bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ‘Judicialization’ of International Commercial Arbitration: Pitfall or Virtue?
Authors: TRAKMAN LEON , MONTGOMERY HUGH 
Published: February 2017

AbstractThis article critiques the global concern that international commercial arbitration (ICA) is becoming increasingly ‘judicialized’, addressing the growing sentiment in ICA that arbitral proceedings are too lengthy, expensive, and complex. Assuming a contrarian perspective, it argues that attempts to address the cost and length of arbitration proceedings ought not to undermine the value of finely reasoned arbitral decisions grounded in law and justice. It also argues for a contextual assessment of ICA that extends beyond the debate over ‘judicialization’.Using global illustrations and ICA developments in Australia as an initial guide, this article suggests that balancing party autonomy, accountability, efficiency,andfairness in ICA can help resolve these growing criticisms of ‘judicialization’. Ultimately, the reform of international arbitration should take place within a framework of ‘international best practice’ that is both analytical in nature and functional in operation. As such, ICA should not only be affordable and expeditious, it should serve as a legitimate and effective method of resolving international commercial disputes. In addition, it should balance the virtue of transparent proceedings against the need to respect the confidences of the parties.
Linking the community structure of arbuscular mycorrhizal fungi and plants: a story of interdependence?
Authors: Horn Sebastian , Hempel Stefan , Verbruggen Erik , Rillig Matthias C , Caruso Tancredi 
Published: February 2017

Abstract
Arbuscular mycorrhizal fungi (AMF) are crucial to plants and vice versa, but little is known about the factors linking the community structure of the two groups. We investigated the association between AMF and the plant community structure in the nearest neighborhood of Festuca brevipila in a semiarid grassland with steep environmental gradients, using high-throughput sequencing of the Glomeromycotina (former Glomeromycota). We focused on the Passenger, Driver and Habitat hypotheses: (i) plant communities drive AMF (passenger); (ii) AMF communities drive the plants (driver); (iii) the environment shapes both communities causing covariation. The null hypothesis is that the two assemblages are independent and this study offers a spatially explicit novel test of it in the field at multiple, small scales. The AMF community consisted of 71 operational taxonomic units, the plant community of 47 species. Spatial distance and spatial variation in the environment were the main determinants of the AMF community. The structure of the plant community around the focal plant was a poor predictor of AMF communities, also in terms of phylogenetic community structure. Some evidence supports the passenger hypothesis, but the relative roles of the factors structuring the two groups clearly differed, leading to an apparent decoupling of the two assemblages at the relatively small scale of this study. Community phylogenetic structure in AMF suggests an important role of within-assemblage interactions.
Origin and fate of methane in the Eastern Tropical North Pacific oxygen minimum zone
Authors: Chronopoulou Panagiota-Myrsini , Shelley Felicity , Pritchard William J , Maanoja Susanna T , Trimmer Mark 
Published: February 2017

Abstract
Oxygen minimum zones (OMZs) contain the largest pools of oceanic methane but its origin and fate are poorly understood. High-resolution (&lt;15 m) water column profiles revealed a 300 m thick layer of elevated methane (20–105 nm) in the anoxic core of the largest OMZ, the Eastern Tropical North Pacific. Sediment core incubations identified a clear benthic methane source where the OMZ meets the continental shelf, between 350 and 650 m, with the flux reflecting the concentration of methane in the overlying anoxic water. Further incubations characterised a methanogenic potential in the presence of both porewater sulphate and nitrate of up to 88 nmol g−1day−1 in the sediment surface layer. In these methane-producing sediments, the majority (85%) of methyl coenzyme M reductase alpha subunit (mcrA) gene sequences clustered with Methanosarcinaceae (⩾96% similarity to Methanococcoides sp.), a family capable of performing non-competitive methanogenesis. Incubations with 13C-CH4 showed potential for both aerobic and anaerobic methane oxidation in the waters within and above the OMZ. Both aerobic and anaerobic methane oxidation is corroborated by the presence of particulate methane monooxygenase (pmoA) gene sequences, related to type I methanotrophs and the lineage of Candidatus Methylomirabilis oxyfera, known to perform nitrite-dependent anaerobic methane oxidation (N-DAMO), respectively.
Exploring the microbial community (microflora) associated with ovine Haemonchus contortus (macroflora) field strains
Authors: El-Ashram Saeed , Suo Xun 
Published: February 2017

AbstractHigh-throughput sequencing technology has shown tremendous promise for microbial community composition and diversity. Illumina MiSeq platform was exploited to study the microbial community associated with the different stages of the life-cycle of ovine Haemonchus contortus field strains using two distinct amplification primer sets (targeting V3–V4, and V5–V7). Scanning electron microscope and polymerase chain reaction coupled with Illumina MiSeq platform were employed to confirm the absence of any parasite surface contamination by intact bacteria or their DNA products. Results showed 48 (V3–V4 tags) and 28 (V5–V7 tags) bacterial genera comprised the microbial flora of H. contortus microbiome. The dominant bacterial genera belonged to Escherichia-Shigella, Pseudomonas and Ochrobactrum, which were shared in all the stages of the parasite life-cycle using V3–V4 and V5–V7 amplicons. Moreover, the parasite microbiome could reflect the external micro-organisms (i.e. micro- and macro-habitats). There is abundant room for further progress in comparing microbiome of different helminths, which has, and will continue to offer considerable potential for better understanding a wide-variety of devastating animal and human diseases.
Microbial community assembly and evolution in subseafloor sediment
Authors: Starnawski Piotr , Bataillon Thomas , Ettema Thijs J. G. , Jochum Lara M. , Schreiber Lars , Chen Xihan , Lever Mark A. , Polz Martin F. , Jørgensen Bo B. , Schramm Andreas , Kjeldsen Kasper U. 
Published: February 2017

Significance
Our study shows that deep subseafloor sediments are populated by descendants of rare members of surface sediment microbial communities that become predominant during burial over thousands of years. We provide estimates of mutation rates and strength of purifying selection in a set of taxonomically diverse microbial populations in marine sediments and show that their genetic diversification is minimal during burial. Our data suggest that the ability of subseafloor microbes to subsist in the energy-deprived deep biosphere is not acquired during burial but that these microbes were already capable of living in this unique environment. These findings represent a significant step toward understanding the bounds for life in the deep biosphere and its connection to life in the surface world.
Quantification of labile heme in live malaria parasites using a genetically encoded biosensor
Authors: Abshire James R. , Rowlands Christopher J. , Ganesan Suresh M. , So Peter T. C. , Niles Jacquin C. 
Published: February 2017

Significance
Malaria parasites degrade substantial quantities of hemoglobin to release heme within a specialized digestive vacuole. Most of this heme is sequestered in an inert crystal. However, the concentration of bioavailable, labile heme in the parasite’s cytosol was unknown. We developed a biosensor to provide the first quantitative insights into labile heme concentrations in malaria parasites. We find that ∼1.6 µM labile cytosolic heme is maintained, including during a period coincident with intense hemoglobin degradation. The heme-binding antimalarial drug, chloroquine, which interferes with heme crystallization, specifically induces an increase in labile heme. The ability to quantify labile heme in malaria parasites opens opportunities for better understanding heme homeostasis, signaling, and metabolism, and its association with antimalarial potency.
Human-started wildfires expand the fire niche across the United States
Authors: Balch Jennifer K. , Bradley Bethany A. , Abatzoglou John T. , Nagy R. Chelsea , Fusco Emily J. , Mahood Adam L. 
Published: February 2017

SignificanceFighting wildfires in the United States costs billions of dollars annually. Public dialog and ongoing research have focused on increasing wildfire risk because of climate warming, overlooking the direct role that people play in igniting wildfires and increasing fire activity. Our analysis of two decades of government agency wildfire records highlights the fundamental role of human ignitions. Human-started wildfires accounted for 84% of all wildfires, tripled the length of the fire season, dominated an area seven times greater than that affected by lightning fires, and were responsible for nearly half of all area burned. National and regional policy efforts to mitigate wildfire-related hazards would benefit from focusing on reducing the human expansion of the fire niche.
Structural basis of autoregulatory scaffolding by apoptosis signal-regulating kinase 1
Authors: Weijman Johannes F. , Kumar Abhishek , Jamieson Sam A. , King Chontelle M. , Caradoc-Davies Tom T. , Ledgerwood Elizabeth C. , Murphy James M. , Mace Peter D. 
Published: February 2017

Significance
Phosphorylation catalyzed by protein kinases governs many aspects of cellular behavior. Apoptosis signal-regulating kinases (ASK1–3) trigger responses to stress, but the structural basis of their regulation remains unclear. Here, we show that a domain directly adjacent to the ASK1 kinase domain promotes activity of ASK1 on a key substrate and also orients an additional ASK1 domain nearby to suppress kinase activity. The structure of this regulatory domain appears to be shared by all ASK kinases and provides a versatile mechanism to control ASK activity in response to various stress stimuli.
Was the Devonian geomagnetic field dipolar or multipolar? Palaeointensity studies of Devonian igneous rocks from the Minusa Basin (Siberia) and the Kola Peninsula dykes, Russia
Authors: Shcherbakova V V , Biggin A J , Veselovskiy R V , Shatsillo A V , Hawkins L M A , Shcherbakov V P , Zhidkov G V 
Published: February 2017

Abstract
Defining variations in the behaviour of the geomagnetic field through geological time is critical to understanding the dynamics of Earth's core and its response to mantle convection and planetary evolution. Furthermore, the question of whether the axial dipole dominance of the recent palaeomagnetic field persists through the whole of Earth's history is fundamental to determining the reliability of palaeogeographic reconstructions and the efficacy of the magnetosphere in shielding Earth from solar wind radiation. Previous palaeomagnetic directional studies have suggested that the palaeofield had a complex configuration in the Devonian period (419–359 Ma). Here we present new high-quality palaeointensity determinations from rocks aged between 408 and 375 Ma from the Minusa Basin (southern Siberia), and the Kola Peninsula that enable the first reliable investigation of the strength of the field during this enigmatic period. Palaeointensity experiments were performed using the thermal Thellier, microwave Thellier and Wilson methods on 165 specimens from 25 sites. Six out of eight successful sites from the Minusa Basin and all four successful sites from the Kola Peninsula produced extremely low palaeointensities (&lt;10 μT). These findings challenge the uniformitarian view of the palaeomagnetic field: field intensities of nearly an order of magnitude lower than Neogene values (except during relatively rare geomagnetic excursions and reversals) together with the widespread appearance of strange directions found in the Devonian suggest that the Earth's field during this time may have had a dominantly multipolar geometry. A persistent, low intensity multipolar magnetic field and associated diminished magnetosphere would increase the impact of solar particles on the Earth's magnetosphere, ionosphere and atmosphere with potential major implications for Earth's climate and biosphere.
Mixed Pain Can Be Discerned in the Primary Care and Orthopedics Settings in Spain
Authors: Ibor Pedro J. , Sánchez-Magro Isabel , Villoria Jesús , Leal Ana , Esquivias Ana 
Published: February 2017

Objectives:To assess the value of the concept of mixed pain by investigating its acceptance and interpretation by health care professionals and the differential characteristics in patients with mixed pain.Materials and Methods:Data from 5024 patients with pain from 551 sites in Primary Care and Orthopedics settings were analyzed in this cross-sectional study. Pain characteristics, other factors influencing pain, health care–related data and health-related quality of life were summarized and compared among 3 groups of patients according to the type of pain (nociceptive, neuropathic, or mixed), as assigned by the investigators after considering the pathophysiological mechanisms involved.Results:Pain was of mixed pathophysiology in most patients (59.3%; 95% confidence interval [CI], 59.2%-59.5%), followed by nociceptive (31.8%; 95% CI, 31.6%-32.0%) and neuropathic pathophysiology (8.9%; 95% CI, 8.8%-9.1%). Patients with mixed pain had pain in >1 site more frequently than the other groups. Spinal conditions was the attributed cause of pain in >80% of patients with mixed pain, whereas nonspinal osteoarthritis represented almost a third. Patients with mixed pain showed a greater clinical complexity than the remaining patients, as they reflected: more comorbidities, adverse psycho-social factors, health care resource utilization, undertreatment, and perceived difficulties in patient management, but less perceived effectiveness of treatments and a lower health-related quality of life.Discussion:An independent category in the pathophysiological classification of pain is justified based on the differential characteristics of patients with mixed pain, although conceptualization of mixed pain should be improved. Increasing referrals to other specialists or implementing chronic pain management programs would seem advisable.Conclusions:Patients with mixed pain showed more clinical complexity than patients with other types of pain. The consideration of mixed pain as an independent pathophysiological category may be justifiable on empirical clinical grounds.
Ischemic Stroke in Young Adults
Authors: Montanaro Vinícius V.A. , Freitas Denise d.S. , Ruiz Miguel C.M. , Cavalcanti Eduardo B.U. , Marinho Patricia B.C. , Freitas Maria C.D.N.B. , Oliveira Eleonora M.J.d. 
Published: February 2017

Introduction:
The societal and economic impact of ischemic stroke in young adults is considerable. The etiological investigation of ischemic stroke in this population is also challenging.

Objective:
To describe the characteristics of young patients with ischemic stroke admitted to a neurological rehabilitation program in Brazil.

Methods:
This transversal retrospective study analyzed data from the electronic health records of 134 patients aged 18 to 45 years with ischemic stroke admitted from 2008 to 2012.

Results:
The average patient age at the time of ictus was 33 years; 56% of the subjects were female, and 29.3% had undetermined etiologies of stroke, on the basis of both TOAST and SSS TOAST criteria. Further, 48.7% of the subjects had a known vascular risk factor, which was arterial hypertension in most cases. The results of thrombophilia testing were positive in 13.7% of patients, but in only 3.7% of patients, thrombophilia was determined to be the causal mechanism of the stroke. There was a significant association between thrombophilia and patent foramen ovale, but no significant association was found between thrombophilia and arterial dissection. Among the patients with artery dissections, 46% had a history of trauma, which was statistically significant.

Conclusions:
Etiological diagnosis of stroke in the young is challenging for clinicians. Hence, a more effective classification scheme, better investigative mechanisms, and correct determination of causal associations in ischemic stroke are needed. Thrombophilia screening should be performed in the presence of relevant clinical signs and/or family history.
Enabling cross-study analysis of RNA-Sequencing data
Authors: Wang Qingguo , Armenia Joshua , Zhang Chao , Penson Alexander V. , Reznik Ed , Zhang Liguo , Minet Thais , Ochoa Angelica , Gross Benjamin E. , Iacobuzio-Donahue Christine A. , Betel Doron , Taylor Barry S. , Gao Jianjiong , Schultz Nikolaus 
Published: February 2017

AbstractDriven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data. While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources poses a great challenge, due to differences in sample and data processing. Here, we present a pipeline that processes and unifies RNA-seq data from different studies, which includes uniform realignment and gene expression quantification as well as batch effect removal. We find that uniform alignment and quantification is not sufficient when combining RNA-seq data from different sources and that the removal of other batch effects is essential to facilitate data comparison. We have processed data from the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA) and have successfully corrected for study-specific biases, enabling comparative analysis across studies. The normalized data are available for download via GitHub (athttps://github.com/mskcc/RNAseqDB).
Signaling architectures that transmit unidirectional information despite retroactivity
Authors: Shah Rushina , Del Vecchio Domitilla 
Published: February 2017

AbstractA signaling pathway transmits information from an upstream system to downstream systems, ideally in a unidirectional fashion. A key obstacle to unidirectional transmission is retroactivity, the additional reaction flux that affects a system once its species interact with those of downstream systems. This raises the fundamental question of whether signaling pathways have developed specialized architectures that overcome retroactivity and transmit unidirectional signals. Here, we propose a general procedure based on mathematical analysis that provides an answer to this question. Using this procedure, we analyze the ability of a variety of signaling architectures to transmit one-way (from upstream to downstream) signals, as key biological parameters are tuned. We find that single stage phosphorylation and phosphotransfer systems that transmit signals from a kinase show a stringent design trade-off that hampers their ability to overcome retroactivity. Interestingly, cascades of these architectures, which are highly represented in nature, can overcome this trade-off and thus enable unidirectional transmission. By contrast, phosphotransfer systems, and single and double phosphorylation cycles that transmit signals from a substrate are unable to mitigate retroactivity effects, even when cascaded, and hence are not well suited for unidirectional information transmission. Our results identify signaling architectures that, allowing unidirectional transmission of signals, embody modular processes that conserve their input/output behavior across multiple contexts. These findings can be used to decompose natural signal transduction networks into modules, and, at the same time, they establish a library of devices that can be used in synthetic biology to facilitate modular circuit design.
Rule-based modeling using wildcards
Authors: Andrews Steven S. 
Published: February 2017

SummaryMany biological molecules exist in multiple variants, such as proteins with different post-translational modifications, DNAs with different sequences, and phospholipids with different chain lengths. Representing these variants as distinct species, as most biochemical simulators do, leads to the problem that the number of species, and chemical reactions that interconvert them, typically increase combinatorially with the number of ways that the molecules can vary. This can be alleviated by “rule-based modeling methods,” in which software generates the chemical reaction network from relatively simple “rules.” This article presents a new approach to rule-based modeling. It is based on wildcards that match to species names, much as wildcards can match to file names in computer operating systems. It is much simpler to use than the formal rule-based modeling approaches developed previously but can also lead to unintended consequences if not used carefully. This article demonstrates rule-based modeling with wildcards through examples for: signaling systems, protein complexation, polymerization, nucleic acid sequence copying and mutation, the “SMILES” chemical notation, and others. The method is implemented in Smoldyn, a spatial and stochastic biochemical simulator, for both the generate-first and on-the-fly expansion, meaning whether the reaction network is generated before or during the simulation.