bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple method for data partitioning based on relative evolutionary rates
Authors: Rota Jadranka , Malm Tobias , Chazot Nicolas , Peña Carlos , Wahlberg Niklas 
Published: August 2018

Background
Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns.

Methods
We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k-means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder.

Results
Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset.

Discussion
We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.
ГОЛОЦЕНОВЫЙ МОРФОЛИТОГЕНЕЗ В ОЗЕРНЫХ КОТЛОВИНАХ ЮГО-ВОСТОЧНОГО ЗАБАЙКАЛЬЯ, "Геоморфология"
Authors: Баженова О.И. , Черкашина А.А. 
Published: August 2018

В статье рассматривается функционирование озерных бессточных бассейнов Даурии в голоцене. Выделены типы рельефообразования, связанные с трансгрессивными и регрессивными фазами развития озер, контролируемыми климатическими колебаниями. Трансгрессия сопровождается интеграцией отложений в котловинах за счет береговых процессов, криогенного выветривания, флювиальной, склоновой и биогенной аккумуляции. Регрессия - эоловой деформацией сухих днищ и склонов озерных депрессий, формированием котловин выдувания, выносом рыхлых отложений господствующими ветрами на юго-восток. Установлены события быстрого флювиального сноса большого объема материала в озерные понижения по падям временных водотоков 7-8.5 тыс. кал.л.н. и в переходное время между атлантической и суббореальной климатическими фазами. Наиболее детально прослежена смена условий рельефообразования и осадконакопления в позднем голоцене, отмечавшаяся каждые 500 лет. Выявлен период стабилизации уровней озер и формирования почвы в атлантическое время и два этапа активизации криогенных процессов около 9.2 и 3.5 тыс. кал.л.н., зафиксированные в отложениях первой террасы оз. Хара-Нур. Установлена тенденция сокращения площадей озер и повышения в морфолитогенезе роли эоловых процессов на фоне общей аридизации климата за последние 10 тыс.л.
СЛЕДЫ ПАЛЕОЦУНАМИ НА ПОБЕРЕЖЬЕ ПРИМОРЬЯ В ГОЛОЦЕНЕ, "Геоморфология"
Authors: Ганзей Л.А. , Разжигаева Н.Г. , Арсланов Х.А. , Нишимура Ю. , Гребенникова Т.А. , Горбунов А.О. , Максимов Ф.Е. , ПЕТРОВ А.Ю. , ХАРЛАМОВ А.А. 
Published: August 2018

Проведена реконструкция параметров сильных цунами в историческое время и в позднем голоцене, основанная на изучении осадков в разрезах прибрежных низменностей на участке морского побережья большой протяженности Восточного и Южного Приморья (от бух. Удобная до бух. Анна и о-ва Русский). Установлено, что осадки палеоцунами лучше сохраняются на прибрежных низменностях в устьях низкопорядковых водотоков. При идентификации цунамигенных осадков применялись литолого-фациальные методы и диатомовый анализ. Определены источники поступления материала и оценены параметры цунами в разных бухтах. Определение возраста событий основано на данных радиоуглеродного датирования, вмещающих органогенные отложения и тефростратиграфии. Выполнена корреляция событий, выделенных в частных разрезах, и результаты сопоставлены с данными по региону. Крупные цунами в япономорском регионе происходят каждые 200 лет, хотя не исключены ситуации, когда сильные цунами могут проходить чаще, через небольшие промежутки времени.
ОЦЕНКА МАКСИМАЛЬНОГО ОБЪЕМА ТВЕРДЫХ ОТЛОЖЕНИЙ ДЛЯ СЕЛЕЙ РАЗЛИЧНЫХ ГЕНЕТИЧЕСКИХ ТИПОВ НА ТЕРРИТОРИИ СЕВЕРНОГО КАВКАЗА, "Геоморфология"
Authors: Залиханов М.Ч. , Аджиев А.Х. , Кондратьева Н.В. , Разумов В.В. 
Published: August 2018

Предлагается аналитический метод оценки максимального объема твердых отложений селя для территории Северного Кавказа на основе статистических данных за период более 50 лет. Он предполагает ранжирование селевых бассейнов по преобладающему генетическому типу селеобразования (ледниковый, ледниково-дождевой, дождевой, снегодождевой) в зависимости от абсолютной высоты истока реки. А также оценку максимального объема твердых отложений селя в бассейне с использованием полученных авторами формул взаимосвязи максимального объема твердых отложений селя (W) и площади селевого бассейна (S), среднего уклона ­русла (б), длины реки (L).
Patient‐Reported Outcomes Predict Mortality in Lupus
Authors: Azizoddin Desiree R. , Jolly Meenakshi , Arora Shilpa , Yelin Ed , Katz Patricia 
Published: August 2018

ObjectivePhysician‐assessed disease activity and damage predict mortality in systemic lupus erythematosus (SLE). Patient‐reported outcomes (PROs) are known predictors of mortality in other chronic diseases, but this relationship has not been well examined in SLE. The aim of the present study was to assess whether PROs predict mortality in SLE.MethodsData were derived from the University of California at San Francisco Lupus Outcomes Study (n = 728). PROs (Medical Outcomes Study Short Form 36 [SF‐36] subscales), self‐rated health, and depression (Center for Epidemiologic Studies Depression scale [CES‐D]) from 2007 (baseline data [T0]) were used to predict mortality (censored 2015). Univariate Cox regression analyses were completed for each PRO as a predictor of mortality, and multivariate Cox regression with covariates for each PRO separately. Covariates were age, sex, race/ethnicity, poverty, disease duration, disease activity (Systemic Lupus Activity Questionnaire), and damage (Brief Index of Lupus Damage).ResultsThe mean ± SD age of patients was 50.6 ± 12.6 years. Ninety‐two percent of patients were women and 68.5% were white. There were 71 deaths (9.1%). In univariate analyses, both the SF‐36 physical component subscale score and self‐rated health were associated with mortality, and the SF‐36 mental health subscale and CES‐D scores were not associated with mortality. In multivariate analyses, lower scores of SF‐36 physical function at T0 independently predicted mortality after controlling for all other covariates (hazard ratio 0.97 [95% confidence interval 0.94–0.99]; P < 0.01).ConclusionPatient‐reported physical function independently predicted mortality in SLE, even after accounting for demographics (including poverty) and disease (duration, activity, and damage). Because PROs are easy to assess, they may be used to triage, track, and guide early interventions for those at high risk of mortality in SLE.
Active Control of Electromagnetically Induced Transparency in a Terahertz Metamaterial Array with Graphene for Continuous Resonance Frequency Tuning
Authors: Kindness Stephen J. , Almond Nikita W. , Wei Binbin , Wallis Robert , Michailow Wladislaw , Kamboj Varun S. , Braeuninger‐Weimer Philipp , Hofmann Stephan , Beere Harvey E. , Ritchie David A. , Degl'Innocenti Riccardo 
Published: August 2018

AbstractOptoelectronic terahertz modulators, operated by actively tuning metamaterial, plasmonic resonator structures, have helped to unlock a myriad of terahertz applications, ranging from spectroscopy and imaging to communications. At the same time, due to the inherently versatile dispersion properties of metamaterials, they offer unique platforms for studying intriguing phenomena such as negative refractive index and slow light. Active resonance frequency tuning of a metamaterial working in the terahertz regime is achieved by integrating metal‐coupled resonator arrays with electrically tunable graphene. This metamaterial device exploits coupled plasmonic resonators to exhibit an electromagnetically induced transparency analog, resulting in the splitting of the resonance into coupled hybrid optical modes. By variably dampening one of the resonators using graphene, the coupling condition is electrically modulated and continuous tuning of the metamaterial resonance frequency is achieved. This device, operating at room temperature, can readily be implemented as a fast, optoelectronic, tunable band pass/reject filter with a tuning range of ≈100 GHz operating at 1.5 THz. The reconfigurable dispersion properties of this device can also be implemented for modulation of the group delay for slow light applications.
Breaking the Diffraction Limit with Radially Polarized Light Based on Dielectric Metalenses
Authors: Zuo Ruizhi , Liu Wenwei , Cheng Hua , Chen Shuqi , Tian Jianguo 
Published: August 2018

AbstractDielectric metalenses with high efficiency and compact size have been widely investigated recently, but still suffer from Abbe diffraction limit. Herein, with linear polarization incidence, a dielectric metalens is demonstrated to efficiently generate and focus radially polarized light simultaneously. Two novel methods are proposed to achieve super‐resolution. First, a circular high‐pass aperture is utilized to enhance the longitudinal field component in the vicinity of focus with the focal spot size of 0.138λ2, much smaller than the theoretical limit of 0.212λ2. The key parameters that impact the focusing size are explored in detail, such as radius of the circular aperture and numerical aperture of the metalens. Second, an extra phase distribution is added on the metalens to filter the transversely polarized component, which leads to a focal spot size of 0.144λ2. The approach provides a wide platform for sub‐resolution focusing and imaging, which offers the capability of subdiffraction techniques for microscopy systems and information processing with extensive channels.
Design and Synthesis of Zirconium‐Containing Coordination Polymer Based on Unsymmetric Indolyl Dicarboxylic Acid and Catalytic Application on Borrowing Hydrogen Reaction
Authors: Hu Xinyu , Zhu Haiyan , Sang Xinxin , Wang Dawei 
Published: August 2018

AbstractCatalytic borrowing hydrogen reaction is a very attractive transformation in the field of C‐alkylation reaction. In this work, a new Zr (Zirconium)‐containing coordination polymer containing unsymmetric indolyl dicarboxylic acid 1‐(carboxymethyl)‐1H‐indole‐5‐carboxylic acid (H2CIA) was synthesized by the way of a solvothermal synthetic route and characterized by powder X‐ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Nitrogen adsorption‐desorption, fourier transform infrared spectroscopy and X‐ray photoelectronic spectroscopy (XPS). The coordination polymer Zr‐CIA was employed as the catalyst for C‐alkylation of acetophenone derivatives in the presence of benzyl alcohol. In addition, Zr‐CIA catalyst was also observed to be effective in the reaction of alcohols with alcohols and high yields of alkylation products were achieved. Mechanism investigations were also conducted to better understand the catalysts and transformations. Meanwhile, the Zr‐CIA could be reused at least five times without a notable decrease in activity and selectivity.magnified image
Controlled Non‐Viral Gene Delivery in Cartilage and Bone Repair: Current Strategies and Future Directions
Authors: Gonzalez‐Fernandez Tomas , Kelly Daniel J. , O'Brien Fergal J. 
Published: August 2018

AbstractRecent advances in the approval and commercialization of gene therapeutics have fostered the return of gene therapy to center stage. But despite new optimism, no Food and Drug Administration approved product exists for the treatment of orthopedic disorders. Non‐viral gene delivery is a promising alternative to recombinant protein administration and viral gene transduction for orthopedic tissue engineering. When applied using appropriately designed systems, it enables temporal control of the overexpression of therapeutic genes, leading to local production of regulatory factors at physiologically relevant levels. Incorporating genetic material into 3D scaffold biomaterials, that is, gene activated scaffolds or hydrogels, presents a particular opportunity to utilize non‐viral gene therapy for in situ transfection of host cells and the regeneration of damaged tissues and organs. But controlled non‐viral gene delivery for musculoskeletal regeneration depends on a multifactorial design in which the choice of gene delivery method, therapeutic gene, and supportive biomaterial play a central role for the success of this strategy. This paper reviews the different modalities of non‐viral gene delivery used for the repair of bone and cartilage, and explores the current challenges and opportunities for the engineering of functional orthopedic tissues using gene activated scaffolds.
Effect of carbonized watermelon rind powder on the mechanical and thermal properties of unsaturated polyester composites: A special insight to chemical resistance and value addition
Authors: Wadgaonkar Kunal K. , Mehta Linchon B. , Bamane Pratiket B. , Pon Kumar Ramamoorthy , Jagtap Ramanand N. 
Published: August 2018

AbstractThis study focuses on the preparation and characterization of bio‐based filler derived from natural fruit waste and its utilization in unsaturated polyester composites. Particle size analysis, energy dispersive x‐ray spectroscopy, and Fourier transform spectroscopy were used to characterize the size and composition of the filler namely carbonized watermelon rind filler, called carbonized watermelon rind filler. The filled composites (0%, 5%, 10%, and 15%) were prepared and their mechanical properties such as tensile, flexural, and impact were tested. It was found that tensile modulus had increased to 17% at 10% filler loading as compared to unfilled. These results were supported by scanning electron microscopy measurements of the fractured surface of the composites. All the fabricated composites resisted well against the chemicals and it indicates that the composites have excellent chemical resistance. The thermal properties were characterized by Thermogravimetric analysis which revealed that there was no improvement in thermal degradation temperature of the filled composites suggesting a way of thermally recycling the composites.
Ein vielseitiges Bisallylbor‐Reagenz für die stereoselektive Synthese von chiralen Diolen
Authors: Hetzler Belinda E. , Volpin Giulio , Vignoni Elisa , Petrovic Ana G. , Proni Gloria , Hu Chunhua T. , Trauner Dirk 
Published: August 2018

AbstractAllylische Bor‐Verbindungen haben vielseitige Anwendungsmöglichkeiten und zeichnen sich durch eine gute stereochemische Vorhersagbarkeit in der Reaktion mit Carbonylgruppen aus. Hier beschreiben wir die Synthese von (Z,Z)‐Hexadienylbisboronat 1, das konfigurationsstabil, kristallin und einfach zu handhaben ist. Es ist Teil einer Klasse bis‐allylischer Bor‐Reagenzien mit bislang nicht ausgeschöpftem Synthesepotential. Durch Katalyse mit chiralen Phosphorsäuren kann das Reagenz in enantioselektiven Allyltransferreaktionen und in einer Vielzahl von Eintopfreaktion eingesetzt werden, die einen schnellen Zugang zu funktionalisierten 1,n‐Diolen ermöglichen. Zusätzlich gestattet das in situ generierte bis‐borinische Reagenz den direkten und diastereoselektiven zweifachen Allyltransfer an Aldehyde. Die dadurch synthetisierten C2‐ oder Ci‐symmetrischen Stereotetraden enthalten ein 1,4‐Diol‐Muster, das in der Naturstoffsynthese relevant ist. Vor diesem Hintergrund wurde die Anwendung unserer Methode in einer kurzen Synthese des Lignans (±)‐Neo‐Olivil demonstriert.
A Versatile Bis‐Allylboron Reagent for the Stereoselective Synthesis of Chiral Diols
Authors: Hetzler Belinda E. , Volpin Giulio , Vignoni Elisa , Petrovic Ana G. , Proni Gloria , Hu Chunhua T. , Trauner Dirk 
Published: August 2018

AbstractAllylboron reagents are popular in synthesis owing to their versatility and the predictable stereochemical outcomes of their reactions with carbonyl compounds. Herein, we describe the synthesis of (Z,Z)‐hexadienyl bis‐boronate 1, a configurationally stable, crystalline, and easy to handle compound, which represents a class of bis‐allylic boron reagents with heretofore untapped synthetic potential. In combination with a chiral phosphoric acid catalyst, the reagent can be employed for the enantioselective allyl transfer reaction to a variety of one‐pot transformations, enabling swift access to functionalized 1,n‐diols. The in situ conversion of the reagent into the corresponding bis‐borinic ester allows for the direct and diastereoselective two‐fold allyl transfer to aldehydes. This affords C2‐ or Ci‐symmetric stereotetrads containing a 1,4‐diol moiety for natural product synthesis. The usefulness of our method was demonstrated with a short synthesis of the lignan (±)‐neo‐olivil.
Recognition of Amino Acid Motifs, Rather Than Specific Proteins, by Human Plasma Cell–Derived Monoclonal Antibodies to Posttranslationally Modified Proteins in Rheumatoid Arthritis
Authors: Steen Johanna , Forsström Björn , Sahlström Peter , Odowd Victoria , Israelsson Lena , Krishnamurthy Akilan , Badreh Sara , Mathsson Alm Linda , Compson Joanne , Ramsköld Daniel , Ndlovu Welcome , Rapecki Stephen , Hansson Monika , Titcombe Philip J. , Bang Holger , Mueller Daniel L. , Catrina Anca I. , Grönwall Caroline , Skriner Karl , Nilsson Peter , Lightwood Daniel , Klareskog Lars , Malmström Vivianne 
Published: August 2018

ObjectiveAntibodies against posttranslationally modified proteins are a hallmark of rheumatoid arthritis (RA), but the emergence and pathogenicity of these autoantibodies are still incompletely understood. The aim of this study was to analyze the antigen specificities and mutation patterns of monoclonal antibodies (mAb) derived from RA synovial plasma cells and address the question of antigen cross‐reactivity.MethodsIgG‐secreting cells were isolated from RA synovial fluid, and the variable regions of the immunoglobulins were sequenced (n = 182) and expressed in full‐length mAb (n = 93) and also as germline‐reverted versions. The patterns of reactivity with 53,019 citrullinated peptides and 49,211 carbamylated peptides and the potential of the mAb to promote osteoclastogenesis were investigated.ResultsFour unrelated anti–citrullinated protein autoantibodies (ACPAs), of which one was clonally expanded, were identified and found to be highly somatically mutated in the synovial fluid of a patient with RA. The ACPAs recognized >3,000 unique peptides modified by either citrullination or carbamylation. This highly multireactive autoantibody feature was replicated for Ig sequences derived from B cells from the peripheral blood of other RA patients. The plasma cell–derived mAb were found to target distinct amino acid motifs and partially overlapping protein targets. They also conveyed different effector functions as revealed in an osteoclast activation assay.ConclusionThese findings suggest that the high level of cross‐reactivity among RA autoreactive B cells is the result of different antigen encounters, possibly at different sites and at different time points. This is consistent with the notion that RA is initiated in one context, such as in the mucosal organs, and thereafter targets other sites, such as the joints.
Preschool predictors of reading ability in the first year of schooling in children with ASD
Authors: Westerveld Marleen F. , Paynter Jessica , O'Leary Kathryn , Trembath David 
Published: August 2018

A high percentage of children with Autism Spectrum Disorder (ASD) show elevated challenges in learning to read. We investigated longitudinal predictors of reading skills in 41 children diagnosed with ASD. All children completed measures of precursor literacy skills at the age of 4–5 years, including phonological awareness, letter sound knowledge, rapid automatic naming, name writing, and phonological memory (digit span), along with measures of word‐ and passage‐level reading skills in their first year of formal schooling. Nonverbal cognition and letter sound knowledge accounted for 53.4% of the variance in regular single word reading at school age, with letter sound knowledge a significant individual predictor. Overall, 18 children showed reading ability scores in the average range on a standardized test of passage‐level reading ability, whereas 23 children performed below expectations. These groups differed significantly on all precursor literacy measures (at ages 4–5), except autism symptoms based on parent report. Group membership was significantly predicted by preschool receptive vocabulary, name writing, and rapid automatic naming, with high sensitivity and specificity. These results are discussed in reference to the literature describing early literacy predictors for typically developing children, highlighting key areas for future intervention and support. Autism Res 2018, 11: 1332–1344. © 2018 International Society for Autism Research, Wiley Periodicals, Inc.Lay summaryChildren with autism are at increased risk of persistent reading difficulties. We examined whether preschool reading‐related skills linked to later reading ability. Performance on the following three tasks administered at preschool predicted children who showed early reading success versus below expectations in their first year of school: vocabulary, name writing, and rapid naming of familiar objects and shapes. These results can inform future interventions.
Epigenetic changes due to physical activity
Authors: Rezapour Sadegh , Shiravand Mustafa , Mardani Mahnaz 
Published: August 2018

AbstractOne of the epigenetic‐modifying factors is regular and continuous physical activity. This article attempts to investigate the effects of physical activity and exercise on changes in histone proteins and gene expression, as well as the effect of these exercises on the prevention of certain cancers and the ejection of age‐related illnesses and cellular oxidation interactions. All of this is due to epigenetic changes and gene expression. Most studies have reported the positive effects of regular exercises on the expression of histone proteins. DNA methylation and the prevention of certain diseases such as cancer and respiratory diseases, caused by antioxidative interactions that occur more often in the elderly, have been studied.