bluuebunny/crossref_metadata_2025 huggingface dataset:
Transforming activity of an oncoprotein-encoding circular RNA from human papillomavirus
Authors: Zhao Jiawei , Lee Eunice E. , Kim Jiwoong , Yang Rong , Chamseddin Bahir , Ni Chunyang , Gusho Elona , Xie Yang , Chiang Cheng-Ming , Buszczak Michael , Zhan Xiaowei , Laimins Laimonis , Wang Richard C.
Published: May 2019

Single-stranded circular RNAs (circRNAs), generated through ‘backsplicing’, occur more extensively than initially anticipated. The possible functions of the vast majority of circRNAs remain unknown. Virus-derived circRNAs have recently been described in gamma-herpesviruses. We report that oncogenic human papillomaviruses (HPVs) generate circRNAs, some of which encompass the E7 oncogene (circE7). HPV16 circE7 is detectable by both inverse RT-PCR and northern blotting of HPV16-transformed cells. CircE7 is N6-methyladenosine (m6A) modified, preferentially localized to the cytoplasm, associated with polysomes, and translated to produce E7 oncoprotein. Specific disruption of circE7 in CaSki cervical carcinoma cells reduces E7 protein levels and inhibits cancer cell growth both in vitro and in tumor xenografts. CircE7 is present in TCGA RNA-Seq data from HPV-positive cancers and in cell lines with only episomal HPVs. These results provide evidence that virus-derived, protein-encoding circular RNAs are biologically functional and linked to the transforming properties of some HPV.
Realization of high-efficiency fluorescent organic light-emitting diodes with low driving voltage
Authors: Salehi Amin , Dong Chen , Shin Dong-Hun , Zhu Liping , Papa Christopher , Thy Bui Anh , Castellano Felix N. , So Franky
Published: May 2019

It is commonly accepted that a full bandgap voltage is required to achieving efficient electroluminescence (EL) in organic light-emitting diodes. In this work, we demonstrated organic molecules with a large singlet-triplet splitting can achieve efficient EL at voltages below the bandgap voltage. The EL originates from delayed fluorescence due to triplet fusion. Finally, in spite of a lower quantum efficiency, a blue fluorescent organic light-emitting diode having a power efficiency higher than some of the best thermally activated delayed fluorescent and phosphorescent blue organic light-emitting diodes is demonstrated. The current findings suggest that leveraging triplet fusion from purely organic molecules in organic light-emitting diode materials offers an alternative route to achieve stable and high efficiency blue organic light-emitting diodes.
Collective cell migration and metastases induced by an epithelial-to-mesenchymal transition in Drosophila intestinal tumors
Authors: Campbell Kyra , Rossi Fabrizio , Adams Jamie , Pitsidianaki Ioanna , Barriga Francisco M. , Garcia-Gerique Laura , Batlle Eduard , Casanova Jordi , Casali Andreu
Published: May 2019

Metastasis underlies the majority of cancer-related deaths yet remains poorly understood due, in part, to the lack of models in vivo. Here we show that expression of the EMT master inducer Snail in primary adult Drosophila intestinal tumors leads to the dissemination of tumor cells and formation of macrometastases. Snail drives an EMT in tumor cells, which, although retaining some epithelial markers, subsequently break through the basal lamina of the midgut, undergo a collective migration and seed polyclonal metastases. While metastases re-epithelialize over time, we found that early metastases are remarkably mesenchymal, discarding the requirement for a mesenchymal-to-epithelial transition for early stages of metastatic growth. Our results demonstrate the formation of metastases in adult flies, and identify a key role for partial-EMTs in driving it. This model opens the door to investigate the basic mechanisms underlying metastasis, in a powerful in vivo system suited for rapid genetic and drug screens.
Atomic resolution electron microscopy in a magnetic field free environment
Authors: Shibata N. , Kohno Y. , Nakamura A. , Morishita S. , Seki T. , Kumamoto A. , Sawada H. , Matsumoto T. , Findlay S. D. , Ikuhara Y.
Published: May 2019

Atomic-resolution electron microscopes utilize high-power magnetic lenses to produce magnified images of the atomic details of matter. Doing so involves placing samples inside the magnetic objective lens, where magnetic fields of up to a few tesla are always exerted. This can largely alter, or even destroy, the magnetic and physical structures of interest. Here, we describe a newly developed magnetic objective lens system that realizes a magnetic field free environment at the sample position. Combined with a higher-order aberration corrector, we achieve direct, atom-resolved imaging with sub-Å spatial resolution with a residual magnetic field of less than 0.2 mT at the sample position. This capability enables direct atom-resolved imaging of magnetic materials such as silicon steels. Removing the need to subject samples to high magnetic field environments enables a new stage in atomic resolution electron microscopy that realizes direct, atomic-level observation of samples without unwanted high magnetic field effects.
Dynamics-dependent density distribution in active suspensions
Authors: Arlt Jochen , Martinez Vincent A. , Dawson Angela , Pilizota Teuta , Poon Wilson C. K.
Published: May 2019

Self-propelled colloids constitute an important class of intrinsically non-equilibrium matter. Typically, such a particle moves ballistically at short times, but eventually changes its orientation, and displays random-walk behaviour in the long-time limit. Theory predicts that if the velocity of non-interacting swimmers varies spatially in 1D, v(x), then their density ρ(x) satisfies ρ(x) = ρ(0)v(0)/v(x), where x = 0 is an arbitrary reference point. Such a dependence of steady-state ρ(x) on the particle dynamics, which was the qualitative basis of recent work demonstrating how to ‘paint’ with bacteria, is forbidden in thermal equilibrium. Here we verify this prediction quantitatively by constructing bacteria that swim with an intensity-dependent speed when illuminated and implementing spatially-resolved differential dynamic microscopy (sDDM) for quantitative analysis over millimeter length scales. Applying a spatial light pattern therefore creates a speed profile, along which we find that, indeed, ρ(x)v(x) = constant, provided that steady state is reached.
Contemporaneous 3D characterization of acute and chronic myocardial I/R injury and response
Authors: Merz Simon F. , Korste Sebastian , Bornemann Lea , Michel Lars , Stock Pia , Squire Anthony , Soun Camille , Engel Daniel R. , Detzer Julia , Lörchner Holger , Hermann Dirk M. , Kamler Markus , Klode Joachim , Hendgen-Cotta Ulrike B. , Rassaf Tienush , Gunzer Matthias , Totzeck Matthias
Published: May 2019

Cardioprotection by salvage of the infarct-affected myocardium is an unmet yet highly desired therapeutic goal. To develop new dedicated therapies, experimental myocardial ischemia/reperfusion (I/R) injury would require methods to simultaneously characterize extent and localization of the damage and the ensuing inflammatory responses in whole hearts over time. Here we present a three-dimensional (3D), simultaneous quantitative investigation of key I/R injury-components by combining bleaching-augmented solvent-based non-toxic clearing (BALANCE) using ethyl cinnamate (ECi) with light sheet fluorescence microscopy. This allows structural analyses of fluorescence-labeled I/R hearts with exceptional detail. We discover and 3D-quantify distinguishable acute and late vascular I/R damage zones. These contain highly localized and spatially structured neutrophil infiltrates that are modulated upon cardiac healing. Our model demonstrates that these characteristic I/R injury patterns can detect the extent of damage even days after the ischemic index event hence allowing the investigation of long-term recovery and remodeling processes.
Non-trivial surface states of samarium hexaboride at the (111) surface
Authors: Ohtsubo Yoshiyuki , Yamashita Yuki , Hagiwara Kenta , Ideta Shin-ichiro , Tanaka Kiyohisa , Yukawa Ryu , Horiba Koji , Kumigashira Hiroshi , Miyamoto Koji , Okuda Taichi , Hirano Wataru , Iga Fumitoshi , Kimura Shin-ichi
Published: May 2019

The peculiar metallic electronic states observed in the Kondo insulator, samarium hexaboride (SmB6), has stimulated considerable attention among those studying non-trivial electronic phenomena. However, experimental studies of these states have led to controversial conclusions mainly due to the difficulty and inhomogeneity of the SmB6 crystal surface. Here, we show the detailed electronic structure of SmB6 with angle-resolved photoelectron spectroscopy measurements of the three-fold (111) surface where only two inequivalent time-reversal-invariant momenta (TRIM) exist. We observe the metallic two-dimensional state was dispersed across the bulk Kondo gap. Its helical in-plane spin polarisation around the surface TRIM indicates that SmB6 is topologically non-trivial, according to the topological classification theory for weakly correlated systems. Based on these results, we propose a simple picture of the controversial topological classification of SmB6.
Homochirality in biomineral suprastructures induced by assembly of single-enantiomer amino acids from a nonracemic mixture
Authors: Jiang Wenge , Athanasiadou Dimitra , Zhang Shaodong , Demichelis Raffaella , Koziara Katarzyna B. , Raiteri Paolo , Nelea Valentin , Mi Wenbo , Ma Jun-An , Gale Julian D. , McKee Marc D.
Published: May 2019

Since Pasteur first successfully separated right-handed and left-handed tartrate crystals in 1848, the understanding of how homochirality is achieved from enantiomeric mixtures has long been incomplete. Here, we report on a chirality dominance effect where organized, three-dimensional homochiral suprastructures of the biomineral calcium carbonate (vaterite) can be induced from a mixed nonracemic amino acid system. Right-handed (counterclockwise) homochiral vaterite helicoids are induced when the amino acid l-Asp is in the majority, whereas left-handed (clockwise) homochiral morphology is induced when d-Asp is in the majority. Unexpectedly, the Asp that incorporates into the homochiral vaterite helicoids maintains the same enantiomer ratio as that of the initial growth solution, thus showing chirality transfer without chirality amplification. Changes in the degree of chirality of the vaterite helicoids are postulated to result from the extent of majority enantiomer assembly on the mineral surface. These mechanistic insights potentially have major implications for high-level advanced materials synthesis.
Moisture outgassing from siloxane elastomers containing surface-treated-silica fillers
Authors: Sharma Hom N. , Lenhardt Jeremy M. , Loui Albert , Allen Patrick G. , McLean William , Maxwell Robert S. , Dinh Long N.
Published: May 2019

The outgassing kinetics from siloxane elastomers is dominated by moisture desorption from the reinforcing silica filler and can be detrimental in moisture-sensitive applications. In this study, a custom 3D printable siloxane rubber (LL50) was analyzed in three different states: after a high temperature vacuum heat treatment, limited re-exposure to moisture after vacuum heat treatment, and in the as-received condition. The outgassing kinetics were extracted using isoconversional and iterative regression analyses. Moisture release by physisorbed and chemisorbed water from the samples have activation energies in the range of 50 kJ/mol (physisorbed type) to 220 kJ/mol (chemisorbed type). Overall, moisture outgassing from LL50 was 10 times lower than that from traditionally prepared siloxane rubbers. The vastly diminished moisture content in LL50 is attributed to the existence of a finite low level of silanol groups that remain on the fumed silica surface even after hydrophobic treatment.
Online Stress Measurement During Laser-aided Metallic Additive Manufacturing
Authors: Lu Yi , Sun Guifang , Xiao Xianfeng , Mazumder Jyoti
Published: May 2019

In situ measurement of residual stress is a challenge, and it is a source of many defects during additive manufacturing (AM). Usually, postmortem measurement is too late to save the product once a defect appears. Most of the existing technologies are predictive simulations and postmortem analysis. However, these technologies cannot directly reflect the stress evolution during the fabrication process. This paper introduces a computer vision-based stress monitoring system combined with finite element method (FEM) technology to estimate the stress development inside of the deposition layer. The system uses a CCD camera and a line laser beam to measure the height of the melt pool and solidified layer, forms a real-time FEM model, and uses the surface displacement between the two states to calculate the stress development during the solidification process. The results show that there is no obvious shape change after solidification. The shape of the melt pool and its solid state is similar. The stress distribution obtained through online monitoring is similar to that from the traditional thermal-stress simulation.
Morphological and molecular analysis of cryptic native and invasive freshwater snails in Chile
Authors: Collado Gonzalo A. , Vidal Marcela A. , Aguayo Karina P. , Méndez Marco A. , Valladares Moisés A. , Cabrera Francisco J. , Pastenes Luis , Gutiérrez Gregoric Diego E. , Puillandre Nicolas
Published: May 2019

Species delimitation in minute freshwater snails is often difficult to perform using solely shell morphology. The problem intensifies when invasive species spread within the distribution range of morphologically similar native species. In Chile, the Truncatelloidean snails are represented by the native genera Heleobia and Potamolithus plus the invasive mudsnail Potamopyrgus antipodarum, which can easily be confused. Using an integrative approach, we performed molecular phylogenetic analysis and studied reproductive and morphological features to identify superficially similar forms inhabiting the central area of the country. Truncatelloidean snails were identified in 40 of 51 localities sampled, 10 containing Potamopyrgus antipodarum, 23 Heleobia and 7 Potamolithus. Based on these results and previously published data, the known distribution of the mudsnail in Chile encompasses 6 hydrological basins, including 18 freshwater ecosystems. The finding of the mudsnails in several type localities of native species/subspecies of “Heleobia” that were not find in situ suggests species replacement or significant extinction of native fauna, a hypothesis supported by the restudy of type material that shows that endemic forms belong to the genus Potamolithus. This study shows the usefulness of integrative taxonomy not only resolving complex taxa with cryptic morphology but also measuring the extent of an ongoing invasion.
Exploratory Gene Ontology Analysis with Interactive Visualization
Authors: Zhu Junjie , Zhao Qian , Katsevich Eugene , Sabatti Chiara
Published: May 2019

The Gene Ontology (GO) is a central resource for functional-genomics research. Scientists rely on the functional annotations in the GO for hypothesis generation and couple it with high-throughput biological data to enhance interpretation of results. At the same time, the sheer number of concepts (>30,000) and relationships (>70,000) presents a challenge: it can be difficult to draw a comprehensive picture of how certain concepts of interest might relate with the rest of the ontology structure. Here we present new visualization strategies to facilitate the exploration and use of the information in the GO. We rely on novel graphical display and software architecture that allow significant interaction. To illustrate the potential of our strategies, we provide examples from high-throughput genomic analyses, including chromatin immunoprecipitation experiments and genome-wide association studies. The scientist can also use our visualizations to identify gene sets that likely experience coordinated changes in their expression and use them to simulate biologically-grounded single cell RNA sequencing data, or conduct power studies for differential gene expression studies using our built-in pipeline. Our software and documentation are available at http://aegis.stanford.edu.
Territory location and quality, together with climate, affect the timing of breeding in the white-throated dipper
Authors: Nilsson A. L. K. , Slagsvold T. , Røstad O. W. , Knudsen E. , Jerstad K. , Cadahía L. , Reitan T. , Helberg M. , Walseng B. , Stenseth N. C.
Published: May 2019

Recent climate change has led to advanced spring phenology in many temperate regions. The phenological response to variation in the local environment, such as the habitat characteristics of the territories birds occupy, is less clear. The aim of this study is to understand how ecological conditions affect breeding time, and its consequences for reproduction, in a white-throated dipper Cinclus cinclus population in a river system in Norway during 34 years (1978–2011). Hatching date advanced almost nine days, indicating a response to higher temperatures and the advanced phenology in the area. Earlier breeding was found in warm springs and at lower altitudes. High population density facilitated earlier breeding close to the coast. Furthermore, when population density was low, breeding was early at territories that were rarely occupied, while in years with high density, breeding was early at territories that were frequently occupied. Also, when population density was low, earlier breeding occurred at territories that on average produced more offspring than other territories, while there was no difference in breeding time in high population years. Selection for early breeding was dependent on spring temperatures and high spring temperatures contributed to higher breeding success during the study period. We found that breeding phenology may have strong effects on fitness in the white-throated dipper, and thus that breeding time is an important ecological factor in a species that feeds mainly on aquatic rather than terrestrial prey.
Runx1 contributes to articular cartilage maintenance by enhancement of cartilage matrix production and suppression of hypertrophic differentiation
Authors: Yano Fumiko , Ohba Shinsuke , Murahashi Yasutaka , Tanaka Sakae , Saito Taku , Chung Ung-il
Published: May 2019

Osteoarthritis (OA) results from an imbalance of the dynamic equilibrium between the breakdown and repair of joint tissues. Previously, we reported that Runx1 enhanced chondrogenic differentiation through transcriptional induction ofCOL2A1, and suppressed hypertrophic differentiation. Here, we investigated the involvement of Runx1 in OA development as well as its potential underlying molecular mechanism. When we analysed OA development inCol2a1-Cre;Runx1fl/flandRunx1fl/flmice by surgically inducing joint instability, Cartilage degradation and osteophyte formation ofCol2a1-Cre;Runx1fl/fljoints was accelerated compared with joints inRunx1fl/flanimals 8 weeks after surgery. To investigate chondrocyte regulation by Runx1, we analysed interactions with co-factors and downstream molecules. Runx1 enhanced cartilage matrix production in cooperation with Sox5, Sox6, and Sox9, and co-immunoprecipitation assays showed protein–protein binding between Runx1 and each Sox protein. Knockdown of Runx1 increased expression of a hypertrophic marker, Co10a1, in mouse articular cartilage and primary chondrocytes. This expression was accompanied by decreased expression of Bapx1, a potent suppressor of hypertrophic differentiation. Notably, Runx1-induced suppression of hypertrophic differentiation was diminished by siRNA silencing ofBapx1, whereas chondrogenic markers were unaltered. Thus, Runx1 contributes to articular cartilage maintenance by enhancing matrix production in cooperation with Sox proteins, and suppressing hypertrophic differentiation at least partly via Bapx1 induction.
Transcriptional profiling of coaggregation interactions between Streptococcus gordonii and Veillonella parvula by Dual RNA-Seq
Authors: Mutha Naresh V. R. , Mohammed Waleed K. , Krasnogor Natalio , Tan Geok Y. A. , Wee Wei Yee , Li Yongming , Choo Siew Woh , Jakubovics Nicholas S.
Published: May 2019

Many oral bacteria form macroscopic clumps known as coaggregates when mixed with a different species. It is thought that these cell-cell interactions are critical for the formation of mixed-species biofilms such as dental plaque. Here, we assessed the impact of coaggregation between two key initial colonizers of dental plaque, Streptococcus gordonii and Veillonella parvula, on gene expression in each partner. These species were shown to coaggregate in buffer or human saliva. To monitor gene regulation, coaggregates were formed in human saliva and, after 30 minutes, whole-transcriptomes were extracted for sequencing and Dual RNA-Seq analysis. In total, 272 genes were regulated in V. parvula, including 39 genes in oxidoreductase processes. In S. gordonii, there was a high degree of inter-sample variation. Nevertheless, 69 genes were identified as potentially regulated by coaggregation, including two phosphotransferase system transporters and several other genes involved in carbohydrate metabolism. Overall, these data indicate that responses of V. parvula to coaggregation with S. gordonii are dominated by oxidative stress-related processes, whereas S. gordonii responses are more focussed on carbohydrate metabolism. We hypothesize that these responses may reflect changes in the local microenvironment in biofilms when S. gordonii or V. parvula immigrate into the system.
Co-overexpression of AVP1 and OsSIZ1 in Arabidopsis substantially enhances plant tolerance to drought, salt, and heat stresses
Authors: Esmaeili Nardana , Yang Xiaojie , Cai Yifan , Sun Li , Zhu Xunlu , Shen Guoxin , Payton Paxton , Fang Weiping , Zhang Hong
Published: May 2019

Abiotic stresses such as water deficit, salt, and heat are major environmental factors that negatively affect plant growth, development, and productivity. Previous studies showed that overexpression of the Arabidopsis vacuolar H+-pyrophosphatase gene AVP1 increases salt and water deficit stress tolerance and overexpression of the rice SUMO E3 ligase gene OsSIZ1 improves heat and water deficit stress tolerance in transgenic plants. In this report, the effects of co-overexpression of AVP1 and OsSIZ1 in Arabidopsis on abiotic stress tolerance were studied. It was found that AVP1/OsSIZ1 co-overexpressing plants performed significantly better than AVP1-overexpressing plants and OsSIZ1-overexpressing plants, and produced 100% more seed than wild-type plants under single stress or multiple stress conditions. The increased stress tolerance in AVP1/OsSIZ1 co-overexpressing plants was substantially larger than the increased stress tolerance in AVP1-overexpressing plants and OsSIZ1-overexpressing plants under every abiotic stress condition tested. This research provides the proof-of-concept that crop yields might be substantially improved using this approach.
Visualization of junctional epithelial cell replacement by oral gingival epithelial cells over a life time and after gingivectomy
Authors: Kato Mayu , Tanaka Junichi , Aizawa Ryo , Yajima-Himuro Sara , Seki Tatsuaki , Tanaka Keisuke , Yamada Atsushi , Ogawa Miho , Kamijo Ryutaro , Tsuji Takashi , Mishima Kenji , Yamamoto Matsuo
Published: May 2019

Junctional epithelium (JE), which is derived from odontogenic epithelial cells immediately after eruption, is believed to be gradually replaced by oral gingival epithelium (OGE) over a lifetime. However, the detailed process of replacement remains unclear. The aim of the present study was to clarify the process of JE replacement by OGE cells using a green fluorescent protein (GFP)–positive tooth germ transplantation method. GFP-positive JE was partly replaced by OGE cells and completely replaced on day 200 after transplantation, whereas there was no difference in the expression of integrin β4 (Itgb4) and laminin 5 (Lama5) between JE before and after replacement by OGE cells. Next, GFP-positive JE was partially resected. On day 14 after resection, the regenerated JE consisted of GFP-negative cells and also expressed both Itgb4 and Lama5. In addition, the gene expression profile of JE derived from odontogenic epithelium before gingivectomy was partly different from that of JE derived from OGE after gingivectomy. These results suggest that JE derived from the odontogenic epithelium is gradually replaced by OGE cells over time and JE derived from the odontogenic epithelium might have specific characteristics different to those of JE derived from OGE.
Identification and first characterization of DinJ-YafQ toxin-antitoxin systems in Lactobacillus species of biotechnological interest
Authors: Ferrari Alberto , Maggi Stefano , Montanini Barbara , Levante Alessia , Lazzi Camilla , Yamaguchi Yoshihiro , Rivetti Claudio , Folli Claudia
Published: May 2019

DinJ-YafQ is a type II TA system comprising the ribosome-dependent RNase YafQ toxin and the DinJ antitoxin protein. Although the module has been extensively characterized in Escherichia coli, little information is available for homologous systems in lactic acid bacteria. In this study, we employed bioinformatics tools to identify DinJ-YafQ systems in Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus species, commonly used in biotechnological processes. Among a total of nineteen systems found, two TA modules from Lactobacillus paracasei and two modules from Lactobacillus rhamnosus wild strains were isolated and their activity was verified by growth assays in Escherichia coli either in liquid and solid media. The RNase activity of the YafQ toxins was verified in vivo by probing mRNA dynamics and metabolism with single-cell Thioflavin T fluorescence. Our findings demonstrate that, albeit DinJ-YafQ TA systems are widely distributed in lactic acid bacteria, only few are fully functional, while others have lost toxicity even though they maintain high sequence identity with wild type YafQ and a likely functional antitoxin protein.
Spatially explicit analysis reveals complex human genetic gradients in the Iberian Peninsula
Authors: Pimenta João , Lopes Alexandra M. , Carracedo Angel , Arenas Miguel , Amorim António , Comas David
Published: May 2019

The Iberian Peninsula is a well-delimited geographic region with a rich and complex human history. However, the causes of its genetic structure and past migratory dynamics are not yet fully understood. In order to shed light on them, here we evaluated the gene flow and genetic structure throughout the Iberian Peninsula with spatially explicit modelling applied to a georeferenced genetic dataset composed of genome-wide SNPs from 746 individuals belonging to 17 different regions of the Peninsula. We found contrasting patterns of genetic structure throughout Iberia. In particular, we identified strong patterns of genetic differentiation caused by relevant barriers to gene flow in northern regions and, on the other hand, a large genetic similarity in central and southern regions. In addition, our results showed a preferential north to south migratory dynamics and suggest a sex-biased dispersal in Mediterranean and southern regions. The estimated genetic patterns did not fit with the geographical relief of the Iberian landscape and they rather seem to follow political and linguistic territorial boundaries.
Urinary peptide panel for prognostic assessment of bladder cancer relapse
Authors: Krochmal Magdalena , van Kessel Kim E. M. , Zwarthoff Ellen C. , Belczacka Iwona , Pejchinovski Martin , Vlahou Antonia , Mischak Harald , Frantzi Maria
Published: May 2019

Non-invasive tools stratifying bladder cancer (BC) patients according to the risk of relapse are urgently needed to guide clinical intervention. As a follow-up to the previously published study on CE-MS-based urinary biomarkers for BC detection and recurrence monitoring, we expanded the investigation towards BC patients with longitudinal data. Profiling datasets of BC patients with follow-up information regarding the relapse status were investigated. The peptidomics dataset (n = 98) was split into training and test set. Cox regression was utilized for feature selection in the training set. Investigation of the entire training set at the single peptide level revealed 36 peptides being strong independent prognostic markers of disease relapse. Those features were further integrated into a Random Forest-based model evaluating the risk of relapse for BC patients. Performance of the model was assessed in the test cohort, showing high significance in BC relapse prognosis [HR = 5.76, p-value = 0.0001, c-index = 0.64]. Urinary peptide profiles integrated into a prognostic model allow for quantitative risk assessment of BC relapse highlighting the need for its incorporation in prospective studies to establish its value in the clinical management of BC.
GABA (γ-aminobutyric acid), as a thermo-protectant, to improve the reproductive function of heat-stressed mungbean plants
Authors: Priya Manu , Sharma Lomeshwar , Kaur Ramanpreet , Bindumadhava H. , Nair Ramkrishnan M. , Siddique K. H. M. , Nayyar Harsh
Published: May 2019

Rising global temperatures are proving to be detrimental for the agriculture. Hence, strategies are needed to induce thermotolerance in food crops to sustain the food production. GABA (γ-aminobutyric acid), a non-protein amino acid, can partially protect plants from high-temperature stress. This study hypothesises that declining GABA concentrations in the cells of heat-stressed mungbean plants increases the heat-sensitivity of reproductive function. Mungbean plants were grown in a natural, outdoor environment (29.3/16.1 ± 1 °C as mean day/night temperature, 1350–1550 µmol m−2 s−1 light intensity, 60–65% as mean relative humidity) until the start of the reproductive stage. Subsequently, two temperature treatments were imposed in a controlled environment—control (35/23 °C) and heat stress (45/28 °C)—at about 800 µmol m−2 s−1 light intensity and 65–70% as mean relative humidity, until pod maturity. In heat-stressed (HS) plants, endogenous GABA concentrations in leaf and anther samples had declined by 49 and 60%, respectively, and to a much lesser degree in the plants, exogenously supplemented with 1 mM GABA. The reproductive function of GABA-treated heat-stressed plants improved significantly in terms of pollen germination, pollen viability, stigma receptivity and ovule viability, compared to untreated HS controls. In addition, GABA-treated heat-stressed plants had less damage to membranes, photosynthetic machinery (chlorophyll concentration, chlorophyll fluorescence, RuBisCO activity were functionally normal) and carbon assimilation (sucrose synthesis and its utilisation) than the untreated HS controls. Leaf water status improved significantly with GABA application, including enhanced accumulation of osmolytes such as proline and trehalose due to increase in the activities of their biosynthetic enzymes. GABA-treated heat-stressed plants produced more pods (28%) and seed weight (27%) plant−1 than the untreated controls. This study is the first to report the involvement of GABA in protecting reproductive function in mungbean under heat stress, as a result of improved leaf turgor, carbon fixation and assimilation processes, through the augmentation of several enzymes related to these physiological processes.
Direct observation of vacuum arc evolution with nanosecond resolution
Authors: Zhou Zhipeng , Kyritsakis Andreas , Wang Zhenxing , Li Yi , Geng Yingsan , Djurabekova Flyura
Published: May 2019

Sufficiently high voltage applied between two metal electrodes, even in ultra high vacuum conditions, results in an inevitable discharge that lights up the entire gap, opening a conductive channel through the vacuum and parasitically consuming large amounts of energy. Despite many efforts to understand the processes that lead to this phenomenon, known as vacuum arc, there is still no consensus regarding the role of each electrode in the evolution of such a momentous process as lightning. Employing a high-speed camera, we capture the entire lightning process step-by-step with a nanosecond resolution and find which of the two electrodes holds the main responsibility for igniting the arc. The light that gradually expands from the positively charged electrode (anode), often is assumed to play the main role in the formation of a vacuum arc. However, both the nanosecond-resolution images of vacuum arc evolution and the corresponding theoretical calculations agree that the conductive channel between the electrodes is built in the form of cathodic plasma long before any significant activity develops in the anode. We show evidently that the anode illumination is weaker and plays a minor role in igniting and maintaining the conductive channel.
Improving the homogeneity of diffraction based colours by fabricating periodic patterns with gradient spatial period using Direct Laser Interference Patterning
Authors: Voisiat Bogdan , Wang Wei , Holzhey Max , Lasagni Andrés Fabián
Published: May 2019

This study focuses on the development of a strategy to produce periodic structures with a variable spatial period for increasing the homogeneity of structural colours by means of direct laser interference patterning. Using a four-beam interference configuration, hole-like periodic arrays are produced on stainless steel with a 70 ps pulsed laser source operating at 532 nm laser wavelength. The laser processing parameters are optimised for obtaining patterns with the highest possible diffraction efficiency and thus showing the highest possible colour intensity. A model for calculating the required spatial period to obtain a defined colour under specific conditions of illumination and observation angles is presented. A very good agreement between the captured structural colour spectrum and the real visible spectrum of light was obtained. In addition, a strategy for mixing holographic colours, in particular for obtaining the white colour is developed. Finally, the developed model is successfully integrated into machine software, in order to automatically process images that exhibit required colours at certain viewing conditions. The produced patterns are characterised using confocal microscopy and the efficiency of the first diffraction order was measured by optical spectroscopy.
Spin-dependent scattering induced negative magnetoresistance in topological insulator Bi2Te3 nanowires
Authors: Bhattacharyya Biplab , Singh Bahadur , Aloysius R. P. , Yadav Reena , Su Chenliang , Lin Hsin , Auluck S. , Gupta Anurag , Senguttuvan T. D. , Husale Sudhir
Published: May 2019

Studies of negative magnetoresistance in novel materials have recently been in the forefront of spintronic research. Here, we report an experimental observation of the temperature dependent negative magnetoresistance in Bi2Te3 topological insulator (TI) nanowires at ultralow temperatures (20 mK). We find a crossover from negative to positive magnetoresistance while increasing temperature under longitudinal magnetic field. We observe a large negative magnetoresistance which reaches −22% at 8 T. The interplay between negative and positive magnetoresistance can be understood in terms of the competition between dephasing and spin-orbit scattering time scales. Based on the first-principles calculations within a density functional theory framework, we demonstrate that disorder (substitutional) by Ga+ ion milling process, which is used to fabricate nanowires, induces local magnetic moments in Bi2Te3 crystal that can lead to spin-dependent scattering of surface and bulk electrons. These experimental findings show a significant advance in the nanoscale spintronics applications based on longitudinal magnetoresistance in TIs. Our experimental results of large negative longitudinal magnetoresistance in 3D TIs further indicate that axial anomaly is a universal phenomenon in generic 3D metals.
Defect-induced ultimately fast volume phonon-polaritons in the wurtzite Zn0.74Mg0.26Se mixed crystal
Authors: Dicko H. , Pagès O. , Shoker M. B. , Firszt F. , Strzałkowski K. , Maillard A. , Polian A. , Battie Y. , Broch L. , En Naciri A. , Postnikov A. V. , Paszkowicz W. , Itié J.-P.
Published: May 2019

Volume-phonon-polaritons (VPP’s) propagating at a light-in-vacuum-like speed are identified in the wurtzite-type Zn0.74Mg0.26Se mixed crystal by near-forward Raman scattering. Their detection is selective to both the laser energy and the laser polarization, depending on whether the ordinary (n0) or extraordinary (ne) refractive index is addressed. Yet, no significant linear birefringence (n0 $${\boldsymbol{\simeq }}$$≃ ne) is observed by ellipsometry. The current access to ultrafastVPP’s is attributed to the quasi-resonant Raman probing of an anomalous dispersion ofn0due to impurity levels created deep in the optical band gap by oriented structural defects. The resonance conditions are evidenced by a dramatic enhancement of the Raman signals due to the polar modes. Hence, this work reveals a capacity for the lattice defects’ engineering to “accelerate” theVPP’s of a mixed crystal up to light-in-vacuum-like speeds. This is attractive for ultrafast signal processing in the terahertz range. On the fundamental side we provide an insight into theVPP’s created by alloying ultimately close to the center of the Brillouin zone.
An optimal BMI range associated with a lower risk of mortality among HIV-infected adults initiating antiretroviral therapy in Guangxi, China
Authors: Jiang Junjun , Qin Xionglin , Liu Huifang , Meng Sirun , Abdullah Abu S. , Huang Jinping , Qin Chunwei , Liu Yanfen , Huang Yunxuan , Qin Fengxiang , Huang Jiegang , Zang Ning , Liang Bingyu , Ning Chuanyi , Liao Yanyan , Liang Hao , Wu Fengyao , Ye Li
Published: May 2019

Previous studies investigating HIV-infected patients suggested a direct link between underweight and the mortality rate of AIDS. However, there was a lack of evidence showing the optimal range of initial body mass index (BMI) patients maintain during antiretroviral therapy (ART). We aimed to evaluate associations of the BMI values pre-ART and during the entire ART duration with mortality among HIV-positive individuals. In total, 5101 HIV/AIDS patients, including 1439 (28.2%) underweight, 3047 (59.7%) normal-weight, 548 (10.7%) overweight and 67 (1.3%) obese patients, were included in this cohort. The cumulative mortality of underweight, normal-weight, and overweight were 2.4/100 person-years (95% CI 1.9–2.9), 1.1/100 person-years (95% CI 0.9–1.3), and 0.5/100 person-years (95% CI 0.1–0.9), respectively. Cumulative mortality was lower in both the normal-weight and overweight populations than in the underweight population, with an adjusted hazard ratio (AHR) of 0.5 (95% CI 0.4–0.7, p < 0.001) and 0.3 (95% CI 0.1–0.6, p = 0.002), respectively. Additionally, in the 1176 patients with available viral load data, there was significant difference between the underweight and normal-weight groups after adjustment for all factors, including viral load (p = 0.031). This result suggests that HIV-infected patients in Guangxi maintaining a BMI of 19–28 kg/m2, especially 24–28 kg/m2, have a reduced risk of death.
Non-Monotonic Aerosol Effect on Precipitation in Convective Clouds over Tropical Oceans
Authors: Liu Huan , Guo Jianping , Koren Ilan , Altaratz Orit , Dagan Guy , Wang Yuan , Jiang Jonathan H. , Zhai Panmao , Yung Yuk L.
Published: May 2019

Aerosol effects on convective clouds and associated precipitation constitute an important open-ended question in climate research. Previous studies have linked an increase in aerosol concentration to a delay in the onset of rain, invigorated clouds and stronger rain rates. Here, using observational data, we show that the aerosol effect on convective clouds shifts from invigoration to suppression with increasing aerosol optical depth. We explain this shift in trend (using a cloud model) as the result of a competition between two types of microphysical processes: cloud-core-based invigorating processes vs. peripheral suppressive processes. We show that the aerosol optical depth value that marks the shift between invigoration and suppression depends on the environmental thermodynamic conditions. These findings can aid in better parameterizing aerosol effects in climate models for the prediction of climate trends.
Enhanced auditory disembedding in an interleaved melody recognition test is associated with absolute pitch ability
Authors: Wenhart Teresa , Hwang Ye-Young , Altenmüller Eckart
Published: May 2019

Absolute pitch (AP) and autism have recently been associated with each other. Neurocognitive theories of autism could perhaps explain this co-occurrence. This study investigates whether AP musicians show an advantage in an interleaved melody recognition task (IMRT), an auditory version of an embedded figures test often investigated in autism with respect to the these theories. A total of N = 59 professional musicians (AP = 27) participated in the study. In each trial a probe melody was followed by an interleaved sequence. Participants had to indicate as to whether the probe melody was present in the interleaved sequence. Sensitivity index d′ and response bias c were calculated according to signal detection theory. Additionally, a pitch adjustment test measuring fine-graded differences in absolute pitch proficiency, the Autism-Spectrum-Quotient and a visual embedded figures test were conducted. AP outperformed relative pitch (RP) possessors on the overall IMRT and the fully interleaved condition. AP proficiency, visual disembedding and musicality predicted 39.2% of variance in the IMRT. No correlations were found between IMRT and autistic traits. Results are in line with a detailed-oriented cognitive style and enhanced perceptional functioning of AP musicians similar to that observed in autism.
Variable protein homeostasis in housekeeping and non-housekeeping pathways under mycotoxins stress
Authors: Sun Yu , Wen Jikai , Chen Ruohong , Deng Yiqun
Published: May 2019

Transcript levels are the primary factor determining protein levels, but for the majority of genes, fold changes in transcript levels are larger than the corresponding changes in protein levels, a phenomenon that is termed “protein homeostasis”. However, this phenomenon is not well characterized in the context of environmental changes. In this study, we sequenced the entire transcriptome and proteome of chicken primary hepatocytes administered three mycotoxin treatments Aflatoxin B1 (AFB1), Ochoratoxin A (OTA) and Zearalenone (ZEN). Each mycotoxin induced unique set of differential expressed transcripts and proteins, suggesting variable cytotoxicity and biochemical action in cell. We found a weak positive correlation between transcript and protein changes, and the transcript changes were higher than the protein changes. Furthermore, we observed pathway-specific protein homeostasis pattern under mycotoxin stress. Specifically, the “Metabolism”, “Transcription” and “Translation” pathways (housekeeping pathways) showed lower fold changes in protein/mRNA levels than non-housekeeping pathways such as “Cell growth and death” and “Immune system”. Protein molecular weight had a weak negative effect on protein production, and this effect was stronger for non-housekeeping pathways. Overall, we hypothesize housekeeping pathways maintain stable protein production for baseline cellular function, whereas non-housekeeping pathways is associated with the fitness response to environmental stress.
Vitamin D Receptor gene polymorphisms and plasma levels are associated with lumbar disc degeneration
Authors: Yang Qinghua , Liu Yang , Guan Yewen , Zhan Xinli , Xiao Zengming , Jiang Hua , Wei Qingjun
Published: May 2019

The purpose of this study was to investigate the association of Vitamin D Receptor (VDR) gene polymorphisms and VDR levels with lumbar disc degeneration (LDD). TaqMan SNP Genotyping Assay was utilized to probe VDR gene polymorphisms including the FokI (rs2228570), ApaI (rs7975232) and TaqI (rs731236) in 454 patients with LDD and 485 controls. Enzyme-Linked Immunosorbent Assay (ELISA) was used to detect plasma VDR levels. The patients with LDD were divided into three subgroups (subgroup 1: lumbar disc herniation; subgroup 2: lumbar spinal stenosis; subgroup 3: lumbar spondylolisthesis) to further probe the association of plasma VDR levels and VDR gene polymorphisms and LDD. Moreover, immunohistochemistry (IHC) was implemented to evaluate VDR expression in lumbar degenerated disc and normal disc. Allele and genotype frequency of TaqI (rs731236) were significantly different in patients with LDD and controls (all P < 0.05). For TaqI polymorphism, the frequencies of T allele were significantly higher in the LDD patients compared with controls (OR = 1.319; 95%CI 1.091 to 1.595; P = 0.004, adjusted (OR = 1.319; 95%CI 1.091 to 1.595; P = 0.004, adjusted OR = 1.383; 95%CI 1.135 to 1.684; P = 0.016). Furthermore, the allele distribution showed a higher frequency of the T allele in the patients with lumbar disc herniation in subgroup 1 (OR = 1.384; 95% CI 1.105 to 1.732; P = 0.004, adjusted OR = 1.319; 95%CI 1.091 to 1.595; P = 0.016). Plasma VDR levels and VDR expression were significantly lower in patients with LDD compared with controls (all P < 0.05). Moreover, the TT genotype of TaqI polymorphism was significantly associated with lower plasma VDR levels in patients with LDD (P = 0.002). TaqI (rs731236) polymorphism was associated with a predisposition to LDD. Plasma VDR and VDR expression levels may be the marker for the occurrence and development of LDD.
Fano Metamaterials on Nanopedestals for Plasmon-Enhanced Infrared Spectroscopy
Authors: Jung Yongseok , Hwang Inyong , Yu Jaeyeon , Lee Jihye , Choi Jun-Hyuk , Jeong Jun-Ho , Jung Joo-Yun , Lee Jongwon
Published: May 2019

We report a sensing platform for surface-enhanced infrared absorption (SEIRA) spectroscopy, based on Fano metamaterials (FMMs) on dielectric nanopedestals. FMMs consist of two parallel gold (Au) nanorod antennas, with a small horizontal coupler attached to one of the nanorod antenna. When placed on SiO2 dielectric nanopedestals, which exhibit strong field enhancements caused by the interference between subradiant and superradiant plasmonic resonances, they provide the highly enhanced E-field intensities formed near the Au nanoantenna, which can provide more enhanced molecular detection signals. Here, the sensing characteristics of FMMs on nanopedestals structure was confirmed by comparison with FMMs on an unetched SiO2 substrate as a control sample. The control FMMs and the FMMs on nanopedestals were carefully designed to excite Fano resonance near the target 1-octadecanethiol (ODT) fingerprint vibrations. The FMMs were fabricated by using nanoimprint lithography and the nanopedestal structures were formed by isotropic dry-etching. The experimental reflection spectra containing the enhanced absorption signals of the ODT monolayer molecules was analyzed using temporal coupled-mode theory. The FMMs on nanopedestals achieved over 7% of reflection difference signal, which was 1.7 times higher signal than the one from the control FMMs. Based on the FMMs on nanopedestal structures proposed in this study, it may be widely applied to future spectroscopy and sensor applications requiring ultrasensitive detection capability.
Reconstructing faces from fMRI patterns using deep generative neural networks
Authors: VanRullen Rufin , Reddy Leila
Published: May 2019

Although distinct categories are reliably decoded from fMRI brain responses, it has proved more difficult to distinguish visually similar inputs, such as different faces. Here, we apply a recently developed deep learning system to reconstruct face images from human fMRI. We trained a variational auto-encoder (VAE) neural network using a GAN (Generative Adversarial Network) unsupervised procedure over a large data set of celebrity faces. The auto-encoder latent space provides a meaningful, topologically organized 1024-dimensional description of each image. We then presented several thousand faces to human subjects, and learned a simple linear mapping between the multi-voxel fMRI activation patterns and the 1024 latent dimensions. Finally, we applied this mapping to novel test images, translating fMRI patterns into VAE latent codes, and codes into face reconstructions. The system not only performed robust pairwise decoding (>95% correct), but also accurate gender classification, and even decoded which face was imagined, rather than seen.