bluuebunny/crossref_metadata_2025 huggingface dataset:
The tin1 gene retains the function of promoting tillering in maize
Authors: Zhang Xuan , Lin Zhelong , Wang Jian , Liu Hangqin , Zhou Leina , Zhong Shuyang , Li Yan , Zhu Can , Liu Jiacheng , Lin Zhongwei
Published: December 2019

Sweet maize and popcorn retain tillering growth habit during maize diversification. However, the underlying molecular genetic mechanism remains unknown. Here, we show that the retention of maize tillering is controlled by a major quantitative trait locus (QTL), tin1, which encodes a C2H2-zinc-finger transcription factor that acts independently of tb1. In sweet maize, a splice-site variant from G/GT to C/GT leads to intron retention, which enhances tin1 transcript levels and consequently increases tiller number. Comparative genomics analysis and DNA diversity analysis reveal that tin1 is under parallel selection across different cereal species. tin1 is involved in multiple pathways, directly represses two tiller-related genes, gt1 and Laba1/An-2, and interacts with three TOPLESS proteins to regulate the outgrowth of tiller buds. Our results support that maize tin1, derived from a standing variation in wild progenitor teosinte population, determines tillering retention during maize diversification.
Stabilization of point-defect spin qubits by quantum wells
Authors: Ivády Viktor , Davidsson Joel , Delegan Nazar , Falk Abram L. , Klimov Paul V. , Whiteley Samuel J. , Hruszkewycz Stephan O. , Holt Martin V. , Heremans F. Joseph , Son Nguyen Tien , Awschalom David D. , Abrikosov Igor A. , Gali Adam
Published: December 2019

Defect-based quantum systems in wide bandgap semiconductors are strong candidates for scalable quantum-information technologies. However, these systems are often complicated by charge-state instabilities and interference by phonons, which can diminish spin-initialization fidelities and limit room-temperature operation. Here, we identify a pathway around these drawbacks by showing that an engineered quantum well can stabilize the charge state of a qubit. Using density-functional theory and experimental synchrotron X-ray diffraction studies, we construct a model for previously unattributed point defect centers in silicon carbide as a near-stacking fault axial divacancy and show how this model explains these defects’ robustness against photoionization and room temperature stability. These results provide a materials-based solution to the optical instability of color centers in semiconductors, paving the way for the development of robust single-photon sources and spin qubits.
Strong optical response and light emission from a monolayer molecular crystal
Authors: Zhao Huijuan , Zhao Yingbo , Song Yinxuan , Zhou Ming , Lv Wei , Tao Liu , Feng Yuzhang , Song Biying , Ma Yue , Zhang Junqing , Xiao Jun , Wang Ying , Lien Der-Hsien , Amani Matin , Kim Hyungjin , Chen Xiaoqing , Wu Zhangting , Ni Zhenhua , Wang Peng , Shi Yi , Ma Haibo , Zhang Xiang , Xu Jian-Bin , Troisi Alessandro , Javey Ali , Wang Xinran
Published: December 2019

Excitons in two-dimensional (2D) materials are tightly bound and exhibit rich physics. So far, the optical excitations in 2D semiconductors are dominated by Wannier-Mott excitons, but molecular systems can host Frenkel excitons (FE) with unique properties. Here, we report a strong optical response in a class of monolayer molecular J-aggregates. The exciton exhibits giant oscillator strength and absorption (over 30% for monolayer) at resonance, as well as photoluminescence quantum yield in the range of 60–100%. We observe evidence of superradiance (including increased oscillator strength, bathochromic shift, reduced linewidth and lifetime) at room-temperature and more progressively towards low temperature. These unique properties only exist in monolayer owing to the large unscreened dipole interactions and suppression of charge-transfer processes. Finally, we demonstrate light-emitting devices with the monolayer J-aggregate. The intrinsic device speed could be beyond 30 GHz, which is promising for next-generation ultrafast on-chip optical communications.
Strong time dependence of ocean acidification mitigation by atmospheric carbon dioxide removal
Authors: Hofmann M. , Mathesius S. , Kriegler E. , Vuuren D. P. van , Schellnhuber H. J.
Published: December 2019

In Paris in 2015, the global community agreed to limit global warming to well below 2 $${}^{\circ }$$

∘

C, aiming at even 1.5 $${}^{\circ }$$

∘

C. It is still uncertain whether these targets are sufficient to preserve marine ecosystems and prevent a severe alteration of marine biogeochemical cycles. Here, we show that stringent mitigation strategies consistent with the 1.5 $${}^{\circ }$$

∘

C scenario could, indeed, provoke a critical difference for the ocean’s carbon cycle and calcium carbonate saturation states. Favorable conditions for calcifying organisms like tropical corals and polar pteropods, both of major importance for large ecosystems, can only be maintained if CO$${}_{2}$$

2

emissions fall rapidly between 2025 and 2050, potentially requiring an early deployment of CO$${}_{2}$$

2

removal techniques in addition to drastic emissions reduction. Furthermore, this outcome can only be achieved if the terrestrial biosphere remains a carbon sink during the entire 21st century.
Creation and annihilation of topological meron pairs in in-plane magnetized films
Authors: Gao N. , Je S. -G. , Im M. -Y. , Choi J. W. , Yang M. , Li Q. , Wang T. Y. , Lee S. , Han H. -S. , Lee K. -S. , Chao W. , Hwang C. , Li J. , Qiu Z. Q.
Published: December 2019

Merons which are topologically equivalent to one-half of skyrmions can exist only in pairs or groups in two-dimensional (2D) ferromagnetic (FM) systems. The recent discovery of meron lattice in chiral magnet Co8Zn9Mn3 raises the immediate challenging question that whether a single meron pair, which is the most fundamental topological structure in any 2D meron systems, can be created and stabilized in a continuous FM film? Utilizing winding number conservation, we develop a new method to create and stabilize a single pair of merons in a continuous Py film by local vortex imprinting from a Co disk. By observing the created meron pair directly within a magnetic field, we determine its topological structure unambiguously and explore the topological effect in its creation and annihilation processes. Our work opens a pathway towards developing and controlling topological structures in general magnetic systems without the restriction of perpendicular anisotropy and Dzyaloshinskii–Moriya interaction.
Author Correction: Adaptive individual variation in phenological responses to perceived predation levels
Authors: Abbey-Lee Robin N. , Dingemanse Niels J.
Published: December 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
The Role of Parvalbumin-positive Interneurons in Auditory Steady-State Response Deficits in Schizophrenia
Authors: Metzner Christoph , Zurowski Bartosz , Steuber Volker
Published: December 2019

Despite an increasing body of evidence demonstrating subcellular alterations in parvalbumin-positive (PV+) interneurons in schizophrenia, their functional consequences remain elusive. Since PV+ interneurons are involved in the generation of fast cortical rhythms, these changes have been hypothesized to contribute to well-established alterations of beta and gamma range oscillations in patients suffering from schizophrenia. However, the precise role of these alterations and the role of different subtypes of PV+ interneurons is still unclear. Here we used a computational model of auditory steady-state response (ASSR) deficits in schizophrenia. We investigated the differential effects of decelerated synaptic dynamics, caused by subcellular alterations at two subtypes of PV+ interneurons: basket cells and chandelier cells. Our simulations suggest that subcellular alterations at basket cell synapses rather than chandelier cell synapses are the main contributor to these deficits. Particularly, basket cells might serve as target for innovative therapeutic interventions aiming at reversing the oscillatory deficits.
Relaxin reverses maladaptive remodeling of the aged heart through Wnt-signaling
Authors: Martin Brian , Gabris Beth , Barakat Amr F. , Henry Brian L. , Giannini Marianna , Reddy Rajiv P. , Wang Xuewen , Romero Guillermo , Salama Guy
Published: December 2019

Healthy aging results in cardiac structural and electrical remodeling that increases susceptibility to cardiovascular diseases. Relaxin, an insulin-like hormone, suppresses atrial fibrillation, inflammation and fibrosis in aged rats but the mechanisms-of-action are unknown. Here we show that relaxin treatment of aged rats reverses pathological electrical remodeling (increasing Nav1.5 expression and localization of Connexin43 to intercalated disks) by activating canonical Wnt signaling. In isolated adult ventricular myocytes, relaxin upregulated Nav1.5 (EC50 = 1.3 nM) by a mechanism inhibited by the addition of Dickkopf-1. Furthermore, relaxin increased the levels of connexin43, Wnt1, and cytosolic and nuclear β-catenin. Treatment with Wnt1 or CHIR-99021 (a GSK3β inhibitor) mimicked the relaxin effects. In isolated fibroblasts, relaxin blocked TGFβ-induced collagen elevation in a Wnt dependent manner. These findings demonstrate a close interplay between relaxin and Wnt-signaling resulting in myocardial remodeling and reveals a fundamental mechanism of great therapeutic potential.
A multistage elastocaloric refrigerator and heat pump with 28 K temperature span
Authors: Snodgrass Ryan , Erickson David
Published: December 2019

Elastocaloric refrigerators are a promising alternative to the vapor compression cycle because they do not require refrigerants with high global warming potential. However, these coolers have yet to achieve temperatures low enough to — for example — be used as standard household refrigerators. We built one-stage, two-stage, and three-stage elastocaloric cooling systems to determine if staging of the elastocaloric effect could significantly expand temperature span. Our three-stage system achieved 1.5 times the maximum temperature span of our single-stage system, and produced the highest temperature span of any elastocaloric device to-date at 28.3 °C, where previously the record was 19.9 °C. Interestingly, we found that multistage systems can achieve equivalent temperature spans but at higher coefficients of performance compared to similarly-constructed single-stage systems.
ThSSim: A novel tool for simulation of reservoir thermal stratification
Authors: Noori Roohollah , Tian Fuqiang , Ni Guangheng , Bhattarai Rabin , Hooshyaripor Farhad , Klöve Bjön
Published: December 2019

This study presents a novel tool, ThSSim, for simulation of thermal stratification (ThS) in reservoirs. ThSSim is a simple and flexible reduced-order model-based the basis function (RMBF) that combines CE-QUAL-W2 (W2) and proper orthogonal decomposition (POD). In a case study, it was used to simulate water temperature in the Karkheh Reservoir (KR), Iran, for the period 2019–2035. ThSSim consists of two space- and time-dependent components that add predictive ability to the RMBF, a major refinement that extends its practical applications. Water temperature simulations by the W2 model at three-hour time intervals for the KR were used as input data to the POD model to develop ThSSim. To add predictive ability to ThSSim and considering that space-dependent components are not a function of time, we extrapolated the first three time-dependent components by September 30, 2035. We checked the predictive ability of ThSSim against water temperature profiles measured during eight sampling campaigns. We then applied ThSSim to simulate water temperature in the KR for 2019–2035. Simulated water temperature values matched well those measured and obtained by W2. ThSSim results showed an increasing trend for surface water temperature during the simulation period, with a reverse trend observed for water temperature in the bottom layers for three seasons (spring, summer and autumn). The results also indicated decreasing and increasing trends in onset and breakdown of thermal stability, respectively, so that the duration of ThS increased from 278 days in 2019 to 293 days in 2035. ThSSim is thus useful for reservoir temperature simulations. Moreover, the approach used to develop ThSSim is widely applicable to other fields of science and engineering.
Patient-specific Hemodynamics of Severe Carotid Artery Stenosis Before and After Endarterectomy Examined by 4D Flow MRI
Authors: Ko Seungbin , Lee Jeesoo , Song Simon , Kim Doosang , Lee Sang Hyung , Cho Jee-Hyun
Published: December 2019

Carotid endarterectomy (CEA) influences the carotid endoluminal anatomy, which results in hemodynamic changes before and after surgery. We investigated the hemodynamics of severe carotid artery stenosis before and after conventional endarterectomy with/without patch repair. An in vitro experiment utilizing carotid phantoms, which underwent a procedure that emulated CEA with/without the patch repair, was performed with a high-spatiotemporal resolution using 4D flow MRI. We evaluated an abnormal region of carotids, which consists of the normalized time-averaged wall shear stress (NTA|WSS|) and the oscillatory shear index (OSI), to account for continuous high-shear regions (high NTA|WSS| and low OSI) and chaotic low-shear regions, i.e., stenosis-prone regions (low NTA|WSS| and high OSI). The use of normalized hemodynamic parameters (e.g., NTA|WSS|) allowed comparison of diverse cases with different conditions of hemodynamics and vessel geometry. We observed that the stenosis-prone regions of the carotids with patches were noticeably larger than the corresponding regions in no-patch carotids. A large recirculating flow zone found in the stenosis-prone region of the internal carotid artery (ICA) of the postoperative carotids with patches partially blocks the flow path into ICA, and consequently the flow rate was not recovered after surgery unlike an expectation.
Reference gene screening of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans for quantitative real-time PCR studies
Authors: Verbrugghe Elin , Pasmans Frank , Martel An
Published: December 2019

Real-time quantitative PCR studies largely depend on reference genes for the normalization of gene expression. Stable reference genes should be accurately selected in order to obtain reliable results. We here present a study screening commonly used reference genes (TEF1F,α-centractin,Ctsyn1,GAPDH,R6046,APRTandTUB) in the chytrid fungiBatrachochytrium dendrobatidis(Bd) andBatrachochytrium salamandrivorans(Bsal), which cause the lethal amphibian skin disease chytridiomycosis. We evaluated the stability of the reference gene candidates during different growth stages of the fungi, using different statistical software packages: ΔCT, BestKeeper, GeNorm, NormFinder and RefFinder. In order to reflect thein vivosituation, the stability of the candidates was assessed when taking all growth stages into account. Using anex-vivoapproach, we tested whether the expression ofGAPDH,TUB,R6046andAPRT(Bd) andGAPDH,TUB,R6046andα-centractin(Bsal) remained stable when these fungi came in contact with host tissue. Finally, their role asin vivoreference genes was examined in skin tissue of experimentally infected midwife toads (Alytes obstetricans) (Bd) and fire salamanders (Salamandra salamandra) (Bsal). Summarized, the present study provides guidance for selecting appropriate reference genes when analyzing expression patterns of these fungal organisms during different growth stages and inBd- orBsal-infected tissues.
Trim33 (Tif1γ) is not required for skeletal muscle development or regeneration but suppresses cholecystokinin expression
Authors: Parks Cassie A. , Pak Katherine , Pinal-Fernandez Iago , Huang Wilson , Derfoul Assia , Mammen Andrew L.
Published: December 2019

The expression of Trim33 (Tif1γ) increases in skeletal muscles during regeneration and decreases upon maturation. Although Trim33 is required for the normal development of other tissues, its role in skeletal muscle is unknown. The current study aimed to define the role of Trim33 in muscle development and regeneration. We generated mice with muscle-specific conditional knockout of Trim33 by combining floxed Trim33 and Cre recombinase under the Pax7 promoter. Muscle regeneration was induced by injuring mouse muscles with cardiotoxin. We studied the consequences of Trim33 knockdown on viability, body weight, skeletal muscle histology, muscle regeneration, and gene expression. We also studied the effect of Trim33 silencing in satellite cells and the C2C12 mouse muscle cell line. Although Trim33 knockdown mice weighed less than control mice, their skeletal muscles were histologically unremarkable and regenerated normally following injury. Unexpectedly, RNAseq analysis revealed dramatically increased expression of cholecystokinin (CCK) in regenerating muscle from Trim33 knockout mice, satellite cells from Trim33 knockout mice, and C2C12 cells treated with Trim33 siRNA. Trim33 knockdown had no demonstrable effect on muscle differentiation or regeneration. However, Trim33 knockdown induced CCK expression in muscle, suggesting that suppression of CCK expression requires Trim33.
Murine xenograft bioreactors for human immunopeptidome discovery
Authors: Heather James M. , Myers Paisley T. , Shi Feng , Aziz-Zanjani Mohammad Ovais , Mahoney Keira E. , Perez Matthew , Morin Benjamin , Brittsan Christine , Shabanowitz Jeffrey , Hunt Donald F. , Cobbold Mark
Published: December 2019

The study of peptides presented by MHC class I and class II molecules is limited by the need for relatively large cell numbers, especially when studying post-translationally modified or otherwise rare peptide species. To overcome this problem, we pose the hypothesis that human cells grown as xenografts in immunodeficient mice should produce equivalent immunopeptidomes as cultured cells. Comparing human cell lines grown eitherin vitroor as murine xenografts, we show that the immunopeptidome is substantially preserved. Numerous features are shared across both sample types, including peptides and proteins featured, length distributions, and HLA-binding motifs. Peptides well-represented in both groups were from more abundant proteins, or those with stronger predicted HLA binding affinities. Samples grownin vivoalso recapitulated a similar phospho-immunopeptidome, with common sequences being those found at high copy number on the cell surface. These data indicate that xenografts are indeed a viable methodology for the production of cells for immunopeptidomic discovery.
Investigating the energy crisis in Alzheimer disease using transcriptome study
Authors: Dharshini S. Akila Parvathy , Taguchi Y.-h. , Gromiha M. Michael
Published: December 2019

Alzheimer disease (AD) is a devastating neurological disorder, which initiates from hippocampus and proliferates to cortical regions. The neurons of hippocampus require higher energy to preserve the firing pattern. In AD, aberrant energy metabolism is the critical factor for neurodegeneration. However, the reason for the energy crisis in hippocampus neurons is still unresolved. Transcriptome analysis enables us in understanding the underlying mechanism of energy crisis. In this study, we identified variants/differential gene/transcript expression profiles from hippocampus RNA-seq data. We predicted the effect of variants in transcription factor (TF) binding using in silico tools. Further, a hippocampus-specific co-expression and functional interaction network were designed to decipher the relationships between TF and differentially expressed genes (DG). Identified variants predominantly influence TF binding, which subsequently regulates the DG. From the results, we hypothesize that the loss of vascular integrity is the fundamental attribute for the energy crisis, which leads to neurodegeneration.
In Vitro Expansion of Keratinocytes on Human Dermal Fibroblast-Derived Matrix Retains Their Stem-Like Characteristics
Authors: Wong Chee-Wai , LeGrand Catherine F. , Kinnear Beverley F. , Sobota Radoslaw M. , Ramalingam Rajkumar , Dye Danielle E. , Raghunath Michael , Lane E. Birgitte , Coombe Deirdre R.
Published: December 2019

The long-term expansion of keratinocytes under conditions that avoid xenogeneic components (i.e. animal serum- and feeder cell-free) generally causes diminished proliferation and increased terminal differentiation. Here we present a culture system free of xenogeneic components that retains the self-renewal capacity of primary human keratinocytes. In vivo the extracellular matrix (ECM) of the tissue microenvironment has a major influence on a cell’s fate. We used ECM from human dermal fibroblasts, cultured under macromolecular crowding conditions to facilitate matrix deposition and organisation, in a xenogeneic-free keratinocyte expansion protocol. Phospholipase A2 decellularisation produced ECM whose components resembled the core matrix composition of natural dermis by proteome analyses. Keratinocytes proliferated rapidly on these matrices, retained their small size, expressed p63, lacked keratin 10 and rarely expressed keratin 16. The colony forming efficiency of these keratinocytes was enhanced over that of keratinocytes grown on collagen I, indicating that dermal fibroblast-derived matrices maintain the in vitro expansion of keratinocytes in a stem-like state. Keratinocyte sheets formed on such matrices were multi-layered with superior strength and stability compared to the single-layered sheets formed on collagen I. Thus, keratinocytes expanded using our xenogeneic-free protocol retained a stem-like state, but when triggered by confluence and calcium concentration, they stratified to produce epidermal sheets with a potential clinical use.
Tracing the mass flow from glucose and phenylalanine to pinoresinol and its glycosides in Phomopsis sp. XP-8 using stable isotope assisted TOF-MS
Authors: Zhang Yan , Shi Junling , Ni Yongqing , Liu Yanlin , Zhao Zhixia , Zhao Xixi , Gao Zhenhong
Published: December 2019

Phomopsis sp. XP-8, an endophytic fungus from the bark of Tu-Chung (Eucommia ulmoides Oliv) showed capability to biosynthesize pinoresinol (Pin) and pinoresinol diglucoside (PDG) from glucose (glu) and phenylalanine (Phe). To verify the mass flow in the biosynthesis pathway, [13C6]-labeled glu and [13C6]-labeled Phe were separately fed to the strain as sole substrates and [13C6]-labeled products were detected by ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry. As results, [13C6]-labeled Phe was incorporated into [13C6]-cinnamylic acid (Ca) and p-coumaric acid (p-Co), and [13C12]-labeled Pin, which revealed that the Pin benzene ring came from Phe via the phenylpropane pathway. [13C6]-Labeled Ca and p-Co, [13C12]-labeled Pin, [13C18]-labeled pinoresinol monoglucoside (PMG), and [13C18]-labeled PDG products were found when [13C6]-labeled glu was used, demonstrating that the benzene ring and glucoside of PDG originated from glu. It was also determined that PMG was not the direct precursor of PDG in the biosynthetic pathway. The study identified the occurrence of phenylalanine- lignan biosynthesis pathway in fungi at the level of mass flow.
Simulated CO2-induced ocean acidification for ocean in the East China: historical conditions since preindustrial time and future scenarios
Authors: Zhang Han , Wang Kuo
Published: December 2019

Since preindustrial times, as atmospheric CO2 concentration increases, the ocean continuously absorbs anthropogenic CO2, reducing seawater pH and $$[{{\rm{C}}{\rm{O}}}_{3}^{2-}]$$
[

C

O

3

2
−

]
, which is termed ocean acidification. We perform Earth system model simulations to assess CO2-induced acidification for ocean in the East China, one of the most vulnerable areas to ocean acidification. By year 2017, ocean surface pH in the East China drops from the preindustrial level of 8.20 to 8.06, corresponding to a 35% rise in [H+], and reduction rate of pH becomes faster in the last two decades. Changes in surface seawater acidity largely result from CO2-induced changes in surface dissolved inorganic carbon (DIC), alkalinity (ALK), salinity and temperature, among which DIC plays the most important role. By year 2300, simulated reduction in sea surface $$[{{\rm{C}}{\rm{O}}}_{3}^{2-}]$$
[

C

O

3

2
−

]
is 13% under RCP2.6, contrasted to 72% under RCP8.5. Furthermore, simulated results show that CO2-induced warming acts to mitigate reductions in $$[{{\rm{C}}{\rm{O}}}_{3}^{2-}]$$
[

C

O

3

2
−

]
, but the individual effect of oceanic CO2 uptake is much greater than the effect of CO2-induced warming on ocean acidification. Our study quantifies ocean acidification induced by anthropogenic CO2, and indicates the potentially important role of accelerated CO2 emissions in projections of future changes in biogeochemistry and ecosystem of ocean in the East China.
RAG-2 deficiency results in fewer phosphorylated histone H2AX foci, but increased retinal ganglion cell death and altered axonal growth
Authors: Álvarez-Lindo Noemí , Baleriola Jimena , de los Ríos Vivian , Suárez Teresa , de la Rosa Enrique J.
Published: December 2019

DNA double-strand breaks (DSBs), selectively visualized as γ-H2AX+ foci, occur during the development of the central nervous system, including the retina, although their origin and biological significance are poorly understood. Mutant mice with DSB repair mechanism defects exhibit increased numbers of γ-H2AX+ foci, increased cell death during neural development, and alterations in axonogenesis in the embryonic retina. The aim of this study was to identify putative sources of DSBs. One of the identified DSBs sources is LINE-1 retrotransposition. While we did not detect changes in LINE-1 DNA content during the early period of cell death associated with retinal neurogenesis, retinal development was altered in mice lacking RAG-2, a component of the RAG-1,2-complex responsible for initiating somatic recombination in lymphocytes. Although γ-H2AX+ foci were less abundant in the rag2−/− mouse retina, retinal ganglion cell death was increased and axonal growth and navigation were impaired in the RAG-2 deficient mice, a phenotype shared with mutant mice with defective DNA repair mechanisms. These findings demonstrate that RAG-2 is necessary for proper retinal development, and suggest that both DSB generation and repair are genuine processes intrinsic to neural development.
Emotion-related impulsivity moderates the cognitive interference effect of smartphone availability on working memory
Authors: Canale Natale , Vieno Alessio , Doro Mattia , Rosa Mineo Erika , Marino Claudia , Billieux Joël
Published: December 2019

Although recent studies suggest that the mere presence of a smartphone might negatively impact on working memory capacity, fluid intelligence, and attentional processes, less is known about the individual differences that are liable to moderate this cognitive interference effect. This study tested whether individual differences in emotion-related impulsivity traits (positive urgency and negative urgency) moderate the effect of smartphone availability on cognitive performance. We designed an experiment in which 132 college students (age 18–25 years) completed a laboratory task that assessed visual working memory capacity in three different conditions: two conditions differing in terms of smartphone availability (smartphone turned off and visible, smartphone in silent mode and visible) and a condition in which the smartphone was not available and was replaced by a calculator (control condition). Participants also completed self-reports that assessed their thoughts after the task performance, positive/negative urgency, and problematic smartphone use. The results showed that participants with higher positive urgency presented increased cognitive interference (reflected by poorer task performance) in the “silent-mode smartphone” condition compared with participants in the “turned-off smartphone” condition. The present study provides new insights into the psychological factors that explain how smartphone availability is liable to interfere with high-level cognitive processes.
Double-parabolic-reflectors acoustic waveguides for high-power medical ultrasound
Authors: Chen Kang , Irie Takasuke , Iijima Takashi , Morita Takeshi
Published: December 2019

High intensity focused ultrasound therapeutics are widely used to noninvasively treat various types of primary tumors and metastasis. However, ultrasound penetration depth is shallowed with increasing frequency which limits the therapeutic accuracy for deep tissues. Although acoustic waveguides are commonly inserted into tissue for localized therapy, powerful ultrasound delivery is difficult. Here, we invent double-parabolic-reflectors acoustic waveguides, where high-power ultrasound emission and large mechanical vibration enhance the therapeutic efficiency. High-energy-density ultrasound with around 20 times amplification by two parabolic reflectors propagates through the thin waveguide between 1 to 2 MHz, and wideband large mechanical vibration at the waveguide tip from 1 kHz to 2.5 MHz accelerates the therapeutics. This fundamental work serves as a milestone for future biomedical applications, from therapeutics to diagnostics. Since the high-power ability at high frequencies, our waveguide will also open up new research fields in medical, bio, physics and so on.
Cryo-Electron Microscopy Reveals That Sperm Modification Coincides with Female Fertility in the Mosquito Aedes aegypti
Authors: Noble Jade M. , Degner Ethan C. , Harrington Laura C. , Kourkoutis Lena F.
Published: December 2019

Manipulating mosquito reproduction is a promising approach to reducing mosquito populations and the burden of diseases they carry. A thorough understanding of reproductive processes is necessary to develop such strategies, but little is known about how sperm are processed and prepared for fertilization within female mosquitoes. By employing cryo-electron microscopy for the first time to study sperm of the mosquito Aedes aegypti, we reveal that sperm shed their entire outer coat, the glycocalyx, within 24 hours of being stored in the female. Motility assays demonstrate that as their glycocalyx is shed in the female’s sperm storage organs, sperm transition from a period of dormancy to rapid motility—a critical prerequisite for sperm to reach the egg. We also show that females gradually become fertile as sperm become motile, and that oviposition behavior increases sharply after females reach peak fertility. Together, these experiments demonstrate a striking coincidence of the timelines of several reproductive events in Ae. aegypti, suggesting a direct relationship between sperm modification and female reproductive capacity.
Vibrational communication between a myrmecophilous butterfly Spindasis lohita (Lepidoptera: Lycaenidae) and its host ant Crematogaster rogenhoferi (Hymenoptera: Formicidae)
Authors: Lin Yueh-Hsien , Liao Yi-Chang , Yang Chin-Cheng Scotty , Billen Johan , Yang Man-Miao , Hsu Yu-Feng
Published: December 2019

Ants are a dominant insect group in terrestrial ecosystems and many myrmecophilous species evolve to associate with ants to gain benefits. One iconic example is myrmecophilous butterflies that often produce ant-mimicking vibrational calls to modulate ant behaviors. Despite its popularity, empirical exploration of how butterflies utilize vibrational signals to communicate with ants is scarce. In this study, we reported that the myrmecophilous butterflySpindasis lohitaproduce three types of larval calls and one type of pupal call, while its tending ant,Crematogaster rogenhoferiemit a single type of call. The results of discriminant analysis revealed that calls of the two species are quantitatively similar in their signal attributes; the potential role of butterfly calls are further confirmed by the playback experiments in which certain ant behaviors including antennation, aggregation, and guarding were induced when one of the butterfly calls was played toC.rogenhoferiworkers. The findings in the current study represent the very first evidence on vibrational communication betweenSpindasisandCrematogasterand also imply thatS.lohitamay have been benefited from ant attendance due to the ability to produce similar calls of the antC.rogenhoferi.
General scaling in bidirectional flows of self-avoiding agents
Authors: Cristín Javier , Méndez Vicenç , Campos Daniel
Published: December 2019

The analysis of the classical radial distribution function of a system provides a possible procedure for uncovering interaction rules between individuals out of collective movement patterns. A formal extension of this approach has revealed recently the existence of a universal scaling in the collective spatial patterns of pedestrians, characterized by an effective potential of interaction $$V(\tau )$$V(τ) conveniently defined in the space of the times-to-collision $${\boldsymbol{\tau }}$$τ between the individuals. Here we significantly extend and clarify this idea by exploring numerically the emergence of that scaling for different scenarios. In particular, we compare the results of bidirectional flows when completely different rules of self-avoidance between individuals are assumed (from physical-like repulsive potentials to standard heuristic rules commonly used to reproduce pedestrians dynamics). We prove that all the situations lead to a common scaling in the t-space both in the disordered phase ($$V(\tau ) \sim {\tau }^{-2}$$V(τ)~τ−2) and in the lane-formation regime ($$V(\tau ) \sim {\tau }^{-1}$$V(τ)~τ−1), independent of the nature of the interactions considered. Our results thus suggest that these scalings cannot be interpreted as a proxy for how interactions between pedestrians actually occur, but they rather represent a common feature for bidirectional flows of self-avoiding agents.
A stochastic generative model of the World Trade Network
Authors: García-Algarra Javier , Mouronte-López Mary Luz , Galeano Javier
Published: December 2019

The World Trade Network (WTN) is a network of exchange flows among countries whose topological and statistical properties are a valuable source of information. Degree and strength (weighted degree) are key magnitudes to understand its structure and generative mechanisms. In this work, we describe a stochastic model that yields synthetic networks that closely mimic the properties of annual empirical data. The model combines two popular mechanisms of network generation: preferential attachment and multiplicative process. Agreement between empirical and synthetic networks is checked using the available series from 1962 to 2017.
Future large hydropower dams impact global freshwater megafauna
Authors: Zarfl Christiane , Berlekamp Jürgen , He Fengzhi , Jähnig Sonja C. , Darwall William , Tockner Klement
Published: December 2019

Dam construction comes with severe social, economic and ecological impacts. From an ecological point of view, habitat types are altered and biodiversity is lost. Thus, to identify areas that deserve major attention for conservation, existing and planned locations for (hydropower) dams were overlapped, at global extent, with the contemporary distribution of freshwater megafauna species with consideration of their respective threat status. Hydropower development will disproportionately impact areas of high freshwater megafauna richness in South America, South and East Asia, and the Balkan region. Sub-catchments with a high share of threatened species are considered to be most vulnerable; these are located in Central America, Southeast Asia and in the regions of the Black and Caspian Sea. Based on this approach, planned dam locations are classified according to their potential impact on freshwater megafauna species at different spatial scales, attention to potential conflicts between climate mitigation and biodiversity conservation are highlighted, and priorities for freshwater management are recommended.
Morpho-physiological and proteomic responses to water stress in two contrasting tobacco varieties
Authors: Chen Zheng , Xu Jiayang , Wang Fazhan , Wang Lin , Xu Zicheng
Published: December 2019

To gain insight into the molecular mechanisms underpinning tobacco (Nicotiana tabacum) tolerance to drought stress, we integrated anatomical, physiological, and proteomic analyses of drought-tolerant (Yuyan6, [Y6]) and -sensitive (Yunyan87 [Y87]) varieties. In comparison to Y87, Y6 exhibited higher water retention capability, improved photosynthetic performance, delayed leaf-senescence, stable leaf ultrastructure, a stronger antioxidant defense, and lesser ROS accumulation when subjected to water stress. Using an iTRAQ-based proteomics approach, 405 and 1,560 differentially accumulated proteins (DAPs) were identified from Y6 and Y87 plants, respectively, of which 114 were found to be present in both cultivars. A subsequent functional characterization analysis revealed that these DAPs were significantly enriched in eight biological processes, six molecular functions, and six cellular components and displayed differential expression patterns in Y6 and Y87 plants, suggesting that the response to water stress between both varieties differed at the proteomic level. Furthermore, we constructed protein coexpression networks and identified hub proteins regulating tobacco defenses to water stress. Additionally, qPCR analysis indicated that the majority of genes encoding selected proteins showed consistency between mRNA levels and their corresponding protein expression levels. Our results provide new insights into the genetic regulatory mechanisms associated with drought response in tobacco plants.
Author Correction: Tracing microplastics in aquatic environments based on sediment analogies
Authors: Enders Kristina , Käppler Andrea , Biniasch Oliver , Feldens Peter , Stollberg Nicole , Lange Xaver , Fischer Dieter , Eichhorn Klaus-Jochen , Pollehne Falk , Oberbeckmann Sonja , Labrenz Matthias
Published: December 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Dose-response of different dietary leucine levels on growth performance and amino acid metabolism in piglets differing for aminoadipate-semialdehyde synthase genotypes
Authors: Bertocchi Micol , Bosi Paolo , Luise Diana , Motta Vincenzo , Salvarani Chiara , Ribani Anisa , Bovo Samuele , Simongiovanni Aude , Matsunaga Keiko , Takimoto Tetsuya , Bannai Makoto , Corrent Etienne , Fontanesi Luca , Chalvon-Demersay Tristan , Trevisi Paolo
Published: December 2019

Dose-response studies of dietary leucine (Leu) in weaners are needed for a proper diet formulation. Dietary Leu effect was assessed in a 3-weeks dose-response trial with a 2 (genotype) x 5 (diets) factorial arrangement on one-hundred weaned pigs (9 to 20 kg body weight (BW)). Pigs differed for a polymorphism at the aminoadipate-semialdehyde synthase (AASS) gene, involved in lysine (Lys) metabolism. Pigs received experimental diets (d7 to d28) differing for the standardized ileal digestible (SID) Leu:Lys: 70%, 85%, 100%, 115%, 130%. Daily feed intake (ADFI), daily gain (ADG) and feed:gain (F:G) in all pigs and ADG and F:G in two classes of BW were analyzed using regression analysis with curvilinear-plateau (CLP) and linear quadratic function (LQ) models. Amino acid (AA) concentrations in plasma, liver, muscle and urine were determined. AASS genotype did not affect the parameters. Dietary Leu affected performance parameters, with a maximum response for ADG and F:G between 100.5% and 110.7% SID Leu:Lys, higher than the usually recommended one, and between 110.5% and 115.4% and between 94.9% and 110.2% SID Leu:Lys for ADG for light and heavy pigs respectively. AA variations in tissues highlighted Leu role in protein synthesis and its influence on the other branched chain AAs.
Genomic characterization of an emerging blaKPC-2 carrying Enterobacteriaceae clinical isolates in Thailand
Authors: Kerdsin Anusak , Deekae Saowarat , Chayangsu Sunee , Hatrongjit Rujirat , Chopjitt Peechanika , Takeuchi Dan , Akeda Yukihiro , Tomono Kazunori , Hamada Shigeyuki
Published: December 2019

The rapidly increasing prevalence of carbapenem-resistant Enterobacteriaceae (CRE) over the past decade has increased concern in healthcare facilities and the impact on public health. The prevalence of blaKPC (KPC) in Thailand remains very low; only blaKPC-13 has been described previously. This study is the first to describe the characteristics of blaKPC-2-carrying Klebsiella pneumoniae, Escherichia coli, and Enterobacter asburiae in Thailand. The prevalence rate of blaKPC-2-carrying isolates was 0.13% among CRE isolates in our study. Based on carbapenem susceptibility testing, K. pneumoniae C1985 was resistant to meropenem and ertapenem, E. coli C1992 was resistant to meropenem, imipenem, and ertapenem, and E. asburiae C2135 was only resistant to imipenem. K. pneumoniae C1985 carried blaKPC-2, blaSHV-11, fosA, oqxA, and oqxB, while E. coli C1992 contained blaKPC-2 and mdf(A) and E. asburiae C2135 harbored blaKPC-2, blaACT-2, and qnrE1. The genetic features of blaKPC-2 in the 3 isolates revealed identical rearrangement and flanking regions. Analysis of genomic sequences from these 3 isolates revealed that the sequence types of K. pneumoniae C1985, E. coli C1992, and E. asburiae C2135 were ST4008, ST7297, and ST1249, respectively. The 3 blaKPC-2 isolates were from individual living cases. Two cases were colonization for K. pneumoniae C1985 and E. asburiae C2135 and the third case was hospital-acquired infection of E. coli C1992. Although the prevalence of blaKPC-2-carrying CRE is relatively low in this study, continued surveillance and close monitoring are warranted. In addition, prompt or early detection of CRE and strict implementation of infection control are essential to prevent outbreaks or rapid spread in hospitals.
Author Correction: Sole coloration as an unusual aposematic signal in a Neotropical toad
Authors: Rößler Daniela C. , Lötters Stefan , Mappes Johanna , Valkonen Janne K. , Menin Marcelo , Lima Albertina P. , Pröhl Heike
Published: December 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
StructureDistiller: Structural relevance scoring identifies the most informative entries of a contact map
Authors: Bittrich Sebastian , Schroeder Michael , Labudde Dirk
Published: December 2019

Protein folding and structure prediction are two sides of the same coin. Contact maps and the related techniques of constraint-based structure reconstruction can be considered as unifying aspects of both processes. We present the Structural Relevance (SR) score which quantifies the information content of individual contacts and residues in the context of the whole native structure. The physical process of protein folding is commonly characterized with spatial and temporal resolution: some residues are Early Folding while others are Highly Stable with respect to unfolding events. We employ the proposed SR score to demonstrate that folding initiation and structure stabilization are subprocesses realized by distinct sets of residues. The example of cytochrome c is used to demonstrate how StructureDistiller identifies the most important contacts needed for correct protein folding. This shows that entries of a contact map are not equally relevant for structural integrity. The proposed StructureDistiller algorithm identifies contacts with the highest information content; these entries convey unique constraints not captured by other contacts. Identification of the most informative contacts effectively doubles resilience toward contacts which are not observed in the native contact map. Furthermore, this knowledge increases reconstruction fidelity on sparse contact maps significantly by 0.4 Å.
Differences in the diagnosis and management of pyriform sinus fistula between newborns and children
Authors: Sheng Qingfeng , Lv Zhibao , Xu Weijue , Liu Jiangbin
Published: December 2019

Pyriform sinus fistula (PSF) is a rare congenital entity. We hypothesized that clinical features, diagnosis and treatment may differ between newborns and children. 190 patients diagnosed with PSF were divided into two groups: neonatal (n = 15) and childhood (n = 175). The medical records including demographic and clinical data were retrospectively analyzed. There were 102 boys and 88 girls in this study. Most patients presented as a left-sided neck lesion. A neck mass, with or without infection and respiratory distress, was the common finding in newborn patients. Prenatal diagnosis was made in three cases. However, in childhood group, initial symptoms were neck abscess (78.8%), acute thyroiditis (11.4%), neck mass (6.9%), and thyroid lesion (2.8%). The presence of a cervical mass with air pocket showed on CT image was thought to be the pathognomonic finding of neonatal PSF. The diagnosis was usually established by barium esophagography in older children. Delayed accurate diagnosis was detected in both groups. The median time from onset to diagnosis was 22 months and 1 year respectively. Endoscopic-assisted open surgery was performed successfully in all patients, with good outcomes in majority cases of both groups (93.3% and 95.4%). Recurrence was developed in 5 patients. PSF should be suspected in newborns with cervical mass and in children with recurrent neck infection, especially on the left side. Early diagnosis and treatment might avoid repeated surgical procedures. Complete resection of the cyst and fistula in non-infected state is essential for good outcomes.
DNA methylation of a NF-κB binding site in the aquaporin 5 promoter impacts on mortality in sepsis
Authors: Rump Katharina , Unterberg Matthias , Dahlke Agnes , Nowak Hartmuth , Koos Björn , Bergmann Lars , Siffert Winfried , Schäfer Simon T. , Peters Jürgen , Adamzik Michael , Rahmel Tim
Published: December 2019

Altered aquaporin 5 (AQP5) expression in immune cells impacts on key mechanisms of inflammation and is associated with sepsis survival. Since epigenetic regulation via DNA methylation might contribute to a differential AQP5 expression in sepsis, we tested the hypotheses that DNA methylation of the AQP5 promotor (1) influences AQP5 expression, (2) is associated with the 30-day survival of septic patients, and (3) alters the nuclear transcription factor NF-κB binding. AQP5 mRNA expression was quantified by real-time PCR in whole blood samples of 135 septic patients. In silico computer analysis of the AQP5 promoter (nt-567 to nt-975) revealed seven putative inflammatory transcription factor binding sites and methylation of these sites was analyzed. Electrophoretic mobility shift assays were performed to assess the binding of nuclear NF-κB to the AQP5 promoter region nt-937. After adjustment for multiple testing, a greater methylation rate was found at cytosine site nt-937 in the AQP5 promoter linked to NF-κB binding in non-survivors compared to survivors (p = 0.002, padj = 0.014). This was associated with greater AQP5 mRNA expression in non-survivors (p = 0.037). Greater (≥16%) promoter methylation at nt-937 was also associated with an independently increased risk of death within 30 days (HR: 3.31; 95% CI: 1.54–6.23; p = 0.002). We detected a functionally important AQP5 promoter cytosine site (nt-937) linked to the binding of the inflammatorily acting nuclear transcription factor NF-κB, with increased methylation in sepsis non-survivors. Thus, nt-937 APQ5 promoter methylation, presumably related to NF-κB binding, is prognostically relevant in sepsis and demonstrates that epigenetic changes impact on sepsis outcome.