bluuebunny/crossref_metadata_2025_split huggingface dataset:
Island extinctions: processes, patterns, and potential for ecosystem restoration
Authors: WOOD JAMIE R. , ALCOVER JOSEP A. , BLACKBURN TIM M. , BOVER PERE , DUNCAN RICHARD P. , HUME JULIAN P. , LOUYS JULIEN , MEIJER HANNEKE J.M. , RANDO JUAN C. , WILMSHURST JANET M. 
Published: July 2017

SUMMARYExtinctions have altered island ecosystems throughout the late Quaternary. Here, we review the main historic drivers of extinctions on islands, patterns in extinction chronologies between islands, and the potential for restoring ecosystems through reintroducing extirpated species. While some extinctions have been caused by climatic and environmental change, most have been caused by anthropogenic impacts. We propose a general model to describe patterns in these anthropogenic island extinctions. Hunting, habitat loss and the introduction of invasive predators accompanied prehistoric settlement and caused declines of endemic island species. Later settlement by European colonists brought further land development, a different suite of predators and new drivers, leading to more extinctions. Extinctions alter ecological networks, causing ripple effects for islands through the loss of ecosystem processes, functions and interactions between species. Reintroduction of extirpated species can help restore ecosystem function and processes, and can be guided by palaeoecology. However, reintroduction projects must also consider the cultural, social and economic needs of humans now inhabiting the islands and ensure resilience against future environmental and climate change.
Natural variation of macrophage activation as disease-relevant phenotype predictive of inflammation and cancer survival
Authors: Buscher Konrad , Ehinger Erik , Gupta Pritha , Pramod Akula Bala , Wolf Dennis , Tweet George , Pan Calvin , Mills Charles D. , Lusis Aldons J. , Ley Klaus 
Published: July 2017

AbstractAlthough mouse models exist for many immune-based diseases, the clinical translation remains challenging. Most basic and translational studies utilize only a single inbred mouse strain. However, basal and diseased immune states in humans show vast inter-individual variability. Here, focusing on macrophage responses to lipopolysaccharide (LPS), we use the hybrid mouse diversity panel (HMDP) of 83 inbred strains as a surrogate for human natural immune variation. Since conventional bioinformatics fail to analyse a population spectrum, we highlight how gene signatures for LPS responsiveness can be derived based on an Interleukin-12β and arginase expression ratio. Compared to published signatures, these gene markers are more robust to identify susceptibility or resilience to several macrophage-related disorders in humans, including survival prediction across many tumours. This study highlights natural activation diversity as a disease-relevant dimension in macrophage biology, and suggests the HMDP as a viable tool to increase translatability of mouse data to clinical settings.
Selective production of arenes via direct lignin upgrading over a niobium-based catalyst
Authors: Shao Yi , Xia Qineng , Dong Lin , Liu Xiaohui , Han Xue , Parker Stewart F. , Cheng Yongqiang , Daemen Luke L. , Ramirez-Cuesta Anibal J. , Yang Sihai , Wang Yanqin 
Published: July 2017

AbstractLignin is the only large-volume renewable source of aromatic chemicals. Efficient depolymerization and deoxygenation of lignin while retaining the aromatic functionality are attractive but extremely challenging. Here we report the selective production of arenes via direct hydrodeoxygenation of organosolv lignin over a porous Ru/Nb2O5 catalyst that enabled the complete removal of the oxygen content from lignin. The conversion of birch lignin to monomer C7–C9 hydrocarbons is nearly quantitative based on its monomer content, with a total mass yield of 35.5 wt% and an exceptional arene selectivity of 71 wt%. Inelastic neutron scattering and DFT calculations confirm that the Nb2O5 support is catalytically unique compared with other traditional oxide supports, and the disassociation energy of Caromatic–OH bonds in phenolics is significantly reduced upon adsorption on Nb2O5, resulting in its distinct selectivity to arenes. This one-pot process provides a promising approach for improved lignin valorization with general applicability.
Dissimilatory Nitrate Reduction to Ammonium in the Yellow River Estuary: Rates, Abundance, and Community Diversity
Authors: Bu Cuina , Wang Yu , Ge Chenghao , Ahmad Hafiz Adeel , Gao Baoyu , Ni Shou-Qing 
Published: July 2017

AbstractDissimilatory nitrate reduction to ammonium (DNRA) is an important nitrate reduction process in estuarine sediments. This study reports the first investigation of DNRA in the Yellow River Estuary located in Eastern Shandong, China. Saltwater intrusion could affect the physicochemical characteristics and change the microbial community structure of sediments. In this study, the activity, abundance and community diversity of DNRA bacteria were investigated during saltwater intrusion. The slurry incubation experiments combined with isotope-tracing techniques and qPCR results showed that DNRA rates and nrfA (the functional gene of DNRA bacteria) gene abundance varied over wide ranges across different sites. DNRA rates had a positive and significant correlation with sediment organic content and extractable NH4+, while DNRA rates were weakly correlated with nrfA gene abundance. In comparison, the activities and abundance of DNRA bacteria did not change with a trend along salinity gradient. Pyrosequencing analysis of nrfA gene indicated that delta-proteobacteria was the most abundant at all sites, while epsilon-proteobacteria was hardly found. This study reveals that variability in the activities and community structure of DNRA bacteria is largely driven by changes in environmental factors and provides new insights into the characteristics of DNRA communities in estuarine ecosystems.
Regulation of Sema3c and the Interaction between Cardiac Neural Crest and Second Heart Field during Outflow Tract Development
Authors: Kodo Kazuki , Shibata Shinsuke , Miyagawa-Tomita Sachiko , Ong Sang-Ging , Takahashi Hiroshi , Kume Tsutomu , Okano Hideyuki , Matsuoka Rumiko , Yamagishi Hiroyuki 
Published: July 2017

AbstractThe cardiac neural crest cells (cNCCs) and the second heart field (SHF) play key roles in development of the cardiac outflow tract (OFT) for establishment of completely separated pulmonary and systemic circulations in vertebrates. A neurovascular guiding factor, Semaphorin 3c (Sema3c), is required for the development of the OFT, however, its regulation of the interaction between cNCCs and SHF remains to be determined. Here, we show that a Sema3c is a candidate that mediates interaction between cNCCs and the SHF during development of the OFT. Foxc1/c2 directly activates the transcription of Sema3c in the OFT, whereas, a hypomorph of Tbx1, a key SHF transcription factor, resulted in the ectopic expression of Sema3c in the pharyngeal arch region. Fgf8, a downstream secreted factor of Tbx1, inhibited the expression of Sema3c in cNCCs via activation of ERK1/2 signaling. Blocking of FGF8 caused ectopic expression of SEMA3C and a migration defect of cNCCs, resulting in abnormal chick pharyngeal arch development. These results suggest that proper spatio-temporal expression of Sema3c, regulated positively by Foxc1/c2 and negatively by the Tbx1-Fgf8 cascade, respectively, is essential for the interaction between cNCCs and the SHF that correctly navigates cNCCs towards the OFT, composed of SHF-derived cells.
Transitions between classes of neuronal excitability and bifurcations induced by autapse
Authors: Zhao Zhiguo , Gu Huaguang 
Published: July 2017

AbstractNeuronal excitabilities behave as the basic and important dynamics related to the transitions between firing and resting states, and are characterized by distinct bifurcation types and spiking frequency responses. Switches between class I and II excitabilities induced by modulations outside the neuron (for example, modulation to M-type potassium current) have been one of the most concerning issues in both electrophysiology and nonlinear dynamics. In the present paper, we identified switches between 2 classes of excitability and firing frequency responses when an autapse, which widely exists in real nervous systems and plays important roles via self-feedback, is introduced into the Morris-Lecar (ML) model neuron. The transition from class I to class II excitability and from class II to class I spiking frequency responses were respectively induced by the inhibitory and excitatory autapse, which are characterized by changes of bifurcations, frequency responses, steady-state current-potential curves, and nullclines. Furthermore, we identified codimension-1 and -2 bifurcations and the characteristics of the current-potential curve that determine the transitions. Our results presented a comprehensive relationship between 2 classes of neuronal excitability/spiking characterized by different types of bifurcations, along with a novel possible function of autapse or self-feedback control on modulating neuronal excitability.
Half‐mode substrate integrated waveguide‐based leaky‐wave antenna loaded with meandered lines
Authors: Zhang Huan , Jiao Yong‐Chang , Zhao Gang , Zhang Chi 
Published: July 2017

A novel meandered‐line‐loaded leaky‐wave antenna (LWA) is proposed. Two half‐mode substrate integrated waveguide‐based LWAs are placed face to face for obtaining high peak gains, and the meandered lines are introduced to acquire larger ratio of the beam scanning range to the operating frequency bandwidth. It is demonstrated that the operating frequency band can be narrowed by almost 1 GHz due to the meandered‐line structure under the condition that the scanning range keeps unchanged. The proposed LWA is fabricated and measured. Both simulated and measured results indicate that the designed antenna is a balanced LWA operating in frequency band 10.8–16 GHz (5.2 GHz centred at 13.4 GHz). Continuous beam scanning characteristic is observed from −60° to +34°, and comparisons are given out to validate the proposed design.
Design considerations for charge‐compensated fast‐switching power MOSFET in the medium‐voltage range
Authors: Siemieniec Ralf , Braz Cesar , Blank Oliver 
Published: July 2017

Low‐voltage power metal–oxide–semiconductor field‐effect transistors (MOSFETs) based on charge compensation using a field plate offer a significant reduction of the area‐specific on‐resistance. The extension of their blocking capability into the so‐called medium‐voltage range of 150–300 V promises devices with excellent properties being attractive for a wide range of applications. There are two approaches how this voltage‐range extension can be realised. Both concepts are linked to different device performance and different development effort. This study discusses both concepts using the example of the 150 V device class and compares the performance gained at the device and application level.
Optical wireless communication using a fully integrated 400 µm diameter APD receiver
Authors: Milovančev Dinka , Jukić Tomislav , Steindl Bernhard , Brandl Paul , Zimmermann Horst 
Published: July 2017

An optical wireless communication (OWC) system is demonstrated which uses a highly sensitive lens‐less optoelectronic integrated circuit with a 400 µm diameter avalanche photodiode as a high‐speed receiver, and a transmitter with highly collimated steerable beam at 680 nm wavelength. The benefits of integrated receiver with large‐area photodiode in an OWC scenario are proven experimentally. At a data rate of 2 Gb/s OWC is established over a distance of 12 m without using any optics at the receiver side to increase the collection area. The maximum receiving angle of the lens‐less receiver is 18°. The receiver is tested under different lighting conditions and immunity to background light is validated up to 2000 lux without using any filter to reduce the photons outside the wavelength range of interest.
Nanohybrid optical sensor for simultaneous measurements of strain, temperature, and vibration for civil application
Authors: Kaur Gurpreet , Kaler Rajinder Singh 
Published: July 2017

A design of a nanooptical sensor, i.e. hybrid Bragg gratings over photonic crystal waveguide is proposed to monitor the strain, temperature, and vibration simultaneously. The shift in wavelength, i.e. red shift (towards the right) and blue shift (towards the left), is observed in response to applied strain, vibration, and temperature, respectively. The proposed sensor gives a better performance to measure the strain (with a 9 nm wavelength shift), temperature (with 8 nm wavelength shifting), and the vibration (with 10 nm wavelength shifting).
Anatomical and Microsurgical Implications in Total and Midarm Transplantation
Authors: Iglesias Martin , Salazar-Hernández Fernanda , Ramírez-Berumen María , Butrón Patricia , Alberú-Gómez Josefina , Leal-Villalpando Rafael , Zamudio-Bautista Jorge , Acosta Victor , Jauregui-Flores Luis , Espinosa-Cruz Verónica , Vázquez-Lamadrid Jorge , González-Sánchez Judith , Hinojosa Carlos , Laparra-Escareño Hugo , Montejo-Vargas Juan , Macias-Gallardo Julio 
Published: July 2017

Background Arm transplantations are performed less frequently than forearm and hand transplantations. We present the surgical and microsurgical technique and its relationship with the clinical results in a patient with bilateral arm transplantation.
Methods A 51-year-old male patient underwent bilateral arm transplantation in October 2015. The right arm was transplanted at the glenohumeral joint. The vascular repair was at the axillary level, and the nerves were repaired at their origin. The total ischemia time was 3 hours and 48 minutes. The left arm was transplanted at the midhumeral level; all muscles were completely transplanted. The nerves were repaired at the distal third of the arm. Additionally, terminolateral neurorrhaphy was performed from the donor musculocutaneous nerve to the recipient radial nerve. The total ischemia time was 6 hours and 35 minutes.
Results At 15 months posttransplantation, the right shoulder had an abduction of 90 degrees and muscle strength of M4; flexion of 100 degrees and M4; internal and external rotation of M1; elbow flexion of 120 degrees and M3; elbow extension of M5; pronosupination of M2; and wrist extension of M2. There was no mobility in the fingers. The left transplanted limb had total elbow flexion and extension of M5, pronosupination of M2, wrist extension of M4, and finger flexion of M2. Both extremities had thermal sensitivity that allowed discrimination of cold and heat with residual deep pressure.
Conclusion Although the functional results of arm transplantation are so far unknown, they may be considered beneficial compared with the devastating disability caused by arm amputation.
Pictorial Review of the Congenital Abnormalities of the Facial Nerve, on CT and MRI
Authors: Bonfort Gratien , Debry Christian , Charpiot Anne , Veillon Francis , Venkatasamy Aina 
Published: July 2017

AbstractThe frequency and importance of the imaging evaluation of the temporal bone and middle ear have increased significantly over the past 30 years, especially prior to ear surgery. Nowadays, conventional computed tomography (CT) of the temporal bone and in fewer cases magnetic resonance imaging (MRI) of the middle ear allow a detailed evaluation of the small and complex structures of the ear and the surrounding nerves. Familiarity with the spectrum of congenital anomalies of the facial nerve and knowledge of normal facial nerve anatomy lead to simple well-defined diagnostic imaging criteria. The purpose of this article is to discuss the different imaging features of the congenital anomalies of the facial nerve, including agenesia, hypoplasia, anomalies of the course, size, and nerve duplications, compared with normal anatomical images at the same level of section for a better understanding, as the facial nerve must always be analyzed on temporal bone imaging, and any modification of its size or course has to be reported prior to any surgical procedure.
Genomic Analysis Reveals Genetic Distinctiveness of the Paiute Cutthroat Trout Oncorhynchus clarkii seleniris
Authors: Saglam Ismail K. , Prince Daniel J. , Meek Mariah , Ali Omar A. , Miller Michael R. , Peacock Mary , Neville Helen , Goodbla Alisha , Mellison Chad , Somer William , May Bernie , Finger Amanda J. 
Published: July 2017

AbstractThe Paiute Cutthroat Trout (PCT) Oncorhynchus clarkii seleniris is classified as a subspecies within the greater Cutthroat Trout O. clarkii ssp. complex and is federally listed as threatened under the Endangered Species Act. However, genetic studies to date have revealed very little genetic differentiation between the PCT and its closest relative, the Lahontan Cutthroat Trout (LCT) O. clarkii henshawi. These results casted doubt on whether the PCT is a genetically distinct subspecies or merely a phenotypic variant of the LCT. Here, we present a genomic analysis of Cutthroat Trout subspecies and populations to resolve the genetic and phylogenetic relationship between PCT and LCT. Our results demonstrate substantial genetic structure and differentiation between PCT and LCT populations. In contrast to current thinking, our phylogenetic reconstructions show the PCT to be a distinct evolutionary lineage that diverged from LCT before the LCT differentiated into its current populations (i.e., rather than PCT divergence due to geographic isolation from an LCT population in the Carson River). We conclude that the PCT is genetically distinct from the LCT.
MWASTools: an R/bioconductor package for metabolome-wide association studies
Authors: Rodriguez-Martinez Andrea , Posma Joram M , Ayala Rafael , Neves Ana L , Anwar Maryam , Petretto Enrico , Emanueli Costanza , Gauguier Dominique , Nicholson Jeremy K , Dumas Marc-Emmanuel 
Published: July 2017

Abstract

Summary
MWASTools is an R package designed to provide an integrated pipeline to analyse metabonomic data in large-scale epidemiological studies. Key functionalities of our package include: quality control analysis; metabolome-wide association analysis using various models (partial correlations, generalized linear models); visualization of statistical outcomes; metabolite assignment using statistical total correlation spectroscopy (STOCSY); and biological interpretation of metabolome-wide association studies results.

Availability and implementation
The MWASTools R package is implemented in R (version  &gt; =3.4) and is available from Bioconductor: https://bioconductor.org/packages/MWASTools/.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Association of Inflammatory Markers With Nonalcoholic Fatty Liver Disease Differs by Human Immunodeficiency Virus Serostatus
Authors: Price Jennifer C , Wang Ruibin , Seaberg Eric C , Budoff Matthew J , Kingsley Lawrence A , Palella Frank J , Witt Mallory D , Post Wendy S , Thio Chloe L 
Published: July 2017

Abstract

Background
We aimed to determine the relationship of circulating adipokines and inflammatory biomarkers with fatty liver among men in the Multicenter AIDS Cohort Study.

Methods
Noncontrast computed tomography was used to assess fatty liver and measure abdominal visceral adipose tissue (VAT) area in 526 participants without history of cardiovascular disease, heavy alcohol use, or viral hepatitis infection. Multivariable logistic regression was used to assess associations of circulating biomarker levels with fatty liver.

Results
Three hundred twenty-nine human immunodeficiency virus (HIV)-infected men had higher levels of several inflammatory biomarkers compared with 197 HIV-uninfected men. Among HIV-uninfected men, increased adiponectin was associated with lower odds of fatty liver (odds ratio [OR] = 0.51 per doubling, P = .02), whereas higher odds of fatty liver was observed with increased levels of the proinflammatory markers intercellular adhesion molecule (ICAM)-1 (OR = 5.30, P = .004), C-reactive protein (OR = 1.66, P = .002), interleukin (IL)-6 (OR = 1.67, P = .03), and tumor necrosis factor α receptor 2 (OR = 6.55, P = .003). Among HIV-infected men, ICAM-1 was the only proinflammatory marker associated with greater odds of fatty liver (OR = 2.67, P = .02), whereas higher adiponectin (OR = 0.57, P = .003), and osteoprotegerin levels (OR = 0.48, P = .03) were associated with lower odds. These associations were all independent of VAT.

Conclusions
Fatty liver is associated with a heightened inflammatory state independent of visceral adiposity in HIV-uninfected men but not in HIV-infected men. However, a heightened anti-inflammatory state may protect against fatty liver regardless of HIV serostatus.
Safety and Efficacy of Ombitasvir, Paritaprevir With Ritonavir ± Dasabuvir With or Without Ribavirin in Patients With Human Immunodeficiency Virus-1 and Hepatitis C Virus Genotype 1 or Genotype 4 Coinfection: TURQUOISE-I Part 2
Authors: Rockstroh Jürgen K , Orkin Chloe , Viani Rolando M , Wyles David , Luetkemeyer Anne F , Lazzarin Adriano , Soto-Malave Ruth , Nelson Mark R , Bhagani Sanjay R , Klinker Hartwig H F , Rizzardini Giuliano , Girard Pierre-Marie , Tural Cristina , Shulman Nancy S , Mobashery Niloufar , Hu Yiran B , Fredrick Linda M , Pilot-Matias Tami , Trinh Roger , Gane Edward 
Published: July 2017

Abstract

Background
Ombitasvir, paritaprevir with ritonavir, and dasabuvir (OBV/PTV/r ± DSV) ±ribavirin (RBV) are approved to treat hepatitis C virus (HCV) genotype 1 and 4 infection. Here, we investigate the safety and efficacy of OBV/PTV/r + DSV ±RBV for HCV genotype 1, and OBV/PTV/r + RBV for HCV genotype 4, in human immunodeficiency virus (HIV)-1 coinfected patients with or without compensated cirrhosis.

Methods
TURQUOISE-I, Part 2 is a phase 3 multicenter study. Patients with or without cirrhosis were HCV treatment-naive or -experienced, on an HIV-1 antiretroviral regimen containing atazanavir, raltegravir, dolutegravir, or darunavir (for genotype 4 only), and had plasma HIV-1 ribonucleic acid &lt;40 copies/mL at screening. Patients received OBV/PTV/r ± DSV ±RBV for 12 or 24 weeks.

Results
In total, 228 patients were treated according to guidelines. Sustained virologic response at posttreatment week 12 (SVR12) was achieved by 194 of 200 (97%) and 27 of 28 (96%) patients with HCV genotype 1 and genotype 4 infection, respectively. There were 2 virologic failures: 1 breakthrough and 1 relapse in a cirrhotic and a noncirrhotic patient with genotype 1b and 1a infection, respectively. One reinfection occurred at posttreatment week 12 in a genotype 1a-infected patient. Excluding nonvirologic failures, the SVR12 rates were 98% (genotype 1) and 100% (genotype 4). Adverse events were mostly mild in severity and did not lead to discontinuation. Laboratory abnormalities were rare.

Conclusions
The OBV/PTV/r ±DSV was well tolerated and yielded high SVR12 rates in patients with HCV genotype 1 or genotype 4/HIV-1 coinfection. The OBV/PTV/r ± DSV ±RBV is a potent HCV treatment option for patients with HIV-1 coinfection, regardless of treatment experience.