicated and transmitted to daughter cells. The recent discovery of consecutive DNA conversions by TET family proteins of 5-methylcytosine into 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine (5caC) suggests these modified cytosines act as DNA lesions, which could threaten genome integrity. Here, we have shown that although 5caC pairs with guanine during DNA replication in vitro, G·5caC pairs stimulated DNA polymerase exonuclease activity and were recognized by the mismatch repair (MMR) proteins. Knockdown of thymine DNA glycosylase increased 5caC in genome, affected cell proliferation via MMR, indicating MMR is a novel reader for 5caC. These results suggest the epigenetic modification products of 5caC behave as DNA lesions.
IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance
Creators: name: Urban, Thomas J.
name: Weeks, Kevin M.
name: Goldstein, David B.
name: Lu, Yi-Fan
name: Mauger, David M.
name: Bradrick, Shelton S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Polymorphisms near the interferon lambda 3 (IFNL3) gene strongly predict clearance of hepatitis C virus (HCV) infection. We analyzed a variant (rs4803217 G/T) located within the IFNL3 mRNA 3′ untranslated region (UTR); the G allele (protective allele) is associated with elevated therapeutic HCV clearance. We show that the IFNL3 3′ UTR represses mRNA translation and the rs4803217 allele modulates the extent of translational regulation. We analyzed the structures of IFNL3 variant mRNAs at nucleotide resolution by SHAPE-MaP. The rs4803217 G allele mRNA forms well-defined 3′ UTR structure while the T allele mRNA is more dynamic. The observed differences between alleles are among the largest possible RNA structural alterations that can be induced by a single nucleotide change and transform the UTR from a single well-defined conformation to one with multiple dynamic interconverting structures. These data illustrate that non-coding genetic variants can have significant functional effects by impacting RNA structure.
Inhibition of miR-29 has a significant lipid-lowering benefit through suppression of lipogenic programs in liver
Creators: name: Sethupathy, Praveen
name: Toth, Cynthia L.
name: Vickers, Kasey C.
name: Kurtz, C. Lisa
name: Pearson, Daniel S.
name: Fannin, Emily E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: MicroRNAs (miRNAs) are important regulators and potential therapeutic targets of metabolic disease. In this study we show by in vivo administration of locked nucleic acid (LNA) inhibitors that suppression of endogenous miR-29 lowers plasma cholesterol levels by ~40%, commensurate with the effect of statins, and reduces fatty acid content in the liver by ~20%. Whole transcriptome sequencing of the liver reveals 883 genes dysregulated (612 down, 271 up) by inhibition of miR-29. The set of 612 down-regulated genes are most significantly over-represented in lipid synthesis pathways. Among the up-regulated genes are the anti-lipogenic deacetylase sirtuin 1 (Sirt1) and the anti-lipogenic transcription factor aryl hydrocarbon receptor (Ahr), the latter of which we demonstrate is a direct target of miR-29. In vitro radiolabeled acetate incorporation assays confirm that pharmacologic inhibition of miR-29 significantly reduces de novo cholesterol and fatty acid synthesis. Our findings indicate that miR-29 controls hepatic lipogenic programs, likely in part through regulation of Ahr and Sirt1, and therefore may represent a candidate therapeutic target for metabolic disorders such as dyslipidemia.
Additional file 2 of Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study
Creators: name: Carda-Diéguez, Miguel
name: Moazzez, Rebecca
name: Mira, Alex
Publisher: name: figshare
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics

description: Additional file 2: Additional Figure 1. Relationship between sequencing effort and bacterial species and gene functions in human dental plaque. Rarefaction curves of all samples used for the current study when using metagenomic (A and B) or metatranscriptomic (C and D) data represent the number of species (left) and functions (right) detected relative to the number of sequence reads. Gene functions were calculated based on the KEGG database. Thresholds of 1x105 reads/sample from the MTG and 5x104 reads/sample for the MTT were used for annotation and subsequent analysis. Rarefaction curves at species level when samples were sequenced using 16S rRNA sequencing approach were also studied (E). Finally, the curves using metagenomics were also analyzed at species level when only species above 0.1% were considered (F).