bluuebunny/crossref_metadata_2025_split huggingface dataset:
A paradox for air pollution controlling in China revealed by “APEC Blue” and “Parade Blue”
Authors: Liu Haoran , Liu Cheng , Xie Zhouqing , Li Ying , Huang Xin , Wang Shanshan , Xu Jin , Xie Pinhua 
Published: September 2016

AbstractA series of strict emission control measures were implemented in Beijing and surrounding regions to ensure good air quality during the 2014 Asia-Pacific Economic Cooperation (APEC) summit and 2015 Grand Military Parade (Parade), which led to blue sky days during these two events commonly referred to as “APEC Blue” and “Parade Blue”. Here we calculated Multi-Axis Differential Optical Absorption Spectroscopy (MAX-DOAS) and Ozone Monitoring Instrument (OMI) NO2 and HCHO results based on well known DOAS trace gas fitting algorithm and WRF-Chem model (with measured climatology parameter and newest emission inventor) simulated trace gases profiles. We found the NO2 columns abruptly decreased both Parade (43%) and APEC (21%) compared with the periods before these two events. The back-trajectory cluster analysis and the potential source contribution function (PSCF) proved regional transport from southern peripheral cities plays a key role in pollutants observed at Beijing. The diminishing transport contribution from southern air mass during Parade manifests the real effect of emission control measures on NO2 pollution. Based on the ratios of HCHO over NO2 we found there were not only limited the NO2 pollutant but also suppress the O3 contaminant during Parade, while O3 increased during the APEC.
Cigarette smoke reversibly activates hypoxia-inducible factor 1 in a reactive oxygen species-dependent manner
Authors: Daijo Hiroki , Hoshino Yuma , Kai Shinichi , Suzuki Kengo , Nishi Kenichiro , Matsuo Yoshiyuki , Harada Hiroshi , Hirota Kiichi 
Published: September 2016

AbstractCigarette smoke (CS) is a major contributor to the development of a large number of fatal and debilitating disorders. However, the precise molecular mechanisms underlying the effects of CS in lung disease are largely unknown. To elucidate these pathophysiological processes, we examined the in vitro and in vivo effects of CS extract (CSE) and CS on the transcription factor, hypoxia-inducible factor 1 (HIF-1). CSE induced concentration- and time-dependent accumulation of HIF-1α protein in human lung epithelial-like cells under non-hypoxic conditions. Genes upregulated by HIF-1, including vascular endothelial growth factor and regulated in development and DNA damage response 1, both of which are involved in smoking-induced emphysematous changes, were increased by CSE treatment under non-hypoxic conditions in vitro and in vivo. Further investigation revealed that reactive oxygen species were generated in cells exposed to CSE and were required for CSE-mediated induction of HIF-1α protein, as was activation of phosphoinositide 3-kinase and mitogen-activated protein kinase pathways. In conclusion, we demonstrated that CSE and CS induced HIF-1 activation in vitro and in vivo, respectively. The evidence warrants further investigation to indicate that HIF-1 plays an important role in CS-induced gene expression, which is deeply involved in pulmonary cellular stress and small airway remodelling.
A multilevel nonvolatile magnetoelectric memory
Authors: Shen Jianxin , Cong Junzhuang , Shang Dashan , Chai Yisheng , Shen Shipeng , Zhai Kun , Sun Young 
Published: September 2016

AbstractThe coexistence and coupling between magnetization and electric polarization in multiferroic materials provide extra degrees of freedom for creating next-generation memory devices. A variety of concepts of multiferroic or magnetoelectric memories have been proposed and explored in the past decade. Here we propose a new principle to realize a multilevel nonvolatile memory based on the multiple states of the magnetoelectric coefficient (α) of multiferroics. Because the states of α depends on the relative orientation between magnetization and polarization, one can reach different levels of α by controlling the ratio of up and down ferroelectric domains with external electric fields. Our experiments in a device made of the PMN-PT/Terfenol-D multiferroic heterostructure confirm that the states of α can be well controlled between positive and negative by applying selective electric fields. Consequently, two-level, four-level, and eight-level nonvolatile memory devices are demonstrated at room temperature. This kind of multilevel magnetoelectric memory retains all the advantages of ferroelectric random access memory but overcomes the drawback of destructive reading of polarization. In contrast, the reading of α is nondestructive and highly efficient in a parallel way, with an independent reading coil shared by all the memory cells.
Spina Bifida Occulta in an Adult Presenting as Perilesional Hemorrhage
Authors: Agrawal Amit , Santhi Vissa , Jena Ranjan , Reddy V Umamaheswara , Sandeep Yashwant 
Published: September 2016

AbstractOccult spinal dysraphism with spinal lipoma, is a rare congenital spinal dysraphic anomaly which usually involves lumbosacral region and manifests in childhood. In the present article, we discuss a case of a 26-year-old man who developed sudden low back pain following intercourse. Magnetic resonance imaging of the lumbosacral spine was suggestive of spina bifida occulta with hemorrhage. The patient underwent a L4–5 laminectomy in the emergency. There was the presence of altered blood in the vicinity of the lesion suggestive of recent hemorrhage. Histopathological examination of the lesion was suggestive of the lipoma. In the present case, the patient had occult spina bifida due to lumbosacral lipoma leading to the tethering of the dura. Strenuous activity resulted in overstretching of the tethered structures and subsequent hemorrhage and intense low back pain which responded well to the surgical treatment.
Atrioesophageal Fistula after Minimally Invasive Video-Assisted Epicardial Ablation for Lone Atrial Fibrillation
Authors: Kik Charles , Mokhles Mostafa , Bekkers Jos , Bogers Ad , van Valen Richard 
Published: September 2016

AbstractMinimally invasive video-assisted epicardial beating heart ablation for lone atrial fibrillation claims to be safe and effective. We, however, report on three patients with an atrioesophageal fistula after this procedure. The exact pathogenesis of this complication is unknown. All patients presented around 6 weeks after surgery with either fever or neurological deficits. Diagnosis can be made by computed tomography scan. We advocate an aggressive surgical approach with closure of the atrial defect on cardiopulmonary bypass and closure and reinforcement of the esophagus with an intercostal muscle flap in a single-stage surgery. Some caution as to the low-risk character of this procedure seems to be realistic.
Psychosoziale Belastungen zu verschiedenen Zeitpunkten nach Brandverletzung
Authors: Berg Lea , Meyer Stefanie , Ipaktchi Ramin , Vogt Peter , Müller Astrid , de Zwaan Martina 
Published: September 2016

ZusammenfassungBrandverletzte leiden unter psychischen und sozialen Folgebeeinträchtigungen. In der vorliegenden Studie wurde geprüft, ob sich Patienten mit unterschiedlichen Zeitintervallen seit der Verbrennung im Hinblick auf psychosoziale Belastungen unterscheiden. Patienten, die in der Zeit zwischen 2006 und 2012 aufgrund einer Verbrennung stationär behandelt wurden, beantworteten Fragebögen zu Lebensqualität (Burn Specific Health Scale – Brief; BSHS-B), Angst und Depression (Hospital Anxiety and Depression Scale – Deutsche Version; HADS-D), posttraumatischer Belastungsstörung (PTBS, Impact of Event Scale – Revidierte Version; IES-R), Stigmatisierung (Perceived Stigmatization Questionnaire; PSQ) und sozialer Unterstützung (Fragebogen zur sozialen Unterstützung; F-SozU-7). Auf Basis der unterschiedlichen Zeiträume zwischen Unfall und Erhebungszeitpunkt der Daten fand eine Einteilung der Stichprobe (146 Patienten) in 4 Gruppen statt. Es zeigten sich keine signifikanten Unterschiede im Ausmaß der psychischen Belastung. Auch lagen keine Differenzen in soziodemografischen und verbrennungsspezifischen Merkmalen vor. Insgesamt lagen 18 (12,4%) Patienten im Bereich Angst und 22 (15,2%) Personen im Bereich Depression bei einem Cut-off von ≥11 im HADS. Ein Verdacht auf die Diagnose einer PTBS konnte bei 16 (11,1%) Patienten gestellt werden. Bezüglich laufender Psycho(pharmako)therapie und dem Wunsch nach Psychotherapie glichen sich die Gruppen. Die Ergebnisse deuten auf chronische psychische Beeinträchtigungen nach Verbrennungen hin. Psychosoziale Interventionen können daher auch noch mehrere Jahre nach der Brandverletzung indiziert sein.
Bursts of activity in collective cell migration
Authors: Chepizhko Oleksandr , Giampietro Costanza , Mastrapasqua Eleonora , Nourazar Mehdi , Ascagni Miriam , Sugni Michela , Fascio Umberto , Leggio Livio , Malinverno Chiara , Scita Giorgio , Santucci Stéphane , Alava Mikko J. , Zapperi Stefano , La Porta Caterina A. M. 
Published: September 2016

Significance
During wound healing and in cancer invasion, cells migrate collectively driven by active internal forces and invade the available space. Here we show that this motion occurs by intermittent bursts of activity described by universal scaling laws similar to the ones observed in other driven systems where a front propagates in response to an external force, such as in fracture and fluid imbibition. Our results demonstrate that living systems display universal nonequilibrium critical fluctuations, induced by cell mutual interactions, that are usually associated with externally driven inanimate media.
Two subdivisions of macaque LIP process visual-oculomotor information differently
Authors: Chen Mo , Li Bing , Guang Jing , Wei Linyu , Wu Si , Liu Yu , Zhang Mingsha 
Published: September 2016

Significance
The lateral intraparietal cortex (LIP) in primates links circuits for vision and saccadic eye movements. Neurons in LIP discharge during visually evoked saccades, but it is not certain whether LIP activity is primarily related to vision or to eye movement. From neuroanatomical evidence, we propose that LIP has two distinct subdivisions, dorsal and ventral LIP, with the dorsal division more concerned with visual processing and the ventral division more concerned with saccades. We provide evidence from both electrophysiological recordings and local inactivation to support our hypothesis. We therefore demonstrate that the two subdivisions of LIP play distinct roles in linking vision with visually guided action.
Comparing co-evolution methods and their application to template-free protein structure prediction
Authors: de Oliveira Saulo Henrique Pires , Shi Jiye , Deane Charlotte M 
Published: September 2016

Abstract

Motivation
Co-evolution methods have been used as contact predictors to identify pairs of residues that share spatial proximity. Such contact predictors have been compared in terms of the precision of their predictions, but there is no study that compares their usefulness to model generation.

Results
We compared eight different co-evolution methods for a set of ∼3500 proteins and found that metaPSICOV stage 2 produces, on average, the most precise predictions. Precision of all the methods is dependent on SCOP class, with most methods predicting contacts in all α and membrane proteins poorly. The contact predictions were then used to assist in de novo model generation. We found that it was not the method with the highest average precision, but rather metaPSICOV stage 1 predictions that consistently led to the best models being produced. Our modelling results show a correlation between the proportion of predicted long range contacts that are satisfied on a model and its quality. We used this proportion to effectively classify models as correct/incorrect; discarding decoys classified as incorrect led to an enrichment in the proportion of good decoys in our final ensemble by a factor of seven. For 17 out of the 18 cases where correct answers were generated, the best models were not discarded by this approach. We were also able to identify eight cases where no correct decoy had been generated.

Availability and Implementation
Data is available for download from: http://opig.stats.ox.ac.uk/resources.

Supplementary information
Supplementary data are available at Bioinformatics online.
Granular clustering of de novo protein models
Authors: Guzenko Dmytro , Strelkov Sergei V 
Published: September 2016

Abstract

Motivation
Modern algorithms for de novo prediction of protein structures typically output multiple full-length models (decoys) rather than a single solution. Subsequent clustering of such decoys is used both to gauge the success of the modelling and to decide on the most native-like conformation. At the same time, partial protein models are sufficient for some applications such as crystallographic phasing by molecular replacement (MR) in particular, provided these models represent a certain part of the target structure with reasonable accuracy.

Results
Here we propose a novel clustering algorithm that natively operates in the space of partial models through an approach known as granular clustering (GC). The algorithm is based on growing local similarities found in a pool of initial decoys. We demonstrate that the resulting clusters of partial models provide a substantially more accurate structural detail on the target protein than those obtained upon a global alignment of decoys. As the result, the partial models output by our GC algorithm are also much more effective towards the MR procedure, compared to the models produced by existing software.

Availability and Implementation
The source code is freely available at https://github.com/biocryst/gc

Supplementary information
Supplementary data are available at Bioinformatics online.
Building Collaboration: Examining the Relationship between Collaborative Processes and Activities
Authors: Sedgwick Donna 
Published: September 2016

Abstract
This study investigates if the collaborative process differs among a group of public programs involved in varying levels of interorganizational activities. Thomson and Perry (2006) suggest five process dimensions underlie collaboration: governance, administration, norms of trust, mutuality, and organizational autonomy. While these dimensions are clearly unique, it is unclear if any of these dimensions are necessary or sufficient for varying degrees of interorganizational involvement. Inventorying the interorganizational activities of pairs of government-funded preschools as ranging along a continuum of no relationship, cooperation, coordination, and collaboration, I conduct a qualitative comparative analysis (QCA) to assess the relationship between collaborative processes and activities. The findings suggest that the collaborative processes dimensions differ depending on the level of involvement. The QCA results also reveal substitutable combinations of process dimensions that underlie respective degrees of interorganizational involvement, offering insight to public managers about different skill sets they can focus on when managing interorganizational activities.
A robust measurement point for dose verification in delivery quality assurance for a robotic radiosurgery system
Authors: Kurosu Keita , Sumida Iori , Shiomi Hiroya , Mizuno Hirokazu , Yamaguchi Hiroko , Okubo Hirofumi , Tamari Keisuke , Seo Yuji , Suzuki Osamu , Ota Seiichi , Inoue Shinichi , Ogawa Kazuhiko 
Published: September 2016

Abstract
In this CyberKnife® dose verification study, we investigated the effectiveness of the novel potential error (PE) concept when applied to the determination of a robust measurement point for targeting errors. PE was calculated by dividing the differences between the maximum increases and decreases in dose distributions by the original distribution after obtaining the former by shifting the source-to-axis and off-axis distances of each beam by ±1.0 mm. Thus, PE values and measurement point dose heterogeneity were analyzed in 48 patients who underwent CyberKnife radiotherapy. Sixteen patients who received isocentric dose delivery were set as the control group, whereas 32 who received non-isocentric dose delivery were divided into two groups of smaller PE (SPE) and larger PE (LPE) by using their median PE value. The mean dose differences (± standard deviations) were 1.0 ± 0.9%, 0.5 ± 1.4% and 4.1 ± 2.8% in the control, SPE and LPE groups, respectively. We observed significant correlations of the dose difference with the PE value (r = 0.582, P &lt; 0.001) and dose heterogeneity (r = 0.471, P &lt; 0.001). We concluded that when determining a robust measurement point for CyberKnife point dose verification, PE evaluation was more effective than the conventional dose heterogeneity-based method that introduced optimal measurement point dose heterogeneity of &lt;10% across the detector.
Retracted: AKAP12 mediates PKA-induced phosphorylation of ATR to enhance nucleotide excision repair
Authors: Jarrett Stuart G. , Wolf Horrell Erin M. , D'Orazio John A. 
Published: September 2016

AbstractLoss-of-function in melanocortin 1 receptor (MC1R), a GS protein-coupled receptor that regulates signal transduction through cAMP and protein kinase A (PKA) in melanocytes, is a major inherited melanoma risk factor. Herein, we report a novel cAMP-mediated response for sensing and responding to UV-induced DNA damage regulated by A-kinase-anchoring protein 12 (AKAP12). AKAP12 is identified as a necessary participant in PKA-mediated phosphorylation of ataxia telangiectasia mutated and Rad3-related (ATR) at S435, a post-translational event required for cAMP-enhanced nucleotide excision repair (NER). Moreover, UV exposure promotes ATR-directed phosphorylation of AKAP12 at S732, which promotes nuclear translocation of AKAP12–ATR-pS435. This complex subsequently recruits XPA to UV DNA damage and enhances 5΄ strand incision. Preventing AKAP12's interaction with PKA or with ATR abrogates ATR-pS435 accumulation, delays recruitment of XPA to UV-damaged DNA, impairs NER and increases UV-induced mutagenesis. Our results define a critical role for AKAP12 as an UV-inducible scaffold for PKA-mediated ATR phosphorylation, and identify a repair complex consisting of AKAP12–ATR-pS435-XPA at photodamage, which is essential for cAMP-enhanced NER.
RETRACTION: Illuminating the dark road from schizophrenia genetic associations to disease mechanisms
Authors: Li Ming , Weinberger Daniel R 
Published: September 2016

Abstract
Recent large-scale genome-wide association studies (GWAS) have enabled the discovery of common genetic variations contributing to risk architectures of schizophrenia in human populations; however, the majority of GWAS-identified variants are located in large genomic regions spanning multiple genes, and recognizing the precise targets and mechanisms of these clinical associations is now the major challenge. Here, we review recent progress in schizophrenia genetics, functional genomics and related neuroscience research, and propose a functional pipeline to translate schizophrenia GWAS risk loci into disease biology and information for drug discovery. The pipeline includes identification of underlying molecular mechanisms using transcriptomic data in human brain, prioritization of putative functional causative variants by the integration of genetic epidemiological and bioinformatics methods as well as molecular approaches, and in vitro and in vivo experimental characterizations of the identified targeted species and causative variants to dissect the relevant disease biology. These approaches will accelerate progress from schizophrenia genetic studies to biological mechanisms and ultimately guide the development of prognostic, preventive and therapeutic measures.
Severe Human Illness Caused by Rift Valley Fever Virus in Mauritania, 2015
Authors: Boushab Boushab Mohamed , Fall-Malick Fatima Zahra , Ould Baba Sidi El Wafi , Ould Salem Mohamed Lemine , Belizaire Marie Roseline Darnycka , Ledib Hamade , Ould Baba Ahmed Mohamed Mahmoud , Basco Leonardo Kishi , Ba Hampaté 
Published: September 2016

Abstract

Background
Rift Valley Fever epizootics are characterized by numerous abortions and mortality among young animals. In humans, the illness is usually characterized by a mild self-limited febrile illness, which could progress to more serious complications.Objectives. The aim of the present prospective study was to describe severe clinical signs and symptoms of Rift Valley Fever in southern Mauritania.

Patients and methods
Suspected cases were enrolled in Kiffa (Assaba) and Aleg (Brakna) Hospital Centers from September 1 to November 7, 2015, based on the presence of fever, hemorrhagic or meningoencephalitic syndromes, and probable contact with sick animals. Suspected cases were confirmed by enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR).

Results
There were thirty-one confirmed cases. The sex ratio M/F and the average age were 2.9 and 25 years old [range, 4-70 years old], respectively. Mosquito bites, direct contact with aborted or dead animals, and frequent ingestion of milk from these animals were risk factors observed in all patients. Hemorrhagic and neurological manifestations were observed in 81% and 13% of cases, respectively. The results of laboratory analysis showed high levels of transaminases, creatinine, and urea associated with thrombocytopenia, anemia, and leukopenia. All patients who died (42%) had a hemorrhagic syndrome and 3 of them had a neurological complication. Among the cured patients, none had neurologic sequelae.

Conclusion
The hemorrhagic form was the most common clinical manifestation of RVF found in southern Mauritania and was responsible for a high mortality rate. Our results justify the implementation of a continuous epidemiological surveillance.
Update on second-trimester surgical abortion
Authors: Shaw Kate A. , Lerma Klaira 
Published: September 2016

Purpose of review
To review the recent literature on surgical second-trimester abortion, with specific attention to cervical preparation techniques.

Recent findings
Confirming previous studies, a recent retrospective observational cohort study, including 54 911 abortions, estimated the total abortion-related complication rate to be 0.41% for second-trimester or later procedures. Cervical preparation is known to reduce risks associated with second-trimester dilation and evacuation (D&E). When considering adjuncts to osmotic dilators for cervical preparation prior to D&E after 16 weeks, both misoprostol and mifepristone are effective alone and in combination or as adjuncts to osmotic dilators. Misoprostol consistently has been shown to cause more pain and cramping than placebo, but is an effective adjunct to osmotic dilators after 16 weeks. Although mifepristone has fewer side-effects, at its current price, it may not be as cost-effective as misoprostol.

Summary
Second-trimester abortion is safe. The use of mifepristone and misoprostol for second-trimester abortion has improved safety and efficacy of medical and surgical methods when used alone or in combination and as adjuncts to osmotic dilators. An important aspect of D&E, cervical preparation, is not a one-size-fits-all practice; the approach and methods are contingent on patient, provider and setting and should consider all the evidence-based options.