bluuebunny/crossref_metadata_2025_split huggingface dataset:
Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms
Authors: Martin Belinda C. , George Suman J. , Price Charles A. , Shahsavari Esmaeil , Ball Andrew S. , Tibbett Mark , Ryan Megan H. 
Published: September 2016

Abstract. Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg−1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g−1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography–mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.
DNA Barcoding of Philippine Herbal Medicinal Products
Authors: Pedales Ronniel D , Damatac Amor M , Limbo Carlo A , Marquez Cielo Mae D , Navarro Anna Isabel B , Molina Jeanmaire 
Published: September 2016

Abstract
The Philippine government established the Traditional and Alternative Medicine Act in 1997 to promote traditionally used herbal products and to provide an effective yet affordable alternative to conventional medicines. However, government regulation of herbal medicinal products (HMPs) is not stringent, relying only on submitted quality data from the manufacturer. In this study we validated the taxonomic identity of 26 plant samples contained within 22 HMPs, each produced by different local manufacturers, through DNA barcoding of the nuclear internal transcribed spacer-2 (ITS2) region. We recovered 19 ITS2 barcodes from 26 samples. These were compared to sequences in GenBank using MEGABLAST, but ambiguous results (similar max scores for different species) were phylogenetically analyzed. Twelve of the 19 samples matched the indicated species on the product label, three were equivocal in specific identity but were placed in the expected genus, and four other samples from three manufacturers contained contamination and/or substitution. GenBank's reference database was at times problematic because some sequences were lacking or were misidentified, but the database was still useful. Overall, ITS2 barcoding was successful in authenticating the HMPs, and it is recommended during the premarket evaluation process so as to obtain a certificate of registration from the government. The government should also develop a comprehensive database of barcodes for Philippine plants, and should prioritize the development of the traditional pharmacopeia because many locally produced HMPs are not indigenous.
Pulmonary Manifestations of Acute Lung Injury: More Than Just Diffuse Alveolar Damage
Authors: Hughes Kenneth T. , Beasley Mary Beth 
Published: September 2016

Context.—Acute pulmonary injury may occur as a result of myriad direct or indirect pulmonary insults, often resulting in hypoxemic respiratory failure and clinical acute respiratory distress syndrome. Histologically, most patients will exhibit diffuse alveolar damage on biopsy, but other histologic patterns may be encountered, such as acute eosinophilic pneumonia, acute fibrinous and organizing pneumonia, and diffuse alveolar hemorrhage with capillaritis.Objective.—To review the diagnostic features of various histologic patterns associated with a clinical picture of acute lung injury, and to discuss key features in the differential diagnosis.Data Sources.—The review is drawn from pertinent peer-reviewed literature and the personal experience of the authors.Conclusions.—Acute pulmonary injury is a significant cause of morbidity and mortality. In addition to diffuse alveolar damage, pathologists should be aware of alternate histologic patterns of lung disease that may present with a similar clinical presentation because this may impact treatment decisions and disease outcome.
Linking Pluripotency Reprogramming and Cancer
Authors: Iglesias Juan Manuel , Gumuzio Juan , Martin Angel G. 
Published: September 2016

Summary
Tumor development and the generation of induced pluripotent stem cells are highly comparable processes with striking similarities. Cellular plasticity is inherent to tumor evolution, rendering cells that acquire a stem cell-like phenotype, for which Sox2 activation has proved instrumental for the plastic acquisition of stemness properties in tumor cells. Understanding the molecular mechanisms underlying both events might uncover novel approaches for the development of anticancer therapeutics and constitute model systems for understanding tumor generation and ensuring the biosafety of cell-based therapies.
Nanoarchitectonic atomic switch networks for unconventional computing
Authors: Demis Eleanor C. , Aguilera Renato , Scharnhorst Kelsey , Aono Masakazu , Stieg Adam Z. , Gimzewski James K. 
Published: September 2016

Abstract
Developments in computing hardware are constrained by the operating principles of complementary metal oxide semiconductor (CMOS) technology, fabrication limits of nanometer scaled features, and difficulties in effective utilization of high density interconnects. This set of obstacles has promulgated a search for alternative, energy efficient approaches to computing inspired by natural systems including the mammalian brain. Atomic switch network (ASN) devices are a unique platform specifically developed to overcome these current barriers to realize adaptive neuromorphic technology. ASNs are composed of a massively interconnected network of atomic switches with a density of ∼109 units/cm2 and are structurally reminiscent of the neocortex of the brain. ASNs possess both the intrinsic capabilities of individual memristive switches, such as memory capacity and multi-state switching, and the characteristics of large-scale complex systems, such as power-law dynamics and non-linear transformations of input signals. Here we describe the successful nanoarchitectonic fabrication of next-generation ASN devices using combined top-down and bottom-up processing and experimentally demonstrate their utility as reservoir computing hardware. Leveraging their intrinsic dynamics and transformative input/output (I/O) behavior enabled waveform regression of periodic signals in the absence of embedded algorithms, further supporting the potential utility of ASN technology as a platform for unconventional approaches to computing.
A genetic programming approach to oral cancer prognosis
Authors: Tan Mei Sze , Tan Jing Wei , Chang Siow-Wee , Yap Hwa Jen , Abdul Kareem Sameem , Zain Rosnah Binti 
Published: September 2016

BackgroundThe potential of genetic programming (GP) on various fields has been attained in recent years. In bio-medical field, many researches in GP are focused on the recognition of cancerous cells and also on gene expression profiling data. In this research, the aim is to study the performance of GP on the survival prediction of a small sample size of oral cancer prognosis dataset, which is the first study in the field of oral cancer prognosis.MethodGP is applied on an oral cancer dataset that contains 31 cases collected from the Malaysia Oral Cancer Database and Tissue Bank System (MOCDTBS). The feature subsets that is automatically selected through GP were noted and the influences of this subset on the results of GP were recorded. In addition, a comparison between the GP performance and that of the Support Vector Machine (SVM) and logistic regression (LR) are also done in order to verify the predictive capabilities of the GP.ResultThe result shows that GP performed the best (average accuracy of 83.87% and average AUROC of 0.8341) when the features selected are smoking, drinking, chewing, histological differentiation of SCC, and oncogene p63. In addition, based on the comparison results, we found that the GP outperformed the SVM and LR in oral cancer prognosis.DiscussionSome of the features in the dataset are found to be statistically co-related. This is because the accuracy of the GP prediction drops when one of the feature in the best feature subset is excluded. Thus, GP provides an automatic feature selection function, which chooses features that are highly correlated to the prognosis of oral cancer. This makes GP an ideal prediction model for cancer clinical and genomic data that can be used to aid physicians in their decision making stage of diagnosis or prognosis.
Assessment of DSDs of GPM‐DPR with ground‐based disdrometer at seasonal scale over Gadanki, India
Authors: Radhakrishna Basivi , Satheesh S. K. , Narayana Rao T. , Saikranthi K. , Sunilkumar K. 
Published: September 2016

AbstractCharacteristics of raindrop size distribution (DSD) obtained by Global Precipitation Measurement (GPM) mission dual‐frequency precipitation radar (DPR) are assessed over Gadanki region during southwest (SW) and northeast (NE) monsoon seasons utilizing 2 years (2014–2015) of DSD measurements by an impact‐type disdrometer. The mass weighted mean diameter (Dm in mm) and normalized DSD scaling parameter for concentration (Nw in mm−1 m−3) show pronounced seasonal differences at low to medium rain rates in the disdrometer data, in accordance with the previous studies, but not in the GPM‐DPR data. Similar features are observed every year in disdrometer measurements and over different spatial domains in GPM‐DPR measurements, indicating that sampling mismatch errors are insignificant. The reasons for the absence of seasonal differences in DSDs derived from GPM‐DPR are examined by simulating the reflectivities at Ku‐ and Ka‐bands, utilizing the disdrometer measurements and T‐matrix scattering indices. Results suggest that the Dm and Nw retrieved from single‐frequency and dual‐frequency algorithms utilizing the disdrometer data also show seasonal differences in accordance with the observations with under and overestimation of Dm and Nw, respectively. When compared with the disdrometer, the Dm values retrieved from the GPM‐DPR (official products) are severely underestimated at high rain rates (R > 8 mm h−1) during the SW monsoon season. On the other hand, during low rain rates (R < 8 mm h−1), a slight underestimation (overestimation) of Dm is seen during the SW (NE) monsoon. The mean Nw values retrieved from GPM‐DPR agree poorly with disdrometer data during both the monsoon seasons.
Thermochronological evidence of a low‐angle, mid‐crustal detachment plane beneath the central South Island, New Zealand
Authors: Warren‐Smith Emily , Lamb Simon , Seward Diane , Smith Euan , Herman Frédéric , Stern Tim 
Published: September 2016

AbstractOblique continental convergence and uplift in the Southern Alps, New Zealand is largely accommodated by dextral transpression on the Alpine Fault. However, toward the south of the orogen the Alpine Fault becomes increasingly strike‐slip, despite evidence for high exhumation rates in the Pacific plate. Here we present 41 new apatite and zircon fission‐track ages to investigate the role of the southern Alpine Fault in Pacific plate exhumation since the Miocene. Through development of a new, maximum likelihood fission‐track age calculation method (to overcome extremely low (<0.1 ppm) 238U concentrations in apatites) we estimate the width of the fully reset apatite zone (ages <5 Ma) southeast of the southern Alpine Fault, which has been previously overestimated. Instead, this zone is ∼30 km wide, rather than 60 km. We combine our exhumation profile with thermo‐kinematic modeling to impose constraints on fault kinematics and deformation history. The surface cooling age pattern can be well reproduced by exhumation along a listric reverse fault, which shallows to a low‐angle (6–10°) mid‐crustal detachment beneath the Southern Lakes. This structure is comparable to the listric central Alpine Fault geometry previously constrained by thermo‐kinematics models to the north of our study region. We propose this detachment plane is continuous beneath a large region of central South Island and may be acting to accommodate underthrusting of Australian crust beneath the Pacific plate.
New modes and mechanisms of thermospheric mass density variations from GRACE accelerometers
Authors: Calabia Andres , Jin Shuanggen 
Published: September 2016

AbstractMonitoring and understanding the upper atmosphere processes is important for orbital decay and space physics. Nowadays, Low Earth Orbit (LEO) accelerometers provide a unique opportunity to study thermospheric density variations with unprecedented details. In this paper, thermospheric mass densities variations from Gravity Recovery and Climate Experiment (GRACE) accelerometers are investigated for the period 2003–2016 using the principal component analysis (PCA). The resulting modes are analyzed and parameterized in terms of solar and magnetospheric forcing, local solar time (LST), and annual variations. A better understanding of global thermospheric air density variations is presented, which validates the suitability of our technique and model. The parameterization of the subsolar‐point annual variation shows two maxima around June and only one in December. The LST parameterization shows a new fluctuation controlling a middle latitude four‐wave pattern, with two maxima at 12 h and 21 h LST and two minima at 1 h and 17 h LST. Our parameterizations are suitable to represent small‐scale variations including, e.g., the equatorial mass density anomaly (EMA) and the midnight density maximum (MDM). Finally, the residuals are analyzed in the spectral domain, and additional contributions are found at the frequencies of the radiational tides and at the periods of 83, 93, 152, and 431 days.
Suprathermal particle energization in dipolarization fronts: Particle‐in‐cell simulations
Authors: Lu San , Angelopoulos V. , Fu Huishan 
Published: September 2016

AbstractWithin dipolarization fronts (DFs) in the Earth's magnetotail, significant magnetic energy is converted to plasma energy, and a significant portion of the electrons and ions therein are accelerated to suprathermal energies. The mechanism that produces these suprathermal particles while simultaneously reducing magnetic field energy is poorly understood, however. We use two‐dimensional particle‐in‐cell simulations to explore this process in conventional flux bundle‐type DFs, which are formed by single X line reconnection and connected to the Earth, and in newly proposed flux rope‐type DFs, which are formed and bracketed by two X lines. In flux bundle‐type DFs, electrons are betatron accelerated near the Bz peak, and ions are energized through reflection at the front. In flux rope‐type DFs, most suprathermal electrons and ions are confined to the flux rope's magnetic structure and are accelerated through repeated reflections at the structure's two ends.
Numerical simulation of the 6 day wave effects on the ionosphere: Dynamo modulation
Authors: Gan Quan , Wang Wenbing , Yue Jia , Liu Hanli , Chang Loren C. , Zhang Shaodong , Burns Alan , Du Jian 
Published: September 2016

AbstractThe Thermosphere‐Ionosphere‐Mesosphere Electrodynamics General Circulation Model (TIME‐GCM) is used to theoretically study the 6 day wave effects on the ionosphere. By introducing a 6 day perturbation with zonal wave number 1 at the model lower boundary, the TIME‐GCM reasonably reproduces the 6 day wave in temperature and horizontal winds in the mesosphere and lower thermosphere region during the vernal equinox. The E region wind dynamo exhibits a prominent 6 day oscillation that is directly modulated by the 6 day wave. Meanwhile, significant local time variability (diurnal and semidiurnal) is also seen in wind dynamo as a result of altered tides due to the nonlinear interaction between the 6 day wave and migrating tides. More importantly, the perturbations in the E region neutral winds (both the 6 day oscillation and tidal‐induced short‐term variability) modulate the polarization electric fields, thus leading to the perturbations in vertical ion drifts and ionospheric F2 region peak electron density (NmF2). Our modeling work shows that the 6 day wave couples with the ionosphere via both the direct neutral wind modulation and the interaction with atmospheric tides.
Reply to comment by Kil et al. on “The night when the auroral and equatorial ionospheres converged”
Authors: Martinis Carlos , Baumgardner Jeffrey , Mendillo Michael , Wroten Joei , Coster Anthea J. , Paxton Larry J. 
Published: September 2016

AbstractOne of the goals of the Martinis et al. (2015) (M15) paper was to stimulate interest in the topic of “severe events during moderate geomagnetic storms”—and we succeeded. We welcome the Comment by Kil et al. (2016) (K16) who identified weak signatures related to medium‐scale traveling ionospheric disturbances (MSTIDs) and tried to argue that airglow depletion signatures of equatorial spread F (ESF) were not present. We agree with K16 in that MSTIDs were present to the north of the all‐sky imager, but only during the early observations. They are easily distinguished from the ESF‐related dark structures observed at the same time to the south of the imager. We stress some observational facts that K16 overlooked or erroneously used to support their case. M15 offered evidence and discussion evidence and discussion of a dynamical pattern—both in space and time domains—and the counter arguments by K16 should have dealt with the same places and same times. We also point out that the GPS data shown by K16 do not provide any information below ~30° geographic latitude in the longitude sector covered by the all‐sky imager. This is the region where the ESF structures appeared first and grew to reach higher latitudes. We believe that the issues addressed by K16 do not provide conclusive evidence to rule out the interpretation given by M15 on the nature of the airglow depletions observed at McDonald Observatory.
Resonance vibrations of the Ross Ice Shelf and observations of persistent atmospheric waves
Authors: Godin Oleg A. , Zabotin Nikolay A. 
Published: September 2016

AbstractRecently reported lidar observations have revealed a persistent wave activity in the Antarctic middle and upper atmosphere that has no counterpart in observations at midlatitude and low‐latitude locations. The unusual wave activity suggests a geographically specific source of atmospheric waves with periods of 3–10 h. Here we investigate theoretically the hypothesis that the unusual atmospheric wave activity in Antarctica is generated by the fundamental and low‐order modes of vibrations of the Ross Ice Shelf (RIS). Simple models are developed to describe basic physical properties of resonant vibrations of large ice shelves and their coupling to the atmosphere. Dispersion relation of the long surface waves, which propagate in the floating ice sheet and are responsible for its low‐order resonances, is found to be similar to the dispersion relation of infragravity waves in the ice‐free ocean. The phase speed of the surface waves and the resonant frequencies determine the periods and wave vectors of atmospheric waves that are generated by the RIS resonant oscillations. The altitude‐dependent vertical wavelengths and the periods of the acoustic‐gravity waves in the atmosphere are shown to be sensitive to the physical parameters of the RIS, which can be difficult to measure by other means. Predicted properties of the atmospheric waves prove to be in a remarkable agreement with the key features of the observed persistent wave activity.
Tsunami generation and associated waves in the water column and seabed due to an asymmetric earthquake motion within an anisotropic substratum
Authors: Bagheri Amirhossein , Greenhalgh Stewart , Khojasteh Ali , Rahimian Mohammad , Attarnejad Reza 
Published: September 2016

AbstractIn this paper, closed‐form integral expressions are derived to describe how surface gravity waves (tsunamis) are generated when general asymmetric ground displacement (due to earthquake rupturing), involving both horizontal and vertical components of motion, occurs at arbitrary depth within the interior of an anisotropic subsea solid beneath the ocean. In addition, we compute the resultant hydrodynamic pressure within the seawater and the elastic wavefield within the seabed at any position. The method of potential functions and an integral transform approach, accompanied by a special contour integration scheme, are adopted to handle the equations of motion and produce the numerical results. The formulation accounts for any number of possible acoustic‐gravity modes and is valid for both shallow and deep water situations as well as for any focal depth of the earthquake source. Phase and group velocity dispersion curves are developed for surface gravity (tsunami mode), acoustic‐gravity, Rayleigh, and Scholte waves. Several asymptotic cases which arise from the general analysis are discussed and compared to existing solutions. The role of effective parameters such as hypocenter location and frequency of excitation is examined and illustrated through several figures which show the propagation pattern in the vertical and horizontal directions. Attention is directed to the unexpected contribution from the horizontal ground motion. The results have important application in several fields such as tsunami hazard prediction, marine seismology, and offshore and coastal engineering. In a companion paper, we examine the effect of ocean stratification on the appearance and character of internal and surface gravity waves.
Using the Model Statement to Elicit Information and Cues to Deceit from Native Speakers, Non‐native Speakers and Those Talking Through an Interpreter
Authors: Ewens Sarah , Vrij Aldert , Leal Sharon , Mann Samantha , Jo Eunkyung , Shaboltas Alla , Ivanova Maria , Granskaya Juliana , Houston Kate 
Published: September 2016

SummaryWe examined how the presence of an interpreter during an interview affects eliciting information and cues to deceit, whilst using a method that encourages interviewees to provide more detail (model statement, MS). Sixty native English speakers were interviewed in English, and 186 non‐native English speakers were interviewed in English or through an interpreter. Interviewees either lied or told the truth about a mock security meeting, which they reported twice: in an initial free recall and after listening to the MS. The MS resulted in the native English speakers and those interviewed with an interpreter providing more reminiscences (additional detail) than the non‐native English speakers interviewed without an interpreter. As a result, those interviewed through an interpreter provided more detail than the non‐native English speakers, but only after the MS. Native English participants were most detailed in both recalls. No difference was found in the amount of reminiscences provided by liars and truth tellers. Copyright © 2016 John Wiley & Sons, Ltd.