bluuebunny/crossref_metadata_2025 huggingface dataset:
Novel 3D computational method reveals nano-to-microscale particle dispersion behaviors in tubular blood flow
Authors: Zhang Zhengzheng
Published: August 2019

Scientists have developed a 3D multiscale blood flow solver to unravel how the particle transport mechanism varies with particle size across nano-to-micrometer scales.
MHC Class II variability in bare-nosed wombats (Vombatus ursinus)
Authors: Old Julie M. , Hermsen Eden M. , Young Lauren J.
Published: August 2019

Studies of gene diversity are used to investigate population dynamics, including immunological fitness. Aside from the selection of an appropriate gene target, an important factor that underpins these studies is the ability to recover viable DNA samples from native animals that are protected, threatened or difficult to sample or locate such as the bare-nosed wombat (Vombatus ursinus). In this study, we used genomic DNA extracted from muscle tissue samples and also identified the optimal method to extract DNA from fresh wombat scat samples to enable further analyses to be performed using non-invasive techniques. The DNA was probed via the polymerase chain reaction using previously targeted marsupial Major Histocompatibility Complex (MHC) gene primers. These genes are highly variable and associated with binding and presentation of pathogens in the immune system. Twenty-three unique MHC Class II DAB V. ursinus gene sequences were translated to 21 unique predicted peptide sequences from 34 individual tissue or scat samples. Vombatus ursinus MHC Class II DAB gene and peptide sequences were most similar to other marsupial DNA and peptide sequences. Further analysis also indicated the likelihood of MHC Class II DAB family membership through motif identification. Additional sampling is required to assess the full level of diversity of MHC Class II DAB genes among V. ursinus populations; however, this study is the first to identify MHC genes in a wombat and will advance immunological and disease studies of the species.
Nesting ecology of flatback sea turtles Natator depressus from Delambre Island, Western Australia
Authors: Thums Michele , Rossendell Jason , Fisher Rebecca , Guinea Michael L.
Published: August 2019

Nest site selection is likely to be important for the fitness of sea turtle populations, but data on the environmental drivers of nest site selection and other important parameters like nest site fidelity and inter-nesting and remigration intervals are limited. We address these questions using data on flipper tag resightings and track counts from flatback turtles (Natator depressus) from Delambre Island in Western Australia collected over 2–3 weeks each nesting season across six nesting seasons. The median inter-nesting interval was 13 days (range 9–17 days) and the mean±s.d. remigration interval was 1.99±0.95 years. Turtles had around 10% probability of returning to the same sector of the beach (150-m-long sections). The median distance between subsequent emergences (whether false crawls were included or not) was ~450m. The number of turtles both emerging and successfully nesting was higher when air temperature and humidity were lowest and emergences increased slightly with tide height. Sector of the beach was by far the strongest predictor of nest site, with turtles showing preference for the less exposed side of the island. The results of this study will assist with future monitoring of this population and the management of threats related to coastal development and activities.
Reservoirs act as footholds for an invasive freshwater crayfish
Authors: Beatty Stephen J. , Ramsay Ashley , Pinder Adrian M. , Morgan David L.
Published: August 2019

Understanding the modalities of aquatic species introductions is important in predicting and preventing new invasions. Australia’s Pilbara Province is an arid region with no naturally occurring freshwater crayfishes. We assessed the population demographics and reproductive potential of redclaw crayfish (Cherax quadricarinatus) in Lake Poongkaliyarra, a major Pilbara water supply reservoir, in which public access and fishing are prohibited. We found the population to have a high relative abundance with a range of size-cohorts present. The species was believed to have first been introduced into the reservoir from at least 2010 and has subsequently been introduced and established in other lotic systems in the region, probably through deliberate releases from the lake for the purposes of providing fishing opportunities to areas where public access is permitted. Introductions of C. quadricarinatus in other parts of Australia and the world have also initially established in reservoirs before subsequently colonising natural systems. The study highlights the potential for reservoirs to act as primary stepping stones for invasion by freshwater crayfish.
Mapping visual symbols onto spoken language along the ventral visual stream
Authors: Taylor J. S. H. , Davis Matthew H. , Rastle Kathleen
Published: August 2019

Reading involves transforming arbitrary visual symbols into sounds and meanings. This study interrogated the neural representations in ventral occipitotemporal cortex (vOT) that support this transformation process. Twenty-four adults learned to read 2 sets of 24 novel words that shared phonemes and semantic categories but were written in different artificial orthographies. Following 2 wk of training, participants read the trained words while neural activity was measured with functional MRI. Representational similarity analysis on item pairs from the same orthography revealed that right vOT and posterior regions of left vOT were sensitive to basic visual similarity. Left vOT encoded letter identity and representations became more invariant to position along a posterior-to-anterior hierarchy. Item pairs that shared sounds or meanings, but were written in different orthographies with no letters in common, evoked similar neural patterns in anterior left vOT. These results reveal a hierarchical, posterior-to-anterior gradient in vOT, in which representations of letters become increasingly invariant to position and are transformed to convey spoken language information.
Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes
Authors: Agarwal Ipsita , Przeworski Molly
Published: August 2019

Significance

Germline mutations, the accidental changes to the genome that occur during gametogenesis, are the source of all heritable variation. Because they are difficult to study directly, however, their determinants remain poorly understood. We use rare human polymorphisms in large samples as proxies for de novo mutations and compare mutational patterns across regions of the X chromosome and autosomes with unique biochemical and sex-specific properties. We highlight signatures of replication timing and repair of meiotic double-strand breaks and show how these biochemical processes may interact with sex-specific life history traits to shape the mutation spectrum. Our analysis has implications for understanding mutation rate variation along the genome, interpreting differences on the X and autosomes, and for the evolution of mutation rates.
Runx1 promotes murine erythroid progenitor proliferation and inhibits differentiation by preventing Pu.1 downregulation
Authors: Willcockson Michael A. , Taylor Samuel J. , Ghosh Srikanta , Healton Sean E. , Wheat Justin C. , Wilson Tommy J. , Steidl Ulrich , Skoultchi Arthur I.
Published: August 2019

Pu.1 is an ETS family transcription factor (TF) that plays critical roles in erythroid progenitors by promoting proliferation and blocking terminal differentiation. However, the mechanisms controlling expression and down-regulation of Pu.1 during early erythropoiesis have not been defined. In this study, we identify the actions of Runx1 and Pu.1 itself at the Pu.1 gene Upstream Regulatory Element (URE) as major regulators of Pu.1 expression in Burst-Forming Unit erythrocytes (BFUe). During early erythropoiesis, Runx1 and Pu.1 levels decline, and chromatin accessibility at the URE is lost. Ectopic expression of Runx1 or Pu.1, both of which bind the URE, prevents Pu.1 down-regulation and blocks terminal erythroid differentiation, resulting in extensive ex vivo proliferation and immortalization of erythroid progenitors. Ectopic expression of Runx1 in BFUe lacking a URE fails to block terminal erythroid differentiation. Thus, Runx1, acting at the URE, and Pu.1 itself directly regulate Pu.1 levels in erythroid cells, and loss of both factors is critical for Pu.1 down-regulation during terminal differentiation. The molecular mechanism of URE inactivation in erythroid cells through loss of TF binding represents a distinct pattern of Pu.1 regulation from those described in other hematopoietic cell types such as T cells which down-regulate Pu.1 through active repression. The importance of down-regulation of Runx1 and Pu.1 in erythropoiesis is further supported by genome-wide analyses showing that their DNA-binding motifs are highly overrepresented in regions that lose chromatin accessibility during early erythroid development.
Site-specific impairment of perivascular adipose tissue on advanced atherosclerotic plaques using multimodal nonlinear optical imaging
Authors: Kim Suho , Lee Eun-Soo , Lee Sang-Won , Kim Yong-Hoon , Lee Chul-Ho , Jo Dong-Gyu , Kim Se-Hwa
Published: August 2019

Significance

Perivascular adipose tissue (PVAT), adipose tissue surrounding blood vessels, has been reported to secrete inflammatory cytokines and adipokines in a paracrine/autocrine manner to regulate the vascular system in healthy and diseased states. However, how PVAT locally and spatially controls vascular functions as atherosclerosis progresses remains unknown. Using multimodal nonlinear optical imaging and an ex vivo assay, we found that PVAT changed differentially from the initial to advanced stages. Interestingly, PVAT at the atherosclerotic plaques showed highly agglomerated lipid droplets and increased fibrosis, suggesting spatial impairment. Our results provide a new concept of PVAT as modulating a direct interaction between the adipose tissue and cardiovascular system.
The iron-regulated vacuolar
Legionella pneumophila
MavN protein is a transition-metal transporter
Authors: Christenson Eric T. , Isaac Dervla T. , Yoshida Karin , Lipo Erion , Kim Jin-Sik , Ghirlando Rodolfo , Isberg Ralph R. , Banerjee Anirban
Published: August 2019

Significance

Iron is essential for microbial growth, and minimizing iron acquisition by pathogens is a cornerstone of the nutritional immunity response. Nevertheless, strategies by which intracellular pathogens circumvent these defenses are poorly understood. Herein, we demonstrate that the highly conserved
Legionella
effector protein MavN is the conduit for iron piracy by the bacterium. We map the in-membrane topology of MavN and pinpoint mutations that render the protein incompetent for sustaining
Legionella
intracellular proliferation. MavN iron transport activity was reconstituted in vitro and mutations identified as critical for growth were similarly detrimental to iron uptake. Our findings illuminate mechanistic details of iron accrual by
Legionella
and illustrate a scheme by which opportunistic bacteria can procure a limited but crucial nutrient.
Peroxidase evolution in white-rot fungi follows wood lignin evolution in plants
Authors: Ayuso-Fernández Iván , Rencoret Jorge , Gutiérrez Ana , Ruiz-Dueñas Francisco Javier , Martínez Angel T.
Published: August 2019

Significance

We analyze the evolution of ligninolytic peroxidases from wood-rotting fungi using conifer and angiosperm lignin as representatives of 2 steps of lignin evolution. By enzyme resurrection, we show that during fungal evolution, these enzymes improved their activity and switched their degradative preferences with the rise of a surface tryptophan conferring on them the ability to oxidize nonphenolic lignin. We calibrated the peroxidase phylogeny and determined that this residue appeared coincident with angiosperm diversification, characterized by the synthesis of a more complex and less phenolic lignin due to the general incorporation of a new unit in its structure. This way, we show that fungal evolution followed that of lignin synthesis, pointing to a coevolution between fungal saprotrophs and their plant hosts.
Makes caterpillars floppy-like effector-containing MARTX toxins require host ADP-ribosylation factor (ARF) proteins for systemic pathogenicity
Authors: Lee Youngjin , Kim Byoung Sik , Choi Sanghyeon , Lee Eun-Young , Park Shinhye , Hwang Jungwon , Kwon Yumi , Hyun Jaekyung , Lee Cheolju , Kim Jihyun F. , Eom Soo Hyun , Kim Myung Hee
Published: August 2019

Upon invading target cells, multifunctional autoprocessing repeats-in-toxin (MARTX) toxins secreted by bacterial pathogens release their disease-related modularly structured effector domains. However, it is unclear how a diverse repertoire of effector domains within these toxins are processed and activated. Here, we report that Makes caterpillars floppy-like effector (MCF)-containing MARTX toxins require ubiquitous ADP-ribosylation factor (ARF) proteins for processing and activation of intermediate effector modules, which localize in different subcellular compartments following limited processing of holo effector modules by the internal cysteine protease. Effector domains structured tandemly with MCF in intermediate modules become disengaged and fully activated by MCF, which aggressively interacts with ARF proteins present at the same location as intermediate modules and is converted allosterically into a catalytically competent protease. MCF-mediated effector processing leads ultimately to severe virulence in mice via an MCF-mediated ARF switching mechanism across subcellular compartments. This work provides insight into how bacteria take advantage of host systems to induce systemic pathogenicity.
A high-throughput system to identify inhibitors of
Candidatus
Liberibacter asiaticus transcription regulators
Authors: Barnett Melanie J. , Solow-Cordero David E. , Long Sharon R.
Published: August 2019

Citrus greening disease, also known as huanglongbing (HLB), is the most devastating disease of
Citrus
worldwide. This incurable disease is caused primarily by the bacterium
Candidatus
Liberibacter asiaticus and spread by feeding of the Asian Citrus Psyllid,
Diaphorina citri
.
Ca
. L. asiaticus cannot be cultured; its growth is restricted to citrus phloem and the psyllid insect. Management of infected trees includes use of broad-spectrum antibiotics, which have disadvantages. Recent work has sought to identify small molecules that inhibit
Ca
. L. asiaticus transcription regulators, based on a premise that at least some regulators control expression of genes necessary for virulence. We describe a synthetic, high-throughput screening system to identify compounds that inhibit activity of
Ca
. L. asiaticus transcription activators LdtR, RpoH, and VisNR. Our system uses the closely related model bacterium,
Sinorhizobium meliloti
, as a heterologous host for expression of a
Ca
. L. asiaticus transcription activator, the activity of which is detected through expression of an enhanced green fluorescent protein (EGFP) gene fused to a target promoter. We used this system to screen more than 120,000 compounds for compounds that inhibited regulator activity, but not growth. Our screen identified several dozen compounds that inhibit regulator activity in our assay. This work shows that, in addition to providing a means of characterizing
Ca
. L. asiaticus regulators, an
S. meliloti
host can be used for preliminary identification of candidate inhibitory molecules.
Human cytomegalovirus glycoprotein B variants affect viral entry, cell fusion, and genome stability
Authors: Tang Jiajia , Frascaroli Giada , Lebbink Robert J. , Ostermann Eleonore , Brune Wolfram
Published: August 2019

Significance

Human cytomegalovirus (HCMV) is a major cause of morbidity and mortality in transplant patients and the most common infectious cause of birth defects. Although HCMV is not a generally accepted cause of cancer, it shares similarities to cancer-causing viruses: It dysregulates the cell cycle, activates the DNA damage response, and suppresses apoptosis. However, causes and consequences of these viral properties remain poorly understood. Here we show that HCMV activates caspase-2, an apoptosis-related enzyme activated by DNA damage and abnormal mitosis, in a strain-specific manner. Caspase-2 activation depends on envelope glycoprotein B variants with increased fusogenicity, which facilitate viral entry, promote cell fusion, and affect genome stability. These results suggest that specific glycoprotein B variants might affect HCMV transmission and pathogenicity.
Cell-to-cell interaction requires optimal positioning of a pilus tip adhesin modulated by gram-positive transpeptidase enzymes
Authors: Chang Chungyu , Wu Chenggang , Osipiuk Jerzy , Siegel Sara D. , Zhu Shiwei , Liu Xiangan , Joachimiak Andrzej , Clubb Robert T. , Das Asis , Ton-That Hung
Published: August 2019

Assembly of pili on the gram-positive bacterial cell wall involves 2 conserved transpeptidase enzymes named sortases: One for polymerization of pilin subunits and another for anchoring pili to peptidoglycan. How this machine controls pilus length and whether pilus length is critical for cell-to-cell interactions remain unknown. We report here inActinomyces oris, a key colonizer in the development of oral biofilms, that genetic disruption of its housekeeping sortase SrtA generates exceedingly long pili, catalyzed by its pilus-specific sortase SrtC2 that possesses both pilus polymerization and cell wall anchoring functions. Remarkably, thesrtA-deficient mutant fails to mediate interspecies interactions, or coaggregation, even though the coaggregation factor CafA is present at the pilus tip. Increasing ectopic expression ofsrtAin the mutant progressively shortens pilus length and restores coaggregation accordingly, while elevated levels of shaft pilins and SrtC2 produce long pili and block coaggregation by SrtA+bacteria. With structural studies, we uncovered 2 key structural elements in SrtA that partake in recognition of pilin substrates and regulate pilus length by inducing the capture and transfer of pilus polymers to the cell wall. Evidently, coaggregation requires proper positioning of the tip adhesin CafA via modulation of pilus length by the housekeeping sortase SrtA.
Gangliosides interact with synaptotagmin to form the high-affinity receptor complex for botulinum neurotoxin B
Authors: Flores Alessandra , Ramirez-Franco Jorge , Desplantes Richard , Debreux Kévin , Ferracci Géraldine , Wernert Florian , Blanchard Marie-Pierre , Maulet Yves , Youssouf Fahamoe , Sangiardi Marion , Iborra Cécile , Popoff Michel Robert , Seagar Michael , Fantini Jacques , Lévêque Christian , El Far Oussama
Published: August 2019

Significance

Botulism is induced by
Clostridium
botulinum neurotoxins (BoNTs). At neuromuscular junctions, BoNT/B binds to dual receptors: a plasma membrane resident polysialoganglioside and synaptotagmin, a synaptic vesicle protein transiently inserted in neuronal membranes upon exocytosis. It is widely thought that BoNT binds initially to gangliosides and that this binary complex then diffuses to interact with synaptotagmin. Here, we show that the true BoNT/B receptor is the preassembled GT1b–SYT complex and that the α-helical structure of the BoNT/B binding domain of synaptotagmin found in previous structural studies is induced by the ganglioside before it ever meets the toxin. BoNT/B thus exploits a preexisting protein–glycolipid complex of yet unknown physiological function.
Sequential localization of a complex electron fluid
Authors: Martelli Valentina , Cai Ang , Nica Emilian M. , Taupin Mathieu , Prokofiev Andrey , Liu Chia-Chuan , Lai Hsin-Hua , Yu Rong , Ingersent Kevin , Küchler Robert , Strydom André M. , Geiger Diana , Haenel Jonathan , Larrea Julio , Si Qimiao , Paschen Silke
Published: August 2019

Significance

Many of the most fascinating and actively investigated materials classes host strongly correlated electrons. Their understanding is challenging because the strong correlations cause entwining of multiple degrees of freedom of an electron, such as spin, orbital, and charge. This complexity is ubiquitous and underlies many of the rich properties. The question then is whether there are universal organizing principles that provide simplicity to the description. Here, by studying a prototype material with entwined spin and orbital degrees of freedom and a theoretical model pertinent to it, we have demonstrated correlation-driven electron localization–delocalization as such a principle. It happens sequentially, involving a single quantum number at a time, thus deciphering the roles of the individual degrees of freedom.
Risk attitudes and personality traits of entrepreneurs and venture team members
Authors: Kerr Sari Pekkala , Kerr William R. , Dalton Margaret
Published: August 2019

Significance

We quantify personality traits and risk tolerances among entrepreneurs and their venture team members using a unique and in-depth survey of multiple locations of an innovation and coworking center. Our survey captures respondents’ own perceptions of their personality traits and an observational assessment of their risk tolerance via a prize lottery. These detailed profiles allow us to describe similarities and differences between entrepreneurs, nonfounder CEOs/leaders, inventor employees, and noninventor employees. This survey provides a characterization of these different personality profiles in innovative firms and environments that have all roles present and thus controlling for confounding environment factors.
Birch tar production does not prove Neanderthal behavioral complexity
Authors: Schmidt Patrick , Blessing Matthias , Rageot Maxime , Iovita Radu , Pfleging Johannes , Nickel Klaus G. , Righetti Ludovic , Tennie Claudio
Published: August 2019

Significance

We found a previously unknown way to produce birch tar. Instead of creating cognitively demanding structures (underground or in containers), this method consists of simply burning bark close to cobbles in a hearth. The tar is deposited on the stones and can be scraped off for use. This approach to interpreting early tar resolves the mystery of the associated and still not understood early technical complexity and provides a “discoverable” pathway to one of the earliest pyrotechnologies. These results have implications for our interpretation of birch tar in the archaeological record: Birch tar from early archaeological contexts alone can no longer indicate the presence of modern cognition and/or cultural behaviors in Neanderthals.
The dynamic layering of relational pairs in L2 classrooms
Authors: Moutinho Ricardo
Published: August 2019

The focus of this paper will be placed upon the methods people use to interact in second language learning settings, discussing interactional aspects of language use in the ongoing production of classroom events. The extracts selected for analysis were drawn from Portuguese language lessons (for beginner and advanced students) in a Chinese university. The results show how L2 classroom participants secure joint orientation and mutual understanding of the categorial pairs (such as ‘teacher-student’ and ‘native-non-native’) being invoked in the sequential organization of the utterances. In other words, when classroom members show orientation to a categorial pair, their subsequent moves will exhibit predicates (actions) of that pair, which will be available to the analyst as phenomena to be explored. This suggests that the sequential elements of the interaction and the membership categorization work carried out by the participants require attention for praxiological enquiries.
Variation in address practices across languages and nations
Authors: Wide Camilla , Lappalainen Hanna , Rouhikoski Anu , Norrby Catrin , Lindholm Camilla , Lindström Jan , Nilsson Jenny
Published: August 2019

This article compares variation in the use of address practices across languages (Swedish,
Finnish) and national varieties (Sweden Swedish, Finland Swedish). It undertakes quantitative and qualitative
analyses of three sets of transcribed medical consultations. In Sweden Swedish, address pronouns which lower
social distance overwhelmingly dominate. In Finnish, both address forms reducing social distance and practices
maintaining greater distance are found, with age and level of acquaintance revealed as the most salient
factors. Finland Swedish is located somewhere between Sweden Swedish and Finnish, displaying a stronger
tendency than Finnish to use informal direct address forms to reduce social distance, but also showing
similarities with Finnish in the use of direct formal address and indirect address. The differences can be
related to larger socio-cultural patterns which, however, form a continuum rather than a fixed set keeping the
two languages and countries completely apart.
Parts of speech membership as a factor of meaning extension and level of abstraction
Authors: Kanasugi Petra
Published: August 2019

Czech and Japanese show formal differences in adnominal modification. Czech tends to utilize adjectives for both
classification and qualification purposes whereas Japanese tends to express classification by compounding and to use a whole range
of parts of speech for qualification. As a result, part of speech membership often differs between the Czech and Japanese
rendering of the same referential content. It has been shown that parts of speech dispose of schematic meaning which contributes
to conceptualization. Based on the results of corpora analysis, I argue that the difference in parts of speech membership results
in different tendencies in meaning extension and ultimately in different meaning of the two counterparts, Czech adjectives are
more abstract and schematic while Japanese verbs are more concrete.
Evolutionary order of macro-events in Mandarin
Authors: Li Fuyin Thomas
Published: August 2019

This article aims to explore the evolutionary order of the five types of macro-event in Mandarin. As a methodology, a closed corpus is set up for five historical stages. The following is concluded: (1) The “V+C” constructions representing a macro-event started to appear from Stage III and continued to be used until the present stage; (2) The “V+C” constructions can only represent four out of five types of Talmy’s macro-event, and action correlating is not systematically represented; (3) The four types of macro-event appeared at a relatively similar time period, and their proportion is: Motion > State change > Temporal > Realization; (4) Verbs with PATH meaning in the V2 slot are more prone to grammaticalization than in the V1 in the serial verb construction “V1+V2”. This research is significant in bridging the areas of event structure, grammaticalization and typology, and might have implications for other languages as well.
Compounds and culture
Authors: Nesset Tore , Sokolova Svetlana
Published: August 2019

This study explores compounds from the perspective of conceptual blending (conceptual integration), and argues that the meaning of compounds arises through the interaction of three levels: (i) input spaces established for the head and non-head components, (ii) a blended space involving compression and emergent structure, i.e. elements not imported from the input spaces, and (iii) the language system as a whole and the culture this system is part of. With regard to (iii) we propose the “Culture-to-Compound Hypothesis”, according to which compounding can be recruited to represent culturally “novel” content in languages where compounding enjoys a peripheral status in the language system. The examples discussed in the article come from Norwegian (a Germanic language where compounding is a central word-formation mechanism) and Russian (a Slavic language where compounding is more marginal in the language system).
Conceptual metaphors and performativity in the Sunshine Policy
Authors: Kwon Iksoo
Published: August 2019

This paper explores the roles of the cognitive mechanisms of conceptual metaphor and performativity in political policy by conducting a case study on the South Korean government’s Sunshine Policy toward North Korea from 1998 to 2008. This study contends that the policy is metaphorically motivated by an Aesop’s fable,The sun and the wind, a narrative whose entailments have significant implications for the policy. It also systematically accounts for the policy’s performative characteristic, focusing on the fact that the policy makers intended to map the causal relationship of the narrative onto a real-world relationship, even though the real-world causal relationship must be based on the unknown result of the policy. Lastly, this paper discusses theoretical implications of the performativity entangled with the conceptual metaphors in the policy; the real-world concept is usually what limits the mapping possibilities, but in this case, the narrative structure of the fable determines the construal.
Preconditioning inverse problems for hyperbolic equations with applications to photoacoustic tomography
Authors: Beigl Alexander , Scherzer Otmar , Sogn Jarle , Zulehner Walter
Published: August 2019

This paper is concerned with the preconditioning of wave equation-constrained linear inverse problems from boundary observation data, such as, for instance, photoacoustic tomography, which is considered as an application. The main result of this paper is a concept for regularization parameter robust preconditioning. That is, we propose a preconditioner for the PDE-constrained optimization problem such that the condition number of the preconditioned optimality system is uniformly bounded with respect to the regularization parameter. Using an augmented Lagrangian formulation for the discretized optimality system, we employ a discretization strategy which renders the discretized preconditioned system robust with respect to both the regularization parameter and the mesh size. Numerical experiments complement our analysis.
Defects and electrical properties in Al-implanted 4H-SiC after activation annealing*
Authors: Tang Yi-Dan , Liu Xin-Yu , Zhou Zheng-Dong , Bai Yun , Li Cheng-Zhan
Published: August 2019

The defects and electrical properties in Al-implanted 4H-SiC after activation annealing (1600 °C–1800 °C) are investigated. High temperature annealing can reduce the ion implantation-induced damage effectively, but it may induce extended defects as well, which are investigated by using Rutherford backscattering spectroscopy (RBS/C), secondary ion mass spectroscopy (SIMS), and transmission electron microscopy (TEM) analyses. According to the ratio of the channeled intensity to the random intensity in the region just below the surface scattering peak (X
min) and RBS/C analysis results, the ion implantation-induced surface damages can be effectively reduced by annealing at temperatures higher than 1700 °C, while the defects near the bottom of the ion-implanted layer cannot be completely annealed out by high temperature and long time annealing process, which is also demonstrated by SIMS and TEM analyses. Referring to the defect model and TEM analyses, an optimized annealing condition can be achieved through balancing the generation and elimination of carbon vacancies in the ion implanted layers. Furthermore, the electrical and surface properties are also analyzed, and the hole concentration, mobility, and resistivity are obtained through the Hall effect. The optimized activation annealing conditions of 1800 °C/5 min are achieved, under which the lower defects and acceptable electrical properties are obtained.
Unconventional phase transition of phase-change-memory materials for optical data storage*
Authors: Chen Nian-Ke , Li Xian-Bin
Published: August 2019

Recent years, optically controlled phase-change memory draws intensive attention owing to some advanced applications including integrated all-optical nonvolatile memory, in-memory computing, and neuromorphic computing. The light-induced phase transition is the key for this technology. Traditional understanding on the role of light is the heating effect. Generally, the RESET operation of phase-change memory is believed to be a melt-quenching-amorphization process. However, some recent experimental and theoretical investigations have revealed that ultrafast laser can manipulate the structures of phase-change materials by non-thermal effects and induces unconventional phase transitions including solid-to-solid amorphization and order-to-order phase transitions. Compared with the conventional thermal amorphization, these transitions have potential superiors such as faster speed, better endurance, and low power consumption. This article summarizes some recent progress of experimental observations and theoretical analyses on these unconventional phase transitions. The discussions mainly focus on the physical mechanism at atomic scale to provide guidance to control the phase transitions for optical storage. Outlook on some possible applications of the non-thermal phase transition is also presented to develop new types of devices.
Neural network study of hidden-charm pentaquark resonances
Authors: Mutuk Halil
Published: August 2019

Recently, the LHCb experiment announced the observation of hidden-charm pentaquark states

,

, and

near

and

thresholds. In this present work, we studied these pentaquarks in the framework of the nonrelativistic quark model with four types of potential. We solved five-body Schrödinger equation by using the artificial neural network method and made predictions of parities for these states, which are not yet determined by experiment. The mass of another possible pentaquark state near the

with

is also calculated.
Study of the

rare hyperon decays in the Standard Model and new physics *
Authors: Hu Xiao-Hui , Zhao Zhen-Xing
Published: August 2019

FCNC processes offer important tools to test the Standard Model (SM) and to search for possible new physics. In this work, we investigate the

rare hyperon decays in SM and beyond. We find that in SM the branching ratios for these rare hyperon decays range from

to

. When all the errors in the form factors are included, we find that the final branching ratios for most decay modes have an uncertainty of about 5% to 10%. After taking into account the contribution from new physics, the generalized SUSY extension of SM and the minimal 331 model, the decay widths for these channels can be enhanced by a factor of

.
Applicability of 9Be global optical potential to reactions of 7,10,11,12Be *
Authors: Xu Yong-Li , Han Yin-Lu , Liang Hai-Ying , Wu Zhen-Dong , Guo Hai-Rui , Cai Chong-Hai
Published: August 2019

Elastic scattering angular distributions and total reaction cross-sections of 7,10,11,12Be projectiles are predicted by the systematic 9Be global phenomenological optical model potential for target mass numbers ranging from 24 to 209. These predictions provide a detailed analysis by their comparison with the available experimental data. Furthermore, these elastic scattering observables are also predicted for some targets out of the mass number range. The results are in reasonable agreement with the existing experimental data, and they are presented in this study.
Response functions of hot and dense matter in the Nambu-Jona-Lasino model *
Authors: Mu Chengfu , Wang Ziyue , He Lianyi
Published: August 2019

We investigate current-current correlation functions, or the so-called response functions of a two-flavor Nambu-Jona-Lasino model at finite temperature and density. The linear response is investigated introducing the conjugated gauge fields as external sources within the functional path integral approach. The response functions can be obtained by expanding the generational functional in powers of the external sources. We derive the response functions parallel to two well-established approximations for equilibrium thermodynamics, namely mean-field theory and a beyond-mean-field theory, taking into account mesonic contributions. Response functions based on the mean-field theory recover the so-called quasiparticle random phase approximation. We calculate the dynamical structure factors for the density responses in various channels within the random phase approximation, showing that the dynamical structure factors in the baryon axial vector and isospin axial vector channels can be used to reveal the quark mass gap and the Mott dissociation of mesons, respectively. Noting that the mesonic contributions are not taken into account in the random phase approximation, we also derive the response functions parallel to the beyond-mean-field theory. We show that the mesonic fluctuations naturally give rise to three kinds of famous diagrammatic contributions: the Aslamazov-Lakin contribution, the self-energy or density-of-state contribution, and the Maki-Thompson contribution. Unlike the equilibrium case, in evaluating the fluctuation contributions, we need to carefully treat the linear terms in external sources and the induced perturbations. In the chiral symmetry breaking phase, we find an additional chiral order parameter induced contribution, which ensures that the temporal component of the response functions in the static and long-wavelength limit recovers the correct charge susceptibility defined using the equilibrium thermodynamic quantities. These contributions from mesonic fluctuations are expected to have significant effects on the transport properties of hot and dense matter around the chiral phase transition or crossover, where the mesonic degrees of freedom are still important.
Energy staggering parameters in nuclear magnetic rotational bands *
Authors: Sun Wu-Ji , Li Jian
Published: August 2019

This study presents the systematics of energy staggering for magnetic rotational bands with

and

transition properties, which are strictly consistent with the features of good candidates of magnetic rotational bands in the

, 110, 130, and 190 mass regions. The regularities exhibited by these bands with respect to the staggering parameter, which increases with increasing spin, are in agreement with the semiclassical description of shears mechanism. Moreover, the abnormal behaviour in the backbend regions or close to band termination has also been discussed. Taking the magnetic dipole bands with same configuration in three

isotones, i.e.,

,

, and

, as examples, the transition from chiral to magnetic rotation with the proton number approaching

is presented. Moreover, the self-consistent tilted axis and principle axis cranking relativistic mean-field theories are applied to investigate the rotational mechanism in the dipole band of

.
Classical model for diffusion and thermalization of heavy quarks in a hot medium: memory and out-of-equilibrium effects *
Authors: Ruggieri Marco , Frasca Marco , Das Santosh Kumar
Published: August 2019

We consider a simple model for the diffusion of heavy quarks in a hot bath, modeling the latter by an ensemble of oscillators distributed according to either a thermal distribution or to an out-of-equilibrium distribution with a saturation scale. In this model it is easy to introduce memory effects by changing the distribution of oscillators: we model them by introducing a Gaussian distribution,

, which can be deformed continuously from a

function, giving a Markov dissipation, to a broad kernel with memory. Deriving the equation of motion of the heavy quark in the bath, we remark how dissipation comes out naturally as an effect of the back-reaction of the oscillators on the bath. Moreover, the exact solution of this equation allows to define the thermalization time as the time necessary to remove any memory of the initial conditions. We find that the broadening of the dissipative kernel, while keeping the coupling fixed, lowers the thermalization time. We also derive the fluctuation-dissipation theorem for the bath, and use it to estimate the kinematic regime in which momentum diffusion of the heavy quark dominates over drift. We find that diffusion is more important as long as

is small, where

and

denote the initial energy of the heavy quark and the average energy of the bath, respectively.
Perturbative modes and black hole entropy in f (Ricci) gravity *
Authors: Wang Chuanyi , Zhao Liu
Published: August 2019

f (Ricci) gravity is a special kind of higher curvature gravity whose bulk Lagrangian density is the trace of a matrix-valued function of the Ricci tensor. It is shown that under some mild constraints, f (Ricci) gravity admits Einstein manifolds as exact vacuum solutions, and can be ghost-free and tachyon-free around maximally symmetric Einstein vacua. It is also shown that the entropy for spherically symmetric black holes in f (Ricci) gravity calculated via the Wald method and the boundary Noether charge approach are in good agreement.
W-hairs of the black holes in three-dimensional spacetime *
Authors: Wang Jing-Bo
Published: August 2019

In a previous publication, we claimed that a black hole can be considered as a topological insulator. A direct consequence of this claim is that their symmetries should be related. In this paper, we give a representation of the near-horizon symmetry algebra of the BTZ black hole using the W
1+∞ symmetry algebra of the topological insulator in three-dimensional spacetime. Based on the W
1+∞ algebra, we count the number of the microstates of the BTZ black holes and obtain the Bekenstein-Hawking entropy.
Criteria analysis in the selection method of mud pumping in coal mining project
Authors: Aryoseno  , Ahyudanari Ervina
Published: August 2019

The process of discharging water from the pit is one of the stages prior to the continued excavation of coal deposits. Due to the increase of coal price, several areas that were not economically valuable became visible to re-mined. In some mine ponds that are considered economically viable, are necessary to pump the mud before carried out the water before further digging. This requirement needs decision-making for the determination of sludge pumping methods. A large number of criterion variables for selecting the best mud pumping method drives this study. The distance of three mine ponds under the company is quite far each other. Some steps were executed to have the best method to cater to the problem. The results indicate that there are six criteria that suitable to be considered in selecting a method for mud pumping. Those are the productivity of pump, man power, mobilization, supporting facilities, flexibilities, and operational cost.
Design of output power control system based on mass flow rate comparison of air and fuel ratio (AFR) on dual fuel generator set by using pid control method
Authors: Toriki M B , Widjiantoro B L , Abdurrakhman A
Published: August 2019

Generator set is a tool that is used to generate energy or electrical power. The electric power generated by the generator set is used to supply the electrical loads in this thesis is lamp. Power that can be produced by a generator set is ranged between 100-1200 watt. The power generated by generator set is used influenced by a mixture ofair and fuel. Generator set used is dual fuel generator set. From the results of this study, a stable response with overshoot value below 0% and its error is 2%. In addition, the best obtained value of Air Fuel Ratio (AFR) is 15.06, Furthermore, the stability of the power generated by the generator set is also influenced by the flowrate mass of the fuel injected into the combustion chamber. From the simulation results when given a power set point at 1200 watt, obtained value of the air mass flowrate is 0.03754 kg/s, mass flowrate of biogas is 0.002367 kg/s, and gasoline constant mass flowrate is 0.000125 kg/s. Meanwhile, when given a set point of 100 watts of power, a value of 0.009928 kg/s air mass flowrate is injected to the chamber, mass flowrate of biogas is 0.0005341 kg/s and the mass flowrate of gasoline is 0.000125 kg/s. The goal of output power control on generator set is to make generator working to produce output power in accordance to required load.
Risk Assessment on Liquefied Petroleum Gas (LPG) Handling Facility, Case Study: Terminal LPG Semarang
Authors: Akbar T A , Dinariyana A A B , Baheramsyah A , Prastyasari F I , Setyorini P D
Published: August 2019

LPG plays important role in Indonesia as household fuel. With the rapid growth of LPG usage, its handling facility is built across the country. The handling of LPG requires various activity prior to supporting its supply chain. One of the vital facility is Terminal LPG (or on this case Terminal LPG Semarang) which serve as a hub in LPG distribution because it handles a relatively huge amount of LPG. It is exposed to operational risk especially fire risk. This paper is intended to assess the risk of LPG Terminal by using combined both qualitative and quantitative methods. The initial step is to identify the hazard by using HAZOP Study. The next step is to determine the likelihood of the risk by using FTA and ETA resulted in event frequency. The severity level is determined using consequences analysis which involved fire modeling of the intended scenarios. The result from both frequency and consequences will be presented in the risk matrix to determine the unacceptable risk scenario to develop a mitigation plan by using Fire Risk Card to assess the capability of the Terminal firefighting equipment.
The development of the IHL wave-current turbine to convert the ocean energy from both wave and current
Authors: Erwandi  , Rahuna D , Mintarso C S J
Published: August 2019

Indonesia has abundant of renewable sources of energy, among others: geothermal, solar, water, wind and marine therefore the promotion of the utilization of the renewable and sustainable energy is urgent. Since 2006 Indonesian Hydrodynamic Laboratory (IHL) BPPT has conducted research and developed a technology converts the ocean energy resources into electricity, the kinetic energy of marine current and the potential energy of wave. The prototype of marine current turbine, 2 kW and 10 kW respectively, had been installed in Larantuka Strait in 2010 and 2011 (http://www.youtube.com/user/erw4ndi). Since mostly the maximum speed of the marine current of many straits in Indonesia are in order 1.0 - 2.0 m/s, we developed the turbine prototype that can convert not only the kinetic energy of marine current but also the potential energy of the wave, called as wave-current rotor turbine, in 2013. The current usually mixes with wave height with order 0.4 - 0.8 m. A 2 kW prototype was installed under Suramadu (Surabaya - Madura) Bridge close to pier no. 56. The prototype showed a good performance especially in converting the kinetic energy of marine current. The research was continued in 2014-2016 under Ministry of Research and Technology (INSINAS RISTEK) budget scheme. Some innovations have been done to improve the performance of turbines.
Subsurface Analysis Using Gravity Data at Lili Sepporaki Geothermal Area
Authors: Sihombing Jubilate , Lestari Wien , Mariyanto  , Joni Wiwid
Published: August 2019

Gravity survey plays an important role in early stage of subsurface imaging in geothermal system. The aim of this study is to understand the subsurface structure and possibly the heat source based on rock density distribution with three dimensional inversion modeling (3D). In 2010, Center of Mineral Resources, Coal and Geothermal of Indonesia was performed gravity survey at Lili Sepporaki geothermal area with 205 stations within a 10 x 10 km coverage area. The complete Bouguer anomaly was obtained with the density of 2.8 g/cm3 and this density was used to do 3D modelling. Bouguer anomalies ranging from 40 mgal to 62 mgal were observed in the study area with low anomalies values located in the northern part and high anomalies located in the southern part of the study area. Based on the 3D inversion modeling results, there are low density rocks with values between 2.0 - 2.3 g/cm3 around the hot springs of the research area with a depth of <1 km. These rocks are interpreted as rocks that associated with fractures forming a fault zone that controls the surface manifestation of the study area. High density rocks with values between 3.0 - 3.3 gr/cm3 are located south of research area with depth >2 km. This rocks are interpreted as intrusive igneous rocks and are thought as the heat source of geothermal systems in the study area.