bluuebunny/crossref_metadata_2025 huggingface dataset:
Digital transformation of the oil, gas and energy value chain
Authors: Taliangis Paul
Published: May 2018

This paper looks back at 2014–2017 as a period of extraordinary transition of the international and Australian oil and gas industry, with mounting evidence that the industry and broader energy value chain is entering an era of unprecedented digital transformation. This process is expected to accelerate through 2018–2025, with profound implications for industry stakeholders. The key question is: are organisations and the industry more broadly doing enough, well enough, fast enough?
Emerging from the lows of a pronounced industry recession, and subsequent and ongoing consolidation, there is now growing, broad-based acceptance that the industry needs to engage new business models that leverage modern digital technology to reform productivity and broader industry performance. However, the harsh reality is that other industries are delivering superior results, faster, which is driving a need for an elevated and sustainable strategic response.
This paper seeks to illustrate the digital links that must be established along the full value chain between data access and management, predictive analytics, visualisation, team collaboration and communication technology. The digital links are enabled by internet connectivity and cloud-based infrastructure, which presents an opportunity for organisations of all sizes to realise benefits along the complete chain.
This paper is structured in four parts:
• The strategic context – what is driving the need to engage in digital transformation?
• The digital transformation value proposition – what value can be achieved?
• Case studies – what are examples of digital transformation?
• Key learnings – what should we note from thousands of global digital initiatives underway along the energy oil, gas and energy value chain?
The main takeaways from this study are:
• There is an unprecedented opportunity to transform the oil and gas value chain to deliver new growth and improved productivity, linking real-time data, predictive analytics, interactive visualisation and collaboration.
• Digital transformation is affordable, readily implemented and scalable to meet current and changing future needs.
• There are many powerful examples of material value add across exploration, development, operations and business management.
• Many organisations and the industry as a whole is lagging others – the industry is not doing enough, well enough, fast enough.
• The time to act/accelerate is now.
• Digital transformation is not about technology alone. Keys to success include vision, leadership, culture and data quality.
Petroleum production and development across Australia 2017
Authors: Bethune Graeme , Bethune Susan
Published: May 2018

This Petroleum Exploration Society of Australia review looks in detail at the trends and highlights for oil and gas production and development both onshore and offshore Australia during 2017. Gas production soared while oil production plummeted yet again. Liquefied natural gas (LNG) did well; 2017 was a great year for LNG and 2018 should be even better. There are stark contrasts between domestic gas on the west and east coasts. On the west coast, prices are affordable and supply relatively plentiful. On the east, prices are high and gas is in short supply. This paper canvasses these trends and makes conclusions about the condition of the oil and gas industry in Australia.
This paper relies primarily on production and reserves data compiled by EnergyQuest. In its latest review of Australian energy policy, the International Energy Agency comments yet again on the weaknesses of Australian oil and gas statistics. This paper also makes some observations on these weaknesses.
Learned behaviours lead to bone ingestion by phosphorus-deficient cattle
Authors: Dixon R. M. , Fletcher M. T. , Goodwin K. L. , Reid D. J. , McNeill D. M. , Yong K. W. L. , Petherick J. C.
Published: May 2018

Grazing cattle deficient in phosphorus (P) often seek out and chew bones, apparently to obtain dietary P. To investigate this phenomenon heifers naïve to P deficiency were either fed a P-deficient diet (LowP) or grazed P-adequate pasture (AdeqP), and preference tests examined their attraction to weathered bones or a control of wood. During Phase 1 (Days 1–145), the LowP heifers developed severe P deficiency and pica, but demonstrated little attraction to weathered bones. During Phase 2 (Days 146–155), heifers were allowed to interact with and to chew a variety of weathered bones. After this experience LowP heifers were more attracted to bones during Phase 3 (Days 156–166) than during Phase 1 (P < 0.05), and more attracted than AdeqP heifers during either phase. Subsequently, in Phase 4 (Days 167–171), LowP heifers were more attracted than AdeqP heifers (P < 0.01) to weathered bones than to a control of wood, and in Phase 5 (Days 172–176) to bones with more extended weathering. During Phase 6 (Days 177–182), attraction was reduced when bones were placed inside a cloth bag. The olfactory constituents from weathered bones were dominated by aliphatic aldehydes and ketones, consistent with long-chain fatty acid breakdown. It was concluded that attraction of P-deficient cattle to seek and ingest bones is primarily a learned response. Smell, taste and visual appearance all appear to be important cues for attraction. Pica is likely important in causing P-deficient cattle to investigate unusual materials, including bones, resulting in cattle learning by making an association between bone chewing and P ingestion.
'It's not therapy, it's gardening': community gardens as sites of comprehensive primary healthcare
Authors: Marsh Pauline , Brennan Sebrina , Vandenberg Miriam
Published: May 2018

Using a participatory research framework, researchers at the Centre for Rural Health, University of Tasmania, explored the potential of Community Gardens to function as comprehensive primary healthcare (CPHC) environments. Community gardeners, coordinators, volunteers and Neighbourhood House coordinators discussed their understandings of the health benefits of community gardens, how they contribute to broad CPHC aims and the barriers and enablers to greater CPHC contributions in the future. This research identifies therapeutic features of Community Gardens and explores the correlations between these and CPHC. It is concluded that there are strong synergies between the aims and activities of Community Gardens and CPHC. To augment the therapeutic capacity of these sites requires adequate resourcing and skill development, suitable design, funding and policy support, along with innovative partnerships with health professionals.
CASA: tracking the past and plotting the future
Authors: Gallagher M. T. , Smith D. J. , Kirkman-Brown J. C.
Published: May 2018

The human semen sample carries a wealth of information of varying degrees of accessibility ranging from the traditional visual measures of count and motility to those that need a more computational approach, such as tracking the flagellar waveform. Although computer-aided sperm analysis (CASA) options are becoming more widespread, the gold standard for clinical semen analysis requires trained laboratory staff. In this review we characterise the key attitudes towards the use of CASA and set out areas in which CASA should, and should not, be used and improved. We provide an overview of the current CASA landscape, discussing clinical uses as well as potential areas for the clinical translation of existing research technologies. Finally, we discuss where we see potential for the future of CASA, and how the integration of mathematical modelling and new technologies, such as automated flagellar tracking, may open new doors in clinical semen analysis.
Latin parsing grammars from the Carolingian age to the later Middle Ages
Authors: Reinikka Anna
Published: May 2018

This article traces the history of Latin parsing grammars from Late Antiquity up to the 14th century, focusing on the group of texts with the incipitDominus quae pars. These grammars circulating mainly north of the Alps were intended to be studied at the elementary and intermediate levels of education following the study of theDonatus minor. By asking questions about a chosen headword of each part of speech in turn, the parsing manuals offered a technique which allowed the pupil to put into practice what he had already learnt and the teacher to focus on the information he considered as relevant, including different aspects of morphology, semantics, etymology, prosody or accentuation. A number of novelties introduced into the theoretical grammars also filtered down to the lower levels of teaching. Thus, when a section on syntax began to be incorporated into pedagogical grammars in the 12th century, some syntactical concepts also entered into parsing grammars. From the 13th century onwards, elements of Aristotelian logic and physics were also integrated into the theory of the parts of speech and their syntax in theDominus quae parstexts.
The Role of Vernacular Proverbs in Latin Language Acquisition, c. 1200–1600
Authors: Geudens Christophe , Van Hal Toon
Published: May 2018

This paper examines the continuities and discontinuities in language teaching between the Middle Ages and the early modern era by drawing attention to the role of bilingual Latin-vernacular proverb collections in premodern education, a subject that has hitherto been neglected in the historiography of linguistics. The focus is on bilingual collections that are of Dutch origin. The paper aims to show that there was an active culture of teaching Latin through vernacular proverbs in Western Europe from the 11th century to the 17th century. After presenting some collections and surveying the arguments in favour of classroom use, it investigates the impact of humanism and the reformation on proverb-based teaching.
Radical reform, inevitable debts
Authors: Marsico Clementina
Published: May 2018

In a letter to his friend Joan Serra, Lorenzo Valla (1407–1457) shows his contempt for medieval grammars, describing Alexander de Villa-Dei, Evrard de Béthune, Giovanni Balbi, and others as faex hominum. Many traces of Valla’s polemics against medieval authors are woven into his linguistic works, in primis in his Elegantie lingue latine.

The Elegantie represent a monumental attempt to restore Latin to its original splendour after the so-called barbarities of the Middle Ages. Starting from its structure, this work adopts a completely different form compared with the systematic grammatical syntheses of the previous period. It functions as a series of thematic chapters united in the goal of denouncing earlier grammatical, lexical, syntactic, and interpretive usage and decisions. The chapters are built entirely on an expertly assembled collection of quotations. For Valla, only through consulting the best authors can a scholar reach the latine loqui. In practical terms, however, is Valla truly able to reach this goal and break from the medieval tradition?

Beginning with this question, this paper focuses on Valla’s linguistic works, showing both their innovative and traditional facets. The most significant changes Valla proposes in his linguistic analysis – often presented by the author as a strong attack on medieval grammarians – are illustrated. Also, the paper clarifies the humanist’s inevitable debt to the tradition he scorns, particularly evident when considering his use of grammatical terminology.
“Si hoc saeculo natus fuisset”
Authors: Considine John
Published: May 2018

The lexicographical part of theCatholiconof Giovanni Balbi of Genoa (d.1286), compiled in 1286, was the dominant Latin dictionary of the 15th century and the first major Latin dictionary to be printed: 24 editions recorded from the 1460s to 1500, another 7 from 1501 to 1520. In the twenty-five years before the final edition, two attempts were made to refurbish it, one by a certain Master Petrus Aegidius in 1499 and one by the humanist Jodocus Badius Ascensius (1462–1535) in 1506. Their editions were meant to maintain the place of a 13th-century dictionary in the world of humanist reference publishing. This paper gives an account of Aegidius’ and Badius’ additions to theCatholicon, emphasising both the intellectual content of their work and the dictionary’s place in the history of the learned book. The paper concludes with an account of how theCatholiconwas driven out of the market by a dictionary compiled in the late 15th century, theDictionariumof Ambrogio Calepino (c.1435–1511), published from 1502 onwards. An appendix sets out the editions of theCatholiconfrom 1499 onwards, with title page transcriptions.
Crooked Hillary and Dumb Trump
Authors: Hoffmann Christian R.
Published: May 2018

While there is extensive research on the language of twitter, our knowledge of the pragmatics of particular twitter genres (and sub-genres) is still piecemeal. At the same time, in the past decades, political discourse analysis has widened our understanding of how language can be used instrumentally to alter or manipulate public interaction, meanings and opinions. However, it has seldom examined the evaluative load of political communication in much detail. To this end, the paper, on the one hand, serves to illuminate the pragmatics of political tweets as a twitter genre. On the other hand, the study brings to the fore the strategic use of negative evaluations in political online campaigning and discusses its potential (and actual) socio-political ramifications. The quantitative and qualitative analysis of negative evaluations largely draws on Martin and White’s Appraisal framework (2005) and is based on a compatible study byCabrejas-Peñuelas and Díez-Prados (2014). I track down, classify and categorize the negative evaluations of a subset of twitter posts by Donald Trump and Hillary Clinton in a self-compiled corpus of 1965 tweets, with a view to evaluation types, their relative frequencies and dispersion across the corpus, as well as objects and targets of evaluation. The quantitative analysis is then completed by a qualitative examination of the objects and targets of evaluation in both twitter profiles as well as a closer look at the recurrent language used to evaluate the political “other”. The results show that Trump makes more flexible (and strategic) use of negative evaluations (both in terms of types, frequency and distribution), while Clinton’s negative evaluations are less frequent, less diverse and, thus possibly, less convincing.
Self-praise online and offline
Authors: Dayter Daria
Published: May 2018

In contrast to the assumptions of linguistic research on face-to-face interaction, CMC studies have shown that self-promotion is acceptable and even desired in certain online contexts. However, investigations of self-praise online repeatedly refer to the specific features of internet environment or internet communities that cause a temporary suspension of the constraint against self-praise. The constraint itself is treated as somewhat of an axiom. The assumption is, therefore, that the speech act of self-praise is face-threatening and disruptive and can only occur when certain conditions prevail, for example, when a disclaimer #humblebrag is provided. In the present study, I look at self-praise in private WhatsApp chats. Until now, self-praise has been investigated in broadcasting contexts of Twitter and Instagram. On the basis of the existing description of these naturally occurring episodes of self-praise, a retrieval strategy is developed to identify self-praise in a corpus through queries for collocations of lexical markers. An analysis of the episodes of self-praise retrieved from the WhatsApp corpus and some preliminary results from the corpus of spoken American English support the tentative hypothesis that self-praise is an unmarked speech behaviour that is a part of an everyday speech act repertoire. The existing claim about its special status could be explained through a combination of intuitive assumptions carried over from the influential studies of the pre-corpus era, and the retrieval methods that targeted the modified self-praise.
Aponeurosis behaviour during muscular contraction: A narrative review
Authors: Raiteri Brent James
Published: May 2018

There is an abundance of evidence that suggests elastic tendons can enhance both animal and human muscle performance. However, in many terrestrial animals, including humans, a large proportion of the elastic tissue within the muscle‐tendon unit is located within the muscle. This continuous elastic sheet, which provides muscle fibre attachment, is known as the aponeurosis. The aponeurosis has a much more complicated shape than the free tendon and it undergoes a more complicated loading regime during contraction, due to its relationship with the bulging muscle fibres, which remain isovolumetric during force production. Muscle contraction may dynamically modulate the stiffness of the aponeurosis at the same active versus passive force, by increasing the intramuscular pressure and transverse forces within the muscle, which may stretch the aponeurosis in width and subsequently reduce its longitudinal strain. Some evidence also suggests that the aponeurosis mechanical properties may be affected by muscle length, which appears to reduce the fascicle strains for a given muscle force at longer muscle lengths. This narrative review outlines the animal and human studies that have investigated aponeurosis behaviour during contraction and discusses how an elastic sheet with a variable stiffness under activation might be beneficial for muscle performance. While it is clear that our understanding of the role of aponeurosis is lacking, it is hoped that further work will attempt to determine how this tissue contributes to power amplification and elastic energy savings during locomotion and potentially uncover how aponeurosis behaviour contributes to injury risk.
The Portuguese stakeholders’ perspective on social investment and quality assessment in LTC
Authors: Lopes Alexandra , Dias Isabel
Published: May 2018

There has been quite a considerable amount of debate over the last decade about the importance of quality assessment in the field of LTC provision in Portugal, framed by the discourse on social investment. In a context of limited resources, care providers are pressured to demonstrate creation of value. Quality assessment becomes one of the paths to demonstrate worthiness. This, however, has not translated into standardised protocols of evaluation of impacts and quality in particular. The question has been asked why is that? In this article we contribute to answering this question by looking at the discourses of stakeholders on the topic of social investment and quality in LTC. Overall there is a discourse that acknowledges the importance of assessing investments and quality as a reliable proxy to measure return on investments, although there is a general difficulty in translating social investment and the quest for quality into specific examples and tools.
Intra-Areolar Pexy: The “Compass Rose” Suture Technique for Small and Moderate Areola Herniation
Authors: Ionescu Radu , Dima Daniel , Antohi Nicolae
Published: May 2018

Background

Common methods for addressing minor tuberous breast (type 0; normal mammary base breast with isolated areolar herniation) do not solve the underlying pathology and may leave an unsightly scar.

Objectives

To assess the efficacy and safety of a simple, scarless method based on a novel “compass rose” technique, which addresses the etiology of minor tuberous breast and other cases desiring small areolar diameter reductions.

Methods

The technique uses 3 layers of suturing, 1 in a compass pattern and 2 in round block. Retrospective data are provided for 77 consecutive women (141 breasts) undergoing cosmetic breast augmentation surgery and requiring unilateral or bilateral type 0 tuberous breast correction (n = 22) or areolar width reduction ≤ 15 mm (n = 55).

Results

Baseline mean age and body mass index were 29.7 ± 6.0 years and 19.4 ± 1.5 kg/m2, respectively. Patients were followed up for a mean of 27.2 ± 19.5 months. In tuberous breast, mean Northwood Index decreased from 0.55 ± 0.06 at baseline to 0.36 ± 0.02 at ≥ 6 months post surgery, indicating minimal residual deformity. In areolar width reductions without tuberosity, mean width decreases of 11.3 ± 1.8 mm (20.0%) were achieved. Patient satisfaction was high with regard to lack of scarring, stability of the result, and overall breast attractiveness. Eight complications were recorded (n = 2 superficial hematoma; n = 3 hypersensibility; n = 2 knot palpability; n = 1 recurrence); all were resolved.

Conclusions

The method is effective and safe, and may be applicable across patients with type 0 tuberous breast or desiring small areolar diameter reductions.

Level of Evidence: 4
Venous Thromboembolism in Aesthetic Surgery: Risk Optimization in the Preoperative, Intraoperative, and Postoperative Settings
Authors: Pannucci Christopher J
Published: May 2018

The purpose of this Continuing Medical Education (CME) article is to provide a framework for practicing surgeons to conceptualize and quantify venous thromboembolism risk among the aesthetic and ambulatory surgery population. The article provides a practical approach to identify and minimize venous thromboembolism risk in the preoperative, intraoperative, and postoperative settings.
An Extension Problem and Trace Hardy Inequality for the Sub-Laplacian on H-type Groups
Authors: Roncal Luz , Thangavelu Sundaram
Published: May 2018

In this paper we study the extension problem for the sub-Laplacian on an $H$-type group and use the solutions to prove trace Hardy and Hardy inequalities for fractional powers of the sub-Laplacian.
The Impact of Early Corticosteroid Pretreatment Before Initiation of Chemotherapy in Patients With Primary Central Nervous System Lymphoma
Authors: Gessler Florian , Bernstock Joshua D , Behmanesh Bedjan , Brunnberg Uta , Harter Patrick , Ye Daniel , Friedman Gregory K , Hansmann Martin-Leo , Wagner Marlies , Seifert Volker , Weise Lutz , Marquardt Gerhard
Published: May 2018

BACKGROUND

The optimal timing of corticosteroid (CS) treatment in patients with primary central nervous system (CNS) lymphoma (PCNSL) remains controversial. While poor clinical presentation may justify early treatment with CS, this may ultimately result in reduced concentrations of chemotherapeutic agents via perturbations in the permeability of the blood-brain barrier.

OBJECTIVE

To investigate whether early CS exposure is associated with beneficial outcomes and/or reduced occurrence of adverse events as opposed to delayed/concomitant administration.

METHODS

Herein we performed a retrospective observational analysis using patients that were prospectively entered into a database. All patients whom were admitted to the University Hospital between 2009 and 2015 with newly diagnosed PCNSL were included within our study.

RESULTS

Our cohort included 50 consecutive patients diagnosed with PCNSL; of these, in 30 patients CS administration was initiated prior to chemotherapy (early), whilst in the remaining 20 patients CS administration was initiated concomitantly with their chemotherapeutic regimen (concomitant). Within the early vs concomitant CS administration groups, no significant differences were observed with regard to progression-free survival (PFS) (P = .81), overall survival (OS) (P = .75), or remission (P = .68; odds ratio 0.76 and confidence interval [95%] 0.22-2.71). Critically, the timing of CS initiation was not associated with either PFS (P = .81) or PFS (P = .75).

CONCLUSION

Early CS administration was not associated with a deterioration in response to chemotherapy, PFS, or OS. As such, administration of CS prior to initiation of chemotherapy is both reasonable and safe for patients with newly diagnosed PCNSL.
Chronic Meningitis and Hydrocephalus due to Sporothrix brasiliensis in Immunocompetent Adults: A Challenging Entity
Authors: Mialski Rafael , de Oliveira João Nóbrega , da Silva Larissa Honorato , Kono Adriana , Pinheiro Rosangela Lameira , Teixeira Manoel Jacobsen , Gomes Renata Rodrigues , de Queiroz-Telles Flávio , Pinto Fernando Gomes , Benard Gil
Published: May 2018

Chronic meningitis caused by Sporothrix sp. is occasionally described in immunosuppressed patients. We report the challenges in diagnosing and managing 2 nonimmunocompromised patients with hydrocephalus and chronic meningitis caused by Sporothrix brasiliensis. This more virulent species appears to contribute more atypical and severe cases than other related species.
Direct Cervical Carotid Stenting and Angioplasty of Right Internal Carotid Artery and Brachiocephalic Artery Ostial Stenoses With Flow Reversal: 2-Dimensional Operative Video
Authors: Rangel-Castilla Leonardo , Levy Elad I , Siddiqui Adnan H
Published: May 2018

We present a case of tandem stenosis of the great vessels (cervical internal carotid artery [ICA] and brachiocephalic trunk ostium [BTO]) treated with stenting and balloon angioplasty of both lesions under flow arrest. A 70-yr-old woman with a history of hypertension, hyperlipidemia, coronary artery disease, and previous strokes presented with recurrent transient ischemic attacks of the left upper and lower extremities over the last 6 mo. She underwent right cervical endarterectomy (CEA) 16 yr prior. Neurological examination was unremarkable. Carotid Doppler ultrasonography revealed severely increased velocities of the right ICA. Cervical magnetic resonance angiography demonstrated 80% right ICA stenosis and 50% BTO stenosis. Digital subtraction cerebral angiography showed 80% right ICA stenosis and 70% BTO stenosis. The patient was not a candidate for standard carotid artery stenting because the BTO precluded endovascular access or for CEA because of the previous CEA; therefore, direct carotid access and flow reversal was an alternative. Under general anesthesia and systemic heparinization, the patient underwent right carotid artery surgical exposure. Under flow reversal using the Enroute System (Silk Road Medical, Sunnyvale, California), anterograde right ICA stenting angioplasty and retrograde BTO stenting and angioplasty were performed. Successful revascularization of the right ICA and BTO was obtained. No procedure-related complications occurred. The patient was discharged home 2 d postprocedure, neurologically intact. Direct carotid access with flow reversal is a safe and effective therapeutic alternative for patients with ICA (or common carotid artery) stenosis who cannot undergo CEA or when endovascular access from the aortic arch is not possible.

 Patient consent was obtained prior to performing the procedure. Institutional board approval is not required for the report of a single case.
Local Policing in a Nationalized Police Force: A Study on the Local Teams of The Netherlands’ National Police
Authors: Terpstra Jan
Published: May 2018

This article concentrates on the local consequences of the introduction of the Netherlands’ National Police. Six local teams of the National Police were studied, using both interviews with officers and observations of police work. Despite the emphasis on standardization, this study showed that there are important differences between these teams. The scale enlargement of the local teams resulted in several negative side effects, such as an increase in driving time of patrol cars in rural areas, and a loss of social bonds between officers in these teams. The aim to replace traditional patrol work by problem-oriented types of policing is hardly realized in practice. Despite the emphasis on the importance of community policing, in fact community officers now have a more isolated position. The introduction of the National Police created more distance between citizens and the police and made that this relationship is now more dependent on abstract forms of communication.
Extracontextuality and extravalence in quantum mechanics
Authors: Auffèves Alexia , Grangier Philippe
Published: May 2018

We develop the point of view where quantum mechanics results from the interplay between the quantized number of ‘modalities’ accessible to a quantum system, and the continuum of ‘contexts’ that are required to define these modalities. We point out the specific roles of ‘extracontextuality’ and ‘extravalence’ of modalities, and relate them to the Kochen–Specker and Gleason theorems.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Quantum reversibility is relative, or does a quantum measurement reset initial conditions?
Authors: Zurek Wojciech H.
Published: May 2018

I compare the role of the information in classical and quantum dynamics by examining the relation between information flows in measurements and the ability of observers to reverse evolutions. I show that in the Newtonian dynamics reversibility is unaffected by the observer’s retention of the information about the measurement outcome. By contrast—even though quantum dynamics is unitary, hence, reversible—reversing quantum evolution that led to a measurement becomes, in principle, impossible for an observer who keeps the record of its outcome. Thus, quantum irreversibility can result from the information gain rather than just its loss—rather than just an increase of the (von Neumann) entropy. Recording of the outcome of the measurement resets, in effect, initial conditions within the observer’s (branch of) the Universe. Nevertheless, I also show that the observer’s friend—an agent who knows what measurement was successfully carried out and can confirm that the observer knows the outcome but resists his curiosity and does not find out the result—can, in principle, undo the measurement. This relativity of quantum reversibility sheds new light on the origin of the arrow of time and elucidates the role of information in classical and quantum physics. Quantum discord appears as a natural measure of the extent to which dissemination of information about the outcome affects the ability to reverse the measurement.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
The quantum theory of time, the block universe, and human experience
Authors: Vaccaro Joan A.
Published: May 2018

Advances in our understanding of the physical universe have dramatically affected how we view ourselves. Right at the core of all modern thinking about the universe is the assumption that dynamics is an elemental feature that exists without question. However, ongoing research into the quantum nature of time is challenging this view: my recently introduced quantum theory of time suggests that dynamics may be a phenomenological consequence of a fundamental violation of time reversal symmetry. I show here that there is consistency between the new theory and the block universe view. I also discuss the new theory in relation to the human experience of existing in the present moment, able to reflect on the past and contemplate a future that is yet to happen.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Dealing with indistinguishable particles and their entanglement
Authors: Compagno Giuseppe , Castellini Alessia , Lo Franco Rosario
Published: May 2018

Here, we discuss a particle-based approach to deal with systems of many identical quantum objects (particles) that never employs labels to mark them. We show that it avoids both methodological problems and drawbacks in the study of quantum correlations associated with the standard quantum mechanical treatment of identical particles. The core of this approach is represented by the multiparticle probability amplitude, whose structure in terms of single-particle amplitudes we derive here by first principles. To characterize entanglement among the identical particles, this new method uses the same notions, such as partial trace, adopted for non-identical ones. We highlight the connection between our approach and second quantization. We also define spin-exchanged multipartite states which contain a generalization of W states to identical particles. We prove that particle spatial overlap plays a role in the distributed entanglement within multipartite systems and is responsible for the appearance of non-local quantum correlations.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Locality and quantum mechanics
Authors: Unruh W. G.
Published: May 2018

It is argued that it is best not to think of quantum mechanics as non-local, but rather that it is non-realistic.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Exploring the boundaries of quantum mechanics: advances in satellite quantum communications
Authors: Agnesi Costantino , Vedovato Francesco , Schiavon Matteo , Dequal Daniele , Calderaro Luca , Tomasin Marco , Marangon Davide G. , Stanco Andrea , Luceri Vincenza , Bianco Giuseppe , Vallone Giuseppe , Villoresi Paolo
Published: May 2018

Recent interest in quantum communications has stimulated great technological progress in satellite quantum technologies. These advances have rendered the aforesaid technologies mature enough to support the realization of experiments that test the foundations of quantum theory at unprecedented scales and in the unexplored space environment. Such experiments, in fact, could explore the boundaries of quantum theory and may provide new insights to investigate phenomena where gravity affects quantum objects. Here, we review recent results in satellite quantum communications and discuss possible phenomena that could be observable with current technologies. Furthermore, stressing the fact that space represents an incredible resource to realize new experiments aimed at highlighting some physical effects, we challenge the community to propose new experiments that unveil the interplay between quantum mechanics and gravity that could be realizable in the near future.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Quantum theory of the classical: quantum jumps, Born’s Rule and objective classical reality via quantum Darwinism
Authors: Zurek Wojciech Hubert
Published: May 2018

The emergence of the classical world from the quantum substrate of our Universe is a long-standing conundrum. In this paper, I describe three insights into the transition from quantum to classical that are based on the recognition of the role of the environment. I begin with the derivation of preferred sets of states that help to define what exists—our everyday classical reality. They emerge as a result of the breaking of the unitary symmetry of the Hilbert space which happens when the unitarity of quantum evolutions encounters nonlinearities inherent in the process of amplification—of replicating information. This derivation is accomplished without the usual tools of decoherence, and accounts for the appearance of quantum jumps and the emergence of preferred
pointer states
consistent with those obtained via environment-induced superselection, or
einselection
. The pointer states obtained in this way determine what can happen—define events—without appealing to Born’s Rule for probabilities. Therefore,
p

k

=|
ψ

k

|
2
can now be deduced from the entanglement-assisted invariance, or
envariance
—a symmetry of entangled quantum states. With probabilities at hand, one also gains new insights into the foundations of quantum statistical physics. Moreover, one can now analyse the information flows responsible for decoherence. These information flows explain how the perception of objective classical reality arises from the quantum substrate: the effective amplification that they represent accounts for the objective existence of the einselected states of macroscopic quantum systems through the redundancy of pointer state records in their environment—through
quantum Darwinism
.

This article is part of a discussion meeting issue ‘Foundations of quantum mechanics and their impact on contemporary society’.
Cooperative induction of ordered peptide and fatty acid aggregates
Authors: Bomba Radoslaw , Kwiatkowski Witek , Riek Roland , Greenwald Jason
Published: May 2018

Interactions between biological membranes and disease-associated amyloids are well documented and their prevalence suggests that an inherent affinity exists between these two distinct molecular assemblies. Within the framework of our research project on amyloids and the origins of life, we hypothesized here that such interactions could increase both the sequence and structure space of peptide amyloids in a heterogeneous system and that if cooperative in nature, the interaction could be advantageous to the propagation of these entities in a prebiotic context. Thus, we have investigated the interplay between vesicle-forming fatty acids and amyloidogenic peptides, the respective precursors of lipids and proteins. Individually they are able to form ordered structures under a limited range of conditions with the bilayer of fatty acid vesicles and the cross-β core of amyloids both being repetitive structures that could in principle support a cooperative interaction. Here we report that an 8-residue basic peptide that can form an amphipathic β-strand, that is soluble at neutral pH and that can form amyloids above its pI at pH 11, is also able to cooperatively form novel co-aggregates of diverse structure with and in the context of simple fatty acids at neutral pH. Below the critical vesicle concentration (CVC) the mixtures of fatty acid and peptide yield a flocculent precipitate with an underlying β-structure. Above the CVC, the mixtures yield ribbon or tube-like structures that bear some of the hallmarks of amyloids yet have associated with them a significant amount of fatty acids, likely in a bilayer structure. In the context of the origin of cellular life these results expand the phase space of both peptides and fatty acids while providing a simple yet robust physical connection between two distinct biological entities relevant for life.
Soil nutrient stoichiometry affects the initial response of microbial community to trophic perturbation
Authors: Mise Kazumori , Maruyama Runa , Miyabara Yuichi , Kunito Takashi , Senoo Keishi , Otsuka Shigeto
Published: May 2018

Soil microbes are drivers of global ecosystem functionality and are continuously subjected to external perturbations. It is fundamental for ecologists and environmental scientists to understand and further predict the microbes’ responses to these perturbations. A major and ubiquitous perturbation is the addition of chemical nutrients, including fertilizers and animal urine, to soil. Recent biogeographical studies suggest that soil nutrient stoichiometry (i.e., nutritional balance) determines microbial community structure and its functions with regard to material circulation. Given this information, here, we show that soil nutrient stoichiometry, or the bioavailable C:P ratio, determines the impact of nutrient addition on the soil’s microbial communities. We sampled two soils with similar carbon and nitrogen concentrations but with a 20-fold difference in phosphorus bioavailability. Soil microcosms with carbon and nitrogen amendments were constructed for both the soils. The phosphorus-depleted soil received prolonged effect from carbon and nitrogen amendments: the phosphatase activity gradually increased over a 24-day incubation period and the microbial community structure did not present recovery to its initial state. In contrast, in the other soil, both phosphatase activity and microbial community structure gradually returned to those of the control samples. Phosphorus depletion mitigated carbon and nitrogen intake; therefore, the effects of carbon and nitrogen amendment lasted longer. Our results demonstrate that nutritional stoichiometry is a strong predictor of microbial community dynamics in response to trophic perturbation, particularly when considering the length of time the trait of perturbation persists in the soil.
Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis
Authors: Thiel Denise , Conrad Nataša Djurdjevac , Peschutter Ria X , Siebert Heike , Marsico Annalisa
Published: May 2018

Background

Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them has unknown function. Recent evidence has shown the importance of both lncR-NAs and chromatin interactions in transcriptional regulation. Although network-based methods, mainly exploiting gene-lncRNA co-expression, have been applied to characterize lncRNA of unknown function by means of ‘guilt-by-association’ strategies, no method exists which combines co-expression analysis with 3D chromatin interaction data.

Results

To better understand the function of chromatin interactions in the context of lncRNA-mediated gene regulation, we have developed a multi-step graph analysis approach to examine the RNA polymerase II ChIA-PET chromatin interaction network in the K562 human cell line. We have annotated the network with gene and lncRNA coordinates, and chromatin states from the ENCODE project. We used centrality measures, as well as an adaptation of our previously developed Markov State Models (MSM) clustering method, to gain a better understanding of lncRNAs in transcriptional regulation. The novelty of our approach resides into the detection of fuzzy regulatory modules based on network properties and their optimization based on co-expression analysis between genes and gene-lncRNA pairs. This results in our method returning morebona fideregulatory modules than other state-of-the art approaches for clustering on graphs.

Conclusions

Interestingly, we find that lncRNA network hubs tend to be significantly enriched in disease association, positional conservation and enhancer-like functions. We validated regulatory functions for well known lncRNAs, such as MALAT1 and the enhancer-like lncRNA FALEC. In addition, by investigating the modular structure of bigger components we show that we can propose regulatory functional mechanisms for uncharacterized lncRNAs, such FLJ37453, RP11442N24 B.1 and LINC00910.
Deep Neural Network for Protein Contact Prediction by Weighting Sequences in a Multiple Sequence Alignment
Authors: Fukuda Hiroyuki , Tomii Kentaro
Published: May 2018

Protein contact prediction is a crucially important step for protein structure prediction. To predict a contact, approaches of two types are used: evolutionary coupling analysis (ECA) and supervised learning. ECA uses a large multiple sequence alignment (MSA) of homologue sequences and extract correlation information between residues. Supervised learning uses ECA analysis results as input features and can produce higher accuracy. As described herein, we present a new approach to contact prediction which can both extract correlation information and predict contacts in a supervised manner directly from MSA using a deep neural network (DNN). Using DNN, we can obtain higher accuracy than with earlier ECA methods. Simultaneously, we can weight each sequence in MSA to eliminate noise sequences automatically in a supervised way. It is expected that the combination of our method and other meta-learning methods can provide much higher accuracy of contact prediction.
Developmental “awakening” of primary motor cortex to the sensory consequences of movement
Authors: Dooley James C. , Blumberg Mark S.
Published: May 2018

Before primary motor cortex (M1) develops its motor functions, it functions like a somatosensory area. Here, by recording from neurons in the forelimb representation of M1 in postnatal day (P) 8-12 rats, we demonstrate a rapid shift in its sensory responses. At P8-10, M1 neurons respond overwhelmingly to feedback from sleep-related twitches of the forelimb, but the same neurons do not respond to wake-related movements. By P12, M1 neurons suddenly respond to wake movements, a transition that results from opening the sensory gate in the external cuneate nucleus. Also at P12, few M1 neurons respond to twitches, but the full complement of twitch-related feedback observed at P8 can be unmasked through local disinhibition. Finally, through P12, M1 sensory responses originate in the deep thalamorecipient layers, not primary somatosensory cortex. These findings demonstrate that M1 initially establishes a sensory framework upon which its later-emerging role in motor control is built.
UPA-Seq: Prediction of Functional LncRNAs Using Differential Sensitivity to UV Crosslinking
Authors: Komatsu Taiwa , Mito Mari , Fujii Koichi , Iwasaki Shintaro , Nakagawa Shinichi
Published: May 2018

While a large number of long noncoding RNAs (lncRNAs) are transcribed from the genome of higher eukaryotes, systematic prediction of their functionality has been challenging due to the lack of conserved sequence motifs or structures. Assuming that lncRNAs function as large ribonucleoprotein complexes and thus are easily crosslinked to proteins upon UV irradiation, we performed RNA-Seq analyses of RNAs recovered from the aqueous phase after UV irradiation and phenol-chloroform extraction (UPA-Seq). As expected, the numbers of UPA-Seq reads mapped to known functional lncRNAs were remarkably reduced upon UV irradiation. Comparison with ENCODE eCLIP data revealed that lncRNAs that exhibited greater decreases upon UV irradiation preferentially associated with proteins containing prion-like domains (PrLDs). Fluorescent in situ hybridization (FISH) analyses revealed the nuclear localization of novel functional lncRNA candidates, including one that accumulated at the site of transcription. We propose that UPA-Seq provides a useful tool for the selection of lncRNA candidates to be analyzed in depth in subsequent functional studies.
Higher rostral locus coeruleus integrity is associated with better memory performance in older adults
Authors: Dahl Martin J. , Mather Mara , Düzel Sandra , Bodammer Nils C. , Lindenberger Ulman , Kühn Simone , Werkle-Bergner Markus
Published: May 2018

For decades, research into memory decline in human cognitive aging has focused on neocortical regions, the hippocampus, and dopaminergic neuromodulation. Recent findings indicate that the locus coeruleus (LC) and noradrenergic neuromodulation may also play an important role in shaping memory development in later life. However, technical challenges in quantifying LC integrity have hindered the study of LC-cognition associations in humans. Using high-resolution neuromelanin-sensitive magnetic resonance imaging, we found that individual differences in learning and memory were positively associated with LC integrity across a variety of memory tasks in younger (n = 66), and older adults (n = 228). Moreover, we observed functionally relevant age differences confined to rostral LC. Older adults with a more youth-like rostral LC also showed higher memory performance. These findings link non-invasive, in vivo indices of LC integrity to memory in aging and highlight the role of the LC norepinephrine system in the decline of cognition.