bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional Impact of Tinnitus in Patients with Hearing Loss
Authors: Mantello Erika Barioni , Lupoli Luciana de Mata , Rodrigues Paula Cantarella de Padua , Cavalcante Juliana Maria Soares , Massuda Eduardo Tanaka , Anastasio Adriana Ribeiro Tavares
Published: January 2020

Introduction Tinnitus, which is considered the third worst symptom for humans, is a common complaint among people living with hearing loss and may negatively affect the quality of life of those who have it.

Objective To analyze the perception of the handicap in patients with tinnitus and hearing loss as well as the possible associations between the variables hearing loss, loudness, onset, frequency and annoyance by tinnitus, and the correlation between the visual analogue scale (VAS) and the Tinnitus Handicap Inventory (THI).

Methods A total of 30 patients with complaints of tinnitus and the presence of sensorineural hearing impairment were selected for this cross-sectional, observational, and descriptive study. The loudness of the tinnitus was measured by a VAS and classified as mild, moderate, or severe. The THI was classified as slight, mild, moderate, severe, and catastrophic. Data were submitted to statistical analysis using the Fisher exact test and Spearman correlation coefficient.

Results Eleven male (36.7%) and 19 female (63.3%) subjects with a mean age of 56.5 years old were evaluated. There was no significant association between loudness, annoyance, time and frequency of tinnitus, nor between hearing loss and tinnitus. There was a significant association between the variables hearing loss and loudness, and a weak correlation between VAS and THI.

Conclusion Tinnitus has a practical impact in the lives of patients with hearing loss in terms of catastrophic, functional, and emotional aspects, regardless of loudness, frequency, or time of onset. Hearing loss was a factor that had an impact on the loudness of tinnitus. There was no statistically significant correlation between VAS and THI.
Adult Otogenic Meningitis in the Pneumococcal Conjugated Vaccines Era
Authors: Marom Tal , Shemesh Shay , Habashi Nadeem , Gluck Ofer , Tamir Sharon Ovnat
Published: January 2020

Introduction Streptococcus pneumoniae is a major pathogen of otogenic meningitis (OgM), the most commonly reported intra-cranial complication of otitis media (OM).

Objectives To study the changes in adult OgM patients in the pneumococcal conjugated vaccines (PCVs) era.

Methods Retrospective cohort of adults presenting with concurrent OM and meningitis in a secondary medical care center between 2005 and 2015. Data collected included demographics, OM-related symptoms, cerebrospinal fluid (CSF) and ear culture results, pre- and during hospitalization antibiotic treatment, imaging findings, and complications. We compared the pre-PCV years (2005–2009) with the post-PCV years (2010–2015). Outcomes were 1) incidence of all-cause adult OgM from the total meningitis cases; 2) impact of PCVs on the clinical presentation of OgM and bacteriology.

Results Otogenic meningitis was diagnosed in 26 out of 45 (58%) cases of all-cause meningitis admissions. Of those, 10 (38%) were male, with a mean age of 62.4 years old. Ear-related signs and symptoms were documented in 70% of the patients, and OgM was diagnosed following imaging studies in 6 out of 26 (23%) patients. All of the patients received intravenous antibiotic therapy, and 7 (27%) patients required surgical interventions: 6 required myringotomy and 1 required mastoidectomy. There were 12 (46%) patients in the pre-PCV years and 14 (56%) in the post-PCV years. The positive pneumococcal CSF and ear culture rates remained high and unchanged (∼ 75%). There were no significant changes in the clinical presentation or mortality rates.

Conclusion Micro-otoscopy should be included in the routine work-up of any suspected adult meningitis, because OgM is underdiagnosed. Unlike their impact on pediatric otitis media, PCVs did not change the epidemiology and bacteriology of OgM.
Malignancy Rate in Thyroid Nodules with Atypia or Follicular Lesion of Undetermined Significance
Authors: Pasha Hamdan Ahmed , Dhanani Rahim , Mughal Ainulakbar , Ahmed Kaleem S. , Suhail Anwar
Published: January 2020

Introduction Atypia of undetermined significance (AUS) or follicular lesion of undetermined significance (FLUS) is one of the six diagnostic categories of the Bethesda System for Reporting Thyroid Cytopathology. The prevalence of malignancy among Bethesda category III cytology is variable, ranging from 5% to 37% in the literature.

Objective To determine the rate of malignancy in thyroid nodules reported as Bethesda category III.

Methods A total of 495 patients underwent surgical intervention for thyroid nodules from January 2015 to December 2017. The present study included 81 cases reported as Bethesda category III, and their medical records were reviewed.

Results Out of 495 fine-needle aspiration cytology samples, 81 (16.4%) samples were labeled as AUS/FLUS. Among these 81 patients, the mean age was 43.0 years (± 13.9), with only 11 (14%) patients older than 55 years of age. Most of our patients were female (n = 69; 85.2%), and the rest were male. The rate of malignancy based on the final histology was of 33.3% (n = 27). The majority were 17 cases (21%) of papillary carcinoma, followed by follicular carcinoma (n = 6) (7.4%).

Conclusion The risk of malignancy can be higher than it is commonly believed, and guidelines should be based on the data from the institutions themselves for a better assessment of the outcomes.
Image of the Month: Meconium Peritonitis with Pseudocyst—A Spot Diagnosis in Newborns
Authors: Ascherl Rudolph , Vaz Pimentel Duarte , Knüpfer Mathias , Sorge Ina , Lacher Martin , Zimmermann Peter
Published: January 2020

We report on a male preterm newborn with a large abdominal tumor found on prenatal ultrasound 2 weeks prior to delivery at 36 + 0 weeks of gestation. A postnatal abdominal plain film showed a mass with well-defined rim calcifications (“eggshell”), suggestive of a meconium pseudocyst. On the 4th day of life, the boy underwent exploratory laparotomy with resection of the cyst and end-to-back jejunojejunostomy. The postoperative course was uneventful. A meconium pseudocyst is the correlate of a sterile peritonitis caused by antenatal bowel perforation. It is an easily recognizable spot diagnosis any pediatrician and pediatric surgeon should be aware of.
Unclonable photonic keys hardened against machine learning attacks
Authors: Bosworth Bryan T. , Atakhodjaev Iskandar A. , Kossey Michael R. , Grubel Brian C. , Vresilovic Daniel S. , Stroud Jasper R. , MacFarlane Neil , Villalba Jesús , Dehak Najim , Cooper A. Brinton , Foster Mark A. , Foster Amy C.
Published: January 2020

The hallmark of the information age is the ease with which information is stored, accessed, and shared throughout the globe. This is enabled, in large part, by the simplicity of duplicating digital information without error. Unfortunately, an ever-growing consequence is the global threat to security and privacy enabled by our digital reliance. Specifically, modern secure communications and authentication suffer from formidable threats arising from the potential for copying of secret keys stored in digital media. With relatively little transfer of information, an attacker can impersonate a legitimate user, publish malicious software that is automatically accepted as safe by millions of computers, or eavesdrop on countless digital exchanges. To address this vulnerability, a new class of cryptographic devices known as physical unclonable functions (PUFs) are being developed. PUFs are modern realizations of an ancient concept, the physical key, and offer an attractive alternative for digital key storage. A user derives a digital key from the PUF’s physical behavior, which is sensitive to physical idiosyncrasies that are beyond fabrication tolerances. Thus, unlike conventional physical keys, a PUF cannot be duplicated and only the holder can extract the digital key. However, emerging machine learning (ML) methods are remarkably adept at learning behavior via training, and if such algorithms can learn to emulate a PUF, then the security is compromised. Unfortunately, such attacks are highly successful against conventional electronic PUFs. Here, we investigate ML attacks against a nonlinear silicon photonic PUF, a novel design that leverages nonlinear optical interactions in chaotic silicon microcavities. First, we investigate these devices’ resistance to cloning during fabrication and demonstrate their use as a source of large volumes of cryptographic key material. Next, we demonstrate that silicon photonic PUFs exhibit resistance to state-of-the-art ML attacks due to their nonlinearity and finally validate this resistance in an encryption scenario.
Magnetic nanostructures for emerging biomedical applications
Authors: Peixoto L. , Magalhães R. , Navas D. , Moraes S. , Redondo C. , Morales R. , Araújo J. P. , Sousa C. T.
Published: January 2020

Magnetic nanostructures have been widely studied due to their potential applicability into several research fields such as data storage, sensing and biomedical applications. Focusing on the biomedical aspect, some new approaches deserve to be mentioned: cell manipulation and separation, contrast-enhancing agents for magnetic resonance imaging, and magnetomechanically induced cell death. This work focuses on understanding three different magnetic nanostructures, disks in the vortex state, synthetic antiferromagnetic particles and nanowires, first, by explaining their interesting properties and how they behave under an applied external field, before reviewing their potential applications for each of the aforementioned techniques.
Periodic bouncing modes for two uniformly magnetized spheres. I. Trajectories
Authors: Edwards Boyd F. , Johnson Bo A. , Edwards John M.
Published: January 2020

We consider a uniformly magnetized sphere that moves without friction in a plane in response to the field of a second, identical, fixed sphere, making elastic hard-sphere collisions with this sphere. We seek periodic solutions to the associated nonlinear equations of motion. We find closed-form mathematical solutions for small-amplitude modes and use these to characterize and validate our large-amplitude modes, which we find numerically. Our Runge-Kutta integration approach allows us to find 1243 distinct periodic modes with the free sphere located initially at its stable equilibrium position. Each of these modes bifurcates from the finite-amplitude radial bouncing mode with infinitesimal-amplitude angular motion and supports a family of states with increasing amounts of angular motion. These states offer a rich variety of behaviors and beautiful, symmetric trajectories, including states with up to 157 collisions and 580 angular oscillations per period.
Extending the fused-sphere SAFT-γ Mie force field parameterization approach to poly(vinyl butyral) copolymers
Authors: Walker Christopher C. , Genzer Jan , Santiso Erik E.
Published: January 2020

SAFT-γ Mie, a molecular group-contribution equation of state with foundations in the statistical associating fluid theory framework, is a promising means for developing accurate and transferable coarse-grained force fields for complex polymer systems. We recently presented a new approach for incorporating bonded potentials derived from all-atom molecular dynamics simulations into fused-sphere SAFT-γ Mie homopolymer chains by means of a shape factor parameter, which allows for bond distances less than the tangent-sphere value required in conventional SAFT-γ Mie force fields. In this study, we explore the application of the fused-sphere SAFT-γ Mie approach to copolymers. In particular, we demonstrate its capabilities at modeling poly(vinyl alcohol-co-vinyl butyral) (PVB), an important commercial copolymer widely used as an interlayer in laminated safety glass applications. We found that shape factors determined from poly(vinyl alcohol) and poly(vinyl butyral) homopolymers do not in general correctly reproduce random copolymer densities when standard SAFT-γ Mie mixing rules are applied. However, shape factors optimized to reproduce the density of a random copolymer of intermediate composition resulted in a model that accurately represents density across a wide range of chemical compositions. Our PVB model reproduced copolymer glass transition temperature in agreement with experimental data, but heat capacity was underpredicted. Finally, we demonstrate that atomistic details may be inserted into equilibrated fused-sphere SAFT-γ Mie copolymer melts through a geometric reverse-mapping algorithm.
Enhanced room temperature ferromagnetism in MoS2 by N plasma treatment
Authors: Wang Bao , Zhang Daoyu , Wang Hong , Zhao Huihui , Liu Ruobai , Li Qi , Zhou Shengqiang , Du Jun , Xu Qingyu
Published: January 2020

The introduction of ferromagnetism in MoS2 is important for its applications in semiconductor spintronics. MoS2 powders were synthesized by hydrothermal method, followed by the N plasma treatment at room temperature. Weak ferromagnetism with saturated ferromagnetic magnetization of 0.64 memu/g has been observed in the as-synthesized MoS2 at room temperature, which is significant enhanced to 3.67 memu/g after the N plasma treatment for the proper duration. X-ray photoelectron spectroscopy demonstrates the adsorption of N, and higher valence state of Mo than +4 due to the bonding with N after the N plasma treatment. First principle calculation has been performed to disclose the possible origin of ferromagnetism. One chemical adsorbed N ion on S ion may form conjugated π bonds with adjacent two Mo ions to have a total magnetic moment of 0.75 μB, contributing to the enhanced ferromagnetism.
Installation and commissioning of the ion source systems for the new spallation neutron source 2.5 MeV injector
Authors: Welton R. F. , Han B. X. , Stockli M. P. , Murray S. N. , Pennisi T. R. , Stinson C. , Barnett W. , Aleksandrov A. , Piller M. , Saethre R. , Kang Y. , Zhukov A.
Published: January 2020

The U.S. Spallation Neutron Source (SNS) is a state-of-the-art neutron scattering facility delivering the world’s most intense pulsed neutron beams to a wide array of instruments, which are used to conduct investigations in many fields of engineering, physics, chemistry, material science, and biology. Neutrons are produced by spallation of liquid Hg by the bombardment of short (∼1 µs), intense (∼35 A) pulses of protons delivered at 60 Hz by an accumulator ring which is fed by a high-intensity, 1 GeV, H− LINAC (linear accelerator). This facility has operated nearly continuously since 2006 but has recently undergone a 4-month maintenance period, which featured a complete replacement of the 2.5 MeV injector feeding the LINAC. The new injector was developed at ORNL in an off-line beam test facility and consists of an ion source, low energy beam transport, and a Radio Frequency Quadrupole (RFQ). This report first describes the installed configuration of the new injector detailing the ion source system. The first beam current, RFQ transmission, emittance, and energy measurements from the injector installed on the SNS are reported. These data not only show a significant performance improvement for our existing facility but will also make accessible the higher beam current requirements for future SNS upgrade projects: the proton power upgrade and second target station.
Interpreting the dynamic equilibrium during evaporation in a cesium environment
Authors: Fadone M. , Barbisan M. , Cristofaro S. , De Muri M. , Serianni G. , Sartori E.
Published: January 2020

The cesium ovens for the prototype source of the ITER neutral beam injectors are currently tested in the CAesium Test Stand (CATS) facility, with a background pressure of 10−6 mbar. Different diagnostics are here installed: two Langmuir–Taylor detectors allow us to determine the Cs vapour evaporation rate from the oven and the Cs density at different positions in the vacuum chamber; and laser absorption spectroscopy is used to measure the density integrated over a line of sight and a quartz crystal microbalance to detect the cesium mass deposited in time over a surface. In this paper, we present a model to describe the dynamic equilibrium in the evaporation chamber of CATS with the first oven tested in order to gain information about the Cs sticking coefficient at the walls. The model hence includes sticking and energy accommodation of the Cs atoms to the walls, calculates the flux density at the surfaces, and provides the Cs atom density at any location in the volume. By this model, we simulate the Cs evaporation and the equilibrium density, comparing the modeled results with the experimental data. As a result, a sticking coefficient of 2% is obtained.
Quantifying mobile ions and electronic defects in perovskite-based devices with temperature-dependent capacitance measurements: Frequency vs time domain
Authors: Futscher Moritz H. , Gangishetty Mahesh K. , Congreve Daniel N. , Ehrler Bruno
Published: January 2020

Perovskites have proven to be a promising candidate for highly efficient solar cells, light-emitting diodes, and x-ray detectors, overcoming limitations of inorganic semiconductors. However, they are notoriously unstable. The main reason for this instability is the migration of mobile ions through the device during operation as they are mixed ionic–electronic conductors. Here, we show how measuring the capacitance in both the frequency and the time domain can be used to study ionic dynamics within perovskite-based devices, quantifying activation energy, diffusion coefficient, sign of charge, concentration, and the length of the ionic double layer in the vicinity of the interfaces. Measuring the transient of the capacitance furthermore allows for distinguishing between ionic and electronic effects.
Machine learning-based multidomain processing for texture-based image segmentation and analysis
Authors: Borodinov Nikolay , Tsai Wan-Yu , Korolkov Vladimir V. , Balke Nina , Kalinin Sergei V. , Ovchinnikova Olga S.
Published: January 2020

Atomic and molecular resolved atomic force microscopy (AFM) images offer unique insights into materials' properties such as local ordering, molecular orientation, and topological defects, which can be used to pinpoint physical and chemical interactions occurring at the surface. Utilizing machine learning for extracting underlying physical parameters increases the throughput of AFM data processing and eliminates inconsistencies intrinsic to manual image analysis, thus enabling the creation of reliable frameworks for qualitative and quantitative evaluation of experimental data. Here, we present a robust and scalable approach to the segmentation of AFM images based on flexible pre-selected classification criteria. The usage of supervised learning and feature extraction allows us to retain the consideration of specific problem-dependent features (such as types of periodical structures observed in the images and the associated numerical parameters: spacing, orientation, etc.). We highlight the applicability of this approach for the segmentation of molecular resolved AFM images based on the crystal orientation of the observed domains, automated selection of boundaries, and collection of relevant statistics. Overall, we outline a general strategy for machine learning-enabled analysis of nanoscale systems exhibiting periodic order that could be applied to any analytical imaging technique.
Single crystalline boron rich B(Al)N alloys grown by MOVPE
Authors: Vuong P. , Mballo A. , Sundaram S. , Patriarche G. , Halfaya Y. , Karrakchou S. , Srivastava A. , Krishnan K. , Sama N. Y. , Ayari T. , Gautier S. , Voss P. L. , Salvestrini J. P. , Ougazzaden A.
Published: January 2020

Boron rich BAlN alloys have been grown on 2-inch sapphire substrates by Metal-Organic Vapor Phase Epitaxy. The surface morphology of BAlN alloys exhibits a transition stage from a completely two-dimensional to a three-dimensional granular surface with an increased trimethylaluminum/group III (TMAl/III) ratio. Only a shift in the position of the 002 plane reflection peak to higher diffraction angles in the 2θ−ω scan along with a decrease in intensity was observed, specifying formation of layered BAlN alloys up to a TMAl/III ratio of 14. AlN phase separation was observed while increasing the TMAl/III ratio to 25, supporting SEM observations. Secondary-ion mass spectrometry measurements confirmed the presence of up to 17% Al in layered BAlN alloy systems. A cross sectional transmission electron microscopy (TEM) study confirmed the layered nature of single phase BAlN alloys. It also revealed the presence of wurtzite Al rich BAlN phases in a matrix of layered hexagonal B rich BAlN. Band to band transition around 5.86 eV has been observed, which shifted slightly to lower energy with increasing Al incorporation. The bowing parameter (C) in boron rich BAlN alloy systems was evaluated to be around 0.65 ± 0.05 eV. Encouraging results were obtained on boron rich BAlN alloy formation, motivating further exploration of growth conditions and study of BAlN fundamental properties for applications in deep UV optoelectronics.
Effect of couple stresses on the rheology and dynamics of linear Maxwell viscoelastic fluids
Authors: Subramaniam C. G. , Mondal Pranab Kumar
Published: January 2020

The constitutive analog of the linear Maxwell viscoelastic fluid model with the explicit addition of couple stresses is derived from thermodynamic first principles. Furthermore, the concepts of the recently proposed “Consistent Couple Stress theory” are considered to fully determine the rheological description of the fluid model. Finally, the resulting linear momentum equations are used to investigate the couple stress modulated flow dynamics of a few simple flow configurations. The plots of the variations in the elastic behavior of the fluid due to the presence of couple stresses show that the couple stress acts in addition to the conventional force-stress to increase the diffusion of momentum and thereby enhance the dampening of the elastic deformations in the equivalent spring-dashpot interpretation of the linear Maxwell viscoelastic fluid.
Early evidence of microplastics on seagrass and macroalgae
Authors: Seng Nicholas , Lai Samantha , Fong Jenny , Saleh Muhammad Faiq , Cheng Clement , Cheok Zi Yu , Todd Peter A.
Published: January 2020

Microplastic accumulation on marine macrophytes, such as macroalgae and seagrasses, is a potentially critical but overlooked pathway by which microplastics enter the marine food web. Despite the possible significance of this pathway, few studies have examined the presence of microplastics on macrophytes found in situ. We quantified the density of microplastics found on the surfaces of three species of intertidal seagrasses (Cymodocea rotundata, Cymodocea serrulata and Thalassia hemprichii) and two species of subtidal macroalgae (Padina sp. and Sargassum ilicifolium), and found significantly higher microplastic densities on seagrasses than on macroalgae. However, we found no relationships between microplastic density and epibiont cover in either seagrass or macroalgae. Our study has provided early evidence of microplastics on macrophyte surfaces in situ, being the first such evidence for macroalgae, and the second for seagrasses.
Impact of past climate warming on genomic diversity and demographic history of collared lemmings across the Eurasian Arctic
Authors: Fedorov Vadim B. , Trucchi Emiliano , Goropashnaya Anna V. , Waltari Eric , Whidden Susan Erin , Stenseth Nils Chr.
Published: January 2020

The Arctic climate was warmer than today at the last interglacial and the Holocene thermal optimum. To reveal the impact of past climate-warming events on the demographic history of an Arctic specialist, we examined both mitochondrial and nuclear genomic variation in the collared lemming (Dicrostonyx torquatus, Pallas), a keystone species in tundra communities, across its entire distribution in northern Eurasia. The ancestral phylogenetic position of the West Beringian group and divergence time estimates support the hypothesis of continental range contraction to a single refugial area located in West Beringia during high-magnitude warming of the last interglacial, followed by westward recolonization of northern Eurasia in the last glacial period. The West Beringian group harbors the highest mitogenome diversity and its inferred demography indicates a constantly large effective population size over the Late Pleistocene to Holocene. This suggests that northward forest expansion during recent warming of the Holocene thermal optimum did not affect the gene pool of the collared lemming in West Beringia but reduced genomic diversity and effective population size in all other regions of the Eurasian Arctic. Demographic inference from genomic diversity was corroborated by species distribution modeling showing reduction in species distribution during past climate warming. These conclusions are supported by recent paleoecological evidence suggesting smaller temperature increases and moderate northward forest advances in the extreme northeast of Eurasia during the Late Pleistocene-to-Holocene warming events. This study emphasizes the importance of West Beringia as a potential refugium for cold-adapted Arctic species under ongoing climate warming.
Microtubules regulate cardiomyocyte transversal Young’s modulus
Authors: Swiatlowska Pamela , Sanchez-Alonso Jose L. , Wright Peter T. , Novak Pavel , Gorelik Julia
Published: January 2020

The field of cardiomyocyte mechanobiology is gaining significant attention, due to accumulating evidence concerning the significant role of cellular mechanical effects on the integrated function of the heart. To date, the protein titin has been demonstrated as a major contributor to the cardiomyocytes Young’s modulus (YM). The microtubular network represents another potential regulator of cardiac mechanics. However, the contribution of microtubules (MTs) to the membrane YM is still understudied and has not been interrogated in the context of myocardial infarction (MI) or mechanical loading and unloading. Using nanoscale mechanoscanning ion conductance microscopy, we demonstrate that MTs contribute to cardiomyocyte transverse YM in healthy and pathological states with different mechanical loading. Specifically, we show that posttranslational modifications of MTs have differing effects on cardiomyocyte YM: Acetylation provides flexibility, whereas detyrosination imparts rigidity. Further studies demonstrate that there is no correlation between the total protein amount of acetylated and detyrosinated MT. Yet, in the polymerized-only populations, an increased level of acetylation results in a decline of detyrosinated MTs in an MI model.
Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia
Authors: Kolobova Kseniya A. , Roberts Richard G. , Chabai Victor P. , Jacobs Zenobia , Krajcarz Maciej T. , Shalagina Alena V. , Krivoshapkin Andrey I. , Li Bo , Uthmeier Thorsten , Markin Sergey V. , Morley Mike W. , O’Gorman Kieran , Rudaya Natalia A. , Talamo Sahra , Viola Bence , Derevianko Anatoly P.
Published: January 2020

Significance

Neanderthals once inhabited Europe and western Asia, spreading as far east as the Altai Mountains in southern Siberia, but the geographical origin and time of arrival of the Altai populations remain unresolved. Excavations at Chagyrskaya Cave in the Altai foothills have yielded 90,000 stone artifacts, numerous bone tools, 74 Neanderthal fossils, and animal and plant remains recovered from 59,000- to 49,000-year-old deposits. The Chagyrskaya Neanderthals made distinctive stone tools that closely resemble Micoquian artifacts from eastern Europe, whereas other Altai sites occupied by earlier Neanderthal populations lack such artifacts. This suggests at least two dispersals of Neanderthals into southern Siberia, with the likely ancestral homeland of the Chagyrskaya toolmakers located 3,000 to 4,000 kilometers to the west, in eastern Europe.
Antibiotic resistance by high-level intrinsic suppression of a frameshift mutation in an essential gene
Authors: Huseby Douglas L. , Brandis Gerrit , Praski Alzrigat Lisa , Hughes Diarmaid
Published: January 2020

A fundamental feature of life is that ribosomes read the genetic code in messenger RNA (mRNA) as triplets of nucleotides in a single reading frame. Mutations that shift the reading frame generally cause gene inactivation and in essential genes cause loss of viability. Here we report and characterize a +1-nt frameshift mutation, centrally located in
rpoB
, an essential gene encoding the beta-subunit of RNA polymerase. Mutant
Escherichia coli
carrying this mutation are viable and highly resistant to rifampicin. Genetic and proteomic experiments reveal a very high rate (5%) of spontaneous frameshift suppression occurring on a heptanucleotide sequence downstream of the mutation. Production of active protein is stimulated to 61–71% of wild-type level by a feedback mechanism increasing translation initiation. The phenomenon described here could have broad significance for predictions of phenotype from genotype. Several frameshift mutations have been reported in
rpoB
in rifampicin-resistant clinical isolates of
Mycobacterium tuberculosis
(Mtb). These mutations have never been experimentally validated, and no mechanisms of action have been proposed. This work shows that frameshift mutations in
rpoB
can be a mutational mechanism generating antibiotic resistance. Our analysis further suggests that genetic elements supporting productive frameshifting could rapidly evolve de novo, even in essential genes.
Mapping proteome-wide targets of protein kinases in plant stress responses
Authors: Wang Pengcheng , Hsu Chuan-Chih , Du Yanyan , Zhu Peipei , Zhao Chunzhao , Fu Xing , Zhang Chunguang , Paez Juan Sebastian , Macho Alberto P. , Tao W. Andy , Zhu Jian-Kang
Published: January 2020

Protein kinases are major regulatory components in almost all cellular processes in eukaryotic cells. By adding phosphate groups, protein kinases regulate the activity, localization, protein–protein interactions, and other features of their target proteins. It is known that protein kinases are central components in plant responses to environmental stresses such as drought, high salinity, cold, and pathogen attack. However, only a few targets of these protein kinases have been identified. Moreover, how these protein kinases regulate downstream biological processes and mediate stress responses is still largely unknown. In this study, we introduce a strategy based on isotope-labeled in vitro phosphorylation reactions using in vivo phosphorylated peptides as substrate pools and apply this strategy to identify putative substrates of nine protein kinases that function in plant abiotic and biotic stress responses. As a result, we identified more than 5,000 putative target sites of osmotic stress-activated SnRK2.4 and SnRK2.6, abscisic acid-activated protein kinases SnRK2.6 and casein kinase 1-like 2 (CKL2), elicitor-activated protein kinase CDPK11 and MPK6, cold-activated protein kinase MPK6, H
2
O
2
-activated protein kinase OXI1 and MPK6, and salt-induced protein kinase SOS1 and MPK6, as well as the low-potassium-activated protein kinase CIPK23. These results provide comprehensive information on the role of these protein kinases in the control of cellular activities and could be a valuable resource for further studies on the mechanisms underlying plant responses to environmental stresses.
Fig (Ficus caricaL.) leaf tea suppresses allergy by acceleration disassembly of IgE-receptor complexes
Authors: Abe Tatsuya
Published: January 2020

In this study, I investigated the allergy suppressive effect of tea made from fig (Ficus carica L.) leaves. In the rat basophil cell line RBL-2H3, degranulation was significantly suppressed by treatment with fig tea at the same time as addition of IgE antibodies (sensitization). IgE bound to the cell surface was liberated in the medium depending on the treatment time with fig tea. Therefore, it was suggested that the mechanism of action of fig tea is promotion of dissociation of IgE from FcεRI receptors. Such a mechanism is novel in food materials. On oral administration to mice, fig tea showed an inhibitory effect on allergic dermatitis. Furthermore, in tests using an atopic dermatitis model in NC/Nga mice, continued administration of fig tea suppressed symptom exacerbation after antigen administration.

Abbreviations

AD: atopic dermatitis; β-Hex: β-hexosaminidase; FCM: flow cytometory; OA: oral administration; TA: transdermal administration
Triply heavy baryons in the constituent quark model *
Authors: Yang Gang , Ping Jialun , Ortega Pablo G. , Segovia Jorge
Published: January 2020

The constituent quark model is used to compute the ground and excited state masses of QQQbaryons containing either c or bquarks. The quark model parameters previously used to describe the properties of charmonium and bottomonium states were used in this analysis. The non-relativistic three-body bound state problem is solved by means of the Gaussian expansion method which provides sufficient accuracy and simplifies the subsequent evaluation of the matrix elements. Several low-lying states with quantum numbers

and

are reported. We compare the results with those obtained by the other theoretical formalisms. There is a general agreement for the mass of the ground state in each sector of triply heavy baryons. However, the situation is more puzzling for the excited states, and appropriate comments about the most relevant features of our comparison are given.
Possible Odderon exchange in pp and

elastic collisions at the TOTEM experiment *
Authors: Lu Juan , Zhou Li-Juan , Fang Zhi-Jie
Published: January 2020

Based on the Froissart-Martin theorem, the Regge theory and the possible Odderon exchange, the total cross-section

and the ratio of the real to imaginary parts of the forward scattering amplitude

in the

and

elastic collisions in the TOTEM energy region are studied in the FPO model. We consider the contributions of the Froissart bound and of the Pomeron, Reggeon and Odderon exchange terms in the scattering amplitude of the

and

elastic collisions. Using the Odderon intercept

, our theoretical predictions are in good agreement with the recent results of the TOTEM experiment. These results show that the Odderon, corresponding to the odd elastic scattering amplitude, is likely to exist.
Manganese doping on the structural properties of TiO2 and ZnO nanoparticles
Authors: Djaja N F , Taufik A , Saleh R
Published: January 2020

In this study, manganese (Mn) doped ZnO and TiO2 were synthesized through the co-precipitation method. The Mn doping content was set at 6 atomic percent (at.%), and the physical properties of all prepared samples were investigated using energy dispersive X-ray spectroscopy, X-ray diffraction, UV-Vis spectroscopy, and electron spin resonance measurement. The results show that the anatase structure from TiO2 and hexagonal wurtzite from ZnO remained unchanged with the incorporation of the Mn dopant. The grain size of the corresponding TiO2 and ZnO slightly decreased after Mn incorporation, and the band gap energies of TiO2 and ZnO nanoparticles decreased after Mn doping. The electron spin resonance measurement confirmed the existence of oxygen vacancy from the TiO2 and ZnO lattice and increased with the incorporation of the Mn ion. To investigate the potential applications of the samples, the photocatalytic activity of the samples was evaluated to determine the degradation of malachite green from the aqueous solutions under UV light irradiations.
Digital image steganography by using edge adaptive based chaos cryptography
Authors: Delmi A , Suryadi S , Satria Y
Published: January 2020

Steganography and Cryptography is the method used to secure the information. Cryptography is used the principle of a Chaos by using Cat Arnold Map function to assure randomness. While in steganography, the method is used Least Significant Bit Matching Revisited (LSBMR). Embedding region was on edge digital imagery to ensure the message was not detected in the image by visual. The method used to detect the edge region by using Canny edge Detection. The test results obtained by Peak Signal to Ratio (PSNR) are 72-44 dB for data messages with a size of 10 % of the media cover.
Preparation and characterisation of bismuth-doped TiO2 nanotubes (Bi–TiO2–NT) and its photocatalytic activity test for rhodamine B elimination under visible light
Authors: Aqil M A , Gunlazuardi J
Published: January 2020

As a photocatalyst, TiO2 nanotubes can effectively degrade dyes; thus, they exhibit a considerable potential to mitigate the problem of river pollution by dye waste originating from the textile industry. However, with a band gap of 3.2 eV (UV light energy range), such nanotubes cannot be completely utilizing under visible light from the sun. Therefore, in this study, the TiO2 nanotubes are modified using bismuth to obtain bismuth-doped TiO2-NT (Bi–TiO2–NT), which exhibits an activity under visible light. Bi-TiO2-NT was successfully synthesized by one-step anodization with Bi(NO3)3 as the dopant source. The optimum synthesis conditions obtained were as follows: 1.0 M Bi(NO3)3 in an ethylene glycol electrolyte with anodization at 40 V for 1 h. In this study, the synthesized photocatalyst was characterized using X-Ray Diffraction (XRD), Fourier Transform Infrared (FTIR), UV-Vis Diffuse Reflectance Spectroscopy (DRS), Scanning Electron Microscopy–Energy Dispersive X-Ray Spectroscopy (SEM-EDS), and Linear Sweep Voltametry (LSV). The results of the photocatalytic activity tests indicated that under visible light illumination the prepared Bi–TiO2–NT was able to eliminate rhodamine B from the tested water, better then bare TiO2.
Synthesis of ion-imprinted polymer with gamma irradiation for the adsorption of Tripolyphosphate
Authors: Anwar S , Saefumillah A , Suhartini M
Published: January 2020

One method of separating tripolyphosphate ion uses ion-imprinted polymer. Chitosan-succinate, tripolyphosphate and methylene bis akrilamida (MBA) were used as the complexing polymer, template, and crosslinker agent, respectively. In the first step, Fe(III)-chitosan-succinate-tripolyphospate was formed. In the second step, Fe(III)-chitosan-succinate-tripolyphospate was crosslinked by MBA and irradiated by gamma rays. Then, tripolyphosphate ion was removed with KOH solution to form a selective cavity for tripolyphosphate ion in the ion-imprinted polymer (IIP). Based on the results of this study, the optimum adsorption of tripolyphosphate ion was found at an MBA crosslinker concentration of 1%, pH 2, irradiation dose 20 kGy, and a tripolyphosphate ion concentration of 1 ppm. This study also included experimental adsorption of tripolyphosphate ion on non-imprinted polymer (NIP-MBA) and an evaluation of the effect of interference ions. The resulting adsorption of tripolyphosphate ion on IIP was found to be higher than those of non-imprinted polymer. The adsorption percentages were found to be 94 % for IIP and 14 % for NIP-MBA. Chloride ion (Cl-) provided greater interference in the adsorption process of tripolyphosphate ion compared to carbonate ions. The percent adsorptions of tripolyphosphates were estimated to be 57.71 % in the presence Cl- ion and 68.28 % in the presence CO3
2−ion.
Selectivity of zinc-molybdenum catalyst to produce gasoil via catalytic hydrocracking of Kapook seed oil (Ceiba pentandra)
Authors: Mirzayanti Y W , Kurniawansyah F , Prajitno D H , Roesyadi A
Published: January 2020

Various type of Zinc (3.25 %) Mo (6.34 %) Hz catalysts have been prepared using incipient wetness impregnation method. The catalysts were characterized by X-ray diffraction (XRD), energy dispersive analysis x-ray (EDAX) and Brunauer-Emmett-Teller (BET) method. The performance of the catalysts, Zinc (3.25 %) Mo (6.34 %) Hz was investigated for the catalytic hydrocracking of Kapook seed oil (KSO) to hydrocarbon biofuel in a slurry pressure batch reactor system with a stirrer. The hydrocracking reaction was carried out at reaction temperatures from 300-400 °C and reactor pressure of 15 bar for 2 h under H2 flowing. The effect of reaction temperature on composition of hydrocarbon compounds, n-paraffin, conversion and selectivity in liquid products was studied with a variation of ZincMoHz catalysts. It showed the highest hydrocarbon content decarboxylation and/or decarbonylation were 18.61 area% of n-paraffin and the highest content for gasoil-range alkanes was 10.44 area% obtained at 400 °C. The result show that the Zinc (3.25%) Mo (6.34%) Hz catalyst activity was found that the gasoil fraction which triglycerides where cracked with long carbon double bonds chains over Zinc (3.25%) Mo (6.34%) Hz catalyst.
The effect of sulphuric acid and oxalic acid on the formation of anodic aluminium oxide templates using two-step anodization method
Authors: Syamdri F D , Wibowo R
Published: January 2020

The prevention of corrosion on the surface of aluminum by formation of a thin coating layer using anodization methods for enhanced applications is an active area of research. In this study, the fabrication of nanoporous anodic aluminum oxide (AAO) templates was performed by a two-step anodization process using aluminum with 99.98% purity in 0.3 M solution of oxalic acid or 0.1, 0.3, or 0.5 M solutions of sulfuric acid as electrolyte. Anodizing time, electrolyte solution and concentration, and current were found to be the main factors determining the pore diameter and interpore size. In addition, the voltage affected the number of pores on the AAO template. The structural features of the nanoporous templates were examined by scanning electron microscopy. The optimum conditions were determined to be 0.3 M sulfuric acid at 25 V.
Cloning gene encoding lysophospholipase from Bacillus halodurans CM1 to Escherichia coli DH5α
Authors: Fernanda S , Abinawanto A , Helianti I
Published: January 2020

Enzyme is a biocatalyst that is widely used in industry, for example detergent, pharmaceutical, food or oil purification. One of the most widely using enzymes for oil purification is lysophospholipase. As much as 50% of the needs of industrial enzyme are obtained from microorganisms. However, enzyme productivity of these wild type microbial strains is usually limited and cannot be applied in industry, so a genetic engineering is necessary. Cloning gene encoding for lysophospholipase was once performed in Aspergillus niger and Cryptococcus neoformans, but has never been conducted from alkalothermophilic bacteria, such as Bacillus halodurans. Bacillus halodurans CM1 is an isolate from Badan Pengkajian dan Penerapan Teknologi (BPPT). Previous research has shown that these bacteria have lipase enzymes, but the study about their properties have not been conducted. This study aims to clone the gene lysophospholipase from Bacillus halodurans CM1 to Escherichia coli DH5α using the pGEM-T easy vector. The recombinant plasmid is sequenced. The gene fragment encoding lysophospholipase was successfully obtained with size 783 base pairs and 100% similarity with gene encoding lysophospholipase from Bacillus halodurans C-125 (No access GenBank: BA000004.3).
Variation of seawater temperature and chlorophyll-a prior to and during upwelling event in Bali Strait, Indonesia: from observation and model
Authors: Rintaka W E , Priyono B
Published: January 2020

Coastal upwelling event can be observed clearly from drastic changes of seawater temperature and chlorophyll-a before and during the event. From observation and model output, time-series data of these variables provide important datasets to be used for further analysis, such as developing gaussian empirical model of net marine primary productivity (NPP). Here, the objectives of this study are to analysis variation of temperature and chlorophyll-a (chl-a) from both observation and model output datasets, and to evaluate model temperature and chl-a for estimating the NPP prior to and during the upwelling event in Bali Strait. The archive CTD collected in April, June and August 2013 and model output datasets were used in this study. It is shown that during peak of upwelling event in August 2013, observed temperature is minimum and chl-a is maximum in the upper 50 m depth. It is found surfacing isotherm of 25-26°C from sub-surface to sea surface. Furthermore, model output of temperature was in good agreement with observed data, complementing the evolution of upwelling for entire year. Estimated NPP from empirical model suggested that a high NPP distribution occurred in the eastern part of Bali Strait during peak of upwelling event.
Variability of ITF front at 115°E in the Eastern Indian Ocean: from 15-years Gridded CTD Argo Float Data
Authors: Susiani I , Atmadipoera A S , Nurjaya I W
Published: January 2020

This study aims to investigate a depth-latitude spatial and temporal variability of ITF front at 115°E, using 15-years (2004–2018) of monthly gridded CTD Argo float dataset in the Indo–Australia Basin. The Empirical Orthogonal Function method was performed to analysis these time-series data. It is shown that mean meridional extent of ITF front is established between 14°S and 10°S. The ITF front can be described by the first five modes of potential temperature and salinity EOF’s, which accounted for 88.6% and 80.7% of the total variance, respectively. The first EOF mode (67.9%) of depth-latitude temperature reveals spatial pattern which is out-of-phase between near-surface layer (<100 m) and thermocline layer, for example, during the northwest monsoon period, warmer and saltier water in the upper-layer and colder and fresher thermocline water are frequently observed, which differ to those observed during the southeast monsoon period. EOF principal components of temperature and salinity exhibit strong annual variation, followed by intraseasonal and interannual scales. On inter-annual scales, fluctuation of temperature and salinity is well correlated with ENSO and IODM, as previously expected.
Study of microfauna foraminifera as bioindicator for coral reef condition in Tambelan Island, Riau Island Province
Authors: Junita D R , Sartimbul A , Gustiantini L , Sahudin
Published: January 2020

Tambelan Islands is one of the coral reef habitats in Indonesia. This area is the southern part of Natuna Sea and South China Sea Throughflow (SCSTF) exit area, which influenced the dynamics of the ocean and climate in Indonesia. Foraminifera is one of the potential bioindicator that can be used to determine the conditions of waters and the environmental health of coral reef. Twenty surface sediment samples were taken and quantitative analysis were made in order to obtain the condition of waters. This analysis including calculation of abundance, community structure, and analysis of biozonation (cluster and SHEBI). Meanwhile, to determine the condition of coral reef was using FORAM Index (FI). The results showed that there were 52 species of benthic foraminifera included in 41 genera. The most abundant genera were Amphistegina (average 28.08%) and Operculina (average 23.85%) which were a type of genera that associated with coral reefs. The FI values range from 3.57–9.12 indicating that environmental conditions are conducive to coral reefs. Biozonation from the cluster and SHEBI showed different results, indicating that the abundance of foraminifera in research area are influenced by complex factors such as substrate conditions and the activities on land.