bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterizing horizontally-polarized shear and infragravity vibrational modes in the Arctic sea ice cover using correlation methods
Authors: Marsan David , Weiss Jérôme , Moreau Ludovic , Gimbert Florent , Doble Martin , Larose Eric , Grangeon Jacques
Published: March 2019

The deployment of three drifting seismic stations on the Arctic sea ice during the winter of 2014–2015 with station inter-spacing between 30 and 80 km enables the characterization of the coherent seismic wavefield at these scales through the use of array methods. Two distinct vibrational modes are observed, corresponding to the fast and non-dispersive horizontally-polarized shear (SH) mode and the slow and dispersive flexural, infragravity mode (ice swell). The excitation of these two modes is not synchronous. The activation of the infragravity mode is linked to the arrival of energetic, dispersive wavetrains that can be readily seen on individual spectrograms, and that, as previous studies have shown, are likely to have their origins in distant storms. In contrast, the SH mode is excited at other time intervals and cannot be isolated on the recording of single stations due to the broadband and emergent nature of these wavetrains; given the horizontal polarization of these waves, the authors hypothesize that SH waves are caused by episodes of rapid SH deformation along major leads located outside the station network. The existence of horizontally-polarized waves propagating over long distances opens the possibility of monitoring ice deformation at the scale of the Arctic basin with unprecedented time resolution.
Close Cassini flybys of Saturn’s ring moons Pan, Daphnis, Atlas, Pandora, and Epimetheus
Authors: Buratti B. J. , Thomas P. C. , Roussos E. , Howett C. , Seiß M. , Hendrix A. R. , Helfenstein P. , Brown R. H. , Clark R. N. , Denk T. , Filacchione G. , Hoffmann H. , Jones G. H. , Khawaja N. , Kollmann P. , Krupp N. , Lunine J. , Momary T. W. , Paranicas C. , Postberg F. , Sachse M. , Spahn F. , Spencer J. , Srama R. , Albin T. , Baines K. H. , Ciarniello M. , Economou T. , Hsu H.-W. , Kempf S. , Krimigis S. M. , Mitchell D. , Moragas-Klostermeyer G. , Nicholson P. D. , Porco C. C. , Rosenberg H. , Simolka J. , Soderblom L. A.
Published: March 2019

Cassini's last look at Saturn's rings

During the final stages of the Cassini mission, the spacecraft flew between the planet and its rings, providing a new view on this spectacular system (see the Perspective by Ida). Setting the scene, Spilker reviews the numerous discoveries made using Cassini during the 13 years it spent orbiting Saturn. Iess
et al.
measured the gravitational pull on Cassini, separating the contributions from the planet and the rings. This allowed them to determine the interior structure of Saturn and the mass of its rings. Buratti
et al.
present observations of five small moons located in and around the rings. The moons each have distinctive shapes and compositions, owing to accretion of ring material. Tiscareno
et al.
observed the rings directly at close range, finding complex features sculpted by the gravitational interactions between moons and ring particles. Together, these results show that Saturn's rings are substantially younger than the planet itself and constrain models of their origin.

Science
, this issue p.
1046
, p.
eaat2965
, p.
eaat2349
, p.
eaau1017
; see also p.
1028
The entorhinal cognitive map is attracted to goals
Authors: Boccara Charlotte N. , Nardin Michele , Stella Federico , O’Neill Joseph , Csicsvari Jozsef
Published: March 2019

Reward and the map in the brain

Recent findings suggest a more complex role of grid cells in the brain than simply coding for space. The grid map in the entorhinal cortex, which is responsible for encoding spatial information, is not as rigid as originally thought and can be distorted by environmental modifications (see the Perspective by Quian Quiroga). Butler
et al.
compared grid cell coding during a free-foraging task and a spatial memory task in rats. They discovered that entorhinal spatial maps restructure to incorporate the location of a learned reward. Boccara
et al.
tested the influence of behaviorally relevant information on the cognitive map that emerges from grid cell firing in the rat medial entorhinal cortex. They found that grid cells participate in neural coding of the goal locality, not the whole environment.

Science
, this issue p.
1447
, p.
1443
; see also p.
1388
Optogenetic manipulation of stomatal kinetics improves carbon assimilation, water use, and growth
Authors: Papanatsiou M. , Petersen J. , Henderson L. , Wang Y. , Christie J. M. , Blatt M. R.
Published: March 2019

Speeding up stomatal responses

A plant's cellular metabolism rapidly adjusts to changes in light conditions, but its stomata—pores that allow gas exchange in leaves—are slower to respond. Because of the lagging response, photosynthesis is less efficient, and excess water is lost through the open pores. Papanatsiou
et al.
introduced a blue light–responsive ion channel into stomata of the small mustard plant
Arabidopsis.
The channel increased the rate of stomata opening and closing in response to light. The engineered plants produced more biomass, especially in the fluctuating light conditions typical of outdoor growth.

Science
, this issue p.
1456
AI for the M.D
Deep Medicine
Eric Topol
Basic Books, 2019. 393 pp.
Authors: Szolovits Peter
Published: March 2019

Deep learning could give doctors of the future more time for the human aspects of health care
Integrating tactics on opioids
Authors: Leshner Alan I.
Published: March 2019

Many parts of the world are in the middle of an opioid addiction crisis. It is an equal opportunity destroyer, affecting rich and poor, urban and rural people alike. The current epidemic differs from the long-standing heroin addiction problem in its broader demographic and in that it has resulted from inappropriate marketing and overprescription of pain medicines and the intrusion of powerful and lethal synthetic opioids. The magnitude of the crisis is also unprecedented: In the United States alone, more than 2 million people are estimated to have “opioid use disorder,” and 47,000 people died of an opioid overdose in 2017. Traditional strategies for dealing with addiction have had limited success. They have primarily used parallel tactics of “supply control” (limiting availability) and “demand control” (trying to prevent or reduce use), which might be considered as criminal justice and public health approaches. But this side-by-side approach may be counterproductive. Last week, the U.S. National Academies of Sciences, Engineering, and Medicine released a report* on the state of medication-based treatments for opioid addiction. What is clear is that in addition to the need for more research, the nature of the epidemic requires new approaches that integrate public health, regulatory, and criminal justice strategies.
Macrolides Inhibit Capsule Formation of Highly Virulent
Cryptococcus gattii
and Promote Innate Immune Susceptibility
Authors: Nakamura Shigeki , Ikeda-Dantsuji Yurika , Jin Lianjin , Higashi Yoshitsugu , Abe Masahiro , Inukai Tatsuya , Nagi Minoru , Urai Makoto , Miyazaki Yoshitsugu
Published: March 2019

Cryptococcus gattii
is a fungal pathogen, endemic in tropical and subtropical regions, the west coast of Canada, and the United States, that causes a potentially fatal infection in otherwise healthy individuals. Because the cryptococcal polysaccharide capsule is a leading virulence factor due to its resistance against innate immunity, the inhibition of capsule formation may be a promising new therapeutic strategy for
C. gattii
.
Postantibiotic and Sub-MIC Effects of Exebacase (Lysin CF-301) Enhance Antimicrobial Activity against Staphylococcus aureus
Authors: Oh Jun Taek , Cassino Cara , Schuch Raymond
Published: March 2019

CF-301 (exebacase) is a recombinantly produced bacteriophage-derived lysin (cell wall hydrolase) and is the first agent of this class to enter clinical development in the United States for treating bacteremia including endocarditis due to
Staphylococcus aureus
. Whereas rapid bactericidal activity is the hallmark
in vitro
and
in vivo
response to CF-301 at exposures higher than the MIC, prolonged antimicrobial activity, mediated by cell wall damage, is predicted at concentrations less than the MIC.
Antimicrobial Activity Evaluation of Tebipenem (SPR859), an Orally Available Carbapenem, against a Global Set of Enterobacteriaceae Isolates, Including a Challenge Set of Organisms
Authors: Arends S. J. Ryan , Rhomberg Paul R. , Cotroneo Nicole , Rubio Aileen , Flamm Robert K. , Mendes Rodrigo E.
Published: March 2019

The antimicrobial activity of tebipenem and other carbapenem agents were tested
in vitro
against a set of recent clinical isolates responsible for urinary tract infection (UTI), as well as against a challenge set. Isolates were tested by reference broth microdilution and included
Escherichia coli
(101 isolates),
Klebsiella pneumoniae
(208 isolates), and
Proteus mirabilis
(103 isolates) species.
Intrahost Selection Pressure Drives Equine Arteritis Virus Evolution during Persistent Infection in the Stallion Reproductive Tract
Authors: Nam Bora , Mekuria Zelalem , Carossino Mariano , Li Ganwu , Zheng Ying , Zhang Jianqiang , Cook R. Frank , Shuck Kathleen M. , Campos Juliana R. , Squires Edward L. , Troedsson Mats H. T. , Timoney Peter J. , Balasuriya Udeni B. R.
Published: March 2019

EAV can persist in the reproductive tract of infected stallions, and consequently, long-term carrier stallions constitute its sole natural reservoir. Previous studies demonstrated that the ampullae of the vas deferens are the primary site of viral persistence in the stallion reproductive tract and the persistence is associated with a significant inflammatory response that is unable to clear the infection. This is the first study that describes EAV full-length genomic evolution during acute and long-term persistent infection in the stallion reproductive tract using next-generation sequencing and contemporary sequence analysis techniques. The data provide novel insight into the intrahost evolution of EAV during acute and persistent infection and demonstrate that persistent infection is characterized by extensive genome-wide purifying selection and a nonstochastic evolutionary pattern mediated by intrahost selective pressure, with important nucleotide substitutions occurring in ORF1a (region encoding nsp2), ORF3, and ORF5.
Voltage-Dependent Anion Channel Protein 2 (VDAC2) and Receptor of Activated Protein C Kinase 1 (RACK1) Act as Functional Receptors for Lymphocystis Disease Virus Infection
Authors: Zhong Ying , Tang Xiaoqian , Sheng Xiuzhen , Xing Jing , Zhan Wenbin
Published: March 2019

Lymphocystis disease virus (LCDV) is the causative agent of lymphocystis disease in fish, which has caused huge economic losses to the aquaculture industry worldwide, but the molecular mechanism underlying the LCDV-host interaction remains unclear. Here, the 27.8-kDa putative cellular receptor for LCDV was identified as voltage-dependent anion channel protein 2 (VDAC2) and receptor of activated protein C kinase 1 (RACK1), and our results revealed that VDAC2 and RACK1 expression was sufficient to allow LCDV entry and that they are functional receptors that initiate LCDV infection for the first time, which leads to a better understanding of the molecular mechanism underlying LCDV infection and virus-host interactions.
Analysis of Coronavirus Temperature-Sensitive Mutants Reveals an Interplay between the Macrodomain and Papain-Like Protease Impacting Replication and Pathogenesis
Authors: Deng Xufang , Mettelman Robert C. , O’Brien Amornrat , Thompson John A. , O’Brien Timothy E. , Baker Susan C.
Published: March 2019

Coronaviruses (CoVs) are emerging human and veterinary pathogens with pandemic potential. Despite the established and predicted threat these viruses pose to human health, there are currently no approved countermeasures to control infections with these viruses in humans. Viral macrodomains, enzymes that remove posttranslational ADP-ribosylation of proteins, and viral multifunctional papain-like proteases, enzymes that cleave polyproteins and remove polyubiquitin chains via deubiquitinating activity, are two important virulence factors. Here, we reveal an unanticipated interplay between the macrodomain and the PLP2 domain that is important for replication and antagonizing the host innate immune response. Targeting the interaction of these enzymes may provide new therapeutic opportunities to treat CoV disease.
African Swine Fever Virus Armenia/07 Virulent Strain Controls Interferon Beta Production through the cGAS-STING Pathway
Authors: García-Belmonte Raquel , Pérez-Núñez Daniel , Pittau Marco , Richt Juergen A. , Revilla Yolanda
Published: March 2019

African swine fever, a devastating disease for domestic pigs and wild boar, is currently spreading in Europe, Russia, and China, becoming a global threat with huge economic and ecological consequences. One interesting aspect of ASFV biology is the molecular mechanism leading to high virulence of some strains compared to more attenuated strains, which produce subclinical infections. In this work, we show that the presently circulating virulent Armenia/07 virus blocks the synthesis of IFN-β, a key mediator between the innate and adaptive immune response. Armenia/07 inhibits the cGAS-STING pathway by impairing STING activation during infection. In contrast, the cGAS-STING pathway is efficiently activated during NH/P68 attenuated strain infection, leading to the production of large amounts of IFN-β. Our results show for the first time the relationship between the cGAS-STING pathway and ASFV virulence, contributing to uncover the molecular mechanisms of ASFV virulence and to the rational development of ASFV vaccines.
Relationship between sociodemographic factors and specialty destination of UK trainee doctors: a national cohort study
Authors: Kumwenda Ben , Cleland Jennifer , Prescott Gordon , Walker Kim , Johnston Peter
Published: March 2019

Objectives

Many countries are driving forward policies to widen the socioeconomic profile of medical students and to train more medical students for certain specialties. However, little is known about how socioeconomic origin relates to specialty choice. Nor is there a good understanding of the relationship between academic performance and specialty choice. To address these gaps, our aim was to identify the relationship between socioeconomic background, academic performance and accepted offers into specialty training.

Design

Longitudinal, cohort study using data from the UK Medical Education Database (https://www.ukmed.ac.uk/).

Participants

6065 (60% females) UK doctors who accepted offers to a specialty training (residency) post after completing the 2-year generic foundation programme (UK Foundation Programme) between 2012 and 2014.

Main outcome measures

Χ2tests were used to examine the relationships between sociodemographic characteristics, academic ability and the dependent variable, specialty choice. Multiple data imputation was used to address the issue of missing data. Multinomial regression was employed to test the independent variables in predicting the likelihood of choosing a given specialty.

Results

Participants pursuing careers in more competitive specialties had significantly higher academic scores than colleagues pursuing less competitive ones. After controlling for the presence of multiple factors, trainees who came from families where no parent was educated to a degree level had statistically significant lower odds of choosing careers in medical specialties relative to general practice (OR=0.78, 95% CI, 0.67 to 0.92). Students who entered medical school as school leavers, compared with mature students, had odds 1.2 times higher (95% CI, 1.04 to 1.56) of choosing surgical specialties than general practice.

Conclusions

The data indicate a direct association between trainees’ sociodemographic characteristics, academic ability and career choices. The findings can be used by medical school, training boards and workforce planners to inform recruitment and retention strategies.
Use of performance reports among trauma medical directors and programme managers in the American College of Surgeons’ Trauma Quality Improvement Program: a qualitative analysis
Authors: Gotlib Conn Lesley , Hoeft Christopher , Neal Melanie , Nathens Avery
Published: March 2019

Background

The American College of Surgeons’ Trauma Quality Improvement Program (TQIP) provides trauma centres with performance reports on their processes and outcomes of care relative to their peers. This study explored how performance reports are used by trauma centre leaders to engage in performance improvement and perceived barriers to use.

Study design

Qualitative focus group study with trauma medical directors (TMDs) and trauma programme managers (TPMs) in US trauma centres. Consistent with qualitative descriptive analysis, data collection and interpretation were inductively and iteratively completed. Major themes were derived using a constant comparative technique.

Results

Six focus groups were conducted involving 22 TMDs and 22 TPMs. Three major themes were captured: (1) technical uses of performance reports; (2) cultural uses of performance reports; (3) opportunities to enhance the role and value of TQIP. First, technical uses included using reports to assess data collection procedures, data quality and areas of poor performance relative to peers. In this domain, barriers to report use included not trusting others’ data quality and challenges with report interpretation. Second, reports were used to influence practice change by fostering inter-specialty discussions, leveraging resources for quality improvement, community engagement and regional collaboratives. Perceived lack of specialist engagement was viewed as an impediment in this domain. Lastly, identified opportunities for TQIP to support report use involved clarifying the relationship between verification and performance reports, and increasing partnerships with nursing associations.

Conclusion

Trauma centre improvement leaders indicated practical and social uses of performance reports that can affect intention and ability to change. Recommendations to optimise programme participation include a focus on data quality, adequate resource provision and enhanced support for regional collaboratives.
Maternity and postpartum care: perspectives
Authors: Heale Roberta
Published: March 2019

EBN Perspectives brings together key issues from the commentaries in one of our nursing topic themes.
Epidemiology and implications of concurrent diagnosis of eosinophilic oesophagitis and IBD based on a prospective population-based analysis
Authors: Limketkai Berkeley N , Shah Shailja C , Hirano Ikuo , Bellaguarda Emanuelle , Colombel Jean-Frederic
Published: March 2019

Objective

Eosinophilic oesophagitis (EoO) and IBD are immune-mediated diseases of the gastrointestinal tract with possible overlapping pathogenic mechanisms. Our aim was to define the epidemiology and clinical implications of concurrent EoO and IBD diagnoses.

Design

We conducted a prospective cohort analysis using the Truven MarketScan database (2009–2016) to estimate the incidence and prevalence of EoO in patients with Crohn’s disease (CD) or UC and vice versa. Cox proportional hazards and Kaplan-Meier methods were used to estimate the risk of EoO-related or IBD-related complications among patients with concurrent diagnoses.

Results

Among 134 013 536 individuals, the incidence of EoO, CD and UC were 23.1, 51.2 and 55.2 per 100 000 person-years, respectively. The risk of EoO was higher among patients with CD (incidence rate ratio [IRR] 5.4, p<0.01; prevalence ratio (PR) 7.8, p<0.01) or UC (IRR 3.5, p<0.01; PR 5.0, p<0.01), while the risk of IBD was higher among patients with EoO (CD: IRR 5.7, p<0.01; PR 7.6, p<0.01; UC: IRR 3.4, p<0.01; PR 4.9, p<0.01) versus individuals without either diagnosis. Concurrent diagnosis of EoO and IBD was associated with greater composite risk of IBD-related complications (CD: adjusted HR (aHR) 1.09, p=0.01; UC: aHR 1.10, p=0.04) but lower composite risk of EoO-related complications (aHR 0.59; p<0.01).

Conclusion

Based on a population-based prospective cohort analysis, the risk of EoO is significantly higher among patients with IBD and vice versa. Concurrent diagnoses might modify the risk of IBD-related and EoO-related complications. Studies defining the mechanisms underlying these observations are needed.
Increased serum/plasma fibroblast growth factor 21 in type 2 diabetes mellitus: a systematic review and meta-analysis
Authors: Wang Yun-Sheng , Ye Jun , Cao Yong-Hong , Zhang Rong , Liu Yan , Zhang Su-Wan , Dai Wu , Zhang Qiu
Published: March 2019

Objectives

Fibroblast growth factor-21 (FGF-21) plays an important role in glucose and lipid metabolism. This study aims to systemically review the evidence regarding the relationship between the FGF-21 levels and type 2 diabetes mellitus (T2DM), as well as the related influential factors.

Methods

Research related to plasma/serum FGF-21 levels in patients with T2DM and healthy controls were searched in PubMed, EMBASE and The Cochrane Library databases (up to 31 March 2017). Pooled standard mean difference (SMD) with 95% CI was calculated by fixed-effect or random-effect model analysis. Heterogeneity test was performed by the Q-statistic and quantified using I2, and publication bias was evaluated using a funnel plot and Egger’s linear regression test.

Results

In total, 317 articles were obtained after searching databases, and 11 studies with 866 patients with T2DM and 629 controls were finally included. Meta-analysis revealed that, compared with the control group, the T2DM group had a significantly higher plasma/serum FGF-21 level (p < 0.001), with the SMD of 1.34% and 95% CI (0.70 to 1.98). Meta-regression analysis and subgroup analyses suggested that body mass index (BMI), triglycerides (TG) and total cholesterol (TC) were likely related to the observed FGF-21 differences between two groups.

Conclusions

Overall, our study suggests that patients with T2DM have significantly higher plasma/serum FGF-21 levels, and the FGF-21 levels were influenced by BMI, TC and TG.
Syphilitic hepatitis and neurosyphilis: an observational study of Danish HIV-infected individuals during a 13-year period
Authors: Salado-Rasmussen Kirsten , Wessman Maria , Cowan Susan A , Gerstoft Jan , Katzenstein Terese Lea
Published: March 2019

Objective

Syphilis is an STI that potentially affects any organ. Syphilitic hepatitis and neurosyphilis have been reported in both HIV-uninfected and HIV-infected individuals. The aim of this study was to investigate syphilitic hepatitis and neurosyphilis among HIV-infected individuals during a 13-year period.

Methods

This retrospective study included all HIV-infected individuals ≥18 years diagnosed with syphilis between 1 May 2004 and 31 December 2016 in Copenhagen, Denmark. We used the unique 10-digit personal identification number assigned to all individuals in Denmark to link data from two nationwide registers to identify the patients. Patient files were revised to obtain clinical and laboratory data.

Results

A total of 509 episodes of syphilis were diagnosed in 427 HIV-infected individuals attending three hospitals in Copenhagen, Denmark. The majority of the patients were men (99.5%), and the majority of men were men who have sex with men (96%). Twenty-seven patients (6%) met the criteria for neurosyphilis, and the neurological symptoms included ocular and auditory abnormalities, headache, paraesthesia, vertigo, facial paresis, motor weakness and unexplained pain in the legs. The patients with neurosyphilis were diagnosed in the secondary stage (84%) and in the early latent (8%) or late latent (8%) stage. Among the patients tested for liver affection, 41% met the criteria for syphilitic hepatitis. The patients with syphilitic hepatitis were diagnosed in the secondary stage (82%), primary stage (10%), and in the early latent (5%) or late latent (3%) stage.

Conclusions

The study emphasises that patients with syphilis, also those seen at STI clinics, should undergo a thorough clinical examination and questioning to reveal neurological symptoms. Identification of patients with neurosyphilis is crucial since these patients undergo a different treatment. The study also emphasises that syphilis should be considered as a diagnosis in sexually active patients with liver .
Esophageal perforations: one is bad, two is worse
Authors: Price Dustin , Skarupa David
Published: March 2019

A 48-year-old man was admitted for medical management of recurrentClostridium difficile(C-dif) colitis. One month prior to presentation, he underwent right thoracotomy and lower lobectomy for a carcinoid tumor at another hospital. His postoperative course was complicated by C-dif colitis, gastroesophageal reflux, and epigastric pain. He underwent two esophagogastroduodenoscopy (EGD) procedures demonstrating mild esophagitis on the first procedure, followed by a linear ulcer on the second procedure 2 weeks later. On hospital day 9 of his current admission, he developed an acute abdomen and underwent an urgent exploratory laparotomy for presumed fulminant colitis. Findings included a healthy-appearing colon with only moderate distension, so a loop ileostomy was created for antegrade colonic irrigation. Postoperatively, a chest X-ray demonstrated a tension-appearing left pleural effusion, prompting tube thoracostomy placement. Initial output was greater than 2L of thin dark-brown fluid. An esophagram demonstrated a distal esophageal perforation (EP) and EGD was performed. Two medium-sized EPs were identified which appeared to arise from chronic-appearing ulcerations, one at 39 cm and one at 45 cm from the incisors (figure 1). A single 19mm×100 mm EndoMAXX fully covered stent was placed. Video-assisted thoracoscopic (VATS) drainage of the left hemithorax was performed in addition to placement of a right tube thoracostomy. Due to continued high output from the left thoracostomy tube, the stent was exchanged for a longer 23mm×100mm EndoMAXX fully covered stent. The patient stabilized for several days but again developed worsened sepsis, with EGD demonstrating inadequate coverage of the proximal perforation.

Figure 1

Endoscopic photograph showing left-sided esophageal perforation/fistula (black arrow). Gastroesophageal junction indicated by white arrow. NG, Nasogastric tube.

What would you have done?

Repeat esophageal stenting with wide drainage of the thoracic cavity.

Esophageal T-tube placement and wide drainage of the thoracic cavity.

Esophageal resection with gastrostomy drainage and proximal diversion.

Bilateral tube thoracostomies and antibiotic/antifungal therapy.
Reshaping fecal gut microbiota composition by growing with Polygonum cuspidatum, Houttuynia cordata, and Ipomoea aquatica
Authors: Zheng Yao , Hu Gengdong , Wu Wei , Qiu Liping , Li Dandan , Bing Xuwen , Chen Jiazhang
Published: March 2019

We carried out sequencing of samples cultivated in floating beds with different Chinese medicinal herbs (Control, Houttuynia cordata Thunb., Polygonum cuspidatum, and a combination of H. cordata with Ipomoea aquatica Forssk.; named groups A, B, C, D, respectively) to analyze changes in the composition of gut microbiota of tilapia feces. Fusobacteria (ranging from 49.0% to 73.3%), Firmicutes (12.3%–37.8%), and Proteobacteria (5.1%–23.0%) were found to be the most dominant phyla present in all samples. The operational taxonomic units and the Ace and Chao1 indices of groups A and D were significantly higher than those of group C. Polygonum cuspidatum decreased the species richness and diversity of microbial communities in tilapia intestinal feces. The phylum WCHB1-60, order Enterobacteriales, and genus Plesiomonas significantly decreased (in group A); the species Plesiomonas shigelloides significantly decreased (in groups B and C); and the genus Leucobacter significantly increased (in group D) when compared with the control. The relative abundance of the class Verrucomicrobiae (groups B vs C) significantly decreased. In the presence of I. aquatica, the phylum Bacteroidetes significantly decreased, while the genera Leucobacter and Pelotomaculum significantly increased. The ratio of Bacteroidetes to Firmicutes was significantly higher in groups B and C relative to the controls, while it decreased significantly in group D. The algae (i.e., Anabaena and Microcystis) and beneficial pathogenic bacteria decreased in groups C and D, respectively. In addition, Enterovibrio decreased in all treatment groups. The present data demonstrate that floating bed cultivation with Chinese medicinal herbs significantly alters the gut microbiota of tilapia, which may enhance its immune activity.
Vibration Analysis of a Shape Memory Oscillator by Harmonic Balance Method Verified Numerically
Authors: Rusinek Rafal , Rekas Joanna , Kecik Krzysztof
Published: March 2019

This paper focuses on periodic solutions for a one-degree-of-freedom oscillator with a spring made of shape memory alloy (SMA). However, when periodic solutions are unstable, irregular motion is identified numerically. The shape memory spring is described by a polynomial characteristic in this model. The harmonic balance method (HBM) is employed to find periodic solutions near the primary resonance. The solutions are confronted with results obtained by the multiple time scales method and numerical simulations. Finally, the effect of system parameters and temperature on the system dynamics is discussed.
Cyclicity of a Family of Generic Reversible Quadratic Systems with One Center
Authors: Wang Jihua , Dai Yanfei
Published: March 2019

This paper is concerned with the quadratic perturbations from one parameter family of generic reversible quadratic vector fields having a simple center and an invariant straight line. It is shown that the system can generate at least two limit cycles. As the parameter is rational, we propose a procedure for finding the upper bound to cyclicity of period annulus based on the Chebyshev criterion for Abelian integrals together with one rationalizing transformation. To illustrate our approach, we determine the cyclicity of three representative reversible systems. Our results may be viewed as a contribution to proving the conjecture on cyclicity proposed by Iliev [1998].
Multivariate Denoising and Missing Data Estimation for Heavy-Tailed Signals
Authors: Gorji Ferdos , Aminghafari Mina
Published: March 2019

This study focuses on heavy-tailed noise reduction in multivariate signals, with no knowledge of their forms. We propose a non-parametric multivariate denoising technique which is robust to heavy-tailed noise. Using a univariate robust linear regression, we construct a multivariate non-parametric method. We design a robust matrix decomposition and, consequently, propose a robust procedure including this new decomposition. In addition, we develop a robust procedure for the imputation of the missing points of the signals. The key advantage of our methods over the previous tools is the robustness to the heavy-tailed observations. The results of our simulation study confirm the good performance of the proposed methods.
Silicene Nanostructures Grown on Graphene Covered SiC (0001) Substrate
Authors: Berbezier I. , Michon A. , Castrucci P. , Scarselli M. , Salvato M. , Scagliotti M. , De Crescenzi M.
Published: March 2019

Large nanostructures of silicene have been successfully grown on graphene covered 6H-SiC (0001) substrates. The graphene plays an important role to obtain honeycomb structures of silicon in the sp2 configuration and acts as an ideal template for 2D materials. The scanning tunneling microscopy images showed nanosheets of silicene with a very small buckling among the Si atoms. Our scanning tunneling spectroscopy confirmed the metallic character of the deposited silicene in excellent agreement with band structure calculations that also exhibit the presence of Dirac cones.
Modification of Electric Transport Properties of CVD Graphene by Electrochemical Deposition of Cobalt Nanoparticles
Authors: Bayev V. , Fedotova J. , Humennik U. , Vorobyova S. , Konakow A. , Fedotov A. , Svito I. , Rybin M. , Obraztsova E.
Published: March 2019

Electrochemical deposition of cobalt nanoparticles was used to modify carrier transport properties of single-layered CVD graphene at the SiO2-on-Si substrate. The structure of graphene with cobalt nanoparticles was analyzed by Raman spectroscopy and scanning electron microscopy. The effect of the deposited cobalt nanoparticles on the sheet resistance of graphene was studied in the temperature range of 4–300[Formula: see text]K.
Nonporous Nitrogen and Ruthenium Co-Doped Titania Films for Photocatalysis
Authors: Linnik O. , Khoroshko L.
Published: March 2019

Nitrogen and ruthenium co-doped titania films synthesized by sol–gel technique exhibit high photocatalytic activity under both UV and visible light. Incorporation of nitrogen and ruthenium ions in titania lattice is proven by XPS. Both doping agents affected the structural properties of the films.
Nitro Derivatives of Silaprismanes as High-Energy Compounds: Theoretical Study
Authors: Salem M. A. , Gimaldinova M. A. , Kochaev A. I. , Katin K. P. , Ryzhuk R. V. , Kargin N. I. , Maslov M. M.
Published: March 2019

We present ab initio study of structures and properties of silaprismanes Si[Formula: see text]H[Formula: see text] and their nitro derivatives Si[Formula: see text]H[Formula: see text]NO2 ([Formula: see text]–10). We found that silaprismane Si[Formula: see text]H9NO2 possesses the highest stability among all studied cages. Attached NO2 group results in weak decreasing of the HOMO–LUMO gap. The smaller prismanes bind with NO2 groups more strongly. The comparison between silaprismanes and carbon prismanes is also discussed.
Middle–late Mesoproterozoic tectonic geography of the North Australia Craton: U–Pb and Hf isotopes of detrital zircon grains in the Beetaloo Sub-basin, Northern Territory, Australia
Authors: Yang B. , Collins A. S. , Blades M. L. , Capogreco N. , Payne J. L. , Munson T. J. , Cox G. M. , Glorie S.
Published: March 2019

The upper Beetaloo Sub-basin of the McArthur Basin, Northern Territory, Australia, records over 500 myr of tectonic history of the North Australian Craton from
c.
1.45 to 0.9 Ga. The basin sequences include shallow-water clastic sedimentary rocks that preserve the oldest global commercial hydrocarbon reserves. New detrital zircon U–Pb age and Lu–Hf isotopes, compiled with published data, provide constraints on the basin provenance and reveal the dynamic tectonic evolution of Mesoproterozoic northern Australia. Data from the oldest formation examined, the
c.
1.4 Ga Bessie Creek Sandstone, suggest provenance from (present-day) eastern sources (e.g. the Mount Isa Province and the palinspastically adjacent Curnamona and Georgetown provinces) with considerable spatial heterogeneity. These eastern source regions are interpreted as uplifted rift-shoulder highs, formed by contemporaneous extension between Proterozoic Australia and Laurentia. Progressively younger formations (the Velkerri Formation, the Moroak Sandstone and the Kyalla Formation) demonstrate a rapid swamping of the basin by detritus from southerly sources (e.g. the Arunta Region) that occurred at
c.
1.4–1.3 Ga. This is particularly characterized by the up-section reduction of
c.
1.6–1.5 Ga detrital zircon grains. This change in provenance is interpreted to relate to closure of an ocean basin during the period 1.35–1.25 Ga, which resulted in uplift of the southern margin of the North Australia Craton. Three ungrouped latest Mesoproterozoic to Neoproterozoic sedimentary units, the lower and upper Jamison sandstone and the Hayfield mudstone, were deposited after the emplacement of the Warakurna Large Igneous Province and are sourced from the Musgrave Province. Detrital zircon U–Pb and Hf isotope affinities between the lower and upper Jamison sandstone and the Hayfield mudstone and the latest Mesoproterozoic to early Neoproterozoic successions along the eastern margin of the North China Craton suggest that they share a similar provenance. This supports correlations between the Mesoproterozoic of the North China Yanshan Basin and the greater McArthur Basin.

Supplementary material:
Sample descriptions, details of data and concordia plots are available at
https://doi.org/10.6084/m9.figshare.c.4444790
Interactive Quality Analytics of User-generated Content
Authors: Sciascio Cecilia Di , Strohmaier David , Errecalde Marcelo , Veas Eduardo
Published: March 2019

Digital libraries and services enable users to access large amounts of data on demand. Yet, quality assessment of information encountered on the Internet remains an elusive open issue. For example, Wikipedia, one of the most visited platforms on the Web, hosts thousands of user-generated articles and undergoes 12 million edits/contributions per month. User-generated content is undoubtedly one of the keys to its success but also a hindrance to good quality. Although Wikipedia has established guidelines for the “perfect article,” authors find it difficult to assert whether their contributions comply with them and reviewers cannot cope with the ever-growing amount of articles pending review. Great efforts have been invested in algorithmic methods for automatic classification of Wikipedia articles (as featured or non-featured) and for quality flaw detection. Instead, our contribution is an interactive tool that combines automatic classification methods and human interaction in a toolkit, whereby experts can experiment with new quality metrics and share them with authors that need to identify weaknesses to improve a particular article. A design study shows that experts are able to effectively create complex quality metrics in a visual analytics environment. In turn, a user study evidences that regular users can identify flaws, as well as high-quality content based on the inspection of automatic quality scores.
Hypercolumn Sparsification for Low-Power Convolutional Neural Networks
Authors: Pilly Praveen K. , Stepp Nigel D. , Liapis Yannis , Payton David W. , Srinivasa Narayan
Published: March 2019

We provide here a novel method, called hypercolumn sparsification, to achieve high recognition performance for convolutional neural networks (CNNs) despite low-precision weights and activities during both training and test phases. This method is applicable to any CNN architecture that operates on signal patterns (e.g., audio, image, video) to extract information such as class membership. It operates on the stack of feature maps in each of the cascading feature matching and pooling layers through the processing hierarchy of the CNN by an explicit competitive process (
k
-WTA, winner take all) that generates a sparse feature vector at each spatial location. This principle is inspired by local brain circuits, where neurons tuned to respond to different patterns in the incoming signals from an upstream region inhibit each other using interneurons, such that only the ones that are maximally activated survive the quenching threshold. We show this process of sparsification is critical for probabilistic learning of low-precision weights and bias terms, thereby making pattern recognition amenable for energy-efficient hardware implementations. Further, we show that hypercolumn sparsification could lead to more data-efficient learning as well as having an emergent property of significantly pruning down the number of connections in the network. A theoretical account and empirical analysis are provided to understand these effects better.
Trained Biased Number Representation for ReRAM-Based Neural Network Accelerators
Authors: Wang Weijia , Lin Bill
Published: March 2019

Recent works have demonstrated the promise of using resistive random access memory (ReRAM) to perform neural network computations in memory. In particular, ReRAM-based crossbar structures can perform matrix-vector multiplication directly in the analog domain, but the resolutions of ReRAM cells and digital/analog converters limit the precisions of inputs and weights that can be directly supported. Although convolutional neural networks (CNNs) can be trained with low-precision weights and activations, previous quantization approaches are either not amenable to ReRAM-based crossbar implementations or have poor accuracies when applied to deep CNNs on complex datasets. In this article, we propose a new CNN training and implementation approach that implements weights using a
trained biased number representation
, which can achieve near full-precision model accuracy with as little as 2-bit weights and 2-bit activations on the CIFAR datasets. The proposed approach is compatible with a ReRAM-based crossbar implementation. We also propose an
activation-side coalescing
technique that combines the steps of batch normalization, non-linear activation, and quantization into a single stage that simply performs a clipped-rounding operation. Experiments demonstrate that our approach outperforms previous low-precision number representations for VGG-11, VGG-13, and VGG-19 models on both the CIFAR-10 and CIFAR-100 datasets.
Negative Sequence Analysis
Authors: Wang Wei , CAO Longbing
Published: March 2019

Negative sequential patterns (NSPs) produced by negative sequence analysis (NSA) capture more informative and actionable knowledge than classic positive sequential patterns (PSPs) due to involving both occurring and nonoccurring items, which appear in many applications. However, the research on NSA is still at an early stage, and NSP mining involves very high computational complexity and a very large search space, there is no widely accepted problem statement on NSP mining, and different settings on constraints and negative containment have been proposed in existing work. Among existing NSP mining algorithms, there are no general and systemic evaluation criteria available to assess them comprehensively. This article conducts a comprehensive technical review of existing NSA research. We explore and formalize a generic problem statement of NSA; investigate, compare, and consolidate the definitions of constraints and negative containment; and compare the working mechanisms and efficiency of existing NSP mining algorithms. The review is concluded by discussing new research opportunities in NSA.
Effect of bacterial flagellin on thiamin uptake by human and mouse pancreatic acinar cells: inhibition mediated at the level of transcription of thiamin transporters 1 and 2
Authors: Srinivasan Padmanabhan , Anandam Kasin Yadunandam , Ramesh Vignesh , Geltz Erica T. , Said Hamid M.
Published: March 2019

Thiamin (vitamin B1) is essential for normal cellular metabolism and function. Pancreatic acinar cells (PACs) obtain thiamin from the circulation via a specific carrier-mediated process that involves the plasma membrane thiamin transporters 1 and 2 (THTR-1 and THTR-2; products of SLC19A2 and SLC19A3 genes, respectively). There is nothing known about the effect of bacterial products/toxins on thiamin uptake by PACs. We addressed this issue in the present investigation by examining the effect of bacterial flagellin on physiological and molecular parameters of thiamin uptake by PACs. We used human primary PACs, mice in vivo, and cultured mouse-derived pancreatic acinar 266-6 cells in our investigation. The results showed that exposure of human primary PACs to flagellin led to a significant inhibition in thiamin uptake; this inhibition was associated with a significant decrease in expression of THTR-1 and -2 at the protein and mRNA levels. These findings were confirmed in mice in vivo as well as in cultured 266-6 cells. Subsequent studies showed that flagellin exposure markedly suppressed the activity of the SLC19A2 and SLC19A3 promoters and that this effect involved the Sp1 regulatory factor. Finally, knocking down Toll-like receptor 5 by use of gene-specific siRNA was found to lead to abrogation in the inhibitory effect of flagellin on PAC thiamin uptake. These results show, for the first time, that exposure of PACs to flagellin negatively impacts the physiological and molecular parameters of thiamin uptake and that this effect is mediated at the level of transcription of the SLC19A2 and SLC19A3 genes.

NEW & NOTEWORTHY The present study demonstrates, for the first time, that prolonged exposure of pancreatic acinar cells to flagellin inhibits uptake of vitamin B1, a micronutrient that is essential for energy metabolism and ATP production. This effect is mediated at the level of transcription of the SLC19A2 and SLC19A3 genes and involves the Sp1 transcription factor.
Oxidative pathophysiology following volumetric muscle loss injury in a porcine model
Authors: Chao Tony , Burmeister David M. , Corona Benjamin T. , Greising Sarah M.
Published: March 2019

Volumetric muscle loss (VML) occurs after severe orthopedic trauma and results in loss of muscle fibers and function that can leave patients permanently disabled. Although animals models of VML are useful to test possible therapeutic strategies, the pathophysiological characteristics of remaining skeletal muscle and changes in metabolism are not thoroughly understood. Herein, alterations of neuromuscular function, muscle fiber morphology, myosin heavy chain expression, and myofiber mitochondrial respiration were evaluated in an adult Yorkshire swine VML injury model. VML injured animals showed reduced peak isometric strength ( P < 0.05) and a shift toward smaller muscle fibers independent of fiber type ( P < 0.001). The muscle remaining after VML had a greater distribution of type I fibers and lower distribution of type II fibers ( P < 0.001). Skeletal muscle mitochondrial state 2 and state 3, reflecting complex I respiration, increased after injury ( P < 0.05) with a consistent trend to display higher oxygen flux per milligram of tissue. However, this was largely driven by increased mitochondrial content after VML which was associated with higher mitochondrial fission (FIS-1 protein levels). This study demonstrates an underlying perturbation of oxidative metabolism within the remaining musculature following surgical creation of an isolated, sterile VML injury in a porcine model that may be influential to the development of insidious pathophysiology and regenerative and rehabilitative therapies.

NEW & NOTEWORTHY The natural injury sequela of volumetric muscle loss (VML) and associated pathophysiology of the remaining muscle is still incompletely understood. Herein we demonstrate a chronic muscle function deficit, with an increase in type I muscle fibers and parallel increase in oxidative capacity of remaining skeletal muscle. It is possible that the alteration in oxidative capacity after VML could largely be due to heightened mitochondrial activity and an increase in mitochondrial abundance.