bluuebunny/crossref_metadata_2025 huggingface dataset:
Is hydrogen Asia's new energy commodity? Opportunities and challenges for Australia
Authors: Low David , Rodger Angus , Gallagher Benjamin , Sharma Prakash
Published: May 2020

Can hydrogen really be the next big energy disruptor? The technological challenges are significant and have suppressed its presence in the energy transition story thus far, but this is changing fast. The hydrogen market faces a chicken-and-egg conundrum. Demand growth remains limited, hindered by uncertainty over supply and cost. But investment in hydrogen supply is restricted by ambiguity over its role in the future energy mix. Nonetheless, government policy and funding in Japan, China and Korea is creating new demand centres. Will the breakthrough be in power generation, transportation or energy storage? The costs associated with hydrogen production and transportation are its biggest hurdles. But new technologies around liquid organic hydrogen carriers and ammonia are emerging. How is this hydrogen+ philosophy evolving, and could it be a future competitive advantage? Over the past decade, we have already seen how new technology has rapidly reduced other renewable energy costs. We outline our view on whether the same could happen with hydrogen. So, where does Australia fit into this picture, and what is its competitive advantage? Australia is well endowed with natural resources, many of which can reliably generate renewable energy. And with numerous ongoing hydrogen pilot programs, it is uniquely positioned to innovate and export green hydrogen know-how. Can Australia become the global laboratory for hydrogen supply-chain technology? Local upstream companies could be catalysts for change, given their existing producer–supplier relationships across north-eastern Asia. What role could hydrogen play in the future upstream portfolio?
Implications of accurate geomechanical modelling and systematic core testing for sanding evaluation and sand control decisions – a case study from Perth Basin
Authors: Asadi Sadegh , Khaksar Abbas , Fabian Mark , Xiang Roger , Dewhurst David N. , Delle Piane Claudio
Published: May 2020

Accurate knowledge of in-situ stresses and rock mechanical properties are required for a reliable sanding risk evaluation. This paper shows an example, from the Waitsia Gas Field in the northern Perth Basin, where a robust well centric geomechanical model is calibrated with field data and laboratory rock mechanical tests. The analysis revealed subtle variations from the regional stress regime for the target reservoir with significant implications for sanding tendency and sand management strategies. An initial evaluation using a non-calibrated stress model indicated low sanding risks under both initial and depleted pressure conditions. However, the revised sanding evaluation calibrated with well test observations indicated considerable sanding risk after 500 psi of pressure depletion. The sanding rate is expected to increase with further depletion, requiring well intervention for existing producers and active sand control for newly drilled wells that are cased and perforated. This analysis indicated negligible field life sanding risk for vertical and low-angle wells if completed open hole. The results are used for sand management in existing wells and completion decisions for future wells. A combination of passive surface handling and downhole sand control methods are considered on a well-by-well basis. Existing producers are currently monitored for sand production using acoustic detectors. For full field development, sand catchers will also be installed as required to ensure sand production is quantified and managed.
The next generation of risk-based inspection for coal seam gas wells
Authors: Collins Scott , Everson Joel
Published: May 2020

The coal seam gas (CSG) industry presents some unique mechanical integrity and assurance challenges, in particular: (1) the large well count (thousands), many of which are not identical (in design, process, equipment and layout), and hence have varying inspection requirements; (2) the geographic spread of wells within a field; (3) relying heavily on inspection to confirm equipment condition; (4) significant water and sand production; and (5) rapidly changing process conditions over the life of the well. One particular challenge for many operators is the potential for loss of containment in well-site pressure equipment from very high erosion rates. This, combined with the large asset count, makes physical inspection of each component to ensure equipment condition a challenging and costly task. So, what can a business do to develop an adaptive maintenance strategy to address changing process conditions, allowing them to intervene proactively before a failure occurs and maximising the opportunity to lengthen inspection intervals and reducing inspection costs on low-risk assets? One CSG operator, in conjunction with a leading integrity management service provider, has developed and implemented a dynamic digital twin of the physical condition of their assets by combining live production, monitoring and inspection data, allowing the current and future condition of equipment to be modelled and a risk-based inspection (RBI) strategy that is evergreen and reacts to the changing process conditions. The system built on the NEXUS Integrity Centre platform uses several different predictive models to prioritise assets and components for inspection using live process data and a consistent RBI approach across all static pressure equipment, essentially providing a live digital representation of the current asset condition, the essence of a digital twin. The system provides a prioritised list of assets requiring inspection before the planned maintenance strategy while also highlighting opportunities to extend inspection intervals and thus take advantage of the potential reduction in on-going maintenance costs.
Re-evaluation of depositional models for the lower Permian Patchawarra Formation, Cooper Basin, South Australia: implications for petroleum exploration
Authors: Wainman Carmine , McCabe Peter
Published: May 2020

The Late Carboniferous–Triassic Cooper Basin is Australia’s most prolific onshore petroleum province. The lower Permian Patchawarra Formation, which is up to 680 m thick and consists of up to 10% coal, is a major exploration target in the basin. Eighteen cores through the formation have been logged to re-evaluate the existing fluviolacustrine depositional model. The siliciclastics form fining- and coarsening-upward sequences that are 1–10 m thick. They are predominately fine-grained with abundant lenticular bedding, wavy bedding and thinly interlaminated siltstones and clays resembling varves. Granules and pebbles, interpreted as dropstones, are present throughout the formation. Coal beds are up to 60 m thick and rich in inertinite. Other than the coal beds, there is little evidence of the establishment of terrestrial conditions: roots are rare and there are no siliciclastic palaeosols. The siliciclastics are interpreted as the deposits of a large glaciolacustrine system, with the fining-upward successions deposited in subaqueous channels cut by hyperpycnal flows and the coarsening-upward successions deposited as overbank splays between those channels. Hyperpycnal flows may have resulted from sediment-laden cold water emanating from glacially-fed rivers, similar to those seen in many large glacial lakes in high latitudes and altitudes today. Much of the coal is interpreted as the accumulation of peats from floating mires that covered large parts of the glaciolacustrine system at certain time intervals. The high inertinite content of many coals is interpreted as the decay of organic matter within the floating mire. These new interpretations have the potential to enhance reservoir characterisation within the basin.
Smashing the stigma in mental health – a strategic blueprint for change
Authors: Feringa Anna , Wentzel Nada
Published: May 2020

The oil and gas industry is known for its strong commitment to safety which often focuses on process safety, physical safety and behaviour, with little attention to mental health. Mental health is a growing issue. It impacts decision making, increases the likelihood of human error which can result in the loss of lives and environmental destruction. If not addressed properly, it can cause excessive stress, anxiety, depression, trauma or even suicide. Mental health is one of the biggest risks to the oil and gas industry today. Research shows that one in five workers suffer from a mental health issue at some point in time during their lives. Experts believe these statistics are higher for workers in the oil and gas industry due to the nature of the work – long working hours, isolation, being away from friends and family, feeling under high pressure to avoid mistakes due to the potentially devastating consequences and being a male dominated industry. Investment in mental health is currently often limited to Employee Assist Programs, RUOK days or wellbeing initiatives. What is needed is a total strategic and integrated approach which organisations can customise to their specific needs, distinct from a series of individual initiatives. By learning from leading practices, other industries and extending experience from building effective safety cultures within the oil and gas industry to mental health, a total strategic approach is presented which will enable organisations build their own customised blueprint and smash the stigma surrounding mental health.
Redefining the relationship between the oil company and its vendor
Authors: Davies Clare E. , Allen Tristan , Dempsey Craig E. , Mishra Kunal
Published: May 2020

During 2016, BHP committed to produce a petroleum systems model for the complete Exmouth Sub-basin area; such a model would require knowledge of the sub-basin’s evolution through time and a uniquely qualified team to deliver within the agreed time frame. Existing seismic coverage rarely illuminated the deepest portion of the basin; however, through a collaboration with WesternGeco Multiclient, a basin-wide broad-band 3D seismic survey was acquired to underpin the new study to ensure its success. To facilitate this acquisition and the development of the petroleum systems model, BHP and WesternGeco Multiclient created a virtual world-wide team to combine their expertise of seismic acquisition and processing, seismic and potential field interpretation, geochemistry and basin modelling. Although the work was coordinated in Perth (WA, Australia), team members were located in Australia, Europe and the US, where particular specific expertise was located. Both companies made a commitment before the commencement of the project to have open exchange of data, interpretations and knowledge transfer, with one project coordinator. Although individual contributors were located in Australia, Europe and the US, monthly video or telephone coordination meetings combined with weekly meetings between individual specialists, as needed, allowed for the project to be completed to the highest technical quality within the scheduled time frame. The collaborative interpretation from this new seismic data and the resulting petroleum system model has created significant value for both companies, with insights benefiting the industry as a whole as a result of this redefined relationship between company and vendor.
Dietary supplementation with protected calcium effects production and egg quality of Hy-line brown laying hens
Authors: Shi H. , Lee K. Y. , Kim I. H.
Published: May 2020

Context
Currently, the commonly used dietary calcium sources are not sufficiently bioavailable to be used for eggshell formation or bone health in laying hens. Protected calcium, a blend of calcium and medium-chain fatty acids with matrix coating, may exert an effective absorption and metabolism ability for calcium consumption in the laying hen.

Aims
The present study was conducted to evaluate the effects of protected-calcium supplementation on egg production, egg quality, and serum calcium and phosphorus concentrations in laying hens.

Methods
In total, 144 Hy-line brown laying hens (25 weeks old) were randomly allotted to three treatments (8 replicates with 6 hens, 1 hen per cage) in a 10-week trial. Treatments consisted of corn–wheat–soybean meal-based basal diet with limestone (coarse limestone:fine limestone = 50:50) as a calcium source (CON) or basal diet supplemented with 0.5% (P1) or 1% (P2) protected calcium in substitution for an equal quantity of coarse limestone. Data were statistically analysed using linear and quadratic contrast with the GLM procedure of SAS. Probability values of <0.05 indicate significance.

Key results
At Weeks 31–33 and 35, the cracked-egg rates were lower in the P1 and P2 groups than in the CON group (P < 0.05; linear, P < 0.05) and, at Weeks 29 and 34, the cracked-egg rates in the P2 group were also significantly (P < 0.05) decreased. At Weeks 26, 30 and 32, the Haugh units in the P2 group were significantly (P < 0.05) higher than those in the CON group. In addition, eggshell strength was increased significantly (P < 0.05) in the P2 group at Weeks 26, 27 and 31–35. The serum calcium concentration of the P2 group was significantly (P < 0.05) greater than that of the CON group in the morning.

Conclusions
In conclusion, a replacement of limestone with 1% protected calcium can increase eggshell quality.

Implications
Protected-calcium supplementation can be used in practice for decreasing the breakage of eggs.
Analysis of Nanoconfined Protein Dielectric Signals Using Charged Amino Acid Network Models
Authors: Pacini Lorenza , Bourgeat Laetitia , Serghei Anatoli , Lesieur Claire
Published: May 2020

Protein slow motions involving collective molecular fluctuations on the timescale of microseconds to seconds are difficult to measure and not well understood despite being essential to sustain protein folding and protein function. Broadband dielectric spectroscopy (BDS) is one of the most powerful experimental techniques to monitor, over a broad frequency and temperature range, the molecular dynamics of soft matter through the orientational polarisation of permanent dipole moments that are generated by the chemical structure and morphological organisation of matter. Its typical frequency range goes from 107 Hz down to 10−3 Hz, being thus suitable for investigations on slow motions in proteins. Moreover, BDS has the advantage of providing direct experimental access to molecular fluctuations taking place on different length-scales, from local to cooperative dipolar motions. The unfolding of the cholera toxin B pentamer (CtxB5) after thermal treatment for 3h at 80°C is investigated by BDS under nanoconfined and dehydrated conditions. From the X-ray structure of the toxin pentamer, network-based models are used to infer the toxin dipoles present in the native state and to compute their stability and dielectric properties. Network analyses highlight three domains with distinct dielectric and stability properties that support a model where the toxin unfolds into three conformations after the treatment at 80°C. This novel integrative approach offers some perspective into the investigation of the relation between local perturbations (e.g. mutation, thermal treatment) and larger scale protein conformational changes. It might help ranking protein sequence variants according to their respective scale of dynamics perturbations.
The effect of animacy on object pronoun distinctions in L2 Spanish
Authors: Olsen Michael Kevin , Juffs Alan
Published: May 2020

When acquiring Spanish object pronouns (OP), English-speaking second language (L2) learners must learn the variety of forms available, word order, and case distinctions. The acquisition of case distinctions in particular is an aspect that has not been thoroughly investigated.Zyzik (2006)showed, through production tasks, that English-speaking L2Spanish learners overgeneralize the dative form to accusative contexts when the referent is animate. This study investigates how L2learners use animacy (human, animal, and inanimate object) instead of case marking as cues to interpret and produce L2Spanish object pronouns. Data from an interpretation task and a fill-in-the-blank production task were collected from 121 intermediate to advanced levels of Spanish learners. Results from linear mixed effects models reveal that learners show effects of the influence of animacy on object pronoun distinction in comprehension as well as production. A key new finding is that learners use the dative form with human referents, reserving accusative forms for animals and inanimate referents. These results provide evidence that animacy cues strongly influence L2Spanish learners in the formation of their OP paradigm, especially at lower-proficiency levels. As proficiency increases, L2learners begin to rely on case cues to distinguish Spanish OPs.
Notes on plurality and the count/mass distinction in Guató
Authors: Godoy Gustavo , Alves Walter
Published: May 2020

Guató is an isolate, nearly extinct indigenous language. Only two elders, VS and EF, remember it. They both live in the Pantanal (State of Mato Grosso do Sul, Brazil). Despite the decline in the number of speakers due to farmers’ invading land that once belonged to Indigenous people, new research has been conducted, resulting in a description of some aspects of its grammar. This paper shows the distribution of plural affixes, as used by EF. In Guató, all nouns combine directly with numerals, whether these nouns are mass or count. The language grammaticalizes the mass-count distinction only in the interpretation of quantifiers.
Individuation, counting, and measuring in the grammar of Kadiwéu
Authors: Sandalo Filomena
Published: May 2020

This work approaches some grammatical differences in the linguistic expression of counting, measuring, aggregating, and quantity comparison and partition in Kadiwéu, a classifier language spoken in Brazil. This paper brings evidence via the grammar of comparison and partition that the counting/measuring distinction is a genuine grammatical distinction. This work also shows that aggregate nouns in Kadiwéu pattern grammatically neither with substance nouns nor with naturally atomic object nouns. That is, Kadiwéu has a specific grammatical expression for groups as atoms.
Maxakalí has suppletion, numerals and associatives but no plurals
Authors: Nevins Andrew , Coelho da Silva Mário
Published: May 2020

The Maxakalí language lacks additive plurals (akin to dog-s) on nouns, but has associative plurals, and a large set of suppletive verbs that indicate whether the internal argument is plural or not. Although it has no plural marking, Maxakalí distinguishes between count nouns and mass nouns. The former can be followed by numerals, while the latter must be coerced or occur with container words. Only count nouns can be distinguished between singular and plural with verbal number. Mass nouns always require plural verbal number. Count nouns are compatible with words like ‘many’ indicating cardinality, while mass nouns are compatible with words like ‘big’ for volume. Granulated substances have variable behavior, depending on whether treated as a whole or as several individuated items. Numerals in Maxakalí show an unusual pattern, whereby 1–3 are treated as unaccusative verbs, and 4 and up, being loanwords, are treated as unergative verbs.
Number morphology in Panará
Authors: Bardagil Bernat
Published: May 2020

In this paper I present a description of number in Panará, with singular, dual and plural, and discuss the mass-count properties of Panará nouns. I also describe an until now unattested instance of omnivorous dual in Panará, where one dual morpheme can map to one or more arguments.
Count and mass nouns in Patxohã
Authors: Bomfim Anari , Lima Suzi
Published: May 2020

This paper describes the count/mass distinction in Patxohã, a revitalized language spoken in Bahia and Minas
Gerais, Brazil. We observe that only count nouns can be directly combined with numerals and that only count nouns can co-occur
with plural determiners. Furthermore, only count nouns can be combined with size adjectives. As for quantifiers, we observe that
at least one quantifier in the language (nitxi) can be combined with count and mass nouns, but trigger different
interpretations depending on the noun it is combined with. We also discuss the use of container phrases in counting and measuring
contexts.
Count-mass distinction in Sakurabiat
Authors: Vilacy Galucio Ana , Nascimento Costa Carla
Published: May 2020

Acknowledging the fact that not all languages seem to distinguish grammatically between mass nouns and count
nouns, this paper aims to provide information on whether or not the count-mass distinction is expressed in the Sakurabiat
language, which belongs to the Tuparic branch of the Tupian linguistic family. The paper presents a brief survey of the
grammatical properties associated with notional mass and notional count nouns in Sakurabiat. The properties of constructions with
nouns and numerals are described and compared to constructions with pluralized nouns and numerals. The question of individual
versus event quantification with numerals, and the role played by quantifiers and comparatives are also analyzed. The Sakurabiat
data contributes to the investigation about the expression (or non-expression) of a count-mass distinction in underrepresented and
understudied languages.
The count-mass distinction in Terena
Authors: Sanchez-Mendes Luciana , Quadros Gomes Ana Paula , Julio Aronaldo
Published: May 2020

This paper examines the count-mass distinction in Terena (Aruák, Brazil) by focusing on plural marking availability, numeral and quantifier distribution and cardinal versus volume interpretation in quantity judgment tests. The data collected from the initial research of these features in Terena reveals the relevancy of the count-mass distinction in the language with some signature properties: (i) only count nouns can be directly combined with numerals; (ii) only count nouns can be used with the quantifier êno with the interpretarion of many individuals rather than a large quantity; and finally, (iii) only count nouns can express cardinality of individuals in a comparative sentence such as John has more N than Peter. Plural morpheme distribution is unsuitable for distinguishing count from mass nouns (such as in English) since mass nouns can be pluralized in Terena, provided noun denotations have individuals to allow for number rather than volume quantity interpretation.
The nominal system in Wapishana (Aruák), preliminary results
Authors: Guerra Vicente Helena , Sanchez-Mendes Luciana , Pires De Oliveira Roberta , Lunguinho Marcus Vinicius , Leandro Wendy Mary
Published: May 2020

The aim of this paper is to provide a preliminary investigation into the nominal system of Wapishana, focusing on the count vs. mass distinction, which is grammatically encoded in this language. Evidence for this distinction can be identified in the constraints imposed by the presence of numerals, number marking, and quantifiers. Nouns such as wyn ‘water’ do not combine with numerals, whereas other words such as baydkury ‘jaguar’ do. The suffixation of the morpheme -nau/-nhau to express plurality seems to be optional and may even be blocked by the presence of numerals. The language exhibits specialized quantifiers for count, liquid, and non-liquid mass nouns.
The count/mass distinction in Ye’kwana
Authors: Coutinho Costa Isabella
Published: May 2020

This paper presents a description of the count/mass distinction in Ye’kwana, a Cariban language spoken in Brazil and Venezuela. The methodology used was based on Lima & Rothstein’s questionnaire this volume). The data shows that Ye’kwana is a bare noun language and that mass and count nouns can be pluralized. However, numerals need a container phrase in order to be directly combined with mass nouns. Nominal quantifierswannaandoojecan be directly combined with count and mass nouns, but they show different interpretations.
“Gracias pana”
Authors: Lower Amanda
Published: May 2020

Compliments and compliment responses are a frequent topic of study in face-to-face interactions (see Chen 2010 for an overview), and are gaining traction in online interactions. This study builds on works on compliment responses online; particularly work by Placencia, Lower, and Powell (2016), by examining compliment responses given by Ecuadorian males on Facebook (FB). The sole focus here is male behavior: how males respond to compliments from other males. Largely ignored in compliment research as a whole, this study demonstrates that Ecuadorian males frequently engage in compliment response behavior on FB, and, appear to be guided by face needs and constraints when responding. Despite the ubiquitous nature of emoticons in online communications, their use in compliment responses by Ecuadorian males on FB was totally absent.
Complimenting behavior in Spanish political discourse on Twitter
Authors: Pano Alamán Ana
Published: May 2020

This study explores complimenting behavior in interactions between Spanish politicians and citizens on Twitter. It adopts a corpus-based methodology, using both quantitative and qualitative analysis to identify the topics which give rise to compliments being paid, the linguistic strategies adopted by users in their complimentary replies to politicians, and the functions of such compliments. The results show that users frequently pay compliments on the basis of performance and ability, and combine explicit and implicit compliments with congratulatory messages, requests, and advice. Finally, in terms of social functions, compliments in this context appear to enhance both the affiliative and the autonomy face of the interactants.
Uniform straw-like cell architecture for three-dimensional cell–cell communication assay
Authors: Inubushi Yusaku , Sakaguchi Yoshiki , Tachibana Akira
Published: May 2020

We fabricated uniform straw-like cell architecture with central lumen using a suture thread within 1 h. The architecture consisting of cancer cells and mature adipocyte was used for cell–cell communication assay, although mature adipocyte could not form spontaneous multi-cellular spheroids. Using the system, it is possible to investigate three-dimensional cell–cell communication as an alternative to animal experiments.

Abbreviations

EB: embryoid body; 2D: two-dimension; 3D: three-dimension; PBS: phosphate buffered saline
Alliances, oppositions and the nature of ephemeral identities in ethnically diversified Basque education (Alianzas, oposiciones y la naturaleza de las identidades efímeras en el sistema educativo vasco étnicamente diverso)
Authors: Pérez-Izaguirre Elizabeth , Roman Gorka
Published: May 2020

This study is part of a broader ethnographically based research project analysing interethnic student interactions in the Basque education system. It focuses on the nature of interethnic student alliances and oppositions within Basque education, which act as identity producers. The research methods include documentary analysis, participant observation, 36 semi-structured interviews and four focus groups. Results indicate that students who had a migrant background allied to oppose learning Basque. Alliances were often transitory and constituted ephemeral identities that were dissolved after such opposition took place. This paper points to the constitutive momentum that leads to the creation of transitory alliances, and its discussion contributes to the theory of identity, in line with the results of the case study.
Ab initio electronic structure and prospects for the formation of ultracold calcium–alkali-metal-atom molecular ions
Authors: Zrafi Wissem , Ladjimi Hela , Said Halima , Berriche Hamid , Tomza Michał
Published: May 2020

Experiments with cold ion–atom mixtures have recently opened the way for the production and application of ultracold molecular ions. Here, in a comparative study, we theoretically investigate ground and several excited electronic states and prospects for the formation of molecular ions composed of a calcium ion and an alkali-metal atom: CaAlk+ (Alk = Li, Na, K, Rb, Cs). We use a quantum chemistry approach based on non-empirical pseudopotentials, operatorial core-valence correlation, large Gaussian basis sets, and full configuration interaction method for valence electrons. Adiabatic potential energy curves, spectroscopic constants, and transition and permanent electric dipole moments are determined and analyzed for the ground and excited electronic states. We examine the prospects for ion-neutral reactive processes and the production of molecular ions via spontaneous radiative association and laser-induced photoassociation. After that, spontaneous and stimulated blackbody radiation transition rates are calculated and used to obtain radiative lifetimes of vibrational states of the ground and first-excited electronic states. The present results pave the way for the formation and spectroscopy of calcium–alkali-metal-atom molecular ions in modern experiments with cold ion–atom mixtures.
Microwave-assisted synthesis of ZnO nanoflakes: structural, optical and dielectric characterization
Authors: Yalcin Mesut
Published: May 2020

In this study, we produced ZnO nanoflakes (ZnO-Nfs) by using microwave-assisted techniques. The structural properties of ZnO-Nfs were analyzed by x-ray diffraction (XRD) technique, Raman scattering spectroscopy and field-emission scanning microscopy (FESEM). The Crystallite size (D) and lattice constants of ZnO-Nfs were calculated. The optical properties of ZnO-Nfs were investigated by using UV-visible diffuse reflectance spectrum and photoluminescence (PL) spectra. Also, dielectric constants of ZnO-Nfs were calculated as related to the refractive index (n) an extinction coefficient (k).
14-3-3 targets keratin intermediate filaments to mechanically sensitive cell–cell contacts
Authors: Mariani Richard A. , Paranjpe Shalaka , Dobrowolski Radek , Weber Gregory F.
Published: May 2020

14-3-3 serves as a major regulator of keratin intermediate filament dynamics in vivo. Migratory mesendoderm tissue of the Xenopus embryo is used to show that the dynamic reorganization of keratin filaments, a consequence of force on cell-cell adhesions, is mediated by a novel association between 14-3-3 and Keratin 19.
Msp1 cooperates with the proteasome for extraction of arrested mitochondrial import intermediates
Authors: Basch Marion , Wagner Mirjam , Rolland Stéphane , Carbonell Andres , Zeng Rachel , Khosravi Siavash , Schmidt Andreas , Aftab Wasim , Imhof Axel , Wagener Johannes , Conradt Barbara , Wagener Nikola
Published: May 2020

During compromised protein import at the mitochondrial outer membrane, Msp1 and the proteasome are required for maintaining organellar biogenesis. Msp1 cooperates with the proteasome, which drives the extraction of arrested and mislocalized proteins at the import pore.
Centriole foci persist in starfish oocytes despite Polo-like kinase 1 inactivation or loss of microtubule nucleation activity
Authors: Pierron Marie , Kalbfuss Nils , Borrego-Pinto Joana , Lénárt Péter , Gönczy Pierre
Published: May 2020

Centrioles are removed from oocytes in most metazoan species through incompletely understood mechanisms. Investigating this question in starfish oocytes, we find that maternal centrioles persist with impaired Plk1 or without MTOC activity, in contrast to the situation in Drosophila, thereby uncovering diversity in centriole removal mechanisms.
Multivariate analysis reveals activation-primed fibroblast geometric states in engineered 3D tumor microenvironments
Authors: Venkatachalapathy Saradha , Jokhun Doorgesh Sharma , Shivashankar G. V.
Published: May 2020

We mimic the tumor-stroma using 3D collagen tissue models of malignant breast cancer spheroids and fibroblasts to understand the factors that contribute to the selective activation of subsets of the stromal fibroblast population. Multiparametric analysis of single cells revealed that such selective activation is coupled to cell geometric states.
Importin binding mediates the intramolecular regulation of anillin during cytokinesis
Authors: Beaudet Daniel , Pham Nhat , Skaik Noha , Piekny Alisa
Published: May 2020

Cytokinesis separates a cell into two daughters at the end of mitosis. We show that anillin, a key component of the cytokinesis machinery, is controlled by importin binding. Active RhoA and importins coordinate to regulate neighboring domains on anillin to stabilize a conformation that is favorable for cortical recruitment.
Aurora B and condensin are dispensable for chromosome arm and telomere separation during meiosis II
Authors: Berthezene Julien , Reyes Céline , Li Tong , Coulon Stéphane , Bernard Pascal , Gachet Yannick , Tournier Sylvie
Published: May 2020

In fission yeast, Aurora B localizes at telomeres during meiosis I and promotes telomere and chromosome arm separation as observed in mitosis. Oppositely, in meiosis II, Aurora B and condensin appear dispensable for telomere and chromosome arm separation illustrating the critical differences in the control of chromosome segregation between mitosis and meiosis II.
Cellular homeostasis in theDrosophilaretina requires the lipid phosphatase Sac1
Authors: Griffiths Nigel W. , Del Bel Lauren M. , Wilk Ronit , Brill Julie A.
Published: May 2020

Using a temperature-sensitive allele, we find that the phosphatidylinositol 4-phosphatase Sac1 is required for ER homeostasis, endosomal degradation, and basal patterning in the developing Drosophila retina.
Solid Tumor Metastases to the Pancreas Diagnosed Using Fine-Needle Aspiration
Authors: Hou Tieying , Stewart John M , Lee Jeffrey H , Gan Qiong
Published: May 2020

Objectives

Solid tumor metastases to the pancreas are rare, and only limited literature on the topic is available. In this retrospective study, we reviewed 107 cases of solid tumor metastases to the pancreas diagnosed by fine-needle aspiration (FNA) from 2005 to 2019.

Methods

Information including the patients’ clinical histories, radiologic and pathologic findings, treatments, and follow-up were collected.

Results

The mean age of the patients was 62.4 years. The mean tumor size was 2.64 cm with even distribution throughout the pancreas (head, neck and body, and tail). The most common primary site was the kidney, followed by the lung, skin, and breast and the gynecologic, gastrointestinal, and genitourinary tracts. The most common tumor type was carcinoma, followed by melanoma and sarcoma. In comparison to patients with nonkidney primary cancers, those with primary renal cell carcinoma had a longer median interval between primary diagnosis and metastasis (8.5 vs 4.0 years; P < .01), less often had metastasis outside the pancreas (38% vs 74%; P < .01), and had a significantly longer 5-year survival rate (65.7% vs 24.8%; P < .01).

Conclusions

FNA plays a crucial role in diagnosing metastases to the pancreas. Metastases originating from kidney and nonkidney primary tumors have distinct clinicopathologic features and prognoses.
Racial/Ethnic Disparities in the Relationship of Alcohol-Related Injury and Perceived Driving Under the Influence from Hours of Exposure to High Blood Alcohol Concentration: Data From Four US National Alcohol Surveys (2000–2015)
Authors: Cherpitel Cheryl J , Williams Edwina , Ye Yu , Kerr William C
Published: May 2020

Aims

To analyze racial/ethnic disparities in risk of two alcohol-related events, alcohol-related injury and self-reported perceived driving under the influence (DUI) from hours of exposure to an elevated blood alcohol concentration (BAC).

Methods

Risk curves for the predicted probability of these two outcomes from the number of hours of exposure to a BAC ≥ 0.08 mg% in the past year were analyzed separately for whites, blacks and Hispanics in a merged sample of respondents from four US National Alcohol Surveys (2000–2015).

Results

Hours of exposure to a BAC ≥ 0.08 showed a stronger association with perceived DUI than with alcohol-related injury for all racial/ethnic groups. Greater risk was found for whites than blacks or Hispanics for outcomes at nearly all BAC exposure levels, and most marked at the highest level of exposure. Risk of both outcomes was significant for whites at all exposure levels, but small for alcohol-related injury. Little association was found for alcohol-related injury for blacks or Hispanics. For perceived DUI, risk for blacks was significantly elevated at lower levels of exposure, while risk for Hispanics was significantly elevated beginning at 30 h of exposure.

Conclusions

Findings showed racial/ethnic differences in risk of alcohol-related injury and perceived DUI from hours of exposure to elevated BAC. Risk increased at relatively low levels of exposure to a BAC ≥ 0.08, especially for whites, highlighting the importance of preventive efforts to reduce harmful outcomes for moderate drinkers.
Genetic variation in early fitness traits across European populations of silver birch (Betula pendula)
Authors: Solé-Medina Aida , Heer Katrin , Opgenoorth Lars , Kaldewey Phillip , Danusevicius Darius , Notivol Eduardo , Robledo-Arnuncio Juan J , Ramírez-Valiente José A
Published: May 2020

Given that the ecological niche of tree species is typically narrower for earlier life stages, intraspecific genetic variation at early fitness traits may greatly influence the adaptive response of tree populations to changing environmental conditions. In this study, we evaluated genetic variation in early fitness traits among 12 populations of Betula pendula from a wide latitudinal range in Europe (41–55°N). We first conducted a chamber experiment to test for population differences in germination and the effect of pre-chilling treatment on seed dormancy release. We then established three common gardens spread across the species latitudinal range in order to evaluate levels of quantitative genetic variation and genotype-by-environment interaction at different early life traits. Our results showed significant variation in chamber germination rates among populations (0–60 %), with southern populations exhibiting lower germination. Pre-chilling treatments did not generally improve germination success. Population seedling emergence rates in the field were correlated with chamber germination rates, though being an order of magnitude lower, with an average ranging from 0 to 1.3 % across gardens. Highly significant variation was found in field emergence rates among populations, and between seed-crop years within populations, but not among families within populations. Populations differed in seedling height, diameter, slenderness and budburst date, with significant among-family variation. Population latitude was positively associated with chamber germination rate and with seedling emergence rate in one of the central field sites. Overall, genetic, environmental and demographic factors seem to influence the observed high levels of variation in early fitness traits among B. pendula populations. Our results suggest limited regeneration capacity for the study species under drier conditions, but further field trials with sufficient replication over environments and seed crops will improve our understanding of its vulnerability to climate change.
Martian oceans
Authors: Dickeson Zachary I , Davis Joel M
Published: May 2020

Zachary Dickeson and Joel Davis review current morphological observations and future questions about the existence, origin and fate of ancient oceans on Mars.
Space for girls
Authors: Bowler Sue
Published: May 2020

The RAS 200 project in partnership with Girlguiding UK and the UK Space Agency is proving successful for all ages, as Sue Bowler reports.
Spathial: an R package for the evolutionary analysis of biological data
Authors: Gardini Erika , Giorgi Federico M , Decherchi Sergio , Cavalli Andrea
Published: May 2020

A primary problem in high-throughput genomics experiments is finding the most important genes involved in biological processes (e.g. tumor progression). In this applications note, we introduce spathial, an R package for navigating high-dimensional data spaces. spathial implements the Principal Path algorithm, which is a topological method for locally navigating on the data manifold. The package, together with the core algorithm, provides several high-level functions for interpreting the results. One of the analyses we propose is the extraction of the genes that are mainly involved in the progress from one state to another. We show a possible application in the context of tumor progression using RNA-Seq and single-cell datasets, and we compare our results with two commonly used algorithms, edgeR and monocle3, respectively.

Availability and implementation

The R package spathial is available on the Comprehensive R Archive Network (https://cran.r-project.org/web/packages/spathial/index.html) and on GitHub (https://github.com/erikagardini/spathial). It is distributed under the GNU General Public License (version 3).

Supplementary information

Supplementary data are available at Bioinformatics online.
SVJedi: genotyping structural variations with long reads
Authors: Lecompte Lolita , Peterlongo Pierre , Lavenier Dominique , Lemaitre Claire
Published: May 2020

Motivation

Studies on structural variants (SVs) are expanding rapidly. As a result, and thanks to third generation sequencing technologies, the number of discovered SVs is increasing, especially in the human genome. At the same time, for several applications such as clinical diagnoses, it is important to genotype newly sequenced individuals on well-defined and characterized SVs. Whereas several SV genotypers have been developed for short read data, there is a lack of such dedicated tool to assess whether known SVs are present or not in a new long read sequenced sample, such as the one produced by Pacific Biosciences or Oxford Nanopore Technologies.

Results

We present a novel method to genotype known SVs from long read sequencing data. The method is based on the generation of a set of representative allele sequences that represent the two alleles of each structural variant. Long reads are aligned to these allele sequences. Alignments are then analyzed and filtered out to keep only informative ones, to quantify and estimate the presence of each SV allele and the allele frequencies. We provide an implementation of the method, SVJedi, to genotype SVs with long reads. The tool has been applied to both simulated and real human datasets and achieves high genotyping accuracy. We show that SVJedi obtains better performances than other existing long read genotyping tools and we also demonstrate that SV genotyping is considerably improved with SVJedi compared to other approaches, namely SV discovery and short read SV genotyping approaches.

Availability and implementation

https://github.com/llecompte/SVJedi.git

Supplementary information

Supplementary data are available at Bioinformatics online.
ProteinFishing: a protein complex generator within the ModelX toolsuite
Authors: Cianferoni Damiano , Radusky Leandro G , Head Sarah A , Serrano Luis , Delgado Javier
Published: May 2020

Accurate 3D modelling of protein–protein interactions (PPI) is essential to compensate for the absence of experimentally determined complex structures. Here, we present a new set of commands within the ModelX toolsuite capable of generating atomic-level protein complexes suitable for interface design. Among these commands, the new tool ProteinFishing proposes known and/or putative alternative 3D PPI for a given protein complex. The algorithm exploits backbone compatibility of protein fragments to generate mutually exclusive protein interfaces that are quickly evaluated with a knowledge-based statistical force field. Using interleukin-10-R2 co-crystalized with interferon-lambda-3, and a database of X-ray structures containing interleukin-10, this algorithm was able to generate interleukin-10-R2/interleukin-10 structural models in agreement with experimental data.

Availability and implementation

ProteinFishing is a portable command-line tool included in the ModelX toolsuite, written in C++, that makes use of an SQL (tested for MySQL and MariaDB) relational database delivered with a template SQL dump called FishXDB. FishXDB contains the empty tables of ModelX fragments and the data used by the embedded statistical force field. ProteinFishing is compiled for Linux-64bit, MacOS-64bit and Windows-32bit operating systems. This software is a proprietary license and is distributed as an executable with its correspondent database dumps. It can be downloaded publicly at http://modelx.crg.es/. Licenses are freely available for academic users after registration on the website and are available under commercial license for for-profit organizations or companies.

Contact

javier.delgado@crg.eu or luis.serrano@crg.eu

Supplementary information

Supplementary data are available at Bioinformatics online.
Higher Solar Irradiance Is Associated With a Lower Incidence of Coronavirus Disease 2019
Authors: Guasp Mar , Laredo Carlos , Urra Xabier
Published: May 2020

We studied the relationship between the incidence of coronavirus disease 2019 (COVID-19), demographical, and climatological measurements in different regions across the world. Lower solar irradiance and higher population density were independent predictors of greater COVID-19 outbreaks. Further studies on the potential protective effect of sunlight over COVID-19 are warranted.
Fine-Scale Position Effects Shape the Distribution of Inversion Breakpoints in Drosophila melanogaster
Authors: McBroome Jakob , Liang David , Corbett-Detig Russell
Published: May 2020

Chromosomal inversions are among the primary drivers of genome structure evolution in a wide range of natural populations. Although there is an impressive array of theory and empirical analyses that have identified conditions under which inversions can be positively selected, comparatively little data are available on the fitness impacts of these genome structural rearrangements themselves. Because inversion breakpoints can disrupt functional elements and alter chromatin domains, the precise positioning of an inversion’s breakpoints can strongly affect its fitness. Here, we compared the fine-scale distribution of low-frequency inversion breakpoints with those of high-frequency inversions and inversions that have gone to fixation between Drosophila species. We identified a number of differences among frequency classes that may influence inversion fitness. In particular, breakpoints that are proximal to insulator elements, generate large tandem duplications, and minimize impacts on gene coding spans which are more prevalent in high-frequency and fixed inversions than in rare inversions. The data suggest that natural selection acts to preserve both genes and larger cis-regulatory networks in the occurrence and spread of rearrangements. These factors may act to limit the availability of high-fitness arrangements when suppressed recombination is favorable.
Analytical spontaneous imbibition model for confined nanofractures
Authors: Zeng Fanhui , Zhang Qiang , Guo Jianchun , Zhang Yu , Ren Wenxi , Jiang Qifeng , Xiang Jianhua
Published: May 2020

The capillary spontaneous imbibition length of slick water in confined rectangular cross-sectional nanofractures is investigated in this paper. In the established model, the effective slip length, effective viscosity, wettability and nanofracture size are incorporated into the modified Hagen–Poiseuille equation. The calculated spontaneous imbibition length as a function of time, viscosity, wettability and pore size is qualitatively validated by experimental and previous theoretical Hagen–Poiseuille flow results. Our model calculation results agree well with the published experimental data. The ratio of the effective and bulk water viscosities is higher than one, and increases with an increase in the ratio of the nanofracture width to height and decreasing contact angle. The spontaneous imbibition capacity of confined water is enhanced ∼0.67–1.28 times, as determined by the Hagen–Poiseuille equation without the slip effect for various contact angles and nanofracture dimensions.
It Takes a Village to Implement a Judgment: Creating a Forum for Multi-Stakeholder Involvement in the Czech Republic
Authors: Schorm Vít Alexander
Published: May 2020

In this practice note, the Government Agent of the Czech Republic before the European Court of Human Rights and other international bodies for the protection of human rights reflects on national implementation, with the help of selected examples.