bluuebunny/crossref_metadata_2025 huggingface dataset:
Demonstration of antibodies to Mycoplasma pneumoniae attachment protein in human sera and respiratory secretions
Authors: Hu P C , Huang C H , Collier A M , Clyde W A
Published: January 2020

Antibodies specific to the attachment protein of Mycoplasma pneumoniae were demonstrated in sera and respiratory secretions of human patients. The results indicate that the attachment protein is a major immunogen.
Blocked herpes simplex virus type 2-specific DNA synthesis in simian virus 40-transformed hamster cells permissive for herpes simplex virus type 1
Authors: Cheresh D A , Haines H
Published: January 2020

Simian virus 40-transformed hamster cells (LL-1) permissive to herpes simplex virus type 1 (HSV-1) were shown to be relatively nonpermissive to HSV-2. When LL-1 cells were infected with HSV-2, there was a 3- to 4-log reduction in infectious viral progeny at 24 h postinfection as compared with HSV-1 under identical cultured conditions. HSV-2 could be carried in the LL-1 cell line for up to 12 passages without any appreciable cytopathology. Various early functions of the replicative cycle of HSV-2 appeared to be normal. Experiments demonstrated that early enzyme activity, HSV-2 thymidine kinase, and DNA polymerase appeared at permissive levels in extracts of HSV-2-infected LL-1 cells. However, DNA analysis of HSV-2 infected LL-1 cells demonstrated a block in HSV-2-specific DNA synthesis, although HSV-2 was capable of inhibiting DNA synthesis in LL-1 cells. Furthermore, indirect immunofluorescence studies indicate that late HSV-2 structural protein synthesis was inhibited in infected LL-1 cells. Thus, the inability of HSV-2 to replicate in LL-1 cells is due to a block at or before HSV-specific DNA synthesis, resulting in a reduction of the structural protein synthesis required for viral maturation.
Genetically manipulated virulence of Yersinia enterocolitica
Authors: Heesemann J , Algermissen B , Laufs R
Published: January 2020

Mobilizable virulence plasmids of Yersinia enterocolitica of serotypes O:3 and O:9 were constructed by cointegration of a mobilizable vector into the virulence plasmids. The obtained cointegrates were mobilized into plasmidless Y. enterocolitica strains of serotypes O:3, O:5, O:8, and O:9. The transfer experiments revealed the existence of two different subgroups of plasmid-associated traits. (i) Animal virulence functions (mouse lethality and conjuctivitis provocation) were only transferable to plasmid-cured derivatives of virulent parent strains (serotypes O:3, O:8, and O:9), but they were not transferable to Y. enterocolitica antigen reference strains (serotypes O:3 and O:8) or to a plasmidless clinical isolate of serotype O:5. A further striking result was that a serotype O:8 strain regained the mouse lethality trait after receipt of a plasmid from a strain not lethal to mice. These results demonstrate that plasmid-mediated animal virulence functions are not uniformly expressed within Y. enterocolitica. (ii) The second subgroup of plasmid-mediated traits (calcium dependency, surface agglutinogens, HEp-2 cell adherence, and protein release) were transferable to all Y. enterocolitica recipient strains tested (serotypes O:3, O:5, O:8, and O:9 of different origin). For the first time HEp-2 cell adherence and temperature-induced release of five major protein species are described as transferable traits.
Draft Genome Sequence of Plant Growth-Promoting
Streptomyces
sp. Strain SA51, Isolated from Olive Trees
Authors: Vurukonda Sai Shiva Krishna Prasad , Mandrioli Mauro , D’Apice Greta , Stefani Emilio
Published: January 2020

A streptomycete was isolated from the rhizosphere of olive trees in the autumn of 2004. Its molecular characterization showed the presence of metabolic pathways promoting plant growth and additional properties that indicate that this strain is a prospective agent for future biocontrol applications
in planta
. We report here the draft genome sequence of
Streptomyces avermitilis
strain SA51.
Draft Genome Sequence of an Escherichia coli Strain Harboring
bla
CTX-M-115
,
bla
CMY-2
, Aminoglycoside, Tetracycline, and Sulfonamide Resistance Genes, Isolated from a Costa Rican Wastewater Treatment Plant
Authors: Barrantes Kenia , Chacón Luz María , Morales Eric , Ramírez-Carvajal Lisbeth
Published: January 2020

We report the draft genome sequence of the multidrug-resistant
Escherichia coli
strain PTA A1517-5, isolated from a wastewater treatment plant in Costa Rica. The genome consists of 4,927,375 bp with a GC content of 50.57% and a total of 4,853 genes. This strain harbors
bla
CTX-M-115
,
bla
CMY-2
, aminoglycoside, tetracycline, and sulfonamide resistance genes.
Partial Genome Sequences of Human Norovirus Strains from Northeast Brazil
Authors: Guarines Klarissa Miranda , Mendes Renata Pêssoa Germano , de Magalhães Jurandy Júnior Ferraz , Pena Lindomar
Published: January 2020

Noroviruses are the leading cause of human gastroenteritis worldwide. Here, we sequenced the open reading frame 1 (ORF1)-ORF2 junction region of norovirus strains isolated from 20 human stool samples. Samples were collected between 2014 and 2017 in Pernambuco State, Brazil. Phylogenetic analyses identified four norovirus GII genotypes circulating in this area of the country.
Draft Genome Sequences of Two Vibrio fortis Strains Isolated from Coral (
Fungia
sp.) from the Andaman Sea
Authors: Deb Sushanta , Badhai Jhasketan , Das Subrata K.
Published: January 2020

We report the draft genome sequences of
Vibrio fortis
strains AN-60 and S7-72, which were isolated from coral (
Fungia
sp.) from the Andaman Sea. The genome sizes for strains AN-60 and S7-72 are 5.43 and 5.53 Mb, respectively. Both strains harbor genes associated with protocatechuate and azathioprine degradation and the sulfate reduction pathway.
Draft Genome Sequences of Clinical K1-Type Klebsiella pneumoniae Strains Isolated in Russia
Authors: Volozhantsev Nikolay V. , Kislichkina Angelina A. , Mukhina Tatiana N. , Fursova Nadezhda K.
Published: January 2020

Klebsiella pneumoniae
of capsular type K1 is the most common causative agent of both health care-associated and community-acquired infections. Here, we report the draft genome sequences of 10 K1-type
K. pneumoniae
strains isolated from patients in an infectious disease hospital and neurosurgical intensive care unit in Russia.
Whole-Genome Shotgun Sequence of
Halomonas
sp. Strain SBS 10, Isolated from a Hypersaline Lake in India
Authors: Kushwaha Bijayendra , Sharma Guru Prasad , Sharma Anshul , Shankar Prem , Geethadevi Anjali , Sharma Nivedita , Sharma Manish Kumar , Jadhav Indrani , Parashar Deepak , Jadhav Kapilesh
Published: January 2020

The whole-genome shotgun sequence of a moderately halophilic bacterium,
Halomonas
sp. strain SBS 10, was assembled and studied. The assembled genome size was 1.5 Mb, with a G+C content of 63.6%. The genome sequence of this
Halomonas
sp. SBS 10 isolate will be valuable in understanding gene clusters and functions involved in the adaptability of this bacterium to hypersaline conditions.
Draft Genome Sequences of Lactobacillus helveticus, Lactobacillus fermentum, and Lactobacillus delbrueckii Strains from African Fermented Nono
Authors: Cho Gyu-Sung , Fagbemigun Olakunle , Brinks Erik , Adewumi Gbenga A. , Oguntoyinbo Folarin A. , Franz Charles M. A. P.
Published: January 2020

The genomes of predominant
Lactobacillus helveticus
,
Lactobacillus fermentum
, and
Lactobacillus delbrueckii
strains from fermented nono were sequenced. The genome sizes were 2.1, 1.9, and 1.7 Mbp, respectively, and the GC contents were 36.5%, 51.5%, and 49.7%, respectively. Annotation revealed some genes for bacteriocin and for the potential production of aroma compounds.
Draft Genome Sequences of Two Pseudomonas aeruginosa Isolates from the Female Urogenital Tract
Authors: Johnson Genevieve , Mores Carine R. , Wolfe Alan J. , Putonti Catherine
Published: January 2020

Pseudomonas aeruginosa
is a Gram-negative bacterium that has the ability to survive in and readily adapt to a variety of environmental conditions. Here, we report 2 genome sequences of
P. aeruginosa
strains, UMB1046 and UMB5686, isolated from the female urogenital tract.
Complete Genome Sequence of Stenotrophomonas maltophilia Myophage Moby
Authors: Vicary Alison , Newkirk Heather , Moreland Russell , Gonzalez Carlos F. , Liu Mei , Ramsey Jolene , Leavitt Justin
Published: January 2020

Stenotrophomonas maltophiliais a prevalent nosocomial pathogen with multidrug resistance. Here, we describe the complete genome ofS. maltophiliamyophage Moby, which shares characteristics withEnterobacteriaphage T4 and is closely related toStenotrophomonasphage IME-SM1. Moby has a 159,365-bp genome with 271 predicted protein-coding genes and 24 predicted tRNAs.
Mortality in a cohort of US firefighters from San Francisco, Chicago and Philadelphia: an update
Authors: Pinkerton Lynne , Bertke Stephen J , Yiin James , Dahm Matthew , Kubale Travis , Hales Thomas , Purdue Mark , Beaumont James J , Daniels Robert
Published: January 2020

Objectives

To update the mortality experience of a previously studied cohort of 29 992 US urban career firefighters compared with the US general population and examine exposure-response relationships within the cohort.

Methods

Vital status was updated through 2016 adding 7 years of follow-up. Cohort mortality compared with the US population was evaluated via life table analyses. Full risk-sets, matched on attained age, race, birthdate and fire department were created and analysed using the Cox proportional hazards regression to examine exposure-response associations between select mortality outcomes and exposure surrogates (exposed-days, fire-runs and fire-hours). Models were adjusted for a potential bias from healthy worker survivor effects by including a categorical variable for employment duration.

Results

Compared with the US population, mortality from all cancers, mesothelioma, non-Hodgkin's lymphoma (NHL) and cancers of the oesophagus, intestine, rectum, lung and kidney were modestly elevated. Positive exposure-response relationships were observed for deaths from lung cancer, leukaemia and chronic obstructive pulmonary disease (COPD).

Conclusions

This update confirms previous findings of excess mortality from all cancers and several site-specific cancers as well as positive exposure-response relations for lung cancer and leukaemia. New findings include excess NHL mortality compared with the general population and a positive exposure-response relationship for COPD. However, there was no evidence of an association between any quantitative exposure measure and NHL.
Factors associated with time to presentation for individuals with symptomatic uncomplicated genital gonorrhoea: a cross sectional cohort study of GToG trial participants
Authors: Ayinde Oluseyi , Tan Wei , Hepburn Trish , Ross Jonathan D C
Published: January 2020

Objectives

To determine the variation in the time from onset of symptoms to clinical presentation (time to presentation [TTP]) in a cohort of sexual health attendees with symptomatic uncomplicated genital gonorrhoea and to identify factors associated with TTP.

Methods

Participants were recruited from 14 clinics across England into the ‘Gentamicin for the Treatment of Gonorrhoea (GToG)’ trial between October 2014 and November 2016. Multivariable analysis was performed using prospectively collected demographic, behavioural and clinical data in a subset of the GToG study cohort presenting with genital discharge and/or dysuria who tested positive forNeisseria gonorrhoeaeusing a nucleic acid amplification test. The results were expressed as geometric mean ratios (GMR) with 95% CI for time to presentation after onset of symptoms.

Results

316 participants (269 men and 47 women) with a median age of 27.6 years (IQR 23.0–34.8) were included. 194 (61%) were Caucasian, 29 (9%) Black African, 27 (9%) Asian and 66 (21%) of other ethnicities. Median TTP was 3 days for men (IQR 2–7) and 14 days for women (IQR 7–21). Participants reported genital discharge (297/316 [94%]), dysuria (251/316 [79%]), both genital discharge and dysuria (232/316 [73%]) and other concurrent symptoms 76/316 (24%) (e.g., rectal bleeding or genital itching). 45/316 (14%) participants reported sexual contact while symptomatic, of whom TTP was more than 7 days in 32/45 (71%). A longer TTP was associated with gender (female cf. male, GMR 2.34 [1.67 to 3.26]), no prior history of gonorrhoea (GMR 1.46 [1.15 to 1.86]), ‘regular’ or ‘ex-regular’ sexual relationship (regular cf. one off GMR 1.35 [1.05 to 1.72]); ex-regular cf. one off GMR 1.88 [1.12 to 3.14]), and being heterosexual (GMR 1.69 [1.31 to 2.19]).

Conclusion

Specific demographic and behavioural factors are associated with a longer TTP in individuals with symptomatic genital gonorrhoea. Detailed knowledge of these factors can be used to prioritise and optimise gonorrhoea management and prevention.
Envisioning the scientific paper of the future
Authors: Sopinka Natalie M. , Coristine Laura E. , DeRosa Maria C. , Rochman Chelsea M. , Owens Brian L. , Cooke Steven J.
Published: January 2020

Consider for a moment the rate of advancement in the scientific understanding of DNA. It is formidable; from Fredrich Miescher’s nuclein extraction in the 1860s to Rosalind Franklin’s double helix X-ray in the 1950s to revolutionary next-generation sequencing in the late 2000s. Now consider the scientific paper, the medium used to describe and publish these advances. How is the scientific paper advancing to meet the needs of those who generate and use scientific information? We review four essential qualities for the scientific paper of the future: ( i) a robust source of trustworthy information that remains peer reviewed and is ( ii) communicated to diverse users in diverse ways, ( iii) open access, and ( iv) has a measurable impact beyond Impact Factor. Since its inception, scientific literature has proliferated. We discuss the continuation and expansion of practices already in place including: freely accessible data and analytical code, living research and reviews, changes to peer review to improve representation of under-represented groups, plain language summaries, preprint servers, evidence-informed decision-making, and altmetrics.
Dynamics of optical solitons and conservation laws of a new (2+1)-dimensional integrable nonlinear evolution equation in deep water oceanic waves
Authors: Singh Sudhir , Sakthivel R. , Inc M. , Yusuf A. , Murugesan K.
Published: January 2020

An integrable extension of the famous Schrödinger equation in (2[Formula: see text]+[Formula: see text]1) dimension, named Kundu–Mukherjee–Naskar (KMN) equation, governing the evolution of ion-acoustic wave in magnetized plasma and oceanic rogue waves is considered, and dark/black as well as gray optical soliton solutions are constructed by using a complex envelope ansatz approach with appropriate conditions for the existence of solitons. Also, a new class of combined gray and black optical soliton solutions is obtained by applying Chupin Liu’s theorem, and it is found to be anti-dark solitons. Additionally, Gaussian wave solutions are derived. Further, the investigation of symmetry analysis, nonlinear self-adjointness and conservation laws (Cls) for the KMN equation are carried out. These results further enrich and deepen the understanding of the dynamics of a higher-dimensional soliton propagation.
On the complex solutions to the (3+1)-dimensional conformable fractional modified KdV–Zakharov–Kuznetsov equation
Authors: Yel Gulnur , Sulaiman Tukur Abdulkadir , Baskonus Hacı Mehmet
Published: January 2020

This paper presents some exponential function solutions of the (3[Formula: see text]+[Formula: see text]1)-dimensional space-time fractional modified KdV–Zakharov–Kuznetsov (mKdV–ZK). The improved Bernoulli sub-equation function method (IBSEFM) is used in carrying out this computation. Choosing the suitable parameters, the 2D and 3D surfaces of solutions are plotted. The constructed results may be useful in explaining the physical meaning of the studied model.
Localized waves and interaction solutions to an extended (3+1)-dimensional Kadomtsev–Petviashvili equation
Authors: Guo Han-Dong , Xia Tie-Cheng , Ma Wen-Xiu
Published: January 2020

In this paper, an extended (3[Formula: see text]+[Formula: see text]1)-dimensional Kadomtsev–Petviashvili (KP) equation is studied via the Hirota bilinear derivative method. Soliton, breather, lump and rogue waves, which are four types of localized waves, are obtained. N-soliton solution is derived by employing bilinear method. Then, line or general breathers, two-order line or general breathers, interaction solutions between soliton and line or general breathers are constructed by complex conjugate approach. These breathers own different dynamic behaviors in different planes. Taking the long wave limit method on the multi-soliton solutions under special parameter constraints, lumps, two- and three-lump and interaction solutions between dark soliton and dark lump are constructed, respectively. Finally, dark rogue waves, dark two-order rogue waves and related interaction solutions between dark soliton and dark rogue waves or dark lump are also demonstrated. Moreover, dynamical characteristics of these localized waves and interaction solutions are further vividly demonstrated through lots of three-dimensional graphs.
Fabrication of Plasmonic Optical Nanopore Platform for Single Molecule Sensing
Authors: Choi Seong Soo , Oh Sae-Joong , Lee Yong Min , Kim Hyun Tae , Choi Soo Bong , Bae Byung Seong
Published: January 2020

Recently there have been significant interests about fabrication of optical nanopore with its diameter range of 5 nm to 10 nm for single molecule analysis and manipulation. However, due to very small amount of the optical intensity through the tiny size of the nano-aperture much smaller than the optical wavelength, the optical intensity enhancement via plasmonic effect by using pore array or periodic groove patterns have been tried. Also, the double slits with nanoscale width are reported to provide the constructive periodic modulation for the transverse-magnetic (TM) wave mode. In this report, the nanoscale double slit with an Au aperture array have been fabricated and optically characterized.
Towards Ultra Low Cobalt Cathodes: A High Fidelity Computational Phase Search of Layered Li-Ni-Mn-Co Oxides
Authors: Houchins Gregory , Viswanathan Venkatasubramanian
Published: January 2020

Layered Li(Ni,Mn,Co,)O2 (NMC) presents an intriguing ternary alloy design space for optimization as a cathode material in Li-ion batteries. In the case of NMC, however, only a select few proportions of transition metal cations have been attempted and even fewer have been adopted on a large scale. Recently, the high cost and resource limitations of Co have added a new design constraint and high Ni-containing NMC alloys have gained enormous attention despite possible performance trade-offs. Although the limited collection of NMC cathodes have been successful in providing the performance needed for many applications, specifically electric vehicles, this concern around Co requires further advancement and optimization within the NMC design space. Additionally, it is not fully understood if this material space is a disordered solid solution at room temperature and any arbitrary combination can be used or if there exist distinct transition metal orderings to which meta-stable solid solutions will decay during cycling and affect performance. Here, we present a high fidelity computational search of the ternary phase diagram with an emphasis on high-Ni, and thus low Co, containing compositional phases to understand the room temperature stability of the ordered and disordered solid solution phases. This is done through the use of density functional theory training data fed into a reduced order model Hamiltonian that accounts for effective electronic and spin interactions of neighboring transition metal atoms at various lengths in a background of fixed composition and position lithium and oxygen atoms. This model can then be solved to include finite temperature thermodynamics into a convex hull analysis to understand the regions of ordered and disordered solid solution as well the transition metal orderings within the ordered region of the phase diagram. We also provide a method to propagate the uncertainty at every level of the analysis to the final prediction of thermodynamically favorable compositional phases thus providing a quantitative measure of confidence for each prediction made. Due to the complexity of the three component system, as well as the intrinsic error of density functional theory, we argue that this propagation of uncertainty, particularly the uncertainty due to exchange-correlation functional choice is necessary to have reliable and interpretable results. We find that for the majority of transition metal compositions of the layered material, specifically medium to high-Ni content, prefer transition metal ordering and predict the collection of preferred compositions in the ordered region.
Review—Electrochemical Sensors and Biosensors Modified with Binary Nanocomposite for Food Safety
Authors: Lu Lin , Hu Xianqiao , Zhu Zhiwei , Li Dan , Tian Shiyi , Chen Zhongxiu
Published: January 2020

Binary nanocomposite has become an excellent modification material for sensors and biosensors, which is superior to single nanomaterial. Multiple electrochemical sensors with four types of binary nanocomposites and biosensors with four biological elements were presented in the application of food safety. Different sensors for the detection of the same food analyte were contrasted. The synergistic effects and interactions of nanocomposites, and analytical performance of modified (bio)sensors are elaborated. The future perspectives for binary nanocomposites used on food (bio)sensors are discussed.
Review—Electrolytic Metal Atoms Enabled Manufacturing of Nanostructured Sensor Electrodes
Authors: Jiang Junhua , Wang Congjian
Published: January 2020

Sensing materials play a key role in the successful implementation of electrochemical sensors, and nanotechnology has emerged as an important and rapidly growing field for stimulating the innovation of high-performance sensors. The fabrication, characterization, and evaluation of the nanostructured electrodes are therefore a focus of this field. Compared to a variety of dry and wet technologies which have been extensively developed for this purpose, electrochemical methods are typically convenient, highly effective, and potentially low-cost for the production of different nanostructures. This minireview is designed to introduce a unique electrochemical method - electrolytic metal-atom enabled manufacturing (EM2) and its application in electrochemical sensors. The EM2 technique employs electrolytic metal atoms generated from their corresponding salt precursor as a tool to nanostructure a wide range of substrate electrodes used in electrochemical sensors, based on a one-pot electrochemical deposition and dissolution of the metal atoms in the same electrolyte bath. Briefly, the metal atoms are electrodeposited on a substrate electrode during the cathode reduction, and they are selectively removed from the substrate during the subsequent anode oxidation. Because of the interactions between the electrolytic metal atoms and the substrate atoms, the repetitive electrodeposition and dissolution of the former on the substrate enable the nanostructuration of the substrate, particularly within its surface layers. The nanostructured electrodes have demonstrated very attractive performance for the determination of numerous analytes, such as high sensitivity and selectivity, high interference tolerance, and low detection limits. However, the EM2 technique and the application of the resulting nanostructured electrodes in electrochemical sensors and beyond have still been very limitedly investigated. In order to bring the community from academic, industries, agencies, and customers together to develop the EM2 technique and advance electrochemical sensor systems, this minireview will introduce the thermodynamic and kinetic fundamentals of this technique, the characterization of resulting nanostructures, the analysis of their electrochemical behavior, and the implementation of this technique for the development of advanced sensor electrodes. Finally, an outlook with a focus on further research areas is provided.
How to Design Lithium Ion Capacitors: Modelling, Mass Ratio of Electrodes and Pre-lithiation
Authors: Madabattula Ganesh , Wu Billy , Marinescu Monica , Offer Gregory
Published: January 2020

Lithium ion capacitors (LICs) store energy using double layer capacitance at the positive electrode and intercalation at the negative electrode. LICs offer the optimum power and energy density with longer cycle life for applications requiring short pulses of high power. However, the effect of electrode balancing and pre-lithiation on usable energy is rarely studied. In this work, a set of guidelines for optimum design of LICs with activated carbon (AC) as positive electrode and lithium titanium oxide (LTO) as negative electrode was proposed. A physics-based model has been developed and used to study the relationship between usable energy at different effective C rates and the mass ratio of the electrodes. The model was validated against experimental data from literature. The model was then extended to analyze the need for pre-lithiation of LTO. The limits for pre-lithiation in LTO and use of negative polarization of the AC electrode to improve the cell capacity have been analyzed using the model. Furthermore, the model was used to relate the electrolyte depletion effects to poorer power performance in a cell with higher mass ratio. The open-source model can be re-parameterised for other LIC electrode combinations, and should be of interest to cell designers.
Review—Recent Progress in the Graphene-Based Electrochemical Sensors and Biosensors
Authors: Coroş Maria , Pruneanu Stela , Stefan-van Staden Raluca-Ioana
Published: January 2020

In this review we shortly discuss about the graphene and graphene-based materials synthesis and present the recent year's research progress (2017−2019) in the enhancement of the analytical performance of sensors and biosensors. Particularly, we covered a very broad range of graphene-based electrochemical sensors and biosensors for the detection of glucose, cholesterol, dopamine (DA), ascorbic acid (AA), uric acid (UA), bisphenol A (BPA), cancer biomarkers and heavy metal ions. We believe that the discussed subjects are useful and may be used as an instruction guide for the future developments in the field of graphene and graphene-based materials for sensors and biosensors.
Critical Review—Approaches for the Electrochemical Interrogation of DNA-Based Sensors: A Critical Review
Authors: Pellitero Miguel Aller , Shaver Alexander , Arroyo-Currás Netzahualcóyotl
Published: January 2020

The desire to improve and decentralize diagnostic platforms to facilitate highly precise and personalized medicine has motivated the development of a large number of electrochemical sensing technologies. Such a development has been facilitated by electrochemistry's unparalleled ability to achieve highly specific molecular measurements in complex biological fluids, without the need for expensive instrumentation. However, for decades, progress in the field had been constrained to systems that depended on the chemical reactivity of the analyte, obstructing the generalizability of such platforms beyond redox- or enzymatically active clinical targets. Thus, the pursuit of alternative, more general strategies, coupled to the timely technological advances in DNA sequencing, led to the development of DNA-based electrochemical sensors. The analytical value of these arises from the structural customizability of DNA and its ability to bind analytes ranging from ions and small molecules to whole proteins and cells. This versatility extends to interrogation methods, as DNA-based sensors work through a variety of detection schemes that can be probed via many electroanalytical techniques. As a reference for those experienced in the field, and to guide the unexperienced scientist, here we review the specific advantages of the electroanalytical methods most commonly used for the interrogation of DNA-based sensors.
Modeling Study of pH Distribution and Non-Equilibrium State of Water in Hydrogen Evolution Reaction
Authors: Feng Zhange , Xie Yuanyuan , Han Qi
Published: January 2020

pH distribution and non-equilibrium state of water in hydrogen evolution reaction are studied using continuum models. In the first model, we analyze the pH distribution in a rotating ring disk electrode system, where the hydrogen evolution occurs on the disk electrode. The model predicts a pH distribution comparable to the experimental data and the nonequilibrium state of water (cH*cOH>1.0 × 10−14) in a small portion of the diffusion layer (ca. 5 μm in thickness) adjacent to the bulk electrolyte under forced convection. The second model explores the pH distribution on an electrode with nanovoids in hydrogen evolution reaction in an acidic media. The value of cH*cOH shifts significantly when close to the electrode surface, e.g., ≤ 2 μm, indicating pH is not viable to assess its impact on an electrochemical reaction involving hydroxide ions. Modeling results also prove that, for an electrode with nanovoids, the concentration gradient of hydroxide between the plain field and the bottom of the nanovoid is minimal. Therefore it should not be the root cause for the differential kinetics of metal electrodeposition inside/outside the nanovoids.
Properly Lumped Lithium-ion Battery Models: A Tanks-in-Series Approach
Authors: Subramaniam Akshay , Kolluri Suryanarayana , Parke Caitlin D. , Pathak Manan , Santhanagopalan Shriram , Subramanian Venkat R.
Published: January 2020

This article introduces a lumped electrochemical model for lithium-ion batteries. The governing equations of the standard ‘pseudo 2-dimensional’ (p2D) model are volume-averaged over each region in a cathode-separator-anode representation. This gives a set of equations in which the evolution of each averaged variable is expressed as an overall balance containing internal source terms and interfacial fluxes. These quantities are approximated to ensure mass and charge conservation. The averaged porous domains may thus be regarded as three ‘tanks-in-series’. Predictions from the resulting equation system are compared against the p2D model and simpler Single Particle Model (SPM). The Tanks-in-Series model achieves substantial agreement with the p2D model for cell voltage, with error metrics of <15 mV even at rates beyond the predictive capability of SPM. Predictions of electrochemical variables are examined to study the effect of approximations on cell-level predictions. The Tanks-in-Series model is a substantially smaller equation system, enabling solution times of a few milliseconds and indicating potential for deployment in real-time applications. The methodology discussed herein is generalizable to any model based on conservation laws, enabling the generation of reduced-order models for different battery types. This can potentially facilitate Battery Management Systems for various current and next-generation batteries.
Phosphor Performance under High Intensity Excitation by InGaN Laser Diodes
Authors: Lenef A. , Raukas M. , Wang J. , Li C.
Published: January 2020

Excitation of phosphors by blue (InGaN) laser diodes is a new area in solid-state lighting applications that is getting notable attention. Such laser-activated remote phosphor (LARP) configurations generate luminances exceeding the brightest high-power LEDs by factors of 2–10, while simultaneously achieving high luminous fluxes in the range of 100s–1000s lumens. To fully take advantage of the LARP approach, a strong understanding of high-intensity phosphor excitation is needed. We develop a general rate-equation model to describe intensity quenching, applicable to common Ce3+- and Eu2+-based phosphors. The model includes the potential impact of traps and recombination from the conduction band. We also simulate the nonlinear propagation of pump and converted light to allow direct comparisons to experimental data. For YAG:Ce and LuAG:Ce model systems, we show that energy-transfer (ET) upconversion to the conduction band likely constitutes the main loss mechanism in high intensity laser pumping. We also show conclusively, via steady-state, low-temperature intensity quenching measurements, that high-intensity excitation alone can be responsible for large drops in quantum efficiency, without the complicating experimental factors of thermal quenching or short-pulse excitation to minimize heating.
The Influence of Excitation Density on Laser Induced White Lighting of Wide-Band-Gap Semiconductor ZnSe:Yb Polycrystallite Ceramics
Authors: Tomala R. , Gerasymchuk Y. , Hreniak D. , Legendziewicz J. , Strek W.
Published: January 2020

The irradiation of ZnSe:Yb polycrystalline ceramics by focused beam of a CW 975 nm laser diode in vacuum conditions leads to generation intense white light in visible range. The emission band was centered at 630 nm. The intensity of white emission increased exponentially with the power density of incident laser light. The influence of excitation power density on generation of broadband emission was investigated. It was found that with increasing excitation power density the total intensity and the slope of exponential enhancement of white light significantly increase. Moreover, for the highest excitation power density there appeared by excitation threshold. The impact of excitation density on white laser induced white emission (LIWE) was discussed in terms of multiphoton excitation and avalanche ionization
Broadened Bandwidth Amplified Spontaneous Emission from Blue GaN-Based Short-Cavity Superluminescent Light-Emitting Diodes
Authors: Zhang Hezhi , Shih Ching-Wen , Martin Denis , Caut Alexander , Carlin Jean-François , Butté Raphaël , Grandjean Nicolas
Published: January 2020

We report broad bandwidth blue superluminescent light-emitting diodes (SLEDs) based on a short-cavity active region. The dependencies of amplified spontaneous emission (ASE) output power and gain bandwidth on cavity length were investigated in devices whose gain medium consists of a ridge waveguide with embedded InGaN/GaN quantum wells sandwiched between one etched facet coated with a high reflectivity distributed Bragg mirror and one cleaved facet with an anti-reflection coating. 250 μm-long blue SLEDs exhibit a spectral bandwidth up to 7.5 nm at 1.72 mW output power at a wavelength of 427 nm. As cavity length decreases, the bandwidth gradually broadens up to 15 nm for the shortest, 40 μm-long, SLED devices. ASE is confirmed by current-dependent electroluminescence spectra and polarization-dependent emission intensity measurements. The optical features of those short-cavity devices could be helpful for designing broad bandwidth SLEDs aiming for various applications such as optical coherence tomography, next generation displays, on-chip biosensing and imaging.
Improvement of The Light Output of Blue InGaN-Based Light Emitting Diodes by Using a Buried Stripe-Type n-Contact and Reflective Bonding Pad
Authors: Kim Jong-Ho , Lee Yong Won , Im Hyeong-Seop , Oh Chan-Hyoung , Shim Jong-In , Kang Daesung , Seong Tae-Yeon , Amano Hiroshi
Published: January 2020

To enhance the light output of blue InGaN-based light emitting diodes (LEDs), a buried stripe-type n-electrode, expanded stripe-type p-electrode, and reflective p-bonding pad were employed. Flip-chip (FC) LEDs with the expanded p-electrode gave forward voltages of 2.99–3.11 V at 100 mA and series resistances of 3.28–3.94 Ω. The expanded p-electrode FCLED fabricated with 375 nm-thick window and TiO2 adhesion layers produced 22.7% higher light output at 21 A/cm2 than conventional FCLEDs. The expanded p-electrode FCLEDs revealed better current spreading efficiency than the c-FCLED, indicating the importance of the use of an optimised window and TiO2 adhesion layers.
Anticorrosive Behavior of SiCxNyOz Film Formed by Non-Heat Assistance Plasma-Enhanced Chemical Vapor Deposition Using Monomethylsilane, Nitrogen and Argon Gases
Authors: Watanabe Toru , Hori Kenta , Habuka Hitoshi
Published: January 2020

A SiC
x
N
y
O
z
film was formed on an aluminum substrate without any heating assistance using monomethylsilane, nitrogen and argon gases at 10–30 Pa by the parallel plate plasma-enhanced chemical vapor deposition method. The obtained film did not have any considerable pinhole and crack, based on the evaluation using a concentrated hydrogen chloride aqueous solution. The anti-corrosive behavior of the obtained film was studied by means of chlorine trifluoride gas etching at the concentration of 100% at atmospheric pressure and at various temperatures. The etching rate increased with the increasing temperature and with the increasing nitrogen concentration in the film. The increase in the nitrogen concentration in the film enhanced the fluorine diffusion through the film during the etching. The anticorrosive behavior was determined to be adjustable by the nitrogen concentration contained in the film.
Metabonomic-Transcriptome Integration Analysis on Osteoarthritis and Rheumatoid Arthritis
Authors: Gao Ningyang , Ding Li , Pang Jian , Zheng Yuxin , Cao Yuelong , Zhan Hongsheng , Shi Yinyu
Published: January 2020

Purpose. This study is aimed at exploring the potential metabolite/gene biomarkers, as well as the differences between the molecular mechanisms, of osteoarthritis (OA) and rheumatoid arthritis (RA).Methods. Transcriptome dataset GSE100786 was downloaded to explore the differentially expressed genes (DEGs) between OA samples and RA samples. Meanwhile, metabolomic dataset MTBLS564 was downloaded and preprocessed to obtain metabolites. Then, the principal component analysis (PCA) and linear models were used to reveal DEG-metabolite relations. Finally, metabolic pathway enrichment analysis was performed to investigate the differences between the molecular mechanisms of OA and RA.Results. A total of 976 DEGs and 171 metabolites were explored between OA samples and RA samples. The PCA and linear module analysis investigated 186 DEG-metabolite interactions including Glycogenin 1- (GYG1-) asparagine_54, hedgehog acyltransferase- (HHAT-) glucose_70, and TNF receptor-associated factor 3- (TRAF3-) acetoacetate_35. Finally, the KEGG pathway analysis showed that these metabolites were mainly enriched in pathways like gap junction, phagosome, NF-kappa B, and IL-17 pathway.Conclusions. Genes such as HHAT, GYG1, and TRAF3, as well as metabolites including glucose, asparagine, and acetoacetate, might be implicated in the pathogenesis of OA and RA. Metabolites like ethanol and tyrosine might participate differentially in OA and RA progression via the gap junction pathway and phagosome pathway, respectively. TRAF3-acetoacetate interaction may be involved in regulating inflammation in OA and RA by the NF-kappa B and IL-17 pathway.
New Generalized Soliton Solutions for a (3+1)-Dimensional Equation
Authors: Chen Yiren
Published: January 2020

In this paper, we investigate the nonlinear wave solutions for a (3+1)-dimensional equation which can be reduced to the potential KdV equation. We present generalized N-soliton solutions in which some arbitrarily differentiable functions are involved by using a simplified Hirota’s method. Our work extends some previous results.
Iterative Deep Neighborhood: A Deep Learning Model Which Involves Both Input Data Points and Their Neighbors
Authors: Liu Rong , Liu Yan , Yan Yonggang , Wang Jing-Yan
Published: January 2020

Deep learning models, such as deep convolutional neural network and deep long-short term memory model, have achieved great successes in many pattern classification applications over shadow machine learning models with hand-crafted features. The main reason is the ability of deep learning models to automatically extract hierarchical features from massive data by multiple layers of neurons. However, in many other situations, existing deep learning models still cannot gain satisfying results due to the limitation of the inputs of models. The existing deep learning models only take the data instances of an input point but completely ignore the other data points in the dataset, which potentially provides critical insight for the classification of the given input. To overcome this gap, in this paper, we show that the neighboring data points besides the input data point itself can boost the deep learning model’s performance significantly and design a novel deep learning model which takes both the data instances of an input point and its neighbors’ classification responses as inputs. In addition, we develop an iterative algorithm which updates the neighbors of data points according to the deep representations output by the deep learning model and the parameters of the deep learning model alternately. The proposed algorithm, named “Iterative Deep Neighborhood (IDN),” shows its advantages over the state-of-the-art deep learning models over tasks of image classification, text sentiment analysis, property price trend prediction, etc.
Network Inference Analysis Identifies SETDB1 as a Key Regulator for Reverting Colorectal Cancer Cells into Differentiated Normal-Like Cells
Authors: Lee Soobeom , Lee Chansu , Hwang Chae Young , Kim Dongsan , Han Younghyun , Hong Sung Noh , Kim Seok-Hyung , Cho Kwang-Hyun
Published: January 2020

Cancer cells exhibit properties of cells in a less differentiated state than the adjacent normal cells in the tissue. We explored whether cancer cells can be converted to a differentiated normal-like state by restoring the gene regulatory network (GRN) of normal cells. Here, we report that colorectal cancer cells exhibit a range of developmental states from embryonic and intestinal stem-like cells to differentiated normal-like cells. To identify the transcription factors (TF) that commit stem-like colorectal cancer cells into a differentiated normal-like state, we reconstructed GRNs of normal colon mucosa and identified core TFs (CDX2, ELF3, HNF4G, PPARG, and VDR) that govern the cellular state. We further found that SET Domain Bifurcated 1 (SETDB1), a histone H3 lysine 9–specific methyltransferase, hinders the function of the identified TFs. SETDB1 depletion effectively converts stem-like colorectal cancer cells into postmitotic cells and restores normal morphology in patient-derived colorectal cancer organoids. RNA-sequencing analyses revealed that SETDB1 depletion recapitulates global gene expression profiles of normal differentiated cells by restoring the transcriptional activity of core TFs on their target genes.

Implications:

Our study provides insights into the molecular regulatory mechanism underlying the developmental hierarchy of colorectal cancer and suggests that induction of a postmitotic state may be a therapeutic alternative to destruction of cancer cells.
Translating Science into Survival: Report on the Fifth International Cancer Immunotherapy Conference
Authors: Diken Mustafa , Kepp Oliver , Brodsky Arthur N.
Published: January 2020

From September 25 to 28, 2019, in Paris, France, the Fifth International Cancer Immunotherapy Conference was hosted jointly by the Cancer Research Institute, the Association for Cancer Immunotherapy, the European Academy of Tumor Immunology, and the American Association for Cancer Research. This year, roughly 1,300 people attended the 4-day event, which covered the latest advances in cancer immunology and immunotherapy.
Evaluation of Corneal Curvature and Astigmatism in Patients with Persistent Pupillary Membrane by Partial Coherence Interferometry Measurements
Authors: Hu Huiling , Yang Mingmin , Du Bing , Fang Min , Liu Xinhua , Wang Jiantao
Published: January 2020

Purpose: To evaluate and compare the corneal curvature and astigmatism in patients with persistent pupillary membrane (PPM) and healthy controls by partial coherence interferometry. Methods: This study included 14 eyes (9 patients) with PPM and 16 eyes (16 subjects) without PPM or other ocular disease, which were age and gender matched. The horizontal corneal radius of curvature (hCRC), vertical CRC (vCRC), average CRC (aveCRC), corneal astigmatic vectors (CAV), and axis were recorded using partial coherence interferometry. Uncorrected visual acuity and best corrected visual acuity (BCVA) were also recorded using a logMAR chart. Results: In the PPM group, the vCRC (45.46 ± 0.52 D) was significantly larger than that in the control group (44.05 ± 0.24 D) (p = 0.009). The aveCRC in the PPM group (43.90 ± 0.46 D) was also significantly larger than that in the control group (43.34 ± 0.23 D) (p = 0.018). In the PPM group, the hCRC (42.35 ± 0.41 D) was significantly smaller than that in the control group (42.63 ± 0.24 D) (p = 0.049). The astigmatisms were with-the-rule in both groups. The absolute value of CAV in PPM group (3.17 ± 0.23 D) was significantly higher than that of control (1.36 ± 0.09 D) (p = 0.001). BCVA (0.42 ± 0.08) in PPM group was significantly worse than that in control (0.90 ± 0.03) (p = 0.009). Conclusions: The larger vertical and smaller horizontal corneal curvature resulted in higher corneal astigmatism with the rule, which is a characteristic feature in patients with PPM. More attention should be paid to astigmatism status and correction treatment for these patients.
Renal Nerve Deafferentation Attenuates the Fall in GFR during Intravenous Infusion of Furosemide in Anesthetized Rats
Authors: Araujo Magali , Solis Glenn , Welch William J. , Wilcox Christopher S.
Published: January 2020

Introduction: Furosemide reduces the glomerular filtration rate (GFR) and increases the renal vascular resistance (RVR) despite inhibiting tubuloglomerular feedback but increases proximal tubule pressure, renin release, and renal nerve activity. Objective: This study tested the hypothesis that the fall in GFR with furosemide is due to volume depletion or activation of angiotensin type 1 (AT1) receptors or renal nerves. Methods: Furosemide was infused for 60 min at 1.0 mg·kg−1·h−1 in groups of 5–8 anesthetized rats. Additional groups received intravenous volume replacement to prevent fluid and Na+ losses or volume replacement plus losartan or plus sham denervation or plus renal denervation or renal nerve deafferentation. Results: At 60 min of infusion, furosemide alone reduced the GFR (–37 ± 4%; p < 0.01). This fall was not prevented by volume replacement or pretreatment with losartan, although losartan moderated the increase in RVR with furosemide (+44 ± 3 vs. +82 ± 7%; p < 0.01). Whereas the GFR fell after furosemide in rats after sham procedure (–31 ± 2%), it was not changed significantly after prior renal deafferentation. Proximal tubule pressure increased significantly but returned towards baseline over 60 min of furosemide, while urine output remained elevated, and GFR and renal blood flow depressed. Conclusions: The fall in GFR over 60 min of furosemide infusion is independent of volume depletion or activation of AT1 receptors but is largely dependent on renal afferent nerves.