bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteome-wide modulation of degradation dynamics in response to growth arrest
Authors: Zhang Tian , Wolfe Clara , Pierle Andrew , Welle Kevin A. , Hryhorenko Jennifer R. , Ghaemmaghami Sina 
Published: November 2017

Significance
In dividing cells, long-lived proteins are continuously diluted by being partitioned into newly formed daughter cells. Conversely, short-lived proteins are cleared from a cell primarily by proteolysis rather than cell division. Thus, when a cell stops dividing, there is a natural tendency for long-lived proteins to accumulate relative to short-lived proteins. This effect is disruptive to cells and leads to the accumulation of aged and damaged proteins over time. Here, we analyzed the degradation of thousands of proteins in dividing and nondividing (quiescent) skin cells. Our results demonstrate that quiescent cells avoid the accumulation of long-lived proteins by enhancing their degradation through pathways involving the lysosome. This mechanism may be important for promotion of protein homeostasis in aged organisms.
Early Neolithic wine of Georgia in the South Caucasus
Authors: McGovern Patrick , Jalabadze Mindia , Batiuk Stephen , Callahan Michael P. , Smith Karen E. , Hall Gretchen R. , Kvavadze Eliso , Maghradze David , Rusishvili Nana , Bouby Laurent , Failla Osvaldo , Cola Gabriele , Mariani Luigi , Boaretto Elisabetta , Bacilieri Roberto , This Patrice , Wales Nathan , Lordkipanidze David 
Published: November 2017

Significance
The earliest biomolecular archaeological and archaeobotanical evidence for grape wine and viniculture from the Near East, ca. 6,000–5,800 BC during the early Neolithic Period, was obtained by applying state-of-the-art archaeological, archaeobotanical, climatic, and chemical methods to newly excavated materials from two sites in Georgia in the South Caucasus. Wine is central to civilization as we know it in the West. As a medicine, social lubricant, mind-altering substance, and highly valued commodity, wine became the focus of religious cults, pharmacopoeias, cuisines, economies, and society in the ancient Near East. This wine culture subsequently spread around the globe. Viniculture illustrates human ingenuity in developing horticultural and winemaking techniques, such as domestication, propagation, selection of desirable traits, wine presses, suitable containers and closures, and so on.
Experiments on transient melting of tungsten by ELMs in ASDEX Upgrade
Authors: Krieger K. , Balden M. , Coenen J.W. , Laggner F. , Matthews G.F. , Nille D. , Rohde V. , Sieglin B. , Giannone L. , Göths B. , Herrmann A. , de Marne P. , Pitts R.A. , Potzel S. , Vondracek P. ,   ASDEX-Upgrade Team,   EUROfusion MST1 Team
Published: November 2017

Abstract
Repetitive melting of tungsten by power transients originating from edge localized modes (ELMs) has been studied in ASDEX Upgrade. Tungsten samples were exposed to H-mode discharges at the outer divertor target plate using the divertor manipulator II (DIM-II) system (Herrmann et al 2015 Fusion Eng. Des. 98–9 1496–9). Designed as near replicas of the geometries used also in separate experiments on the JET tokamak (Coenen et al 2015 J. Nucl. Mater. 463 78–84; Coenen et al 2015 Nucl. Fusion
55 023010; Matthews et al 2016 Phys. Scr. T167 7), the samples featured a misaligned leading edge and a sloped ridge respectively. Both structures protrude above the default target plate surface thus receiving an increased fraction of the parallel power flux. Transient melting by ELMs was induced by moving the outer strike point to the sample location. The temporal evolution of the measured current flow from the samples to vessel potential confirmed transient melting. Current magnitude and dependency from surface temperature provided strong evidence for thermionic electron emission as main origin of the replacement current driving the melt motion. The different melt patterns observed after exposures at the two sample geometries support the thermionic electron emission model used in the MEMOS melt motion code, which assumes a strong decrease of the thermionic net current at shallow magnetic field to surface angles (Pitts et al 2017 Nucl. Mater. Energy
12 60–74). Post exposure ex situ analysis of the retrieved samples show recrystallization of tungsten at the exposed surface areas to a depth of up to several mm. The melt layer transport to less exposed surface areas leads to ratcheting pile up of re-solidified debris with zonal growth extending from the already enlarged grains at the surface.
A new wave of marine evidence-based management: emerging challenges and solutions to transform monitoring, evaluating, and reporting
Authors: Addison P F E , Collins D J , Trebilco R , Howe S , Bax N , Hedge P , Jones G , Miloslavich P , Roelfsema C , Sams M , Stuart-Smith R D , Scanes P , von Baumgarten P , McQuatters-Gollop A 
Published: November 2017

Abstract
Sustainable management and conservation of the world’s oceans requires effective monitoring, evaluation, and reporting (MER). Despite the growing political and social imperative for these activities, there are some persistent and emerging challenges that marine practitioners face in undertaking these activities. In 2015, a diverse group of marine practitioners came together to discuss the emerging challenges associated with marine MER, and potential solutions to address these challenges. Three emerging challenges were identified: (i) the need to incorporate environmental, social and economic dimensions in evaluation and reporting; (ii) the implications of big data, creating challenges in data management and interpretation; and (iii) dealing with uncertainty throughout MER activities. We point to key solutions to address these challenges across MER activities: (i) integrating models into marine management systems to help understand, interpret, and manage the environmental and socio-economic dimensions of uncertain and complex marine systems; (ii) utilizing big data sources and new technologies to collect, process, store, and analyze data; and (iii) applying approaches to evaluate, account for, and report on the multiple sources and types of uncertainty. These solutions point towards a potential for a new wave of evidence-based marine management, through more innovative monitoring, rigorous evaluation and transparent reporting. Effective collaboration and institutional support across the science–management–policy interface will be crucial to deal with emerging challenges, and implement the tools and approaches embedded within these solutions.
Effective Faithful Tropicalizations Associated to Adjoint Linear Systems
Authors: Kawaguchi Shu , Yamaki Kazuhiko 
Published: November 2017

AbstractLet R be a complete discrete valuation ring of equi-characteristic zero with fraction field K. Let X be a connected smooth projective variety of dimension d over K, and let L be an ample line bundle over X. We assume that there exist a regular strictly semistable model ${\mathscr {X}}$ of X over R and a relatively ample line bundle ${\mathscr {L}}$ over ${\mathscr {X}}$ with $\left .{{\mathscr {L}}}\right \vert_{{X}} \cong L$. Let $S({\mathscr {X}})$ be the skeleton associated to ${\mathscr {X}}$ in the Berkovich analytification Xan of X. In this article, we study when $S({\mathscr {X}})$ is faithfully tropicalized into tropical projective space by the adjoint linear system |L⊗m ⊗ ωX|. Roughly speaking, our results show that if m is an integer such that the adjoint bundle is basepoint free, then the adjoint linear system admits a faithful tropicalization of $S({\mathscr {X}})$.
Microbiota and HDL metabolism
Authors: Nakaya Kazuhiro , Ikewaki Katsunori 
Published: November 2017

Purpose of review
Accumulating evidence has provided new insights regarding potentially effective therapeutic options targeting modulation of HDL metabolism, resulting in the prevention of cardiovascular diseases. The gut microbiota has now been convincingly linked to host health, but its impact on host lipid metabolism, especially HDL metabolism, remains poorly understood. This review focuses on the recent progress in establishing associations between gut microbiota and host HDL metabolism. It also discusses causality and mechanisms, and how to translate the findings into clinical use.

Recent findings
Recent human and animal studies have demonstrated that the gut microbiota composition can explain a substantial proportion of the individual variation in host blood lipid profiles. In addition, signaling molecules produced by gut microbiota have been shown to have potent effects on reverse cholesterol transport, a crucial atheroprotective function of HDL, which could subsequently influence the development of atherosclerosis. Ultimately, selective manipulation of gut microbiota may serve as an ideal therapeutic approach for improving HDL function and cardiovascular risk, although further studies are needed for a better understanding of which specific bacteria, or alternatively, which bacterial metabolites, are appropriate targets.

Summary
We are just beginning to understand how the gut microbiota, a newly recognized endocrine organ system, influences HDL metabolism and atherosclerotic diseases. From recent experimental and clinical perspectives, it can be targeted for therapeutic benefit with respect to HDL function and cardiovascular diseases.
Pediatric and adolescent anterior shoulder instability: clinical management of first-time dislocators
Authors: Lin Kenneth M. , James Evan W. , Spitzer Elad , Fabricant Peter D. 
Published: November 2017

Purpose of reviewThe purpose of this review is to discuss the epidemiology, pathoanatomy, diagnosis, and clinical management of pediatric and adolescent patients following a first-time shoulder dislocation.Recent findingsShoulder instability is becoming increasingly common as pediatric and adolescent patients engage in earlier organized sports competition. Recommended treatment following a first-time glenohumeral dislocation event in adolescents depends on several factors, but surgical stabilization is becoming more frequently performed. Surgical indications include bony Bankart lesion, ALPSA lesion, bipolar injury (e.g. Hill–Sachs humeral head depression fracture) or off-season injury in an overhead or throwing athlete. Complications following surgical treatment are rare but most commonly are associated with recurrent instability. Young children (eg. open proximal humerus growth plate), individuals averse to surgery, or in-season athletes who accept the risk of redislocation may complete an accelerated rehabilitation program for expedited return to play in the absence of the structural abnormalities listed above.SummaryFollowing a first-time dislocation event in pediatric and adolescent patients, a detailed discussion of the risks and benefits of nonoperative versus operative management is critical to match the recommended treatment with the patient's injury pattern, risk factors, and activity goals.
Management of hypertonia in cerebral palsy
Authors: Nahm Nickolas J. , Graham H. Kerr , Gormley Mark E. , Georgiadis Andrew G. 
Published: November 2017

Purpose of review
The review provides an update on the treatment of hypertonia in cerebral palsy, including physical management, pharmacotherapy, neurosurgical, and orthopedic procedures.

Recent findings
Serial casting potentiates the effect of Botulinum neurotoxin A injections for spasticity. Deep brain stimulation, intraventricular baclofen, and ventral and dorsal rhizotomy are emerging tools for the treatment of dystonia and/or mixed tone. The long-term results of selective dorsal rhizotomy and the timing of orthopedic surgery represent recent advances in the surgical management of hypertonia.

Summary
Management of hypertonia in cerebral palsy targets the functional goals of the patient and caregiver. Treatment options are conceptualized as surgical or nonsurgical, focal or generalized, and reversible or irreversible. The role of pharmacologic therapies is to improve function and mitigate adverse effects. Further investigation, including clinical trials, is required to determine the role of deep brain stimulation, intraventricular baclofen, orthopedic procedures for dystonia, and rhizotomy.
All dispersal functions are wrong, but many are useful: A response to Cousens et al.
Authors: Bullock James M. , Hooftman Danny A. P. , Tamme Riin , Götzenberger Lars , Pärtel Meelis , Mallada González Laura , White Steven M. 
Published: November 2017

Abstract

To address the lack of information about the shape and extent of real dispersal kernels, Bullock et al. (Journal of Ecology 105:6‐19, 2017) synthesised empirical information on seed dispersal distances. Testing the fit of a variety of probability density functions, they found no function was the best‐fitting for all datasets but some outperformed others. Cousens et al. (Journal of Ecology, 2017) focus on the specific finding of the generally poor fit of the WALD function to wind dispersal data and use this to argue that mechanistically derived functions would not be expected to fit data particularly well.

We agree in part with this argument and discuss the issues that may lead to poor fit, including the simplifying assumptions of the WALD and the complexity of the dispersal process. We explain the fundamental linkage between the mechanistic form of the WALD and the derived function used for fitting to data.

We demonstrate, however, that the logic that a mechanistically based function could fit to data is valid, under the hypothesis that it encompasses the key processes determining the dispersal kernel. This argument is supported by the facts that: (1) our analyses and others have shown the WALD performs well in a number of cases; and (2) the WALD is the best‐fitting function for an example in which we simulate dispersal data using a realistic representation of variability in the wind dispersal process.

Synthesis. While there are reasons that mechanistically derived functions may not fit well to empirical data, they do in some empirical and simulated cases and this suggests they can capture the dispersal behaviour of real systems. Mechanistic functions should be explored along with other more general functions when describing empirical data to investigate their simplifying assumptions and to add to our arsenal of functions for analysing dispersal data. Analyses using these functions are critical if we are to move from simply describing the system in which the data were gathered to gaining more general insights into dispersal and predicting its consequences.
Characterization of Volatile Sulfur Compounds in Moutai Liquors by Headspace Solid‐Phase Microextraction Gas Chromatography‐Pulsed Flame Photometric Detection and Odor Activity Value
Authors: Chen Shuang , Sha Sha , Qian Michael , Xu Yan 
Published: November 2017

AbstractThis study investigated the aroma contribution of volatile sulfur compounds (VSCs) in Moutai liquors. The VSCs were analyzed using headspace solid‐phase microextraction‐gas chromatography‐pulsed flame photometric detection (HS‐SPME‐GC‐PFPD). The influences of SPME fibers, ethanol content in the sample, pre‐incubation time, and extraction temperature and time on the extraction of VSCs were optimized. The VSCs were optimally extracted using a divinylbenzene/carboxen/polydimethylsiloxane fiber, by incubating 10 mL diluted Chinese liquor (5% vol.) with 3 g NaCl at 30 °C for 15 min, followed by a subsequent extraction for 40 min at 30 °C. The optimized method was further validated. A total of 13 VSCs were identified and quantified in Moutai liquors. The aroma contribution of these VSCs were evaluated by their odor activity values (OAVs), with the result that 7 of 13 VSCs had OAVs > 1. In particular, 2‐furfurylthiol, methanethiol, dimethyl trisulfide, ethanethiol, and methional had relatively high OAVs and could be the key aroma contributors to Moutai liquors.Practical ApplicationIn this study, a method for analyzing volatile sulfur compounds in Chinese liquors has been developed. This method will allow an in‐depth study the aroma contribution of volatile sulfur compounds in Chinese liquors. Seven volatile sulfur compounds were identified as potential key aroma contributors for Moutai liquors, which can help to the quality control of Moutai liquors.
Competitive foreclosure
Authors: Burguet Roberto , Sákovics József 
Published: November 2017

AbstractWe model oligopolistic firms, producing substitutes, who compete for inputs from capacity constrained suppliers in a decentralized market. Compared to a price‐taking input market, the incentive to foreclose downstream competitors leads to higher input prices and to a higher aggregate amount of input acquired. This novel feature mitigates the output reducing effect of downstream market power and may even restore efficiency in the unique (input) market clearing equilibrium. Other equilibria, where firms coordinate on which suppliers to target, result in excess supply (involuntary unemployment, if input is labor) and even higher input prices. Our insights generalize to alternative vertical structures.
Association between plasma fibrinogen and survival in patients with small‐cell lung carcinoma
Authors: Fan Shanshan , Guan Yin , Zhao Guanfei , An Guangyu 
Published: November 2017

BackgroundElevated plasma fibrinogen (Fbg) levels contribute to tumor progression and metastasis; however, limited research on Fbg in small cell lung cancer (SCLC) has been conducted. This study evaluated the prognostic value of Fbg levels in patients with SCLC.MethodsData on plasma Fbg level, clinical features, and overall survival were retrospectively collected. Kaplan–Meier estimates and log‐rank tests were used to analyze the relationship between Fbg level and survival. Multivariate analyses were performed to determine independent prognostic factors. Subgroup analyses were performed based on extensive/limited disease and Eastern Cooperative Oncology Group status.ResultsA total of 120 patients with SCLC were included. The one, three, and five‐year survival rates for the entire cohort were 48.3%, 9.2%, and 1.7%, respectively. Univariate analyses revealed that age, alcohol use, clinical stage, pleural effusion, Eastern Cooperative Oncology Group grade, and Fbg and lactate dehydrogenase levels were associated with survival (P < 0.05). The median survival time for patients with high Fbg levels (> 400 mg/dL) was shorter than for those with low Fbg levels (8 vs. 14 months; P = 0.013). Furthermore, multivariate analysis revealed that Fbg was negatively and independently associated with SCLC prognosis (hazard ratio 1.505, 95% confidence interval 1.018–2.226; P = 0.041). Higher Fbg levels were associated with shorter survival in the extensive disease subgroup (7 vs. 12 months; P = 0.004).ConclusionsElevated plasma Fbg was an independent factor associated with poor outcomes in SCLC patients and could serve as a prognostic biomarker.
Multiresponse algorithms for community‐level modelling: Review of theory, applications, and comparison to species distribution models
Authors: Nieto‐Lugilde Diego , Maguire Kaitlin C. , Blois Jessica L. , Williams John W. , Fitzpatrick Matthew C. 
Published: November 2017

Abstract

Community‐level models (CLMs) consider multiple, co‐occurring species in model fitting and are lesser known alternatives to species distribution models (SDMs) for analysing and predicting biodiversity patterns. Community‐level models simultaneously model multiple species, including rare species, while reducing overfitting and implicitly considering drivers of co‐occurrence. Many CLMs are direct extensions of well‐known SDMs and therefore should be familiar to ecologists. However, CLMs remain underutilized, and there have been few tests of their potential benefits and no systematic reviews of their assumptions and implementations. Here, we review this emerging field and provide examples in r to fit common CLMs. Our goal is to introduce CLMs to a broader audience, and discuss their attributes, benefits and limitations relative to SDMs.

We review (1) statistical implementations and applications of CLMs, (2) their advantages and limitations, and (3) comparative analyses of CLMs and SDMs. We also suggest directions for future research.

We identify seven CLM algorithms with similar data structures and predictive outputs as SDMs that should be most accessible to ecologists familiar with species‐level modelling, including five methods that predict assemblage composition and individual species distributions and two methods that model compositional turnover along environmental gradients. Community‐level models have been applied to numerous taxa, regions, and spatial scales, and a variety of topics (e.g. studying drivers of community structure or assessing relationships between community composition and functional traits). Studies suggest that the relative benefits of CLMs and SDMs may be case specific, especially in terms of predicting species distributions and community composition. However, CLMs may offer advantages in terms of computational efficiency, modelling rare species, and projecting to no‐analog climates. A major shortcoming of CLMs is their reliance on presence–absence community composition data.

Studies are needed to assess the relative merits of SDMs and CLMs, and different CLM algorithms, with a focus on three key areas: (1) under which circumstances CLMs improve predictions for rare species, (2) how CLMs perform under different community compositions (e.g. relative abundance of rare vs. common species), including the extent to which co‐occurrence patterns are structured by biotic interactions, and (3) ability to project across time/space.
A simple centrifugation protocol for metagenomic studies increases mitochondrial DNA yield by two orders of magnitude
Authors: Macher Jan‐Niklas , Zizka Vera Marie Alida , Weigand Alexander Martin , Leese Florian 
Published: November 2017

Abstract

DNA (meta)barcoding is applied to study biodiversity and is available for standardized biodiversity assessments. However, it suffers from PCR bias, which can lead to the loss of specific taxa. PCR‐free techniques such as shotgun metagenomics are therefore thought to be more suited for biodiversity assessments, but are currently limited by incomplete reference libraries.

The technique of “mitogenome‐skimming” or “mitogenomics,” in which complete mitochondrial genomes are sequenced, is ideal to bridge the techniques of (meta)barcoding and metagenomics. However, without the enrichment of mitochondria, roughly 99% of all sequencing reads are of non‐mitochondrial origin and mostly useless for common applications, e.g. species identification.

Here, we present a simple centrifugation protocol that leads to an average 140‐fold enrichment of mitochondrial DNA. By sequencing six ‘mock’‐communities—comprising the freshwater taxa Corbicula fluminea, Gammarus roeselii and Hydropsyche exocellata each—we recovered whole mitochondrial genomes of these species and the acanthocephalan endoparasite Pomphorhynchus laevis.

The enrichment protocol will speed up building reference libraries for whole mitochondrial genomes, as dozens of species can be sequenced on a single MiSeq run. Subsequently, it will also allow biodiversity assessments, using mitogenomics at greatly reduced costs in comparison to mitogenomic approaches without prior enrichment for mitochondria.