bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inflamed neutrophils sequestered at entrapped tumor cells via chemotactic confinement promote tumor cell extravasation
Authors: Chen Michelle B. , Hajal Cynthia , Benjamin David C. , Yu Cathy , Azizgolshani Hesham , Hynes Richard O. , Kamm Roger D. 
Published: June 2018

Significance
Systemic inflammation that occurs during the course of tumor treatment is often correlated with adverse oncological outcomes independent of the infectious insult. As the first line of defense against infection, it is likely that neutrophils play an important role in modulating the progression of distant metastases in these scenarios. This study uses a multiplexed microfluidic model of human microcirculation combined with LPS-stimulated neutrophils as a model of systemic infection to probe the dynamic interactions between intravascular tumor cells and neutrophils at high spatiotemporal resolutions. We uncover chemokine-dependent neutrophil migration patterns which result in enhanced tumor cell extravasation rates. These findings may provide a basis for inhibiting the proextravasation and possibly prometastatic effect of inflamed neutrophils.
Genomic organization underlying deletional robustness in bacterial metabolic systems
Authors: Hosseini Sayed-Rzgar , Wagner Andreas 
Published: June 2018

Significance
From the organismal and the anatomical levels down to the molecular level, all complex biological systems manifest astonishing organization and order that are counterintuitive and challenging to explain by evolutionary mechanisms. In this study, we focus specifically on one aspect of this biological organization: the arrangement of metabolic genes in bacterial genomes. We show that this organization ensures a substantially higher robustness to large-scale gene deletions than expected from random genomic ordering. We systematically investigate the possible evolutionary mechanisms behind the emergence of such robust organizations. Our analysis provides several lines of evidence indicating that bacteria may have gained a robust genome organization through pervasive gene loss events.
Serine metabolism in the brain regulates starvation-induced sleep suppression in
Drosophila melanogaster
Authors: Sonn Jun Young , Lee Jongbin , Sung Min Kyung , Ri Hwajung , Choi Jung Kyoon , Lim Chunghun , Choe Joonho 
Published: June 2018

Significance
Foraging and sleep are two conflicting behaviors in starved animals; however, it remains elusive how metabolic status governs sleep drive. In this study, we show that a biosynthetic pathway for the amino acid serine is transcriptionally up-regulated by starvation in adult fly brains. The behavioral response to genetic manipulation of key enzymes involved in serine metabolism supports the sleep-suppressing effect of serine in response to starvation. In a society where daily diet is becoming increasingly important to the sleep quality of individuals, our study defines an amino acid metabolic pathway that underlies adaptive sleep behaviors upon dietary stress.
Nonlocal supercurrent of quartets in a three-terminal Josephson junction
Authors: Cohen Yonatan , Ronen Yuval , Kang Jung-Hyun , Heiblum Moty , Feinberg Denis , Mélin Régis , Shtrikman Hadas 
Published: June 2018

Significance
In this work we present detailed studies of a nondissipative current, called “quartet supercurrent,” where two distinct Cooper pairs, originating in different terminals, recombine into a four-electron quasiparticle: a quartet. Employing conductance measurements and highly sensitive cross-correlation of current fluctuation, we identified the existence of such a coherent nonlocal state.
Decimation by sea star wasting disease and rapid genetic change in a keystone species,
Pisaster ochraceus
Authors: Schiebelhut Lauren M. , Puritz Jonathan B. , Dawson Michael N 
Published: June 2018

Significance
Opportunities to study microevolution in wild populations are rare and challenging. Annual monitoring allowed us to capture both the prelude to and aftermath of one of the largest marine mass mortality events on record in a keystone marine species. Median mortality of 81% across populations was recorded along with significant allele frequency shifts at multiple loci in the adult population. Shifts were consistent across locations and also occurred in new recruits, with few exceptions. These results indicate a long-term species-wide change in allele frequencies will persist through future generations. Population genomic monitoring, at a time when marine diseases and mass mortalities are on the rise, will be essential for documenting rapid genetic shifts in response to chronic and extreme events.
Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA
Authors: Kwon Sunghark , Watanabe Satoshi , Nishitani Yuichi , Kawashima Takumi , Kanai Tamotsu , Atomi Haruyuki , Miki Kunio 
Published: June 2018

Significance
The large subunit of [NiFe] hydrogenase undergoes Ni insertion into the active site by the Ni chaperone HypA during its posttranslational process (maturation process). However, the detailed mechanism of the Ni insertion has been elusive. Here, we report the structures of an immature large subunit HyhL in complex with HypA, which enable us to infer a series of conformational changes involved in the Ni delivery. The structures show that the N-terminal tail of HyhL interacts with the Ni-binding domain of HypA. Structural comparison of the immature large subunit HyhL with a mature one reveals that the Ni insertion may induce spatial rearrangement of the N- and C-terminal tails of HyhL.
Multiple feedback loops of the Arabidopsis circadian clock provide rhythmic robustness across environmental conditions
Authors: Shalit-Kaneh Akiva , Kumimoto Roderick W. , Filkov Vladimir , Harmer Stacey L. 
Published: June 2018

Significance
While all eukaryotic circadian clocks depend on transcriptional feedback loops, the plant circadian network is uniquely complex. An apparent redundancy in the plant clock is two types of transcription factors that antagonistically regulate common target genes. Here, we show that, although loss of either repressor- or activator-type factors perturbs clock pace and plant development, simultaneous loss of both types of factors restores near–wild-type development and largely rescues circadian period and phase phenotypes at ambient temperatures. However, in the higher-order mutant, rhythmic amplitude is reduced under optimal temperature, and rhythmicity is lost at low or high temperatures within the physiologically relevant range. Our data suggest that the multiple feedback loops of the plant clock help ensure rhythmicity under adverse environmental conditions.
The complexities of written Chinese and the cognitive-linguistic precursors to reading, with consequent implications for reading interventions
Authors: Kalindi Sylvia Chanda , Chung Kevin Kien Hoa , Liu Duo Phil , Wang Li-Chih Angus 
Published: June 2018

Abstract
This chapter will review universal and unique cognitive-linguistic precursors to reading acquisition and impairment, such as reading disabilities and dyslexia, in the Chinese language. The chapter will examine research evidence linking phonological awareness, morphological awareness, orthographic awareness, rapid automatized naming (RAN), and visual skills to reading acquisition among children in mainland China, Hong Kong, and Taiwan. Understanding these cognitive-linguistic constructs and their mechanisms underlying reading acquisition is essential in order to explain reading impairment. Compared to dyslexic children of alphabetic languages, Chinese children with dyslexia present different and often multiple profiles of cognitive-linguistic deficits, the most dominant being RAN, orthographic awareness, and morphological awareness and the less dominant being phonological awareness. In particular, the review will examine the causes, characteristics, uniqueness or idiosyncrasies found in speakers of Chinese, and consequences of dyslexia in children in the three Chinese societies. Such a review will offer insight into and lay foundations for developing effective evidence-based interventions for children with reading impairment both inside and outside of school. Implications for current evidence-based practices in interventions are also discussed.
Brain mechanisms of Chinese word reading
Authors: Cao Fan 
Published: June 2018

Abstract
Research on Chinese reading provides important insights into the understanding of language-universal and script-specific mechanisms of reading, because Chinese is contrastively different from alphabetic languages. In this chapter, I will first summarize neuroimaging findings of Chinese word reading in adults in comparison to English word reading. Then, I will discuss how the brain adapts to one’s language with learning and development. Then, I will focus on the topic of second language learning, including how one brain processes Chinese and English in bilinguals, how first language influences second language learning, and whether there are different optimal learning methods for different second languages. This chapter will address these important questions based on neuroimaging studies.
Loan verbs in Egyptian Arabic
Authors: Hassan Ashraf F. 
Published: June 2018

Abstract
This paper will explain the strategies of loan verbs integration in Egyptian Arabic (EA). As a recipient language, EA adopts
two strategies: (a) insertion with ‘Light Verb Strategy’; and (b) Direct Insertion either with or without ‘Reduction to
Root.’
While direct insertion strategy without ‘reduction to root’ is used almost exclusively for imperative loan verbs, the same
strategy with ‘reduction to root’ is open to any ‘input form’. To each loan verb EA assigns a root and the loan verb assumes
one of the EA verbal forms.
An investigation of new loan verbs passed to EA through Social Media, while they are being integrated, gives us further
insight, and therefore a better understanding, into the integration process of loan verbs in general.
The disappearance of bromuconazole fungicide in domestic waste anaerobic fermentation
Authors: Hariyadi H R 
Published: June 2018

Abstract
A previous study recommended observing degradation of bromuconazole in waste anaerobic fermentation. This research, therefore, was carried out to study the disappearance of bromuconazole in waste anaerobic fermentation. Bromuconazole is a fungicide which is effective against Ascomycetes, Basidiomycetes and fungi imperfecti in cereals, grapes, top fruits and vegetables. It is also effective against Alternaria and Fusarium sp. In this study, one-month old refuse added with bromuconazole was anaerobically incubated in the 500 ml bottles at 30°C with no shaking in the dark room. Bromuconazole with total concentration of 200 mg/L was added in day 0 and 31. As a control, a bottle with refuse and bromuconazole at concentration of 200 mg/L was autoclaved and incubated at the same condition. High-performance Liquid Chromatography with UV detector and a 100 RP18 5µm Lichrosphere column was used to determine bromuconazole concentration. Methane content was determined by Gas Chromatography method equipped with a flame ionization detector and a metal column packed with 5% neopentyl glycol sebacate and 1% H3PO4 on Chromosorb W-AW (mesh 80-100). The disappearance of bromuconazole in anaerobic enrichments can be observed from mass balance determination after incubation for 225 days. The result showed that there was no change in bromuconazole mass balance. Bromuconazole was mostly adsorbed by the refuse. Bromuconazole inhibited the production of methane (99.58 mM), less than that of the control bottle with no added bromuconazole (121.78 mM). This phenomenon indicated the persistence of bromuconazole and its toxicity against methanogen bacterial activity. The presence of bromuconazole in the anaerobic process caused the refuse to be imperfectly fermented and so the production of methane was inhibited and volatile fatty acids were accumulated. Accumulation of the volatile fatty acids may cause further pollution in aquatic environment around the landfills site.
The future of Heritage Science and Technologies from a legal point of view
Authors: Segnalini S. 
Published: June 2018

Abstract
The development and the prospect of future cultural heritage should certainly be confronted with the development of new technologies applied to the arts which, from a legal point of view, implies mainly three important aspects.
1.
Copyrights for software
: this seems to be the least interesting for the jurists as many aspects have already been addressed and solved, and therefore on will just quickly list some of them. In fact the copyright explicitely protects the software as work of wit and consequently it is clear that the author is the dominus of his creation in the sense that he is the only person who can decide how to allow other people use his software. So f.e. the relationship between the copyright legislation and open source is actually less difficult than it maybe thought. In addition open source use is fully regulated by Law no. 633/1941 (so called “legge sul diritto d’autore”) which guarantees its proper use.
2.
Legal issues related to the so-called BIM technology
: Building Information Modelling (BIM) is a software for plannig and implementing building projects based on 3D modeling of buildings or structures models. The BIM has already been adopted internationally for the realization of major project and one of the most exciting challenges for a lawyer is to develop a specific BIM contract for the particular field of art and cultural heritage.
3.
Legal issues related to artificial intelligence
: this certainly represents a field yet to be discovered by jurists and here I will present a series of legal concerns that will engage jurists in the coming years. Such as responsibility and ethics of artificial intelligence. For the above-mentioned considerations, the European Parliament’s Legal Affairs Committee approved a report calling on the European Commission to introduce a set of regulations on robotics.
RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure
Authors: Lu Jacob S , Bindewald Eckart , Kasprzak Wojciech K , Shapiro Bruce A 
Published: June 2018

Abstract

Summary
Creating clear, visually pleasing 2D depictions of RNA and DNA strands and their interactions is important to facilitate and communicate insights related to nucleic acid structure. Here we present RiboSketch, a secondary structure image production application that enables the visualization of multistranded structures via layout algorithms, comprehensive editing capabilities, and a multitude of simulation modes. These interactive features allow RiboSketch to create publication quality diagrams for structures with a wide range of composition, size and complexity. The program may be run in any web browser without the need for installation, or as a standalone Java application.

Availability and implementation
https://rnastructure.cancer.gov/ribosketch
BioStructMap: a Python tool for integration of protein structure and sequence-based features
Authors: Guy Andrew J , Irani Vashti , Richards Jack S , Ramsland Paul A 
Published: June 2018

Abstract

Summary
A sliding window analysis over a protein or genomic sequence is commonly performed, and we present a Python tool, BioStructMap, that extends this concept to three-dimensional (3D) space, allowing the application of a 3D sliding window analysis over a protein structure. BioStructMap is easily extensible, allowing the user to apply custom functions to spatially aggregated data. BioStructMap also allows mapping of underlying genomic sequences to protein structures, allowing the user to perform genetic-based analysis over spatially linked codons—this has applications when selection pressures arise at the level of protein structure.

Availability and implementation
The Python BioStructMap package is available at https://github.com/andrewguy/biostructmap and released under the MIT License. An online server implementing standard functionality is available at https://biostructmap.burnet.edu.au.

Supplementary information
Supplementary data are available at Bioinformatics online.
panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data
Authors: Treepong Panisa , Guyeux Christophe , Meunier Alexandre , Couchoud Charlotte , Hocquet Didier , Valot Benoit 
Published: June 2018

Abstract

Motivation
The advent of next-generation sequencing has boosted the analysis of bacterial genome evolution. Insertion sequence (IS) elements play a key role in prokaryotic genome organization and evolution, but their repetitions in genomes complicate their detection from short-read data.

Results
PanISa is a software pipeline that identifies IS insertions ab initio in bacterial genomes from short-read data. It is a highly sensitive and precise tool based on the detection of read-mapping patterns at the insertion site. PanISa performs better than existing IS detection systems as it is based on a database-free approach. We applied it to a high-risk clone lineage of the pathogenic species Pseudomonas aeruginosa, and report 43 insertions of five different ISs (among which three are new) and a burst of ISPa1635 in a hypermutator isolate.

Availability and implementation
PanISa is implemented in Python and released as an open source software (GPL3) at https://github.com/bvalot/panISa.

Supplementary information
Supplementary data are available at Bioinformatics online.
The ancestral KH peptide at the root of a domain family with three different folds
Authors: Pereira Joana , Lupas Andrei N 
Published: June 2018

Abstract

Motivation
The direct ancestor of the DNA-protein world of today is considered to have been an RNA-peptide world, in which peptides were co-factors of RNA-mediated catalysis and replication. Evidence for these ancestral peptides, from which folded proteins evolved, can be derived even today from regions of local sequence similarity within globally dissimilar folds. One of these is the 45-residue motif common to both folds of the hnRNP K homology (KH) domain.

Results
In a survey of KH domains, we found a third fold that contains the KH motif at its core. This corresponds to the Small Domain of bacterial Ribonucleases G/E and, like type I and type II KH domains, it cannot be related to the others by a single genetic event, providing further support for the KH motif as an ancestral peptide predating folded proteins.

Supplementary information
Supplementary data are available at Bioinformatics online.
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks
Authors: Hanson Jack , Paliwal Kuldip , Litfin Thomas , Yang Yuedong , Zhou Yaoqi 
Published: June 2018

AbstractMotivationAccurate prediction of a protein contact map depends greatly on capturing as much contextual information as possible from surrounding residues for a target residue pair. Recently, ultra-deep residual convolutional networks were found to be state-of-the-art in the latest Critical Assessment of Structure Prediction techniques (CASP12) for protein contact map prediction by attempting to provide a protein-wide context at each residue pair. Recurrent neural networks have seen great success in recent protein residue classification problems due to their ability to propagate information through long protein sequences, especially Long Short-Term Memory (LSTM) cells. Here, we propose a novel protein contact map prediction method by stacking residual convolutional networks with two-dimensional residual bidirectional recurrent LSTM networks, and using both one-dimensional sequence-based and two-dimensional evolutionary coupling-based information.ResultsWe show that the proposed method achieves a robust performance over validation and independent test sets with the Area Under the receiver operating characteristic Curve (AUC) &gt; 0.95 in all tests. When compared to several state-of-the-art methods for independent testing of 228 proteins, the method yields an AUC value of 0.958, whereas the next-best method obtains an AUC of 0.909. More importantly, the improvement is over contacts at all sequence-position separations. Specifically, a 8.95%, 5.65% and 2.84% increase in precision were observed for the top L∕10 predictions over the next best for short, medium and long-range contacts, respectively. This confirms the usefulness of ResNets to congregate the short-range relations and 2D-BRLSTM to propagate the long-range dependencies throughout the entire protein contact map ‘image’.Availability and implementationSPOT-Contact server url: http://sparks-lab.org/jack/server/SPOT-Contact/.Supplementary informationSupplementary data are available at Bioinformatics online.
Participatory planning in a low-income neighbourhood in Ontario, Canada: building capacity and collaborative interactions for influence
Authors: Nasca Tessa F , Changfoot Nadine , Hill Stephen D 
Published: June 2018

AbstractThis research evaluated a community-led participatory planning process that sought to involve citizens who are often marginalized within planning processes. Participatory planning – which is theoretically informed by communicative planning theory – may shift the legacy of power and marginalization within planning processes and improve planning outcomes, foster social cohesion, and enhance the quality of urban life. The two-year Stewart Street Active Neighbourhoods Canada (ANC) project aimed to build capacity among residents of a low-income neighbourhood in Peterborough, Ontario and to influence City planning processes impacting the neighbourhood. The project, led by a community-based organization, GreenUP, fostered collaborative interactions between residents and planning experts and supported residents to build and leverage collective power within planning processes. The participatory planning approach applied in the Stewart Street ANC transformed – and at times unintentionally reproduced – inequitable power relations within the planning process. Importantly, we found that GreenUP was a vital power broker between marginalized residents and more formal power holders, and successfully supported residents to voice their collective visions within professionalized planning contexts.
Dialogues on the Threshold: Dialogical Learning for Humanism and Justice
Authors: Kumagai Arno K. , Richardson Lisa , Khan Sarah , Kuper Ayelet 
Published: June 2018

Given the constant pressures of overflowing clinics, hospital wards, and emergency departments; shortened duty hours; and increased accreditation requirements, overburdened clinician teachers ask, “How does one teach for humanism and justice?” How does one step away—even momentarily—and focus teaching on the individual in front of us, the person who requires our attention and care? This approach must not only involve content (the patient’s perspective of illness, social context, and life story) but also must be tightly linked with the ways in which these lessons in living are learned and taught. In this article, the authors propose recognition and use of a style of communication that is already implicitly present in clinical conversations and that is uniquely capable of stimulating reflection on the human dimensions of medicine: that of dialogue.
Dialogue involves committing one’s whole self to communicative exchange and emphasizes interpersonal relationships and trust. Its result is often not a specific answer; rather, it is enhanced understanding through the generation of new questions and possibilities and action in implementing solutions. It requires a reorientation of the teacher–learner relationship from top-down to one of open exchange and shared authority and responsibility. In the context of professional identity development, these conversations become dialogues on the threshold of transformative change. Through an exploration of dialogical teaching, the authors envision clinical education as constantly stepping in and out of goal-oriented discussions and reflective dialogues, all with the overall goal to educate physicians who practice with excellence, compassion, and justice.