bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulations of QCD and QED with C* boundary conditions
Authors: Hansen Martin , Lucini Biagio , Patella Agostino , Tantalo Nazario 
Published: March 2018

We present exploratory results from dynamical simulations of QCD in isolation, as well as QCD coupled to QED, with C* boundary conditions. In finite volume, the use of C* boundary conditions allows for a gauge invariant and local formulation of QED without zero modes. In particular we show that the simulations reproduce known results and that masses of charged mesons can be extracted in a completely gauge invariant way. For the simulations we use a modified version of the HiRep code. The primary features of the simulation code are presented and we discuss some details regarding the implementation of C* boundary conditions and the simulated lattice action.
Preprint: CP3-Origins-2017-046 DNRF90, CERN-TH-2017-214
Topological susceptibility with a single light quark flavour
Authors: Frison Julien , Kitano Ryuichiro , Yamada Norikazu 
Published: March 2018

One of the historical suggestions to tackle the strong CP problem is to take the up quark mass to zero while keeping md finite. The θ angle is then supposed to become irrelevant, i.e. the topological susceptibility vanishes. However, the definition of the quark mass is scheme-dependent and identifying the mu = 0 point is not trivial, in particular with Wilson-like fermions. More specifically, up to our knowledge there is no theoretical argument guaranteeing that the topological susceptibility exactly vanishes when the PCAC mass does.
We will present our recent progresses on the empirical check of this property using Nf = 1 + 2 flavours of clover fermions, where the lightest fermion is tuned very close to [see formula in PDF] and the mass of the other two is kept of the order of magnitude of the physical ms. This choice is indeed expected to amplify any unknown non-perturbative effect caused by mu ≠ md. The simulation is repeated for several βs and those results, although preliminary, give a hint about what happens in the continuum limit.
Verification of real-time WSA−ENLIL+Cone simulations of CME arrival-time at the CCMC from 2010 to 2016
Authors: Wold Alexandra M. , Mays M. Leila , Taktakishvili Aleksandre , Jian Lan K. , Odstrcil Dusan , MacNeice Peter 
Published: March 2018

The Wang-Sheeley-Arge (WSA)−ENLIL+Cone model is used extensively in space weather operations world-wide to model coronal mass ejection (CME) propagation. As such, it is important to assess its performance. We present validation results of the WSA−ENLIL+Cone model installed at the Community Coordinated Modeling Center (CCMC) and executed in real-time by the CCMC space weather team. CCMC uses the WSA−ENLIL+Cone model to predict CME arrivals at NASA missions throughout the inner heliosphere. In this work we compare model predicted CME arrival-times to in situ interplanetary coronal mass ejection leading edge measurements at Solar TErrestrial RElations Observatory-Ahead (STEREO-A), Solar TErrestrial RElations Observatory-Behind (STEREO-B), and Earth (Wind and ACE) for simulations completed between March 2010 and December 2016 (over 1,800 CMEs). We report hit, miss, false alarm, and correct rejection statistics for all three locations. For all predicted CME arrivals, the hit rate is 0.5, and the false alarm rate is 0.1. For the 273 events where the CME was predicted to arrive at Earth, STEREO-A, or STEREO-B, and was actually observed (hit event), the mean absolute arrival-time prediction error was 10.4 ± 0.9 h, with a tendency to early prediction error of −4.0 h. We show the dependence of the arrival-time error on CME input parameters. We also explore the impact of the multi-spacecraft observations used to initialize the model CME inputs by comparing model verification results before and after the STEREO-B communication loss (since September 2014) and STEREO-A sidelobe operations (August 2014–December 2015). There is an increase of 1.7 h in the CME arrival time error during single, or limited two-viewpoint periods, compared to the three-spacecraft viewpoint period. This trend would apply to a future space weather mission at L5 or L4 as another coronagraph viewpoint to reduce CME arrival time errors compared to a single L1 viewpoint.
Acute Cellular Rejection: Is It Still Relevant?
Authors: Koutsokera Angela , Levy Liran , Pal Prodipto , Orchanian-Cheff Ani , Martinu Tereza 
Published: March 2018

AbstractDespite significant progress in the field of transplant immunology, acute cellular rejection (ACR) remains a very frequent complication after lung transplantation (LTx), with almost 30% of LTx recipients experiencing at least one episode of treated ACR during the first year of follow-up. Most episodes respond to the first-line immunosuppressive treatment and are rarely a direct cause of death. However, the association of ACR with later adverse outcomes, such as chronic lung allograft dysfunction, bronchial stricture, and infectious complications associated with the intensification of immunosuppression, negatively impacts long-term survival. The burden imposed on patients and health-care resources is even higher in cases of refractory or recurrent ACR, which accelerates lung function decline. Although important laboratory and clinical research conducted over the last two decades has improved our understanding of the mechanisms underlying ACR, there are still many uncertainties about the risk factors for ACR, the optimal monitoring strategies, and the prediction of long-term outcomes. These knowledge gaps contribute to the large variability in clinical practice among LTx centers, which renders multicenter studies of ACR challenging. In this review, we summarize current evidence on the epidemiology, pathogenesis, and risk factors of ACR. We describe diagnostic and therapeutic approaches that are currently used in the clinical practice and also review promising diagnostic tools that are under investigation. Associations between ACR and other adverse outcomes of LTx are examined. Finally, within each topic of discussion, we highlight the main areas of controversy and opportunities for future research.
Fungal Infections Complicating Lung Transplantation
Authors: Clark Nina , Weigt S. , Fishbein Michael , Kubak Bernard , Belperio John , Lynch Joseph 
Published: March 2018

AbstractLung transplantation is an increasingly utilized modality for treating advanced lung disease. However, lung transplant recipients (LTRs) experience high rates of infection-related mortality and, compared with other solid organ transplant recipients, are at increased risk of infectious complications given the intensity of immunosuppression employed, the presence of airway abnormalities after surgery and exposure of the allograft to the environment. Fungal infections, particularly mold infections, are problematic after transplantation as they are often associated with limited treatment options and poor outcomes. We describe the non-Candida fungal infections occurring in LTRs, including their epidemiology, clinical features, and treatment.
Chronic Lung Allograft Dysfunction: Evolving Concepts and Therapies
Authors: DerHovanessian Ariss , Wallace W. , Lynch Joseph , Belperio John , Weigt S. 
Published: March 2018

AbstractLung transplantation has become an established therapeutic option for a variety of end-stage lung diseases. Technical advances in graft procurement, implantation, perioperative care, immunosuppression, and posttransplant medical management have led to significant improvements in 1-year survival, but outcomes after the first year have improved minimally over the last two decades. The main limitation to better long-term survival after lung transplantation is chronic lung allograft dysfunction (CLAD). CLAD also impairs quality of life and increases the costs of medical care. Our understanding of CLAD manifestations, risk factors, and mechanisms is rapidly evolving. Recognition of different CLAD phenotypes (e.g., bronchiolitis obliterans syndrome and restrictive allograft syndrome) and the unique pathogenic mechanisms will be important for developing novel therapies. In addition to alloimmune-mediated rejection, we now recognize the importance of alloimmune-independent mechanisms of injury to the allograft. CLAD is the consequence of dysregulated repair of allograft injury. Unfortunately, currently available therapies for CLAD are usually not effective. However, the advances in knowledge, reviewed in this manuscript, should lead to novel strategies for CLAD prevention and treatment, as well as improvement in long-term outcomes after lung transplantation. We provide an overview of the evolving terminology related to CLAD, its varying clinical phenotypes and their diagnosis, natural history, pathogenesis, and potential treatments.
Homeopathy for Perennial Asthma in Adolescents: Pilot Feasibility Study Testing a Randomised Withdrawal Design
Authors: Mitchiguian Hotta Livia , de Toledo Cesar Amarilys , Martinez Edson , Demarzo Marcelo , Cardinalli Adler Ubiratan 
Published: March 2018

Introduction Previous findings from a pragmatic trial suggest that usual care compared with usual care plus individualised homeopathy is not a feasible design to address homeopathic interventions for asthma.
Objective The main purpose of this article was to investigate the feasibility of the randomised withdrawal design as a strategy to assess the effectiveness of a standardised clinical–pharmaceutical homeopathic protocol (Organon.modus) on perennial asthma in adolescents.
Methods Randomised withdrawal, double-blind, parallel, placebo-controlled, 12-week study. Patients: 12 to 17 years old adolescents, with the diagnosis of perennial asthma, using inhalatory beclomethasone (plus fenoterol for wheezing episodes), who achieved 3 months of well-controlled asthma, after a variable period of individualised homeopathic treatment according to Organon.modus protocol. Setting: a secondary care medical specialist centre. Intervention: continuation with the individualised homeopathic medicine or with indistinguishable placebo during 12 weeks of beclomethasone step-down. Primary outcome: number of days of well-controlled asthma. Secondary measures: number of days of fenoterol use, number of visits to an emergency service (without hospitalisation) and percentage of patients excluded due to an exacerbation characterising a partly controlled asthma. Tolerability was assessed by Adverse Events, registered at every visit.
Results Nineteen patients were randomised to continue treatment with homeopathy and 21 with placebo. Effectiveness measures for the homeopathy and placebo groups respectively were median number of days of good clinical control: 84 versus 30 (p = 0.18); median number of days of fenoterol use per patient: 3 versus 5 (p = 0.41); visits to an emergency room: 1 versus 6 (p = 0.35); percentage of exclusion due to partly controlled asthma: 36.8% versus 71.4% (p = 0.05). Few Adverse Events were reported.
Conclusions This pilot study supports the feasibility of the double-blind randomised withdrawal design in studies investigating homeopathy on teenage asthma, when performed by specialists following a standardised clinical–pharmaceutical homeopathic protocol.
Clinical Trial Registration RBR-6XTS8Z.
Risk Factors for Neonatal Hypoxic-Ischemic Encephalopathy in the Absence of Sentinel Events
Authors: Eke Ahize , Ozen Maide , Burd Irina , Graham Ernest , Novak Christopher 
Published: March 2018

Objective Hypoxic-ischemic encephalopathy (HIE) may be associated with intrapartum sentinel events or may be unexplained. We sought to identify risk factors for unexplained HIE cases and compare their morbidity and mortality to cases associated with sentinel events.
Study Design Retrospective cohort study of all neonates admitted with suspected HIE treated with whole-body hypothermia from January 2007 through July 2017. Cases of unexplained HIE were compared with those with a sentinel event.
Results A total of 223 neonates met the inclusion criteria, of which 86 (38.6%) experienced a sentinel event and 137 (61.4%) did not. Placental histopathology was performed for 28/31 (90.3%) and 48/53 (90.6%) inborn neonates with and without sentinel events, respectively. Placentas from unexplained HIE cases more often exhibited histologic chorioamnionitis (43.8% vs. 17.9%, p = 0.02) and funisitis (25% vs. 3.6%, p = 0.02). Neonatal morbidity and mortality were similar. On multivariable regression, nulliparity (odds ratio [OR], 4.11, 95% confidence interval [CI]: 1.24–13.62) and histologic funisitis (OR, 20.33, 95% CI: 1.11–373.4) remained significant.
Conclusion Other than nulliparity and infection which could be identified on umbilical cord examination following delivery but not on clinical assessment prior to delivery, there are no other identifiable risk factors for HIE in the absence of a sentinel event, and morbidity and mortality are similar between groups.
Exploring the structural origins of cryptic sites on proteins
Authors: Beglov Dmitri , Hall David R. , Wakefield Amanda E. , Luo Lingqi , Allen Karen N. , Kozakov Dima , Whitty Adrian , Vajda Sandor 
Published: March 2018

Significance
Cryptic binding sites are absent or occluded in unbound proteins but present in ligand-bound structures. They can provide druggable pockets in cases where the main functional site of the protein cannot be targeted with sufficient potency or specificity. We show that unbound structures of proteins with cryptic sites have strong binding hot spots and above-average flexibility around the incipient pockets. Binding hot spots can be easily identified computationally, and protein flexibility can often be assessed by the analysis of X-ray structures of the unbound protein, including structures with low resolution. The approach presented here helps to assess the potential druggability of cryptic sites prior to running expensive screening experiments and reveals information about how cryptic sites form.
Rapid enhancement of chemical weathering recorded by extremely light seawater lithium isotopes at the Permian–Triassic boundary
Authors: Sun He , Xiao Yilin , Gao Yongjun , Zhang Guijie , Casey John F. , Shen Yanan 
Published: March 2018

Significance
Estimates of seawater Li isotopic composition at the Permian–Triassic boundary (PTB) reveal extremely light seawater Li isotopic signatures accompanying the most severe mass extinction in the history of animal life. Theoretical modeling indicates a rapid enhancement of continental weathering during this time, which was likely triggered by the eruption of the Siberian Traps, rapid global warming, and acid rains. Our results provide independent geochemical evidence for an enhanced continental chemical weathering at the PTB, illustrating that continental weathering may provide a key link between terrestrial and marine ecological crises.
Energetic tradeoffs control the size distribution of aquatic mammals
Authors: Gearty William , McClain Craig R. , Payne Jonathan L. 
Published: March 2018

Significance
The reasons why aquatic mammals exhibit larger average sizes than their terrestrial relatives have long been debated. Most previous hypotheses have focused on releases from terrestrial constraints on large sizes. Through the analysis of mammal size distributions, we find the aquatic realm imposes stronger constraints on body size than does the terrestrial realm, driving and confining aquatic mammals to larger sizes. Calculations of energy intake and demand as a function of body size indicate heat loss imposes a strong lower bound on size, whereas the scaling of feeding rate versus metabolic rate imposes a constraint on maximum size. Rather than freeing animals from body size constraints, living in water appears to impose stronger selective pressures than does living on land.
Grassland biodiversity can pay
Authors: Binder Seth , Isbell Forest , Polasky Stephen , Catford Jane A. , Tilman David 
Published: March 2018

Significance
Ecological research suggests that greater biodiversity could lead to greater economic value, even for private owners of “working” land. However, the studies from which such a conclusion might be inferred do not account for all relevant information in a coherent economic framework. Our paper applies standard economic theory to rigorously account for costs, quality, and risk. Results indicate that higher levels of biodiversity than are typically observed on commercial grasslands would maximize landowner value in the experimental grassland we study. Greater private benefits from biodiversity could encourage private investment in biodiversity and reduce the cost of public conservation efforts.
Cracking the social code of speech prosody using reverse correlation
Authors: Ponsot Emmanuel , Burred Juan José , Belin Pascal , Aucouturier Jean-Julien 
Published: March 2018

Significance
In speech, social evaluations of a speaker’s dominance or trustworthiness are conveyed by distinguishing, but little-understood, pitch variations. This work describes how to combine state-of-the-art vocal pitch transformations with the psychophysical technique of reverse correlation and uses this methodology to uncover the prosodic prototypes that govern such social judgments in speech. This finding is of great significance, because the exact shape of these prototypes, and how they vary with sex, age, and culture, is virtually unknown, and because prototypes derived with the method can then be reapplied to arbitrary spoken utterances, thus providing a principled way to modulate personality impressions in speech.
Escalation of competition into conflict in competitive networks of Formula One drivers
Authors: Piezunka Henning , Lee Wonjae , Haynes Richard , Bothner Matthew S. 
Published: March 2018

Significance
Competition, while often seen as beneficial, can escalate into destructive conflict. This occurs, for instance, when athletes sabotage each other or when rival executives get caught up in a career-derailing fight. These escalations into conflict are especially likely among status-similar competitors, who are fraught with discordant understandings of who is superior to whom. We examine the link between status similarity and conflict as well as the conditions under which this link holds. We find that status-similar Formula One drivers are more prone to collide, especially when they are age-similar, perform well, are embedded in a stable role structure, and feel safe. Our inquiry deepens our understanding of when violent conflict emerges and can guide conflict prevention efforts.
Small proline-rich protein 2B drives stress-dependent p53 degradation and fibroblast proliferation in heart failure
Authors: Burke Ryan M. , Lighthouse Janet K. , Quijada Pearl , Dirkx Ronald A. , Rosenberg Alexander , Moravec Christine S. , Alexis Jeffrey D. , Small Eric M. 
Published: March 2018

Significance
Heart disease is associated with the development of fibrosis, a type of scarring that impedes cardiac function. The primary cellular source of cardiac fibrosis is the resident cardiac fibroblast. We found that cardiac fibroblasts from human heart failure patients or a mouse model of heart disease express excessive amounts of the SPRR2B protein. We provide evidence that SPRR2B is a signal-responsive regulatory subunit of the p53 ubiquitination complex that stimulates the destruction of p53 and the accumulation of pathological fibroblasts. This study defines a unique mechanism of cell cycle control that is dysfunctional in heart disease and may drive the development pathological fibrosis.
Molecular and structural architecture of polyQ aggregates in yeast
Authors: Gruber Anselm , Hornburg Daniel , Antonin Matthias , Krahmer Natalie , Collado Javier , Schaffer Miroslava , Zubaite Greta , Lüchtenborg Christian , Sachsenheimer Timo , Brügger Britta , Mann Matthias , Baumeister Wolfgang , Hartl F. Ulrich , Hipp Mark S. , Fernández-Busnadiego Rubén 
Published: March 2018

Significance
How protein aggregation leads to neurodegenerative disorders such as Huntington’s disease remains poorly understood. Here we show that polyglutamine (polyQ) aggregation in yeast results in the formation of amorphous inclusions and less frequent fibrils. This is accompanied by significant changes in proteome composition as well as distortions in mitochondria and lipid droplet morphology that do not arise from direct interactions of these organelles with polyQ inclusions or fibrils. This contrasts with recent observations in mammalian cells, where the same polyQ proteins formed amyloid-like fibrils that distort endoplasmic reticulum membranes. These results demonstrate that the same polyQ expansion protein can adopt different nonnative conformations that utilize distinct mechanisms to target a variety of cellular structures.
NAA80 is actin’s N-terminal acetyltransferase and regulates cytoskeleton assembly and cell motility
Authors: Drazic Adrian , Aksnes Henriette , Marie Michaël , Boczkowska Malgorzata , Varland Sylvia , Timmerman Evy , Foyn Håvard , Glomnes Nina , Rebowski Grzegorz , Impens Francis , Gevaert Kris , Dominguez Roberto , Arnesen Thomas 
Published: March 2018

Significance
More than 80% of human proteins are N-terminal (Nt)–acetylated during translation. In contrast, actin, the most abundant protein in the cytoplasm of animal cells, is Nt-acetylated posttranslationally and following a unique multistep mechanism that has remained poorly characterized. Here, we describe the discovery of actin’s N-terminal acetyltransferase (NAT), NAA80. We further demonstrate that actin Nt-acetylation plays essential roles in filament assembly, cytoskeleton organization, and cell motility, resulting in a net increase in the ratio of monomeric to filamentous actin and fewer lamellipodia and filopodia. These effects converge to reduce cell hypermotility. This work establishes the role of Nt-acetylation for the most abundant cytoskeletal protein in animals and reveals a NAT acting posttranslationally and on a single dedicated substrate.
RNA-mediated gene regulation is less evolvable than transcriptional regulation
Authors: Payne Joshua L. , Khalid Fahad , Wagner Andreas 
Published: March 2018

Significance
Cells regulate the activity of genes in a variety of ways. For example, they regulate transcription through DNA binding proteins called transcription factors, and they regulate mRNA stability and processing through RNA binding proteins. Based on current knowledge, transcriptional regulation is more widespread and is involved in many more evolutionary adaptations than posttranscriptional regulation. The reason could be that transcriptional regulation is studied more intensely. We suggest instead that transcriptional regulation harbors an intrinsic evolutionary advantage: when mutations change transcriptional regulation, they are more likely to bring forth novel patterns of such regulation. That is, transcriptional regulation is more evolvable. Our analysis suggests a reason why a specific kind of gene regulation is especially abundant in the living world.
Crystal structure of human lysyl oxidase-like 2 (hLOXL2) in a precursor state
Authors: Zhang Xi , Wang Qifan , Wu Jianping , Wang Jiawei , Shi Yigong , Liu Minhao 
Published: March 2018

Significance
Lysyl oxidases (LOXs) catalyze oxidative deamination of peptidyl lysines on collagen and elastin, generating a highly reactive aldehyde group to initiate intermolecular cross-linking. In humans, this reaction plays fundamental roles in the formation and repair of extracellular matrix fiber networks and the development of connective tissues. Moreover, a relationship between LOX proteins and tissue fibrosis and cancer has been established. Since the identification of prototypic LOX, the atomic structure of LOX protein has remained to be elucidated. Here, we present the high-resolution structure of human lysyl oxidase-like 2 protein. The zinc-bound precursor-state structure provides an important framework for understanding the structure–function relationship of the LOX family and for drug discovery that aims to block LTQ generation of LOX proteins.