bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated evolutionary analysis reveals antimicrobial peptides with limited resistance
Authors: Spohn Réka , Daruka Lejla , Lázár Viktória , Martins Ana , Vidovics Fanni , Grézal Gábor , Méhi Orsolya , Kintses Bálint , Számel Mónika , Jangir Pramod K. , Csörgő Bálint , Györkei Ádám , Bódi Zoltán , Faragó Anikó , Bodai László , Földesi Imre , Kata Diána , Maróti Gergely , Pap Bernadett , Wirth Roland , Papp Balázs , Pál Csaba
Published: October 2019

Antimicrobial peptides (AMPs) are promising antimicrobials, however, the potential of bacterial resistance is a major concern. Here we systematically study the evolution of resistance to 14 chemically diverse AMPs and 12 antibiotics in Escherichia coli. Our work indicates that evolution of resistance against certain AMPs, such as tachyplesin II and cecropin P1, is limited. Resistance level provided by point mutations and gene amplification is very low and antibiotic-resistant bacteria display no cross-resistance to these AMPs. Moreover, genomic fragments derived from a wide range of soil bacteria confer no detectable resistance against these AMPs when introduced into native host bacteria on plasmids. We have found that simple physicochemical features dictate bacterial propensity to evolve resistance against AMPs. Our work could serve as a promising source for the development of new AMP-based therapeutics less prone to resistance, a feature necessary to avoid any possible interference with our innate immune system.
Ultrafast self-trapping of photoexcited carriers sets the upper limit on antimony trisulfide photovoltaic devices
Authors: Yang Zhaoliang , Wang Xiaomin , Chen Yuzhong , Zheng Zhenfa , Chen Zeng , Xu Wenqi , Liu Weimin , Yang Yang , Zhao Jin , Chen Tao , Zhu Haiming
Published: October 2019

Antimony trisulfide (Sb2S3) is considered to be a promising photovoltaic material; however, the performance is yet to be satisfactory. Poor power conversion efficiency and large open circuit voltage loss have been usually ascribed to interface and bulk extrinsic defects By performing a spectroscopy study on Sb2S3 polycrystalline films and single crystal, we show commonly existed characteristics including redshifted photoluminescence with 0.6 eV Stokes shift, and a few picosecond carrier trapping without saturation at carrier density as high as approximately 1020 cm−3. These features, together with polarized trap emission from Sb2S3 single crystal, strongly suggest that photoexcited carriers in Sb2S3 are intrinsically self-trapped by lattice deformation, instead of by extrinsic defects. The proposed self-trapping explains spectroscopic results and rationalizes the large open circuit voltage loss and near-unity carrier collection efficiency in Sb2S3 thin film solar cells. Self-trapping sets the upper limit on maximum open circuit voltage (approximately 0.8 V) and thus power conversion efficiency (approximately 16 %) for Sb2S3 solar cells.
Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing
Authors: Hamilton Thomas A. , Pellegrino Gregory M. , Therrien Jasmine A. , Ham Dalton T. , Bartlett Peter C. , Karas Bogumil J. , Gloor Gregory B. , Edgell David R.
Published: October 2019

The selective regulation of bacteria in complex microbial populations is key to controlling pathogenic bacteria. CRISPR nucleases can be programmed to kill bacteria, but require an efficient and broad-host range delivery system to be effective. Here, using an Escherichia coli and Salmonella enterica co-culture system, we show that plasmids based on the IncP RK2 conjugative system can be used as delivery vectors for a TevSpCas9 dual nuclease. Notably, a cis-acting plasmid that encodes the conjugation and CRISPR machinery conjugates from E. coli to S. enterica with high frequency compared to a trans system that separates conjugation and CRISPR machinery. In culture conditions that enhance cell-to-cell contact, conjugation rates approach 100% with the cis-acting plasmid. Targeting of single or multiplexed sgRNAs to non-essential genes results in high S. enterica killing efficiencies. Our data highlight the potential of cis-acting conjugative plasmids as a delivery system for CRISPR nucleases or other microbial-altering agents for targeted bacterial killing.
Dendronized fluorosurfactant for highly stable water-in-fluorinated oil emulsions with minimal inter-droplet transfer of small molecules
Authors: Chowdhury Mohammad Suman , Zheng Wenshan , Kumari Shalini , Heyman John , Zhang Xingcai , Dey Pradip , Weitz David A. , Haag Rainer
Published: October 2019

Fluorosurfactant-stabilized microfluidic droplets are widely used as pico- to nanoliter volume reactors in chemistry and biology. However, current surfactants cannot completely prevent inter-droplet transfer of small organic molecules encapsulated or produced inside the droplets. In addition, the microdroplets typically coalesce at temperatures higher than 80 °C. Therefore, the use of droplet-based platforms for ultrahigh-throughput combination drug screening and polymerase chain reaction (PCR)-based rare mutation detection has been limited. Here, we provide insights into designing surfactants that form robust microdroplets with improved stability and resistance to inter-droplet transfer. We used a panel of dendritic oligo-glycerol-based surfactants to demonstrate that a high degree of inter- and intramolecular hydrogen bonding, as well as the dendritic architecture, contribute to high droplet stability in PCR thermal cycling and minimize inter-droplet transfer of the water-soluble fluorescent dye sodium fluorescein salt and the drug doxycycline.
Atomically ordered non-precious Co3Ta intermetallic nanoparticles as high-performance catalysts for hydrazine electrooxidation
Authors: Feng Guang , An Li , Li Biao , Zuo Yuxuan , Song Jin , Ning Fanghua , Jiang Ning , Cheng Xiaopeng , Zhang Yuefei , Xia Dingguo
Published: October 2019

Nano-ordered intermetallic compounds have generated great interest in fuel cell applications. However, the synthesis of non-preciousearly transition metal intermetallic nanoparticles remains a formidable challenge owing to the extremely oxyphilic nature and very negative reduction potentials. Here, we have successfully synthesized non-precious Co3Ta intermetallic nanoparticles, with uniform size of 5 nm. Atomic structural characterizations and X-ray absorption fine structure measurements confirm the atomically ordered intermetallic structure. As electrocatalysts for the hydrazine oxidation reaction, Co3Ta nanoparticles exhibit an onset potential of −0.086 V (vs. reversible hydrogen electrode) and two times higher specific activity relative to commercial Pt/C (+0.06 V), demonstrating the top-level performance among reported electrocatalysts. The Co-Ta bridge sites are identified as the location of the most active sites thanks to density functional theory calculations. The activation energy of the hydrogen dissociation step decreases significantly upon N2H4 adsorption on the Co-Ta bridge active sites, contributing to the significantly enhanced activity.
Synthesis of magnesium-nitrogen salts of polynitrogen anions
Authors: Laniel Dominique , Winkler Bjoern , Koemets Egor , Fedotenko Timofey , Bykov Maxim , Bykova Elena , Dubrovinsky Leonid , Dubrovinskaia Natalia
Published: October 2019

The synthesis of polynitrogen compounds is of fundamental importance due to their potential as environmentally-friendly high energy density materials. Attesting to the intrinsic difficulties related to their formation, only three polynitrogen ions, bulk stabilized as salts, are known. Here, magnesium and molecular nitrogen are compressed to about 50 GPa and laser-heated, producing two chemically simple salts of polynitrogen anions, MgN4 and Mg2N4. Single-crystal X-ray diffraction reveals infinite anionic polythiazyl-like 1D N-N chains in the crystal structure of MgN4 and cis-tetranitrogen N44− units in the two isosymmetric polymorphs of Mg2N4. The cis-tetranitrogen units are found to be recoverable at atmospheric pressure. Our results respond to the quest for polynitrogen entities stable at ambient conditions, reveal the potential of employing high pressures in their synthesis and enrich the nitrogen chemistry through the discovery of other nitrogen species, which provides further possibilities to design improved polynitrogen arrangements.
Shape memory polymer resonators as highly sensitive uncooled infrared detectors
Authors: Adiyan Ulas , Larsen Tom , Zárate Juan José , Villanueva Luis Guillermo , Shea Herbert
Published: October 2019

Uncooled infrared detectors have enabled the rapid growth of thermal imaging applications. These detectors are predominantly bolometers, reading out a pixel’s temperature change due to infrared radiation as a resistance change. Another uncooled sensing method is to transduce the infrared radiation into the frequency shift of a mechanical resonator. We present here highly sensitive resonant infrared sensors, based on thermo-responsive shape memory polymers. By exploiting the phase-change polymer as transduction mechanism, our approach provides 2 orders of magnitude improvement of the temperature coefficient of frequency. Noise equivalent temperature difference of 22 mK in vacuum and 112 mK in air are obtained using f/2 optics. The noise equivalent temperature difference is further improved to 6 mK in vacuum by using high-Q silicon nitride membranes as substrates for the shape memory polymers. This high performance in air eliminates the need for vacuum packaging, paving a path towards flexible non-hermetically sealed infrared sensors.
Observation of a phonon bottleneck in copper-doped colloidal quantum dots
Authors: Wang Lifeng , Chen Zongwei , Liang Guijie , Li Yulu , Lai Runchen , Ding Tao , Wu Kaifeng
Published: October 2019

Hot electrons can dramatically improve the efficiency of solar cells and sensitize energetically-demanding photochemical reactions. Efficient hot electron devices have been hindered by sub-picosecond intraband cooling of hot electrons in typical semiconductors via electron-phonon scattering. Semiconductor quantum dots were predicted to exhibit a “phonon bottleneck” for hot electron relaxation as their quantum-confined electrons would couple very inefficiently to phonons. However, typical cadmium selenide dots still exhibit sub-picosecond hot electron cooling, bypassing the phonon bottleneck possibly via an Auger-like process whereby the excessive energy of the hot electron is transferred to the hole. Here we demonstrate this cooling mechanism can be suppressed in copper-doped cadmium selenide colloidal quantum dots due to femtosecond hole capturing by copper-dopants. As a result, we observe a lifetime of ~8.6 picosecond for 1Pe hot electrons which is more than 30-fold longer than that in same-sized, undoped dots (~0.25 picosecond).
Nanomechanical characterization of quantum interference in a topological insulator nanowire
Authors: Kim Minjin , Kim Jihwan , Hou Yasen , Yu Dong , Doh Yong-Joo , Kim Bongsoo , Kim Kun Woo , Suh Junho
Published: October 2019

Aharonov–Bohm conductance oscillations emerge as a result of gapless surface states in topological insulator nanowires. This quantum interference accompanies a change in the number of transverse one-dimensional modes in transport, and the density of states of such nanowires is also expected to show Aharonov–Bohm oscillations. Here, we demonstrate a novel characterization of topological phase in Bi2Se3 nanowire via nanomechanical resonance measurements. The nanowire is configured as an electromechanical resonator such that its mechanical vibration is associated with its quantum capacitance. In this way, the number of one-dimensional transverse modes is reflected in the resonant frequency, thereby revealing Aharonov–Bohm oscillations. Simultaneous measurements of DC conductance and mechanical resonant frequency shifts show the expected oscillations, and our model based on the gapless Dirac fermion with impurity scattering explains the observed quantum oscillations successfully. Our results suggest that the nanomechanical technique would be applicable to a variety of Dirac materials.
Visible and infrared three-wavelength modulated multi-directional actuators
Authors: Zuo Bo , Wang Meng , Lin Bao-Ping , Yang Hong
Published: October 2019

In recent years, light-guided robotic soft actuators have attracted intense scientific attention and rapidly developed, although it still remains challenging to precisely and reversibly modulate the moving directions and shape morphing modes of soft actuators with ease of stimulating operation. Here we report a strategy of building a multi-stimuli-responsive liquid crystal elastomer soft actuator system capable of performing not only multi-directional movement, but also different shape morphing modes. This strategy is based on the selective stimulation of specific domains of the hierarchical structured actuator through the modulation of three wavelength bands (520, 808, 980 nm) of light stimulus, which release the actuation system from light scanning position/direction restriction. Three near-infrared dual-wavelength modulated actuators and one visible/infrared tri-wavelength modulated multi-directional walker robot are demonstrated in this work. These devices have broad application prospects in robotic and biomimetic technology.
Tacticity in chiral phononic crystals
Authors: Bergamini A. , Miniaci M. , Delpero T. , Tallarico D. , Van Damme B. , Hannema G. , Leibacher I. , Zemp A.
Published: October 2019

The study of vibrational properties in engineered periodic structures relies on the early intuitions of Haüy and Boscovich, who regarded crystals as ensembles of periodically arranged point masses interacting via attractive and repulsive forces. Contrary to electromagnetism, where mechanical properties do not couple to the wave propagation mechanism, in elasticity this paradigm inevitably leads to low stiffness and high-density materials. Recent works transcend the Haüy-Boscovich perception, proposing shaped atoms with finite size, which relaxes the link between their mass and inertia, to achieve unusual dynamic behavior at lower frequencies, leaving the stiffness unaltered. Here, we introduce the concept of tacticity in spin-spin-coupled chiral phononic crystals. This additional layer of architecture has a remarkable effect on their dispersive behavior and allows to successfully realize material variants with equal mass density and stiffness but radically different dynamic properties.
Blautia genus associated with visceral fat accumulation in adults 20–76 years of age
Authors: Ozato Naoki , Saito Shinichiro , Yamaguchi Tohru , Katashima Mitsuhiro , Tokuda Itoyo , Sawada Kaori , Katsuragi Yoshihisa , Kakuta Masanori , Imoto Seiya , Ihara Kazushige , Nakaji Shigeyuki
Published: October 2019

The gut microbiota is reported to be related to obesity, and visceral fat is reported to be strongly associated with cardiovascular disease and overall mortality. However, the association between the gut microbiota and obesity has mainly been studied using body mass index (BMI) as a proxy for obesity. We investigated the relationship of both visceral fat and BMI with the gut microbiota stratified by sex in a population-based cross-sectional study of Japanese men and women 20–76 years of age (n = 1001). Women with a higher visceral fat area (VFA) harboured a higher relative abundance of the Firmicutes phylum (P for trend <0.001) and a lower relative abundance of the Bacteroidetes phylum (P for trend 0.030), whereas men with higher VFA harboured a lower relative abundance of the Firmicutes phylum (P for trend 0.076) and a higher relative abundance of the Bacteroidetes phylum (P for trend 0.013). Similar results were obtained using BMI as an index, but the differences were not significant in men. At the genus level, Blautia was the only gut microbe significantly and inversely associated with VFA regardless of sex. In conclusion, at the genus level we found that Blautia was the only gut microbe significantly and inversely associated with VFA, regardless of sex.
Carbon-based polymer nanocomposite membranes for oily wastewater treatment
Authors: Noamani Sadaf , Niroomand Shirin , Rastgar Masoud , Sadrzadeh Mohtada
Published: October 2019

Increasing oil contaminants in water is one of the major environmental concerns due to negative impacts on human health and aquatic and terrestrial ecosystems. The objective of this review paper is to highlight recent advances in the application carbon-based polymer nanocomposite membranes for oily wastewater treatment. Carbon-based nanomaterials, including graphene and graphene-oxide (GO), carbon nanotubes (CNTs), and carbon nanofibers (CNFs), have gained tremendous attention due to their unique physicochemical properties, such as excellent chemical and mechanical stability, electrical conductivity, reinforcement capability, and their antifouling properties. This review encompasses innovative carbon-based membranes for effective oil–water separation and provides a critical comparison of these membranes regarding the permeation flux, wettability, and flux recovery. The current challenges for the successful development of carbon-based nanocomposite membranes and opportunities for future research are also discussed.
Convergent and Divergent Paired Electrodeposition of Metal-Organic Framework Thin Films
Authors: Alizadeh Saber , Nematollahi Davood
Published: October 2019

Employing the environmentally friendly methods for synthesis of the metal-organic frameworks (MOFs) is an urgent need and sustainable development in the synthesis of these compounds is essential. In this way, ignoring the counter electrode reaction is a potentially negative point from green chemistry standpoint which increases some issues like energy consumption and reaction time. We wish to introduce the “paired electrodeposition” (PED) technique as a new method for the simultaneous synthesis and deposition of the MOF thin films (MOFTFs). This protocol implements the uniform pattern of two MOFTF modified substrates by “convergent (CPED: Zna/Znc-MOFTFs) and divergent (DPED: Cua/Znc-MOFTFs) paired electrodeposition” via a one-step synthesis. With the rule of thumb, enhanced energy efficiency and atom economy, increasing electrochemical yield, time-saving along with a variety of products are advantages of this technique. Besides, the “Electrode Modification Efficiency” has introduced for the evaluation of functionality and modification efficiency of electrochemical heterogeneous systems, especially MOFTFs. To investigate this concept, we synthesized Zn3(BTC)2 and Cu3(BTC)2 as MOF models under constant current electrolysis in water and at room temperature. This work can make a breakthrough in the green synthesis of metal-organic frameworks.
Solution blow spinning of polymer/nanocomposite micro-/nanofibers with tunable diameters and morphologies using a gas dynamic virtual nozzle
Authors: Vasireddi Ramakrishna , Kruse Joscha , Vakili Mohammad , Kulkarni Satishkumar , Keller Thomas F. , Monteiro Diana C. F. , Trebbin Martin
Published: October 2019

Uniform endless fibers are ubiquitous and their applications range from functional textiles over biomedical engineering to high-performance filtering and drug delivery systems. Here, we report a new method for the direct, reproducible fabrication of uniform polymer and composite micro-/nanofibers using a microfluidic gas flow focusing nozzle (Gas Dynamic Virtual Nozzle (GDVN)) relinquishing the need for external fiber pulling mechanisms. Compared to other methods, this technique is inexpensive, user-friendly and permits precise fiber diameter control (~250 nm to ~15 µm), high production rate (m/s-range) and direct fiber deposition without clogging due to stable, gas-focused jetting. Control over shape (flat or round) and surface patterning are achieved by simply tuning the air pressure and polymer concentration. The main thinning process happens after the polymer exits the device and is, therefore, mostly independent of the nozzle’s internal geometry. Nevertheless, the lithography-based device design is versatile, allowing for precise flow-field control for operation stability as well as particle alignment control. As an example, we demonstrate the successful production of endless hematite nanocomposite fibers which highlights this technology’s exciting possibilities that can lead to the fabrication of multifunctional/stimuli-responsive fibers with thermal and electrical conductivity, magnetic properties and enhanced mechanical stability.
Association between underweight and pulmonary function in 282,135 healthy adults: A cross-sectional study in Korean population
Authors: Do Jong Geol , Park Chul-Hyun , Lee Yong-Taek , Yoon Kyung Jae
Published: October 2019

In contrast to obesity, studies on the relationship between underweight and pulmonary function are still sparse. Thus, the objective of this study was to investigate the effect of being underweight on pulmonary function in a general population without apparent lung disease. A total of 282,135 retrospective cohort subjects between January 2012 and December 2014 in Korea were included. Using multivariate-adjusted analysis, the relationship between body mass index (BMI) and pulmonary function were assessed. Underweight individuals represented 5.5% of the total study population (n = 282,135), with most (87.9%) of them being females. Compare to normal weight and obese, underweight was associated with decreased pulmonary function. Forced expiratory volume in first second (FEV1), predicted FEV1 (%), forced vital capacity (FVC), predicted FVC (%), and peak expiratory flow (PEF) were lower in the underweight group than those in other groups after adjusting for age, sex, height, status of smoking, frequency of vigorous exercise, diabetes, and high-sensitivity C-reactive protein (hsCRP) (P < 0.001). Lower BMI tended to decrease pulmonary function parameters such as FEV1 (L), predicted FEV1 (%), FVC (L), predicted FVC (%), and PEF (L/sec) (P for trend <0.001). After adjusting for possible confounders, odds ratios (ORs; 95% confidence interval) for subjects with predicted FEV1% < 80% in underweight and normal weight groups compared to obese group (reference) were 2.10 (1.98–2.21), and 0.93 (0.90–0.97), respectively. ORs for subjects with predicted FVC% < 80% in underweight and normal weight groups compared to obese group (reference) were 4.90 (4.62–5.18) and 1.32 (1.27–1.38), respectively. This study demonstrated a proportional relationship between pulmonary function and the degree of BMI. We found that underweight status was independently associated with decreased pulmonary function in Korean population.
Population co-divergence in common cuttlefish (Sepia officinalis) and its dicyemid parasite in the Mediterranean Sea
Authors: Drábková Marie , Jachníková Nikola , Tyml Tomáš , Sehadová Hana , Ditrich Oleg , Myšková Eva , Hypša Václav , Štefka Jan
Published: October 2019

Population structure and biogeography of marine organisms are formed by different drivers than in terrestrial organisms. Yet, very little information is available even for common marine organisms and even less for their associated parasites. Here we report the first analysis of population structure of both a cephalopod host (Sepia officinalis) and its dicyemid parasite, based on a homologous molecular marker (cytochrome oxidase I). We show that the population of common cuttlefish in the Mediterranean area is fragmented into subpopulations, with some areas featuring restricted level of gene flow. Amongst the studied areas, Sardinia was genetically the most diverse and Cyprus the most isolated. At a larger scale, across the Mediterranean, the population structure of the parasite shows co-diversification pattern with its host, but a slower rate of diversification. Differences between the two counterparts are more obvious at a finer scale, where parasite populations show increased level of fragmentation and lower local diversities. This discrepancy can be caused by local extinctions and replacements taking place more frequently in the dicyemid populations, due to their parasitic lifestyle.
Feasibility of Standardized Human Milk Collection in Neonatal Care Units
Authors: Galante Laura , Vickers Mark H. , Milan Amber M. , Reynolds Clare M. , Alexander Tanith , Bloomfield Frank H. , Pundir Shikha
Published: October 2019

Research in human lactation is a growing field. However, difficulties in studying human milk originate from the dynamicity of its composition. Using standardized collection protocols is mandatory to minimize variation and warrant comparability of findings across different studies. Yet, information on the feasibility of collecting human milk with standardized procedures, especially in neonatal units, are lacking. The present study aims to report on the feasibility and difficulties to collect human milk according to a standardized protocol, during early lactation from women who gave birth to preterm infants. Human milk was collected from 129 mothers of moderate- to late-preterm infants according to two variations of a standard protocol which differed for number of collection time-points. Collection rates and adherence to the sampling protocol were evaluated together with reason for missed collection. Collection of ≥1 sample was successful for 80% of the mothers. However adherence to the standard protocol was overall low (36% and 27%). Collection rates were different between the two protocol variations (73% against 92%, p ≤ 0.001). Amongst the reason for missed collection, low milk supply was the most recurrent (40%). Our findings show that while collecting human milk in neonatal units is achievable, obtaining standard and comparable samples results challenging.
Changes in the microsomal proteome of tomato fruit during ripening
Authors: Pontiggia Daniela , Spinelli Francesco , Fabbri Claudia , Licursi Valerio , Negri Rodolfo , De Lorenzo Giulia , Mattei Benedetta
Published: October 2019

The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress.
ARA: accurate, reliable and active histopathological image classification framework with Bayesian deep learning
Authors: Rączkowska Alicja , Możejko Marcin , Zambonelli Joanna , Szczurek Ewa
Published: October 2019

Machine learning algorithms hold the promise to effectively automate the analysis of histopathological images that are routinely generated in clinical practice. Any machine learning method used in the clinical diagnostic process has to be extremely accurate and, ideally, provide a measure of uncertainty for its predictions. Such accurate and reliable classifiers need enough labelled data for training, which requires time-consuming and costly manual annotation by pathologists. Thus, it is critical to minimise the amount of data needed to reach the desired accuracy by maximising the efficiency of training. We propose an accurate, reliable and active (ARA) image classification framework and introduce a new Bayesian Convolutional Neural Network (ARA-CNN) for classifying histopathological images of colorectal cancer. The model achieves exceptional classification accuracy, outperforming other models trained on the same dataset. The network outputs an uncertainty measurement for each tested image. We show that uncertainty measures can be used to detect mislabelled training samples and can be employed in an efficient active learning workflow. Using a variational dropout-based entropy measure of uncertainty in the workflow speeds up the learning process by roughly 45%. Finally, we utilise our model to segment whole-slide images of colorectal tissue and compute segmentation-based spatial statistics.
Ecotoxicological hazard of a mixture of glyphosate and aminomethylphosphonic acid to the mussel Mytilus galloprovincialis (Lamarck 1819)
Authors: Matozzo Valerio , Munari Marco , Masiero Luciano , Finos Livio , Marin Maria Gabriella
Published: October 2019

Assessment of the effects of chemical mixtures is a very important objective of the ecotoxicological risk assessment. This study was aimed at evaluating for the first time the effects of a mixture of glyphosate and its main breakdown product aminomethylphosphonic acid (AMPA) on various biomarkers in the mussel Mytilus galloprovincialis. Mussels were exposed for 7, 14 and 21 days to either 100 µg/L of glyphosate, 100 µg/L of AMPA or a mixture of both (100 + 100 µg/L). Various haemocyte parameters, such as total haemocyte counts, haemocyte diameter and volume, haemocyte proliferation, haemolymph lactate dehydrogenase activity and haemocyte lysate acid phosphatase activities were measured. In addition, the effects of exposure on the activity of antioxidant enzymes, acetylcholinesterase and glutathione-S-transferase were evaluated in gills and digestive gland from mussels. On the whole, this study demonstrated that the variables considered in the experimental plan, namely treatment, exposure time and their interaction, affect significantly biomarker responses in M. galloprovincialis. The effects of the mixture were comparable to those of the individual compounds, whereas their synergistic effects were occasionally observed, under the experimental conditions tested at least.
Versatile direct laser writing of non-photosensitive materials using multi-photon reduction-based assembly of nanoparticles
Authors: Nishiyama Hiroaki , Umetsu Kan , Kimura Kaito
Published: October 2019

Versatile direct laser writing (DLW), not limited by material photosensitivity, offers opportunities for fundamental and technological innovation for micro-/nanofabrication in integrated photonics, electronics and material science. Although DLW has high potential in micro-/nanodevice fabrication, material choice suffers an intrinsic limitation: DLW cannot be applied to non-photosensitive materials. We describe a newly discovered rapid-assembly phenomenon of fine particles based on femtosecond laser multi-photon-reduction in solution. This phenomenon allowed the writing of micropatterns with thick clad layers filled with nanoparticles. We wrote continuous patterns by moving the laser focus even in the case of non-photosensitive material such as SiO2. By transcending the strict material limitation, this novel laser writing process promises to be a powerful tool in a variety of scientific fields.
Identification, characterization and expression profiles of Fusarium udum stress-responsive WRKY transcription factors in Cajanus cajan under the influence of NaCl stress and Pseudomonas fluorescens OKC
Authors: Kumar Gagan , Bajpai Raina , Sarkar Ankita , Mishra Raj Kumar , Kumar Gupta Vijai , Singh Harikesh B. , Sarma Birinchi K.
Published: October 2019

The WRKY gene family has never been identified in pigeonpea (Cajanus cajan). Therefore, objective of the present study was to identify the WRKY gene family in pigeonpea and characterize the Fusarium udum stress-responsive WRKY genes under normal, NaCl-stressed and Pseudomonas fluorescens OKC (a plant growth-promoting bacterial strain) treated conditions. The aim was to characterize the Fusarium udum stress-responsive WRKY genes under some commonly occurring field conditions. We identified 97 genes in the WRKY family of pigeonpea, using computational prediction method. The gene family was then classified into three groups through phylogenetic analysis of the homologous genes from the representative plant species. Among the 97 identified WRKY genes 35 were further classified as pathogen stress responsive genes. Functional validation of the 35 WRKY genes was done through generating transcriptional profiles of the genes from root tissues of pigeonpea plants under the influence of P. fluorescens OKC after 24 h of stress application (biotic: Fusarium udum, abiotic: NaCl). The entire experiment was conducted in two pigeonpea cultivars Asha (resistant to F. udum) and Bahar (susceptible to F. udum) and the results were concluded on the basis of transcriptional regulation of the WRKY genes in both the pigeonpea cultivars. The results revealed that among the 35 tentatively identified biotic stress responsive CcWRKY genes, 26 were highly F. udum responsive, 17 were better NaCl responsive compared to F. udum and 11 were dual responsive to both F. udum and NaCl. Application of OKC was able to enhance transcript accumulation of the individual CcWRKY genes to both the stresses when applied individually but not in combined challenge of the two stresses. The results thus indicated that CcWRKY genes play a vital role in the defense signaling against F. udum and some of the F. udum responsive CcWRKYs (at least 11 in pigeonpea) are also responsive to abiotic stresses such as NaCl. Further, plant beneficial microbes such as P. fluorescens OKC also help pegionpea to defend itself against the two stresses (F. udum and NaCl) through enhanced expression of the stress responsive CcWRKY genes when the stresses are applied individually.
Combined dental wear and cementum analyses in ungulates reveal the seasonality of Neanderthal occupations in Covalejos Cave (Northern Iberia)
Authors: Sánchez-Hernández Carlos , Gourichon Lionel , Pubert Eric , Rendu William , Montes Ramón , Rivals Florent
Published: October 2019

We propose for the first time the use of the combination of two high-resolution techniques, dental wear (meso- and microwear) and dental cementum analyses, to gain a better understanding of Neanderthal subsistence strategies and occupational patterns. Dental wear analysis provides information not only on ungulate palaeodiet and palaeoenvironments but also on hunting time and seasons. Dental cementum analysis allows the accurate determination of the age and season at death of a prey. Our study has focused on the Cantabrian region and has applied both methods to investigate the Mousterian faunal assemblages in Covalejos Cave. Identification of the ungulate palaeodiet reveals information on the environmental conditions of the studied region. Moreover, it may facilitate observation on the evolution of both palaeodiet and palaeoenvironment throughout the site sequence. Results show a general stability in the palaeoenvironmental conditions and in the ungulate palaeodiet throughout the Mousterian sequence; this finding may be attributed to the role of the area as a climate refuge, and slight differences in levels 8, 7 and 4 suggest long- or short-term but repeated Neanderthal occupations at different seasons in the annual cycle.
Identification of the Sex of Pre-implantation Mouse Embryos Using a Marked Y Chromosome and CRISPR/Cas9
Authors: Zhao Xiuling , Wei Wei , Pan Hong , Nie Junyu , Chen Dongrong , Zhang Pengfei , Chen Fumei , Fu Qiang , Zuo Erwei , Lu Yangqing , Zhang Ming
Published: October 2019

Although numerous attempts have been made to alter the sex ratio of the progeny of mammals, the limitations of current technologies have prevented their widespread use in farm animals. The presence or absence of a Y chromosome determines whether a mammalian embryo develops as a male or female, and non-invasive genetic reporters such as fluorescence protein markers have been intensively applied in a variety of fields of research. To develop a non-invasive and instantaneous method for advance determination of the sex of embryos, we developed a Y chromosome-linked eGFP mouse line that stably expresses green fluorescent protein under the control of the CAG promoter. The development of the CRISPR/Cas9 system has made it easy to deliver an exogenous gene to a specific locus of a genome, and linking a tracer to the Y chromosome has simplified the process of predicting the sex of embryos collected by mating a Y-Chr-eGFP transgenic male with a wild-type female. XY embryos appeared green, under a fluorescence microscope, and XX embryos did not. Y chromosome-linked genes were amplified by nested PCR to further confirm the accuracy of this method, and the simultaneous transplantation of green and non-green embryos into foster mothers indicated that 100% accuracy was achieved by this method. Thus, the Y-Chr-eGFP mouse line provides an expeditious and accurate approach for sexing pre-implantation embryos and can be efficiently used for the pre-selection of sex.
Predators of monarch butterfly eggs and neonate larvae are more diverse than previously recognised
Authors: Hermann Sara L. , Blackledge Carissa , Haan Nathan L. , Myers Andrew T. , Landis Douglas A.
Published: October 2019

Conserving threatened organisms requires knowledge of the factors impacting their populations. The Eastern monarch butterfly (Danaus plexippus L.) has declined by as much as 80% in the past two decades and conservation biologists are actively seeking to understand and reverse this decline. While it is well known that most monarchs die as eggs and young larvae, few studies have focused on identifying what arthropod taxa contribute to these losses. The aim of our study was to identify previously undocumented predators of immature monarchs in their summer breeding range in the United States. Using no-choice feeding assays augmented with field observations, we evaluated 75 arthropod taxa commonly found on the primary host plant for their propensity to consume immature monarchs. Here we report 36 previously unreported monarch predators, including representatives from 4 new orders (Orthoptera, Dermaptera, Lepidoptera and Opiliones) and 11 taxa (Acrididae, Gryllidae, Tettigoniidae, Forficulidae, Anthocoridae, Geocoridae, Lygaeidae, Miridae, Nabidae, Erebidae and Opilliones). Surprisingly, several putative herbivores were found to readily consume immature monarchs, both in a targeted fashion or incidentally as a result of herbivory. This work expands our understanding of the monarch predator community and highlights the importance of unrecognized predation on insects of conservation concern.
Optical Resolution Photoacoustic Microscopy of Ovary and Fallopian Tube
Authors: Rao Bin , Leng Xiandong , Zeng Yifeng , Lin Yixiao , Chen Ruimin , Zhou Qifa , Hagemann Andrea R. , Kuroki Lindsay M. , McCourt Carolyn K. , Mutch David G. , Powell Matthew A. , Hagemann Ian S. , Zhu Quing
Published: October 2019

Ovarian cancer is the leading cause of death among gynecological cancers, but is poorly amenable to preoperative diagnosis. In this study, we investigate the feasibility of “optical biopsy,” using high-optical-resolution photoacoustic microscopy (OR-PAM) to quantify the microvasculature of ovarian and fallopian tube tissue. The technique is demonstrated using excised human ovary and fallopian tube specimens imaged immediately after surgery. Quantitative parameters are derived using Amira software. The parameters include three-dimensional vascular segment count, total volume and length, which are associated with tumor angiogenesis. Qualitative results of OR-PAM demonstrate that malignant ovarian tissue has larger and more tortuous blood vessels as well as smaller vessels of different sizes, while benign and normal ovarian tissue has smaller vessels of uniform size. Quantitative analysis shows that malignant ovaries have greater tumor vessel volume, length and number of segments, as compared with benign and normal ovaries. The vascular pattern of benign fallopian tube is different than that of benign ovarian tissue. Our initial results demonstrate the potential of OR-PAM as an imaging tool for fast assessment of ovarian tissue and fallopian tube and could avoid unnecessary surgery if the risk of the examined ovary is extremely low.
Realizing High Thermoelectric Performance at Ambient Temperature by Ternary Alloying in Polycrystalline Si1-x-yGexSny Thin Films with Boron Ion Implantation
Authors: Peng Ying , Miao Lei , Gao Jie , Liu Chengyan , Kurosawa Masashi , Nakatsuka Osamu , Zaima Shigeaki
Published: October 2019

The interest in thermoelectrics (TE) for an electrical output power by converting any kind of heat has flourished in recent years, but questions about the efficiency at the ambient temperature and safety remain unanswered. With the possibility of integration in the technology of semiconductors based on silicon, highly harvested power density, abundant on earth, nontoxicity, and cost-efficiency, Si1-x-yGexSny ternary alloy film has been investigated to highlight its efficiency through ion implantation and high-temperature rapid thermal annealing (RTA) process. Significant improvement of the ambient-temperature TE performance has been achieved in a boron-implanted Si0.864Ge0.108Sn0.028 thin film after a short time RTA process at 1100 °C for 15 seconds, the power factor achieves to 11.3 μWcm−1 K−2 at room temperature. The introduction of Sn into Si1-xGex dose not only significantly improve the conductivity of Si1-xGex thermoelectric materials but also achieves a relatively high Seebeck coefficient at room temperature. This work manifests emerging opportunities for modulation Si integration thermoelectrics as wearable devices charger by body temperature.
Climatic niche characteristics of native and invasive Lilium lancifolium
Authors: Herrando-Moraira Sonia , Nualart Neus , Herrando-Moraira Albert , Chung Mi Yoon , Chung Myong Gi , López-Pujol Jordi
Published: October 2019

One of the topics currently under discussion in biological invasions is whether the species’ climatic niche has been conserved or, alternatively, has diverged during invasions. Here, we explore niche dynamic processes using the complex invasion history model ofLilium lancifolium, which is the first tested case of a native species (Korea) with two hypothesized spatial (regional and intercontinental) and temporal arrivals: (1) as an archaeophyte in East Asia (before AD 1500); and (2) as a neophyte in Europe, North America, Australia, and New Zealand (after AD 1500). Following a niche examination through both environmental and geographical spaces, the species in the archaeophyte range has apparently filled the ancestral native niche and, rather, would have increased it considerably. The species as a neophyte shows a closer climatic match with the archaeophyte range than with the native one. This pattern of niche similarity suggests that the neophyte range was probably colonized by a subset of archaeophyte propagules adapted to local climate that promoted the species’ establishment. Overall, niche conservatism is proposed at each colonization step, from native to archaeophyte, and from archaeophyte to neophyte ranges. We detected signals of an advanced invasion stage within the archaeophyte range and traces of an early introduction stage in neophyte ranges.
Plant biotransformation of T2 and HT2 toxin in cultured organs of Triticum durum Desf
Authors: Righetti Laura , Körber Tania , Rolli Enrico , Galaverna Gianni , Suman Michele , Bruni Renato , Dall’Asta Chiara
Published: October 2019

The present study aimed at elucidating the uptake and biotransformation of T2 and HT2 toxins in five cultivars of durum wheat, by means of cultured plant organs. An almost complete absorption of T2 toxin (up to 100 µg) was noticed after 7 days, along with the contemporaneous formation of HT2 in planta, whereas HT2 showed a slower uptake by uninfected plant organs. Untargeted MS-analysis allowed to identify a large spectrum of phase I and phase II metabolites, resulting in 26 T2 and 23 HT2 metabolites plus tentative isomers. A novel masked mycotoxin, 3-acetyl-HT2-glucoside, was reported for the first time in wheat. The in vitro approach confirmed its potential to both investigate the contribution of plant metabolism in the biosynthesis of masked mycotoxins and to foresee the development of biocatalytic tools to develop nature-like mixtures to be used as reference materials.
Identification and characterization of jasmonic acid- and linolenic acid-mediated transcriptional regulation of secondary laticifer differentiation in Hevea brasiliensis
Authors: Loh Swee Cheng , Othman Ahmad Sofiman , Veera Singham G.
Published: October 2019

Hevea brasiliensis remains the primary crop commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. Here, we described the transcriptional events related to jasmonic acid (JA)- and linolenic acid (LA)-induced secondary laticifer differentiation (SLD) in H. brasiliensis clone RRIM 600 based on RNA-seq approach. Histochemical approach proved that JA- and LA-treated samples resulted in SLD in H. brasiliensis when compared to ethephon and untreated control. RNA-seq data resulted in 86,614 unigenes, of which 2,664 genes were differentially expressed in JA and LA-induced secondary laticifer harvested from H. brasiliensis bark samples. Among these, 450 genes were unique to JA and LA as they were not differentially expressed in ethephon-treated samples compared with the untreated samples. Most transcription factors from the JA- and LA-specific dataset were classified under MYB, APETALA2/ethylene response factor (AP2/ERF), and basic-helix-loop-helix (bHLH) gene families that were involved in tissue developmental pathways, and we proposed that Bel5-GA2 oxidase 1-KNOTTED-like homeobox complex are likely involved in JA- and LA-induced SLD in H. brasiliensis. We also discovered alternative spliced transcripts, putative novel transcripts, and cis-natural antisense transcript pairs related to SLD event. This study has advanced understanding on the transcriptional regulatory network of SLD in H. brasiliensis.
Phylogeny and morphology of Lasiodiplodia species associated with Magnolia forest plants
Authors: de Silva Nimali I. , Phillips Alan J. L. , Liu Jian-Kui , Lumyong Saisamorn , Hyde Kevin D.
Published: October 2019

Two new species of Lasiodiplodia (Lasiodiplodia endophytica and Lasiodiplodia magnoliae) are described and illustrated from Magnolia forests in Yunnan, China. Endophytic and saprobic Lasiodiplodia pseudotheobromae and endophytic L. thailandica are new records from this host. The internal transcribed spacers (ITS), part of the translation elongation factor-1α (tef1) and partial β-tubulin (tub2) sequence data were analyzed to investigate the phylogenetic relationships of the new species with other Lasiodiplodia species. Lasiodiplodia magnoliae is phylogenetically sister to L. mahajangana and L. pandanicola but morphologically distinct from L. mahajangana in having larger conidia. Lasiodiplodia endophytica is most closely related to L. iraniensis and L. thailandica and the three species can be distinguished from one another by 2 base pair differences in ITS and three or four base pair differences in tef1. The new collections suggest that Magnolia forest plants are good hosts for Lasiodiplodia species with endophytic and saprobic life-styles.