bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vibrational coherence transfer in the ultrafast intersystem crossing of a diplatinum complex in solution
Authors: Monni Roberto , Capano Gloria , Auböck Gerald , Gray Harry B. , Vlček Antonín , Tavernelli Ivano , Chergui Majed 
Published: June 2018

Significance
The observation of vibrational wave packets allows tracking the pathways of energy relaxation in nonadiabatic surface crossing events of (bio)molecular systems, such as conical intersections or charge transfer processes. Here, we identify transfer of vibrational coherence in the course of conversion between electronic excited states of different spin in a diplatinum complex in solution, as an example. Retention of coherence is due to the fact that the conversion rate is dramatically accelerated in an acetonitrile solvent due to the strong solvation of higher-lying electronic states that then provide the channel for the coherent population flow from the singlet to the triplet state. These results highlight the role of the environment in controlling the pathways of energy flow and conversion.
Autoantibodies reactive to adrenocorticotropic hormone can alter cortisol secretion in both aggressive and nonaggressive humans
Authors: Værøy Henning , Adori Csaba , Legrand Romain , Lucas Nicolas , Breton Jonathan , Cottard Caroline , do Rego Jean-Claude , Duparc Céline , Louiset Estelle , Lefebvre Hervé , Déchelotte Pierre , Western Elin , Andersson Stein , Hökfelt Tomas , Fetissov Sergueï O. 
Published: June 2018

Significance
The number of inmates imprisoned for violent aggression is increasing, as are the penitentiaries, but still our understanding of mechanisms underlying criminality is limited. Our analysis of violent aggressor inmates reveals unique properties of IgG reactive with adrenocorticotropic hormone (ACTH). We show that these IgGs can regulate ACTH-induced cortisol secretion in the adrenal gland, and they exhibit a clear-cut difference in ACTH epitope binding in violent aggressors vs. controls. Additionally, IgG from a subset of aggressive subjects selectively bind to hypothalamic vasopressin neurons. Thus, using several in vitro and in vivo approaches, the study reveals a molecular mechanism involved in the variability of stress response relevant to the neurobiology of aggression and possibly other stress-related conditions.
Identification and nanomechanical characterization of the fundamental single-strand protofilaments of amyloid α-synuclein fibrils
Authors: Ruggeri Francesco Simone , Benedetti Fabrizio , Knowles Tuomas P. J. , Lashuel Hilal A. , Sekatskii Sergey , Dietler Giovanni 
Published: June 2018

Significance
Today, more than 40 million people worldwide are affected by neurodegenerative disorders. These diseases are associated at the molecular level with the aggregation of specific proteins into insoluble fibrils, termed amyloids. Increasing evidence suggests that the intermediate aggregates, rather than the final fibrillar products, are implicated in toxicity in vivo. However, the investigation of the conversion of proteins into amyloids represents a formidable experimental challenge because of their nanoscale and heterogeneous nature. Here, we report the identification of a mechanism of early assembly of monomeric proteins into elongated intermediates during amyloid formation. The biophysical characterization of novel intermediate molecular species is fundamental to unravel their mechanism of formation and gain insights into their potential toxicity and role in pathology.
Changes in brain architecture are consistent with altered fear processing in domestic rabbits
Authors: Brusini Irene , Carneiro Miguel , Wang Chunliang , Rubin Carl-Johan , Ring Henrik , Afonso Sandra , Blanco-Aguiar José A. , Ferrand Nuno , Rafati Nima , Villafuerte Rafael , Smedby Örjan , Damberg Peter , Hallböök Finn , Fredrikson Mats , Andersson Leif 
Published: June 2018

Significance
A common feature of all domestic animals is their tame behavior and lack of fear for humans. Consistent with this, we have previously demonstrated that genes with a role in brain or neural development have been particularly targeted during rabbit domestication. Here we show, using high-resolution magnetic resonance imaging, that domestic rabbits have an altered brain architecture consistent with reduced emotional processing, including attention to behaviorally relevant stimulation, such as fear detection, learning, expression, and control, as well as compromised information processing. The results, here based on rabbits, are significant for understanding both domestication-induced reorganization of brain architecture and how adaptions in brain territories and networks supporting emotion, cognition, and behavior coincide with an altered behavioral repertoire.
Disease outbreak thresholds emerge from interactions between movement behavior, landscape structure, and epidemiology
Authors: White Lauren A. , Forester James D. , Craft Meggan E. 
Published: June 2018

Significance
Understanding how emerging infectious and zoonotic diseases spread through space and time is critical for predicting outbreaks and designing interventions; disease models are important tools for realizing these goals. Currently, humans are altering the environment in unprecedented ways through urbanization, habitat fragmentation, and climate change. However, the consequences of increasingly heterogeneous landscapes on pathogen transmission and persistence remain unclear. By synthesizing mathematical modeling and movement ecology approaches, we examined how wildlife movement patterns interact with broad-scale landscape structure to affect population-level disease dynamics. We found that habitat fragmentation could counterintuitively promote disease outbreaks but that, for higher wildlife densities and longer infectious periods, small differences in how hosts navigated their environments could dramatically alter observed disease dynamics.
Unusual duplication mutation in a surface loop of human transthyretin leads to an aggressive drug-resistant amyloid disease
Authors: Klimtchuk Elena S. , Prokaeva Tatiana , Frame Nicholas M. , Abdullahi Hassan A. , Spencer Brian , Dasari Surendra , Cui Haili , Berk John L. , Kurtin Paul J. , Connors Lawreen H. , Gursky Olga 
Published: June 2018

Significance
We identified a one-of-a-kind duplication mutation in human transthyretin (TTR) that causes unusually aggressive systemic amyloidosis. To understand the poor response to treatment with a drug that stabilizes the TTR tetramer, we explored the structure, stability, and drug binding of recombinant proteins. The results suggested that amyloid formation could stem from global destabilization of the monomeric and tetrameric protein as well as the local disordering near the mutation site. This disordering induced proteolysis with release of aggregation-prone fragments. Alternatively, local disordering could trigger misfolding of the full-length protein by exposing an adhesive segment. Drug binding at a dimer interface distant from the mutation site did not significantly influence these pathological processes, indicating the need for alternative therapeutic targets.
Structure of RNA polymerase complex and genome within a dsRNA virus provides insights into the mechanisms of transcription and assembly
Authors: Wang Xurong , Zhang Fuxian , Su Rui , Li Xiaowu , Chen Wenyuan , Chen Qingxiu , Yang Tao , Wang Jiawei , Liu Hongrong , Fang Qin , Cheng Lingpeng 
Published: June 2018

Significance
Double-stranded RNA (dsRNA) viruses infect hosts ranging from fungi to plants and to humans. Like most other dsRNA viruses, the aquareovirus RNA polymerase catalyzes the synthesis of RNA plus strands within the inner capsid, a process vital for the replication of virus progeny. Here we present a near-atomic resolution structure of the RNA polymerase in complex with its cofactor protein and genomic RNA within the aquareovirus. Some asymmetric structures within the elaborate viral machine that have never been previously determined have been resolved in our structure, and key interactions among the polymerase, cofactor protein, and dsRNA have been revealed. These findings provide insights into the mechanism underlying highly coordinated dsRNA virus transcription and assembly.
Focal, remote-controlled, chronic chemical modulation of brain microstructures
Authors: Ramadi Khalil B. , Dagdeviren Canan , Spencer Kevin C. , Joe Pauline , Cotler Max , Rousseau Erin , Nunez-Lopez Carlos , Graybiel Ann M. , Langer Robert , Cima Michael J. 
Published: June 2018

Significance
The brain is composed of distinct microstructures. Many neurologic and neuropsychiatric diseases arise from dysfunction of circuits of neurons and glia affecting multiple brain regions. Novel potential drug therapies are often delivered through acutely inserted cannulas in the brain. We show that such methods target a much larger region than focal chemical dosing using a class of chronically implanted microprobes. We develop techniques to quantify dynamics of deep-brain infusions and show distinct diffusion behavior of different chemicals. Our microprobes can be independently inserted and combine multiple fluidic lumens in a submillimeter footprint. Studies using implanted drug delivery systems in rodents illustrate our system’s ability to remotely control behavior and the importance of volume in modulating brain regions.
In vivo imaging of the pathophysiological changes and neutrophil dynamics in influenza virus-infected mouse lungs
Authors: Ueki Hiroshi , Wang I-Hsuan , Fukuyama Satoshi , Katsura Hiroaki , da Silva Lopes Tiago Jose , Neumann Gabriele , Kawaoka Yoshihiro 
Published: June 2018

SignificanceWe used a state-of-the-art in vivo imaging system and fluorescent influenza viruses (Color-flu) to determine in real time the pathophysiological changes in the lungs of infected mice. We found that influenza virus infections reduced blood flow speed and decreased neutrophil motility. More significantly, infection with a prototypic “bird flu” strain, a highly pathogenic H5N1 influenza virus, caused higher pulmonary permeability than did infection with a mouse-adapted human influenza virus. This in vivo imaging system with quantitative analyses allowed us to reveal the progression of the disease at the cellular level and to perform a multiparameter analysis that is not possible by using conventional histopathology.
Fast charging of lithium-ion batteries at all temperatures
Authors: Yang Xiao-Guang , Zhang Guangsheng , Ge Shanhai , Wang Chao-Yang 
Published: June 2018

Significance
Range anxiety is a key reason that consumers are reluctant to embrace electric vehicles (EVs). To be truly competitive with gasoline vehicles, EVs should allow drivers to recharge quickly anywhere in any weather, like refueling gasoline cars. However, none of today’s EVs allow fast charging in cold or even cool temperatures due to the risk of lithium plating, the formation of metallic lithium that drastically reduces battery life and even results in safety hazards. Here, we present an approach that enables 15-min fast charging of Li-ion batteries in any temperatures (even at −50 °C) while still preserving remarkable cycle life (4,500 cycles, equivalent to >12 y and >280,000 miles of EV lifetime), thus making EVs truly weather-independent.
Piano training enhances the neural processing of pitch and improves speech perception in Mandarin-speaking children
Authors: Nan Yun , Liu Li , Geiser Eveline , Shu Hua , Gong Chen Chen , Dong Qi , Gabrieli John D. E. , Desimone Robert 
Published: June 2018

Significance
Musical training is beneficial to speech processing, but this transfer’s underlying brain mechanisms are unclear. Using pseudorandomized group assignments with 74 4- to 5-year-old Mandarin-speaking children, we showed that, relative to an active control group which underwent reading training and a no-contact control group, piano training uniquely enhanced cortical responses to pitch changes in music and speech (as lexical tones). These neural enhancements further generalized to early literacy skills: Compared with the controls, the piano-training group also improved behaviorally in auditory word discrimination, which was correlated with their enhanced neural sensitivities to musical pitch changes. Piano training thus improves children’s common sound processing, facilitating certain aspects of language development as much as, if not more than, reading instruction.
Female-to-Male Gender-Affirming Chest Reconstruction Surgery
Authors: Ammari Tareq , Sluiter Emily C , Gast Katherine , Kuzon William M 
Published: June 2018

Abstract
There is an increased demand for gender affirmation surgery. Chest contouring, or “top” surgery, is especially important in the female-to-male (FtM) transgender population. This Continuing Medical Education (CME) article critically appraises the available literature on top surgery to allow plastic surgeons to understand current practices and determine the best surgical technique using a decision algorithm and the patient’s preoperative anatomy and characteristics. Because a single best surgical approach does not exist due to significant variance in preoperative patient anatomy, and in order to provide a useful framework for decision making, surgical approaches described are categorized as: approach 1—remote incision procedures without skin excision; approach 2—procedures with periareolar skin excision; and approach 3—mastectomy procedures with skin excision other than periareolar skin excision. Decision algorithms that help determine the most suitable surgical technique for individual patients are reviewed. Data on complication rates and patient satisfaction will improve informed consent discussions and create realistic patient expectations.
Physiological RNA dynamics in RNA-Seq analysis
Authors: Xu Zhongneng , Asakawa Shuichi 
Published: June 2018

AbstractPhysiological RNA dynamics cause problems in transcriptome analysis. Physiological RNA accumulation affects the analysis of RNA quantification, and physiological RNA degradation affects the analysis of the RNA sequence length, feature site and quantification. In the present article, we review the effects of physiological degradation and accumulation of RNA on analysing RNA sequencing data. Physiological RNA accumulation and degradation probably led to such phenomena as incorrect estimations of transcription quantification, differential expressions, co-expressions, RNA decay rates, alternative splicing, boundaries of transcription, novel genes, new single-nucleotide polymorphisms, small RNAs and gene fusion. Thus, the transcriptomic data obtained up to date warrant further scrutiny. New and improved techniques and bioinformatics software are needed to produce accurate data in transcriptome research.
appreci8: a pipeline for precise variant calling integrating 8 tools
Authors: Sandmann Sarah , Karimi Mohsen , de Graaf Aniek O , Rohde Christian , Göllner Stefanie , Varghese Julian , Ernsting Jan , Walldin Gunilla , van der Reijden Bert A , Müller-Tidow Carsten , Malcovati Luca , Hellström-Lindberg Eva , Jansen Joop H , Dugas Martin 
Published: June 2018

Abstract

Motivation
The application of next-generation sequencing in research and particularly in clinical routine requires valid variant calling results. However, evaluation of several commonly used tools has pointed out that not a single tool meets this requirement. False positive as well as false negative calls necessitate additional experiments and extensive manual work. Intelligent combination and output filtration of different tools could significantly improve the current situation.

Results
We developed appreci8, an automatic variant calling pipeline for calling single nucleotide variants and short indels by combining and filtering the output of eight open-source variant calling tools, based on a novel artifact- and polymorphism score. Appreci8 was trained on two data sets from patients with myelodysplastic syndrome, covering 165 Illumina samples. Subsequently, appreci8’s performance was tested on five independent data sets, covering 513 samples. Variation in sequencing platform, target region and disease entity was considered. All calls were validated by re-sequencing on the same platform, a different platform or expert-based review. Sensitivity of appreci8 ranged between 0.93 and 1.00, while positive predictive value ranged between 0.65 and 1.00. In all cases, appreci8 showed superior performance compared to any evaluated alternative approach.

Availability and implementation
Appreci8 is freely available at https://hub.docker.com/r/wwuimi/appreci8/. Sequencing data (BAM files) of the 678 patients analyzed with appreci8 have been deposited into the NCBI Sequence Read Archive (BioProjectID: 388411; https://www.ncbi.nlm.nih.gov/bioproject/PRJNA388411).

Supplementary information
Supplementary data are available at Bioinformatics online.
The Timing of Sensory-Guided Behavioral Response is Represented in the Mouse Primary Somatosensory Cortex
Authors: Camon Jérémy , Hugues Sandrine , Erlandson Melissa A , Robbe David , Lagoun Sabria , Marouane Emna , Bureau Ingrid 
Published: June 2018

Abstract
Whisker-guided decision making in mice is thought to critically depend on information processing occurring in the primary somatosensory cortex. However, it is not clear if neuronal activity in this “early” sensory region contains information about the timing and speed of motor response. To address this question we designed a new task in which freely moving mice learned to associate a whisker stimulus to reward delivery. The task was tailored in such a way that a wide range of delays between whisker stimulation and reward collection were observed due to differences of motivation and perception. After training, mice were anesthetized and neuronal responses evoked by stimulating trained and untrained whiskers were recorded across several cortical columns of barrel cortex. We found a strong correlation between the delay of the mouse behavioral response and the timing of multiunit activity evoked by the trained whisker, outside its principal cortical column, in layers 4 and 5A but not in layer 2/3. Circuit mapping ex vivo revealed this effect was associated with a weakening of layer 4 to layer 2/3 projection. We conclude that the processes controlling the propagation of key sensory inputs to naive cortical columns and the timing of sensory-guided action are linked.
Serological Evidence for the Circulation of Ebolaviruses in Pigs From Sierra Leone
Authors: Fischer Kerstin , Jabaty Juliet , Suluku Roland , Strecker Thomas , Groseth Allison , Fehling Sarah K , Balkema-Buschmann Anne , Koroma Bashiru , Schmidt Kristina M , Atherstone Christine , Weingartl Hana M , Mettenleiter Thomas C , Groschup Martin H , Hoenen Thomas , Diederich Sandra 
Published: June 2018

Abstract
Many human ebolavirus outbreaks have been linked to contact with wildlife including nonhuman primates and bats, which are assumed to serve as host species. However, it is largely unknown to what extent other animal species, particularly livestock, are involved in the transmission cycle or act as additional hosts for filoviruses. Pigs were identified as a susceptible host for Reston virus with subsequent transmission to humans reported in the Philippines. To date, there is no evidence of natural Ebola virus (EBOV) infection in pigs, although pigs were shown to be susceptible to EBOV infection under experimental settings. To investigate the potential role of pigs in the ecology of EBOV, we analyzed 400 porcine serum samples from Sierra Leone for the presence of ebolavirus-specific antibodies. Three samples reacted with ebolavirus nucleoproteins but had no neutralizing antibodies. Our results (1) suggest the circulation of ebolaviruses in swine in Sierra Leone that are antigenically related but not identical to EBOV and (2) could represent undiscovered ebolaviruses with unknown pathogenic and/or zoonotic potential.
Theorizing China’s rise in and beyond international relations
Authors: Pan Chengxin , Kavalski Emilian 
Published: June 2018

AbstractChina's rise, like the demise of the Soviet Union, is one of the defining events in the contemporary world. Yet, while the unexpected Soviet collapse and the end of the Cold War sparked the ‘Third Debate’ in International Relations (IR) theory, it is puzzling that the rise of China has yet to generate a comparable process of shell-shock and soul-searching among IR theorists. Just as the end of the Cold War is more than simply the end of a bipolar power struggle per se, so too China's rise is much more than the familiar ascendancy of another great power. Rather, it is also a complex, evolving and possibly border-traversing and paradigm-shattering phenomenon in global life that, on the one hand, requires fresh and innovative theorizing in and beyond IR and, on the other hand, potentially offers new insights for us to rethink world politics more broadly. This article introduces this Special Issue that seeks to tentatively respond to this theoretical, epistemological and ontological challenge. It draws attention to the blind spot in IR theorizing on China, and calls for deeper engagement between IR theory and China's rise that goes beyond mere ‘theory-testing’ within the existing perimeters of mainstream IR.
A Plasma-Derived Protein-Metabolite Multiplexed Panel for Early-Stage Pancreatic Cancer
Authors: Fahrmann Johannes F , Bantis Leonidas E , Capello Michela , Scelo Ghislaine , Dennison Jennifer B , Patel Nikul , Murage Eunice , Vykoukal Jody , Kundnani Deepali L , Foretova Lenka , Fabianova Eleonora , Holcatova Ivana , Janout Vladimir , Feng Ziding , Yip-Schneider Michele , Zhang Jianjun , Brand Randall , Taguchi Ayumu , Maitra Anirban , Brennan Paul , Max Schmidt C , Hanash Samir 
Published: June 2018

Abstract

Background
We applied a training and testing approach to develop and validate a plasma metabolite panel for the detection of early-stage pancreatic ductal adenocarcinoma (PDAC) alone and in combination with a previously validated protein panel for early-stage PDAC.

Methods
A comprehensive metabolomics platform was initially applied to plasmas collected from 20 PDAC cases and 80 controls. Candidate markers were filtered based on a second independent cohort that included nine invasive intraductal papillary mucinous neoplasm cases and 51 benign pancreatic cysts. Blinded validation of the resulting metabolite panel was performed in an independent test cohort consisting of 39 resectable PDAC cases and 82 matched healthy controls. The additive value of combining the metabolite panel with a previously validated protein panel was evaluated.

Results
Five metabolites (acetylspermidine, diacetylspermine, an indole-derivative, and two lysophosphatidylcholines) were selected as a panel based on filtering criteria. A combination rule was developed for distinguishing between PDAC and healthy controls using the Training Set. In the blinded validation study with early-stage PDAC samples and controls, the five metabolites yielded areas under the curve (AUCs) ranging from 0.726 to 0.842, and the combined metabolite model yielded an AUC of 0.892 (95% confidence interval [CI] = 0.828 to 0.956). Performance was further statistically significantly improved by combining the metabolite panel with a previously validated protein marker panel consisting of CA 19–9, LRG1, and TIMP1 (AUC = 0.924, 95% CI = 0.864 to 0.983, comparison DeLong test one-sided P= .02).

Conclusions
A metabolite panel in combination with CA19-9, TIMP1, and LRG1 exhibited substantially improved performance in the detection of early-stage PDAC compared with a protein panel alone.