bluuebunny/crossref_metadata_2025 huggingface dataset:
Maternal undernutrition during pregnancy and lactation increases transcription factors, ETV5 and GDNF, and alters regulation of apoptosis and heat shock proteins in the testis of adult offspring in the rat
Authors: Pedrana Graciela , Larrañaga Camila , Diaz Alejandra , Viotti Helen , Lombide Paula , Cavestany Daniel , Vickers Mark H. , Martin Graeme B. , Sloboda Deborah M.
Published: April 2021

We tested whether changes in Sertoli cell transcription factors and germ cell heat shock proteins (HSPs) are linked to the effects of maternal undernutrition on male offspring fertility. Rats were fed ad libitum with a standard diet (CONTROL) throughout pregnancy and lactation or with 50% of CONTROL intake throughout pregnancy (UNP) or lactation (UNL) or both periods (UNPL). After postnatal Day 21, 10 male pups per group were fed a standard diet ad libitum until postnatal Day 160 when testes were processed for histological, mRNA and immunohistochemical analyses. Compared with CONTROL: caspase-3 was increased in UNP and UNPL (P = 0.001); Bax was increased in UNL (P = 0.002); Bcl-2 (P < 0.0001) was increased in all underfed groups; glial cell line-derived neurotrophic factor (P = 0.002) was increased in UNP and UNL; E twenty-six transformation variant gene 5 and HSP70 were increased, and HSP90 was diminished in all underfed groups (P < 0.0001). It appears that maternal undernutrition during pregnancy and lactation disrupts the balance between proliferation and apoptosis in germ cells, increasing germ cell production and perhaps exceeding the support capacity of the Sertoli cells. Moreover, fertility could be further compromised by changes in meiosis and spermiogenesis mediated by germ cell HSP90 and HSP70.
Increase in congenital syphilis cases and challenges in prevention in Japan, 2016–2017
Authors: Kanai Mizue , Arima Yuzo , Shimada Tomoe , Hori Narumi , Yamagishi Takuya , Sunagawa Tomimasa , Tada Yuki , Takahashi Takuri , Ohnishi Makoto , Matsui Tamano , Oishi Kazunori
Published: April 2021

In Japan, the increase in congenital syphilis (CS) notifications has become a public health concern. We conducted a case series study to describe the characteristics of CS patients and their mothers. Of the 13 mothers who consented to participate, seven had regular prenatal care visits, including four who had tested negative at their first trimester syphilis screening. Only three mothers noted that their partners were tested, with all three partners being diagnosed with syphilis. Raising awareness for syphilis prevention during pregnancy, partner testing, and considering additional syphilis testing at the third trimester of pregnancy during times of increased syphilis prevalence is imperative.
Thermosensitive TRPV4 channels mediate temperature-dependent microglia movement
Authors: Nishimoto Rei , Derouiche Sandra , Eto Kei , Deveci Aykut , Kashio Makiko , Kimori Yoshitaka , Matsuoka Yoshikazu , Morimatsu Hiroshi , Nabekura Junichi , Tominaga Makoto
Published: April 2021

Significance

Movement is a key feature of the surveillance and protective roles of microglia. This dynamic process is highly modulated by the surrounding environment. We discovered that microglia movement is temperature dependent in vitro and in vivo. Our investigation of thermosensitive TRP channel involvement in this phenomenon revealed several candidates including TRPM2, TRPM4, and TRPV4 channels. Using pharmacological tools and transgenic mice, we showed that the temperature dependency of microglia movement mainly relies on TRPV4 channel activity. Understanding the mechanisms by which temperature modulates microglia movement will improve our comprehension of pathological processes and allow the identification of new leads for the treatment of brain pathologies.
Geography is more important than life history in the recent diversification of the tiger salamander complex
Authors: Everson Kathryn M. , Gray Levi N. , Jones Angela G. , Lawrence Nicolette M. , Foley Mary E. , Sovacool Kelly L. , Kratovil Justin D. , Hotaling Scott , Hime Paul M. , Storfer Andrew , Parra-Olea Gabriela , Percino-Daniel Ruth , Aguilar-Miguel X. , O’Neill Eric M. , Zambrano Luis , Shaffer H. Bradley , Weisrock David W.
Published: April 2021

Significance

Population structure and speciation are shaped by a combination of biotic and abiotic factors. The tiger salamander complex has been considered a key group in which life history variation has led to a rapid rate of speciation, driven in large part by the evolution of obligate paedomorphosis—a condition in which adults maintain an aquatic, larval phenotype. Using a large multilocus dataset, we present evidence of gene flow between taxa with different life history strategies, suggesting that obligate paedomorphosis is not a strong driver of speciation in the tiger salamander complex. Many of these nominal taxa are listed as critically endangered, and our genetic results provide information and guidance that will be useful for their conservation.
Chitinase 3-like 1 is a profibrogenic factor overexpressed in the aging liver and in patients with liver cirrhosis
Authors: Nishimura Norihisa , De Battista Davide , McGivern David R. , Engle Ronald E. , Tice Ashley , Fares-Gusmao Rafaelle , Kabat Juraj , Pomerenke Anna , Nguyen Hanh , Sato Shinya , Bock Kevin W. , Moore Ian N. , Kleiner David E. , Zamboni Fausto , Alter Harvey J. , Govindarajan Sugantha , Farci Patrizia
Published: April 2021

Significance

Older age at the time of hepatitis virus infection and age of liver donors are major determinants of liver fibrosis progression and disease severity. Our study demonstrates that aging is accompanied by significant changes in gene expression and identifies a gene,
chitinase 3-like 1
(
CHI3L1
), as having the greatest age-dependent increase in expression and as being overexpressed in cirrhotic livers. Our in vivo and in vitro results provide evidence that CHI3L1 plays a central role in liver fibrogenesis and support a role for CHI3L1 in the increased susceptibility of aging livers to fibrosis progression. This study may open avenues for specific antifibrotic or microRNA therapy to reduce or prevent hepatic fibrosis and its ominous complications.
Refractive index sensing with hollow metal–insulator–metal metasurfaces
Authors: Vasić Borislav , Isić Goran
Published: April 2021

Refractive index sensing with metal–insulator–metal (MIM) metasurfaces featuring a continuous dielectric film between two metallic layers suffers from a low spatial overlap between high field enhancement regions and the analyte placed above. Recent studies have thus turned toward hollow MIM metasurfaces, particularly suited for fluid analytes which can infiltrate the hollow cavities. Here we describe a general procedure for reaching the optimal design in three most relevant configurations: mushroom-type structures with narrow dielectric pedestals carrying the top metallic ribbon array, hollow structures with the metallic ribbon array resting on a distant lateral support, and hollow structures in which the metallic ribbons are carried by an encapsulating layer from top. We contend that since a majority of the resonant eigenmode energy is contained within the analyte, very high refractive index sensitivities are possible for three different measurement methods: spectral, reflectance and phase interrogation. This is confirmed by numerical simulations demonstrating terahertz spectral sensitivities of above 700 GHz RIU−1 with a normalized sensitivity of around 0.6

 

R
I
U

−
1

(RIU stands for refractive index unit). Detection limits and dynamic ranges are estimated for both bulk refractive index sensing and thin film detection. Refractive index sensitivities and corresponding figure-of-merit factors are shown to reach maxima in the critical coupling regime characterized by equal radiative and non-radiative decay rates of the resonant mode which is controlled by cavity height. Since this regime is associated with a zero reflectance which prevents measurements of any signal, metasurfaces should operate close to the critical coupling point where reflected beam is still measurable. The final optimization is done by decay rate engineering in order to achieve narrower resonances and improve sensing performance.
Prioritization of the influence of different exchange interactions and uniaxial anisotropy on the generation and morphology of skyrmions
Authors: Xu Min , Zhang Jinyu , Meng Dexiang , Li Runshui
Published: April 2021

Different magnetic interactions and anisotropy in the multi-layer structure have different effects on the formation and morphology of skyrmions under zero field. In this paper, we show that the Ruderman–Kittel–Kasuya–Yosida (RKKY) coupling plays a dominant role in the generation of skyrmions but has no significant effect on the size of skyrmions. When the RKKY coupling is weak, if the Dzyaloshinskii–Moriya interaction (DMI) is strong enough, some irregular cruciform domain states can be formed. With the increase of the DMI, the shape of skyrmions is altered from Néel skyrmions to skyrmioniums, and when the Heisenberg exchange is relatively low, complex domain states, such as the labyrinth are formed. However, when the Heisenberg coupling is comparatively high, the spin states of the Néel-skyrmions are reversed. Both the Heisenberg exchange interaction and uniaxial anisotropy have a positive influence on reducing the diameters of skyrmions. However, skyrmions are difficult to generate when the Heisenberg exchange and anisotropy are strong enough. We find the prioritization of the effects of different magnetic interactions and uniaxial anisotropy on the formation and morphology of skyrmions by analyzing the energy diagrams, combined with the magnetization configuration in different pairs of the exchange interactions and anisotropy, in which the RKKY coupling has the greatest influence, followed by the DMI, then the Heisenberg exchange and finally the uniaxial anisotropy.
A fault diagnosis method for an electro-hydraulic directional valve based on intrinsic mode functions and weighted densely connected convolutional networks
Authors: Shi Chong , Ren Yan , Tang Hesheng , Mupfukirei Leaven Romeo
Published: April 2021

Wear caused by contaminated oil or frequent reciprocating of the spool is the chief source of internal leakage in electro-hydraulic directional valves. It is difficult to detect the location and extent of the internal wear of directional valves because the hydraulic transmission works in a closed system. Therefore, this paper focuses on the internal leakage fault diagnosis caused by the wear based on intrinsic mode functions (IMFs) and weighted densely connected convolutional networks (WDenseNets), especially for electro-hydraulic directional valves. First, the empirical mode decomposition is performed in three subsections, respectively, and a series of IMF components are obtained correspondingly. Combined with the ReliefF feature selection algorithm, the optimal IMF component is selected. The weights assigned to the optimal IMF mode are normalized and then weighted as the subsequent diagnostic feature vector. Then, a WDenseNet inspired by squeeze-and-excitation networks is designed. Finally, the weighted optimal IMF component is used as the input for the WDenseNet for fault identification and classification. In addition, an experimental method to investigate the internal leakage faults associated with wear is developed. Theoretical and experimental results indicate that the fault diagnosis method can be used to identify the type of internal leakage and wear location in electro-hydraulic directional valves. Compared with other intelligent diagnosis methods, this method has higher diagnostic accuracy and better training stability. The effectiveness of the proposed method is also verified through an experimental study of the bearing fault in an axial piston pump.
First-principles study of pristine and Li-doped borophene as a candidate to detect and scavenge SO2 gas
Authors: Tu Xianxian , Xu Hong , Wang Xiaohua , Li Chenyin , Fan Guohong , Chu Xiangfeng
Published: April 2021

In this research, the potential application of borophene as gas sensor device is explored. The first-principles theory is employed to investigate the sensing performance of pristine and Li-doped borophene for SO2 and five main atmospheric gases (including CH4, CO2, N2, CO and H2). All gases are found to be adsorbed weakly on pristine borophene, which shows weak physical interaction between the pristine borophene and gases. The gas adsorption performance of borophene is improved by the doping of Li atom. The results of adsorption energy suggest that Li-borophene exhibits high selectivity to SO2 molecule. Moreover, analyses of the charge transfer, density of states and work function also confirm the introduction of Li adatom on borophene significantly enhances the selectivity and sensitivity to SO2. In addition, desorption time of gas from pristine and Li doped borophene indicates the Li-borophene has good desorption characteristics for SO2 molecule at high temperatures. This research would be helpful for understanding the influence of Li doping on borophene and presents the potential application of Li-borophene as a SO2 gas sensor or scavenger.
Carbon nitride/positive carbon black anchoring PtNPs assembled by γ-rays as ORR catalyst with excellent stability
Authors: Liu Liangsen , Shi Xiang , Wang Wei , Pei Mengfan , Hong Chunxia , Xue Yanling , Xu Zhiwei , Tian Feng , Guo Xingfeng
Published: April 2021

Electrocatalytic performance of low-cost graphitic carbon nitride (CN) is greatly limited by its limited conductivity and small specific surface area. Herein, a simple and cost-effective idea to produce novel nanocomposite is constructed by the CN and cetyl trimethyl ammonium bromide functionalized carbon black (CB) anchored platinum nanoparticles as highly efficient oxygen reduction catalysts based on gamma irradiation. The assembled carbon nitride/positive carbon black anchoring PtNPs (Pt/CN2-CB+
1) catalyst exhibits significantly improved specific surface area, high graphitization, and uniformly dispersed ultra-small platinum nanoparticles. For the oxygen reduction reaction (ORR) performance, the catalyst shows more positive onset-potential (0.93 V versus RHE) and larger diffusion limiting current density (5.65 mA cm−2) compared with benchmark Pt/C catalysts in alkaline medium. Moreover, the Pt/CN2-CB+
1 catalyst exhibits a small Tafel slope (92 mV dec−1). Besides, the catalyst was demonstrated the remarkable methanol tolerance and good long-term stability under working conditions. This work provides a new and effective γ-rays irradiation for synthesizing the carbon nitride catalysts for energy conversion and storage applications.
Reliable readings from Arduino voltmeters
Authors: Makan Gergely , Mingesz Robert , Gingl Zoltan
Published: April 2021

Modern instruments use sensors, analogue and digital electronics, and digital processing to measure almost any kind of physical quantities. Arduino is a very useful and widely used platform to build such systems in a school environment. Since it has analogue voltage inputs, it can be used as a digital voltmeter or even as a chart recorder. However, the ways of ensuring the required level of accuracy or just the right estimation of accuracy are often unknown or misunderstood. In this paper we try to fill this gap to aid reliable school experimentation.
Impact of terbium inclusion on the photodetection performance of ZnO thin films
Authors: Kumar S Sathish , Chidhambaram N , Deva Arun Kumar Karuppiah , Isaac R S Rimal , Abdeltawab Ahmed A , Mohammady Sayed Z , Ubaidullah Mohd , Shaik Shoyebmohamad F
Published: April 2021

Terbium (Tb)-doped ZnO thin films were fabricated using the successive ionic layer adsorption and reaction route. Their structural, morphological, optical, and ultraviolet photosensing properties were studied and compared with those of pure ZnO thin films. The x-ray diffraction results illustrate that the pure and Tb-doped ZnO films reveal hexagonal structures with the P63mc space group. The 1% Tb-doped ZnO film shows an increase in the absorption and a decrease in bandgap value from 3.24 eV to 3.15 eV compared to pure ZnO. The photoluminescence results reveal the existence of emission centers at 388, 414, 441, and 477 nm in the fabricated thin films. By increasing the rare earth (Tb) element, the near band edge emission was decreased and correspondingly increased the blue emission due to its 4f orbital energy transition. The photosensing parameters, such as responsivity, external quantum efficiency, and specific detectivity values of the 1% Tb-doped ZnO detector, are 2.21 × 10−1 A W−1, 75%, and 1.84 × 1010 Jones, respectively, which are higher compared to the other fabricated devices due to their better optoelectronic properties. For the 5% Tb-doped ZnO detector, the I–V characteristic curve shows a non-linear behavior, which indicates that a small Schottky barrier is formed in the detector due to widening of the potential barrier and depletion region by Tb. We also investigated the possible energy band diagram of both linear and non-linear (Schottky barrier) behaviors for Tb-doped ZnO detectors.
Enhancement of surge-induced synchronized switch harvesting on inductor strategy
Authors: Onoda Junjiro , Minesugi Kenji , Kwon Seong-Cheol , Oh Hyun-Ung
Published: April 2021

We propose and demonstrate a novel method to enhance vibration harvesting based on surge-induced synchronized switch harvesting on inductor (S3HI). S3HI allows harvesting of a large amount of energy even from low-amplitude vibrations by inducing a surge voltage during the voltage inversion of a synchronized switch harvesting on inductor (SSHI). The surge voltage and the voltage amplification from the conventional voltage inversion improve energy harvesting. S3HI modifies SSHI by both rewiring the circuit without adding components and using a novel switching pattern for voltage inversion, thus maintaining the simplicity of SSHI. We propose a novel switching strategy and circuit topology and analyze six methods that constitute the S3HI family, which includes traditional S3HI and high-frequency S3HI. We demonstrate that the six methods suitably harvest energy even from low-amplitude vibrations. Nevertheless, the harvestable energy per vibration cycle depends on the switching pattern and storage-capacitor voltage. The use of the proposed switching strategy, which allows energy harvesting before energy-dissipative voltage inversion, substantially increases the harvestable energy per vibration cycle. In the typical case considered in this study, the said increase is on the order of 11%–31% and 15%–450% compared to the traditional and existing high-frequency S3HI methods, respectively, depending on the storage-capacitor voltage. Additionally, the proposed circuit can be used as a traditional circuit. It could be considered a promising alternative to S3HI methods owing to its potential auto-reboot capability, which is not found in traditional S3HI circuit.
Addendum: Beyond the limits of 1D coherent synchrotron radiation (2018 New J. Phys.
20 073035)
Authors: Brynes A D , Smorenburg P , Akkermans I , Allaria E , Badano L , Brussaard S , Danailov M , Demidovich A , De Ninno G , Gauthier D , Gaio G , van der Geer S B , Giannessi L , de Loos M J , Mirian N S , Penco G , Rebernik P , Rossi F , Setija I , Spampinati S , Spezzani C , Trovò M , Williams P H , Di Mitri S
Published: April 2021

This paper is an addendum to reference  (Brynes et al 2018 New J. Phys.
20 073035), in which we studied the transverse emittance growth due to coherent synchrotron radiation (CSR) in the bunch compressor of a free-electron laser. Analytic results based on the theory of CSR were compared with results from experiment and simulation. Recent results have been published (Stupakov 2019 arXiv:1901.10745) which correct the theoretical emittance growth, predicting a smaller increase than that which was expected based on previous results. When comparing these new calculations with the emittance growth that was measured experimentally, and with 3D simulations, we find an improved agreement when the bunch compression approaches its maximum value.
Angular-momentum exchange among acoustic and optical waves at the collinear acousto-optic diffraction
Authors: Kostyrko Myroslav , Skab Ihor , Vlokh Rostyslav
Published: April 2021

We consider collinear acousto-optic diffraction of circularly polarized optical waves at circularly polarized acoustic waves in the crystals that reveal both acoustic conical refraction and optical activity. We find that, due to the conical refraction of acoustic waves, these waves produce vector-vortex beam. In this process, the orbital angular momentum (OAM) of the conically refracted acoustic wave is transformed into the OAM of the diffracted optical wave. At the same time, the spin angular momentum of conically refracted phonons is transferred to diffracted photons. The possibility of phonon-photon entanglement is discussed in the work.
Tunable thickness and uniform drop deposition of graphene oxide on porous anodic aluminum oxide and a reliable thickness measurement technique
Authors: Cho Hyeonho , Kim Taehee , Kim Sunghan
Published: April 2021

The pinned contact line of sessile droplets containing micro/nanoparticles on a substrate results in nonuniform depositions with noncontrollable thicknesses, thereby producing the coffee-ring effect. In this study, we demonstrated that the thickness of graphene oxide (GO) films can be engineered using porous anodic aluminum oxide (AAO) substrates to fabricate uniform GO films. The outstanding thickness controllability and uniformity of GO films were obtained via tailorable hydrodynamic flow in a sessile droplet due to the pores of the AAO substrate. Furthermore, we developed a novel approach for measuring the micro/nanoscale thicknesses of GO films using an optical microscope. The thicknesses of the deposited GO film, measured via optical microscopy, demonstrated good agreement with those obtained via atomic force microscopy. These findings are beneficial for GO film applications, such as in wearable sensors, filtration, inkjet printing.
Graphene oxide biohybrid layer enhances sensitivity and anticorrosive properties in refractive index sensor
Authors: Alonso-Murias Monserrat del C , Monzón-Hernández David , Gravagnuolo Alfredo Maria , Márquez Salomón , Giardina Paola , Morales-Narváez Eden
Published: April 2021

Graphene-based materials are capable of enhancing the refractometric response of prism- and optical fiber-based surface plasmon resonance (SPR) sensors; however, complicated multistep and time-consuming attaching processes could limit their practical applications. Herein, for the first time, we demonstrate the immobilization of graphene oxide (GO) submicrometric sheets onto the surface of a gold-coated single-mode fiber using a coating of fungal self-assembling proteins, the hydrophobins (HFBs), as an adhesive nanolayer. Hetero-core fiber tip SPR structures used in this study, consisting of a mirrored multimode–single-mode fiber structure coated with different thin layers (a chromium layer of 3 nm and a gold layer of 30 nm on top) exhibited a refractive index sensitivity (SRI) of 1842 nm RIU−1 (RIU: refractive index unit) at a refractive index (RI) of 1.36. Self-assembly of GO over the SPR fiber tip via HFB, offered an enhancement of up to 20% in the SRI. Moreover, this HFB-GO coating prevented degradation of the Al thin film mirror caused by corrosive salt-water solutions. The process is very simple, harmless, rapid (around 15 min) and scalable, as it is mostly based on one plasma treatment, which can be performed in large chambers and two dip coating steps, in liquid baths. All these features make the use of self-assembled bio/non-bio hybrid coating a green industrial method to improve the performance of SPR fiber biosensors, if compared with traditional chemical methods. Materials applied in this technology, fungal proteins and derivatives of graphite, are sustainable and largely available.
FFT and Equivalent-inclusion approach for effective conductivity of three-phase composites with random coated-ellipse inclusion
Authors: Nguyen Van-Luat
Published: April 2021

Unlike sphere inclusion, every ellipsoid inclusion is anisotropic, but compound-inclusion composite material with random distribution of coated-ellipse inclusion can be considered as isotropic. The paper introduces the Fast Fourier transformation method (FFT) and equivalent inclusion approach to calculate the effective conductivity of the transverse isotropic unidirectional coated-fiber composite with coated-ellipse inclusion. In the equivalent inclusion approximation, the two-phase of coated-ellipse inclusions are substituted by the equivalent homogeneous one of the same size and corresponding mechanical properties, from here we can build a simple approximation formula (EI) to determine effective conductivity of three-phase composites. Beside that, the FFT simulation can be combined with the equivalent inclusion approach to obtain the results FFT-EI.
Samurai: A Very Short Introduction
Authors: Wert Michael
Published: April 2021

A book about the samurai from their origins in the eighth and ninth centuries until their demise in the mid-nineteenth century. It describes samurai life, work, philosophy, and warfare as it changed over time and covers what samurai were doing when they weren’t fighting. The first half of the book tends to focus on warriors who were essentially aristocrats; warrior families who looked to non-warrior nobles for models of behaviour, lifestyle, and politics. It traces the early formation of a warrior regime, how it interacted with an emperor-centered noble court located permanently in Kyoto, and the political and cultural struggles within the warrior class. The second half of the book zeroes in on the details of warlord families, the struggles of “rank-and-file” samurai typically depicted in popular culture—warriors from the seventeenth through nineteenth centuries. It also shows how samurai history, culture, and values were consumed by non-samurai and, in so doing, contributed to an idealized warrior image that even samurai themselves tried to emulate.
5. The politics of arbitration against governments
Authors: Schultz Thomas , Grant Thomas
Published: April 2021

This chapter focuses on the most politically charged type of arbitration: arbitration between an investor and a foreign government. Investment arbitration marks a great step forward for rule of law in international affairs. A government does not escape responsibility by saying that its own law or courts have declared a given abuse against an investor to be lawful. Investment treaties set out substantive protections, such as fair and equitable treatment, full protection and security, and a guarantee against discriminatory expropriation. They give investors legal rights independent of domestic rules that an unfriendly government might have manipulated at the investor’s cost. The chapter then considers the emerging critique of investment arbitration.
Geology or biology?
Authors: Sheppard Charles
Published: April 2021

For centuries, reefs were used and valued for their food and shelter from storms, though for mariners they were a constant danger to be avoided because of their position at shallow depths in tropical seas. Scientific understanding started with European travellers trading with the Caribbean region and then with traders going eastwards to the Indian and Pacific oceans, especially when naturalists, commonly sponsored by patrons, accompanied the traders. The main questions included how the obviously living veneer could make the vast amounts of rock, as well as what the huge variety of sea creatures were. Darwin was the most famous naturalist who became intrigued by them and, following his Beagle voyage, he formed his theory of how they developed, which was proved true a century later. The basic underlying mechanism he proposed unified how they grew and why reefs around the world had so many common characteristics, especially why they nearly all had a similar depth and profile.
The resulting structure—a reef
Authors: Sheppard Charles
Published: April 2021

Reef profiles are remarkably consistent in general design because they are essentially biological constructions responding to environmental factors. All have reef flats, a horizontal expanse at low tide level that develops when the reef can no longer build upwards and extends horizontally. This is commonly the largest expanse and is the only part that early naturalists could examine until the advent of scuba diving relatively recently. However, it is always relatively depauperate because of the extremes of heat, salinity, and light that affect it. To seaward is the reef crest, commonly constructed by calcareous red algae that are the only form of life that can withstand the severe waves that pound the reef. To seaward of the crest, the reef slopes downwards, and is where environmental conditions are most benign and where the greatest biodiversity is found. The rugosity or 3-D structure of a reef is a key factor in reef biodiversity because it provides a vast number of niches for the huge diversity of life. Reefs are constantly subjected to erosion from burrowing and tunnelling forms, whose activity creates sand and sediment. This is then forced into crevices or pushed up onto the island behind it, so this erosion is also the starting point for further reef and island construction. Expanses of sand are associated with all reefs, and are home to another rich assemblage of species.
A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine
Authors: Dotolo Serena , Marabotti Anna , Rachiglio Anna Maria , Esposito Abate Riziero , Benedetto Marco , Ciardiello Fortunato , De Luca Antonella , Normanno Nicola , Facchiano Angelo , Tagliaferri Roberto
Published: April 2021

Motivation

Assessment of genetic mutations is an essential element in the modern era of personalized cancer treatment. Our strategy is focused on ‘multiple network analysis’ in which we try to improve cancer diagnostics by using biological networks. Genetic alterations in some important hubs or in driver genes such as BRAF and TP53 play a critical role in regulating many important molecular processes. Most of the studies are focused on the analysis of the effects of single mutations, while tumors often carry mutations of multiple driver genes. The aim of this work is to define an innovative bioinformatics pipeline focused on the design and analysis of networks (such as biomedical and molecular networks), in order to: (1) improve the disease diagnosis; (2) identify the patients that could better respond to a given drug treatment; and (3) predict what are the primary and secondary effects of gene mutations involved in human diseases.

Results

By using our pipeline based on a multiple network approach, it has been possible to demonstrate and validate what are the joint effects and changes of the molecular profile that occur in patients with metastatic colorectal carcinoma (mCRC) carrying mutations in multiple genes. In this way, we can identify the most suitable drugs for the therapy for the individual patient. This information is useful to improve precision medicine in cancer patients. As an application of our pipeline, the clinically significant case studies of a cohort of mCRC patients with the BRAF V600E-TP53 I195N missense combined mutation were considered.

Availability

The procedures used in this paper are part of the Cytoscape Core, available at (www.cytoscape.org). Data used here on mCRC patients have been published in [55].

Supplementary Information

A supplementary file containing a more detailed discussion of this case study and other cases is available at the journal site as Supplementary Data.
Interpretable principal component analysis for multilevel multivariate functional data
Authors: Zhang Jun , Siegle Greg J , Sun Tao , D’andrea Wendy , Krafty Robert T
Published: April 2021

Many studies collect functional data from multiple subjects that have both multilevel and multivariate structures. An example of such data comes from popular neuroscience experiments where participants’ brain activity is recorded using modalities such as electroencephalography and summarized as power within multiple time-varying frequency bands within multiple electrodes, or brain regions. Summarizing the joint variation across multiple frequency bands for both whole-brain variability between subjects, as well as location–variation within subjects, can help to explain neural reactions to stimuli. This article introduces a novel approach to conducting interpretable principal components analysis on multilevel multivariate functional data that decomposes total variation into subject-level and replicate-within-subject-level (i.e., electrode-level) variation and provides interpretable components that can be both sparse among variates (e.g., frequency bands) and have localized support over time within each frequency band. Smoothness is achieved through a roughness penalty, while sparsity and localization of components are achieved by solving an innovative rank-one based convex optimization problem with block Frobenius and matrix $L_1$-norm-based penalties. The method is used to analyze data from a study to better understand reactions to emotional information in individuals with histories of trauma and the symptom of dissociation, revealing new neurophysiological insights into how subject- and electrode-level brain activity are associated with these phenomena. Supplementary materials for this article are available online.
The mitochondrial landscape of ovarian cancer: emerging insights
Authors: Shukla Pallavi , Singh Keshav K
Published: April 2021

Ovarian cancer (OC) is known to be the most lethal cancer in women worldwide, and its etiology is poorly understood. Recent studies show that mitochondrial DNA (mtDNA) content as well as mtDNA and nuclear genes encoding mitochondrial proteins influence OC risk. This review presents an overview of role of mitochondrial genetics in influencing OC development and discusses the contribution of mitochondrial proteome in OC development, progression and therapy. A role of mitochondrial genetics in racial disparity is also highlighted. In-depth understanding of role of mitochondria in OC will help develop strategies toward prevention and treatment and improving overall survival in women with OC.
Transmission Dynamics of the Rubella Virus Circulating in China During 2010–2019: 2 Lineage Switches Between Genotypes 1E and 2B
Authors: Zhu Zhen , Cui Aili , Zhang Yan , Mao Naiying , Liu Ying , Liu Li , Deng Lili , Chen Ying , Zhao Hua , Gong Tian , Zhou Shujie , Li Fangcai , Lei Yue , Yang Yuying , Wang Yan , Sun Zhaodan , Feng Daxing , Peng Xiaofang , Yuan Fang , Du Hui , Feng Yan , Wang Changyin , Guo Jun , Huang Fang , Gao Hui , Ma Yu , Chen Haiyun , Deng Xiuying , Zhang Ting , Li Liqun , Wang Shuang , Yang Xiuhui , Tian Xiaoling , Fan Lixia , Niu Dandan , Xu Wenbo
Published: April 2021

Background

To provide a better understanding of the progress on rubella control and elimination in China, a genetic analysis was conducted to examine the transmission pattern of the endemic rubella virus in China during 2010–2019.

Methods

A total of 4895 strains were obtained from 29 of the 31 provinces in mainland China during 2010–2019. The genotyping regions of the strains were amplified, determined, and assembled. Genotyping analysis and lineage division were performed by comparisons with the World Health Organization reference strains and reported lineage reference strains, respectively. Further phylogenetic analyses were performed to compare the genetic relationship.

Results

During 2010–2019, the domestic lineage 1E-L1 and multiple imported lineages of rubella viruses including 2B-L1, 1E-L2, and 2B-L2c were identified. Further analysis of the circulation trend of the different lineages indicated that 2 switches occurred among the lineages. The first shift was from lineage 1E-L1 to 2B-L1, which occurred around 2015–2016, followed by the lowest rubella incidence in 2017. The second shift was from lineage 2B-L1 to 1E-L2 and 2B-L2c, which occurred around 2018–2019, coinciding with rubella resurgence and the subsequent nationwide epidemic during 2018–2019. Insufficient genomic information worldwide made it impossible to trace the origin of the imported viruses.

Conclusions

China was moving toward rubella elimination, as evidenced by the fact that previous endemic lineages were not detected. However, rubella reemerged in 2018 2019 due to the newly imported rubella viruses. Therefore, to realize the rubella elimination goal, joint efforts are required for all countries worldwide.
Detection of Pathogenic Bacteria From Septic Patients Using 16S Ribosomal RNA Gene–Targeted Metagenomic Sequencing
Authors: Fida Madiha , Wolf Matthew J , Hamdi Ahmed , Vijayvargiya Prakhar , Esquer Garrigos Zerelda , Khalil Sarwat , Greenwood-Quaintance Kerryl E , Thoendel Matthew J , Patel Robin
Published: April 2021

Background

Conventional blood cultures were compared to plasma cell-free DNA–based 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR)/next-generation sequencing (NGS) for detection and identification of potential pathogens in patients with sepsis.

Methods

Plasma was prospectively collected from 60 adult patients with sepsis presenting to the Mayo Clinic (Minnesota) Emergency Department from March through August 2019. Results of routine clinical blood cultures were compared to those of 16S rRNA gene NGS.

Results

Nineteen (32%) subjects had positive blood cultures, of which 13 yielded gram-negative bacilli, 5 gram-positive cocci, and 1 both gram-negative bacilli and gram-positive cocci. 16S rRNA gene NGS findings were concordant in 11. For the remaining 8, 16S rRNA gene NGS results yielded discordant detections (n = 5) or were negative (n = 3). Interestingly, Clostridium species were additionally detected by 16S rRNA gene NGS in 3 of the 6 subjects with gastrointestinal sources of gram-negative bacteremia and none of the 3 subjects with urinary sources of gram-negative bacteremia. In the 41 remaining subjects, 16S rRNA gene NGS detected at least 1 potentially pathogenic organism in 17. In 15, the detected microorganism clinically correlated with the patient’s syndrome. In 17 subjects with a clinically defined infectious syndrome, neither test was positive; in the remaining 7 subjects, a noninfectious cause of clinical presentation was identified.

Conclusions

16S rRNA gene NGS may be useful for detecting bacteria in plasma of septic patients. In some cases of gram-negative sepsis, it may be possible to pinpoint a gastrointestinal or urinary source of sepsis based on the profile of bacteria detected in plasma.
Exposure to Diverse Plasmodium falciparum Genotypes Shapes the Risk of Symptomatic Malaria in Incident and Persistent Infections: A Longitudinal Molecular Epidemiologic Study in Kenya
Authors: Sumner Kelsey M , Freedman Elizabeth , Mangeni Judith N , Obala Andrew A , Abel Lucy , Edwards Jessie K , Emch Michael , Meshnick Steven R , Pence Brian W , Prudhomme-O’Meara Wendy , Taylor Steve M
Published: April 2021

Background

Repeated exposure to malaria infections could protect against symptomatic progression as people develop adaptive immunity to infections acquired over time.

Methods

We investigated how new, recurrent, and persistent Plasmodium falciparum infections were associated with the odds of developing symptomatic compared with asymptomatic malaria. Using a 14-month longitudinal cohort in Western Kenya, we used amplicon deep sequencing of 2 polymorphic genes (pfama1 and pfcsp) to assess overlap of parasite genotypes (represented by haplotypes) acquired within an individual’s successive infections. We hypothesized infections with novel haplotypes would increase the odds of symptomatic malaria.

Results

After excluding initial infections, we observed 534 asymptomatic and 88 symptomatic infections across 186 people. We detected 109 pfcsp haplotypes, and each infection was classified as harboring novel, recurrent, or persistent haplotypes. Incident infections with only new haplotypes had higher odds of symptomatic malaria when compared with infections with only recurrent haplotypes [odds ratio (OR): 3.24; 95% confidence interval (CI), 1.20–8.78], but infections with both new and recurrent haplotypes (OR: 0.64; 95% CI: 0.15–2.65) did not. Assessing persistent infections, those with mixed (persistent with new or recurrent) haplotypes (OR: 0.77; 95% CI: 0.21–2.75) had no association with symptomatic malaria compared with infections with only persistent haplotypes. Results were similar for pfama1.

Conclusions

These results confirm that incident infections with only novel haplotypes were associated with increased odds of symptomatic malaria compared with infections with only recurrent haplotypes but this relationship was not seen when haplotypes persisted over time in consecutive infections.
Non-bacterial thrombotic endocarditis manifested by ventricular fibrillation in a patient with low grade ovarian carcinoma: case report and literature review
Authors: Kuipers Remko S , Berghuis Meike A T , Ogilvie Aernout C , van Wissen Sanne A , Riezebos Robert K
Published: April 2021

Background

Non-bacterial thrombotic endocarditis (NBTE) is a rare form of endocarditis notably described in patients with advanced malignancy and auto-immune diseases. It is characterized by the formation of sterile, fibrin-containing vegetations on cardiac endothelium, in the absence of positive blood cultures. It is predominantly located on the mitral- and aortic valve (AV). Vegetations in NBTE are prone to embolize. Trousseau syndrome (TS) is defined as unexplained thrombotic events that precede the diagnosis of malignancy.

Case summary

A 49-year-old pre-menopausal woman with a history of visual disturbances, recurrent deep vein thrombosis (DVT) with concurrent pulmonary emboli (PE), and uterine myomas with dysfunctional uterine bleeding was resuscitated for ventricular fibrillation. While echocardiography revealed vegetations on the AV, blood cultures remained negative. Additional work-up for the aetiology of sterile vegetations revealed a low-grade ovarian carcinoma. Cardiac analysis showed evidence of myocardial infarction in the absence of coronary atherosclerosis as a cause for ventricular fibrillation.

Discussion

Unexplained thrombotic events (venous, arterial, or both) warrant further investigation, e.g., with regard to TS. NBTE is a potential source of thromboembolism in TS and a rare ante-mortem finding, which prompts additional investigation of the underlying cause. In our patient, a triad of (suspected) (i) arterial/systemic embolization (i.e. visual disturbances, splenic infarction, coronary embolism), (ii) peripheral thrombophlebitis/hypercoagulability (i.e. DVT and PE), and (iii) malignancy (i.e. gynaecological abnormalities) raised suspicion of NBTE in the setting of TS. Early diagnosis and treatment of NBTE is of importance due to the high incidence of embolization, with possible fatal outcome.
Paper-containing 1-methylcyclopropene treatment suppresses fruit decay of fresh Anxi persimmons by enhancing disease resistance
Authors: Zeng Lingzhen , Shi Lili , Lin Hetong , Lin Yuzhao , Lin Yixiong , Wang Hui
Published: April 2021

Objectives

The purpose of this work was to evaluate the potential application of papers containing 1-methylcyclopropene (1-MCP) postharvest treatment for suppressing fruit decay of fresh Anxi persimmons and its possible mechanism.

Materials and methods

Anxi persimmon fruit were treated with papers containing 1-MCP at the dosage of 1.35 μL/L and stored at 25 ± 1 °C and 85 per cent relative humidity for 35 days. During storage, the fruit decay rate and lignin content were evaluated, and the content of total phenolics, the activities of phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO), peroxidase (POD), chitinase (CHI), and β-1,3-glucanase (GLU) were determined by spectrophotometry.

Results

The 1-MCP–treated persimmons displayed a lower fruit decay rate, but higher contents of lignin and total phenolics, higher activities of PAL, PPO, POD, CHI, and GLU.

Conclusions

The treatment with 1-MCP could inhibit the fruit decay of postharvest Anxi persimmons, which might be because 1-MCP enhanced fruit disease resistance by increasing the activities of disease resistance-associated enzymes and retaining higher contents of disease resistance-related substances in postharvest fresh Anxi persimmons. These findings indicate that papers containing 1-MCP at the dosage of 1.35 μL/L have potential application in suppressing fruit decay and extending storage life of postharvest fresh Anxi persimmons.
INCIPIENT GENOME DIFFERENTIATION IN GOSSYPIUM. III. COMPARISON OF CHROMOSOMES OF G. HIRSUTUM AND ASIATIC DIPLOIDS USING HETEROZYGOUS TRANSLOCATIONS
Authors: Menzel Margaret Y , Hasenkampf Clare A , Stewart James McD
Published: April 2021

Hybrids between upland cotton (G. hirsutum, genome constitution 2AhDh) and either A-genome or D-genome diploid species exhibit 26 paired and 13 unpaired chromosomes at metaphase I. The Ah and Dh genomes are therefore considered homoeologous with those of the respective diploids. Previous studies, nevertheless, revealed a low level of ("incipient") differentiation between Dh and various diploid D genomes. The diploid A genomes have been regarded as more closely homologous to Ah on the basis of low preferential pairing and autotetraploid segregation ratios in allohexaploids.—The present study addressed the following questions: Are the diploid A genomes differentiated from Ah in meiotic homology? If so, is the differentiation manifested equally by all 13 chromosomes or is it localized in certain chromosomes?—Three diploid A-genome lines representing G. herbaceum and G. arboreum were hybridized by in ovulo culture of embryos (1) with a standard line of G. hirsutum, which differs from G. herbaceum by two and from G. arboreum by three naturally occurring reciprocal translocations involving chromosomes 1—5, and (2) with six lines homozygous for experimental translocations involving chromosomes 6, 7, 10, 11, 12 and 13. Chiasma frequencies in hybrids were compared with those in appropriate G. hirsutum controls. In every comparison overall chiasma frequencies were slightly lower in the hybrids. Therefore Ah appears to be differentiated from the diploid A genomes. No localized differentiation was detected in chromosomes marked by experimental translocations. The differentiation may be localized mainly in chromosomes 4 and 5.
IDENTIFICATION OF A SECOND LOCUS IN DROSOPHILA MELANOGASTER REQUIRED FOR EXCISION REPAIR
Authors: Boyd J B , Snyder R D , Harris P V , Presley J M , Boyd S F , Smith P D
Published: April 2021

The mus(2)201 locus in Drosophila is defined by two mutant alleles that render homozygous larvae hypersensitive to mutagens. Both alleles confer strong in vivo somatic sensitivity to treatment by methyl methanesulfonate, nitrogen mustard and ultraviolet radiation but only weak hypersensitivity to X-irradiation. Unlike the excision-defective mei-9 mutants identified in previous studies, the mus(2)201 mutants do not affect female fertility and do not appear to influence recombination proficiency or chromosome segregation in female meiocytes.—Three independent biochemical assays reveal that cell cultures derived from embryos homozygous for the mus(2)  D1 allele are devoid of detectable excision repair. 1. Such cells quantitatively retain pyrimidine dimers in their DNA for 24 hr following UV exposure. 2. No measurable unscheduled DNA synthesis is induced in mutant cultures by UV treatment. 3. Single-strand DNA breaks, which are associated with normal excision repair after treatment with either UV or N-acetoxy-N-acetyl-2-aminofluorene,* are much reduced in these cultures. Mutant cells possess a normal capacity for postreplication repair and the repair of single-strand breaks induced by X-rays.