bluuebunny/crossref_metadata_2025 huggingface dataset:
Programming DNA origami patterning with non-canonical DNA-based metallization reactions
Authors: Jia Sisi , Wang Jianbang , Xie Mo , Sun Jixue , Liu Huajie , Zhang Yinan , Chao Jie , Li Jiang , Wang Lihua , Lin Jianping , Gothelf Kurt V. , Fan Chunhai
Published: December 2019

The inherent specificity of DNA sequence hybridization has been extensively exploited to develop bioengineering applications. Nevertheless, the structural potential of DNA has been far less explored for creating non-canonical DNA-based reactions. Here we develop a DNA origami-enabled highly localized metallization reaction for intrinsic metallization patterning with 10-nm resolution. Both theoretical and experimental studies reveal that low-valence metal ions (Cu2+ and Ag+) strongly coordinate with DNA bases in protruding clustered DNA (pcDNA) prescribed on two-dimensional DNA origami, which results in effective attraction within flexible pcDNA strands for site-specific pcDNA condensation. We find that the metallization reactions occur selectively on prescribed sites while not on origami substrates. This strategy is generically applicable for free-style metal painting of alphabet letters, digits and geometric shapes on all−DNA substrates with near-unity efficiency. We have further fabricated single- and double-layer nanoscale printed circuit board (nano-PCB) mimics, shedding light on bio-inspired fabrication for nanoelectronic and nanophotonic applications.
Responses of unicellular predators to cope with the phototoxicity of photosynthetic prey
Authors: Uzuka Akihiro , Kobayashi Yusuke , Onuma Ryo , Hirooka Shunsuke , Kanesaki Yu , Yoshikawa Hirofumi , Fujiwara Takayuki , Miyagishima Shin-ya
Published: December 2019

Feeding on unicellular photosynthetic organisms by unicellular eukaryotes is the base of the aquatic food chain and evolutionarily led to the establishment of photosynthetic endosymbionts/organelles. Photosynthesis generates reactive oxygen species and damages cells; thus, photosynthetic organisms possess several mechanisms to cope with the stress. Here, we demonstrate that photosynthetic prey also exposes unicellular amoebozoan and excavates predators to photosynthetic oxidative stress. Upon illumination, there is a commonality in transcriptomic changes among evolutionarily distant organisms feeding on photosynthetic prey. One of the genes commonly upregulated is a horizontally transferred homolog of algal and plant genes for chlorophyll degradation/detoxification. In addition, the predators reduce their phagocytic uptake while accelerating digestion of photosynthetic prey upon illumination, reducing the number of photosynthetic cells inside the predator cells, as this also occurs in facultative endosymbiotic associations upon certain stresses. Thus, some mechanisms in predators observed here probably have been necessary for evolution of endosymbiotic associations.
Tuneable reflexes control antennal positioning in flying hawkmoths
Authors: Natesan Dinesh , Saxena Nitesh , Ekeberg Örjan , Sane Sanjay P.
Published: December 2019

Complex behaviours may be viewed as sequences of modular actions, each elicited by specific sensory cues in their characteristic timescales. From this perspective, we can construct models in which unitary behavioural modules are hierarchically placed in context of related actions. Here, we analyse antennal positioning reflex in hawkmoths as a tuneable behavioural unit. Mechanosensory feedback from two antennal structures, Böhm’s bristles (BB) and Johnston’s organs (JO), determines antennal position. At flight onset, antennae attain a specific position, which is maintained by feedback from BB. Simultaneously, JO senses deflections in flagellum-pedicel joint due to frontal airflow, to modulate its steady-state position. Restricting JO abolishes positional modulation but maintains stability against perturbations. Linear feedback models are sufficient to predict antennal dynamics at various set-points. We modelled antennal positioning as a hierarchical neural-circuit in which fast BB feedback maintains instantaneous set-point, but slow JO feedback modulates it, thereby elucidating mechanisms underlying its robustness and flexibility.
Structural order as a genuine control parameter of dynamics in simple glass formers
Authors: Tong Hua , Tanaka Hajime
Published: December 2019

Glass transition is characterised by drastic dynamical slowing down upon cooling, accompanied by growing spatial heterogeneity. Its rationalisation by subtle changes in the liquid structure has been long debated but remains elusive, due to intrinsic difficulty in detecting the underlying complex structural ordering. Here we report that structural order parameter characterising local packing capability can well describe the glassy dynamics not only macroscopically but also microscopically, no matter whether it is driven by temperature or density. A Vogel-Fulcher-Tammann (VFT)-like relation is universally identified between the structural relaxation time and the order parameter for supercooled liquids with isotropic interactions. More importantly, we find such an intriguing VFT-like relation to be statistically valid even at a particle level, between spatially coarse-grained structural order and microscopic particle-level dynamics. Such a unified description of glassy dynamics based solely on structural order is expected to contribute to the ultimate understanding of the long-standing glass-transition problem.
Author Correction: Highly efficient multiplex human T cell engineering without double-strand breaks using Cas9 base editors
Authors: Webber Beau R. , Lonetree Cara-lin , Kluesner Mitchell G. , Johnson Matthew J. , Pomeroy Emily J. , Diers Miechaleen D. , Lahr Walker S. , Draper Garrett M. , Slipek Nicholas J. , Smeester Branden A. , Lovendahl Klaus N. , McElroy Amber N. , Gordon Wendy R. , Osborn Mark J. , Moriarity Branden S.
Published: December 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Publisher Correction: Deep Machine Learning Techniques for the Detection and Classification of Sperm Whale Bioacoustics
Authors: Bermant Peter C. , Bronstein Michael M. , Wood Robert J. , Gero Shane , Gruber David F.
Published: December 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Superfluid Phase Transitions and Effects of Thermal Pairing Fluctuations in Asymmetric Nuclear Matter
Authors: Tajima Hiroyuki , Hatsuda Tetsuo , van Wyk Pieter , Ohashi Yoji
Published: December 2019

We investigate superfluid phase transitions of asymmetric nuclear matter at finite temperature (T) and density (ρ) with a low proton fraction (Yp ≤ 0.2), which is relevant to the inner crust and outer core of neutron stars. A strong-coupling theory developed for two-component atomic Fermi gases is generalized to the four-component case, and is applied to the system of spin-1/2 neutrons and protons. The phase shifts of neutron-neutron (nn), proton-proton (pp) and neutron-proton (np) interactions up to k = 2 fm−1 are described by multi-rank separable potentials. We show that the critical temperature $${{\boldsymbol{T}}}_{{\bf{c}}}^{{\bf{n}}{\bf{n}}}$$Tcnn of the neutron superfluidity at Yp = 0 agrees well with Monte Carlo data at low densities and takes a maximum value $${{\boldsymbol{T}}}_{{\bf{c}}}^{{\bf{n}}{\bf{n}}}$$Tcnn= 1.68 MeV at $${\boldsymbol{\rho }}{\boldsymbol{/}}{{\boldsymbol{\rho }}}_{{\bf{0}}}{\boldsymbol{=}}{\bf{0.14}}$$ρ/ρ0=0.14 with ρ0 = 0.17 fm−3. Also, the critical temperature $${{\boldsymbol{T}}}_{{\bf{c}}}^{{\bf{n}}{\bf{n}}}$$Tcnn of the proton superconductivity for Yp ≤ 0.2 is substantially suppressed at low densities due to np-pairing fluctuations, and starts to dominate over $${{\boldsymbol{T}}}_{{\bf{c}}}^{{\bf{n}}{\bf{n}}}$$Tcnn only above $${\boldsymbol{\rho }}{\boldsymbol{/}}{{\boldsymbol{\rho }}}_{{\bf{0}}}{\boldsymbol{=}}{\bf{0.70}}$$ρ/ρ0=0.70(0.77) for Yp = 0.1(0.2), and (iii) the deuteron condensation temperature $${{\boldsymbol{T}}}_{{\bf{c}}}^{{\bf{d}}}$$Tcd is suppressed at Yp ≤ 0.2 due to a large mismatch of the two Fermi surfaces.
Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies
Authors: Ali Muhammad , Kabir Firoz , Thomson Jason J. , Ma Yinghong , Qiu Caihong , Delannoy Michael , Khan Shahid Y. , Riazuddin S. Amer
Published: December 2019

The ocular lens serves as an excellent system to investigate the intricate details of development and differentiation. Generation of lentoid bodies or lens-like structures using pluripotent stem cells is important for understanding the processes critical for lens morphogenesis and the mechanism of cataractogenesis. We previously reported the generation of peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cells (iPSCs). Here, we report generation of lentoid bodies from human embryonic stem cells (hESCs) and (PBMC)-originated, iPSCs employing the “fried egg” method with brief modifications. The ultrastructure analysis of hESC- and iPSC-derived lentoid bodies identified closely packed lens epithelial- and differentiating fiber-like cells. In addition, we performed RNA sequencing (RNA-Seq) based transcriptome profiling of hESC- and iPSC-derived lentoid bodies at differentiation day 25. Next-generation RNA sequencing (RNA-Seq) of hESC- and iPSC-derived lentoid bodies detected expression (≥0.659 RPKM) of 13,975 and 14,003 genes, respectively. Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies revealed 13,563 (>96%) genes common in both datasets. Among the genes common in both transcriptome datasets, 12,856 (~95%) exhibited a quantitatively similar expression profile. Next, we compared the mouse lens epithelial and fiber cell transcriptomes with hESC- and iPSC-derived lentoid bodies transcriptomes and identified > 96% overlap with lentoid body transcriptomes. In conclusion, we report first-time comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies at differentiation day 25.
Transgenerational role of seed mycobiome – an endosymbiotic fungal composition as a prerequisite to stress resilience and adaptive phenotypes in Triticum
Authors: Vujanovic Vladimir , Islam M. Nazrul , Daida Prasad
Published: December 2019

Illumina-MiSeq next-generation sequencing of ITS 5.8S rRNA gene demonstrated the transgenerational transmission of fungal seed-endophytes (mycobiome) across three consecutive wheat host generations under standard-control and drought conditions in the greenhouse. Drought-stressed plants experienced a positive shift in the seed mycobiome’s composition, moderated by the external acquisition of endophytic Penicillium (E+) at the seed level. Untreated (E−) and unstressed plants harbor a maximal fungal diversity of non-equilibrium ecological communities. While fungal composition in drought-stressed E− plants experienced important fluctuation, E+ plants maintained fungal ecological communities in phase equilibrium across generations. E+ plants hosted a relatively higher abundance of Ascomycota in the 2nd and 3rd seed generations of wheat, whereas higher abundance of Basidiomycota was detected in 1st generation seeds. The dynamic response of ecological communities to environmental stress is conducive to E+ plants’ active recruitment of endosymbiotic consortia in seeds, benefiting host stress resilience and phenotype. In contrast, E− plants showed an erratic distribution of detected OTUs with an increased occurrence of phytopathogens and diminished plant performance under stress. The present study gives insight into the understanding of the seed-mycobiome composition and dynamics with the potential to improve plant host traits in an adverse environment.
Essential roles of autophagy in metabolic regulation in endosperm development during rice seed maturation
Authors: Sera Yuri , Hanamata Shigeru , Sakamoto Shingo , Ono Seijiro , Kaneko Kentaro , Mitsui Yuudai , Koyano Tomoko , Fujita Naoko , Sasou Ai , Masumura Takehiro , Saji Hikaru , Nonomura Ken-Ichi , Mitsuda Nobutaka , Mitsui Toshiaki , Kurusu Takamitsu , Kuchitsu Kazuyuki
Published: December 2019

Autophagy plays crucial roles in the recycling of metabolites, and is involved in many developmental processes. Rice mutants defective in autophagy are male sterile due to immature pollens, indicating its critical role in pollen development. However, physiological roles of autophagy during seed maturation had remained unknown. We here found that seeds of the rice autophagy-deficient mutant Osatg7-1, that produces seeds at a very low frequency in paddy fields, are smaller and show chalky appearance and lower starch content in the endosperm at the mature stage under normal growth condition. We comprehensively analyzed the effects of disruption of autophagy on biochemical properties, proteome and seed quality, and found an abnormal activation of starch degradation pathways including accumulation of α-amylases in the endosperm during seed maturation in Osatg7-1. These results indicate critical involvement of autophagy in metabolic regulation in the endosperm of rice, and provide insights into novel autophagy-mediated regulation of starch metabolism during seed maturation.
Results of multigene panel testing in familial cancer cases without genetic cause demonstrated by single gene testing
Authors: Dominguez-Valentin Mev , Nakken Sigve , Tubeuf Hélène , Vodak Daniel , Ekstrøm Per Olaf , Nissen Anke M. , Morak Monika , Holinski-Feder Elke , Holth Arild , Capella Gabriel , Davidson Ben , Evans D. Gareth , Martins Alexandra , Møller Pål , Hovig Eivind
Published: December 2019

We have surveyed 191 prospectively sampled familial cancer patients with no previously detected pathogenic variant in the BRCA1/2, PTEN, TP53 or DNA mismatch repair genes. In all, 138 breast cancer (BC) cases, 34 colorectal cancer (CRC) and 19 multiple early-onset cancers were included. A panel of 44 cancer-predisposing genes identified 5% (9/191) pathogenic or likely pathogenic variants and 87 variants of uncertain significance (VUS). Pathogenic or likely pathogenic variants were identified mostly in familial BC individuals (7/9) and were located in 5 genes: ATM (3), BRCA2 (1), CHEK2 (1), MSH6 (1) and MUTYH (1), followed by multiple early-onset (2/9) individuals, affecting the CHEK2 and ATM genes. Eleven of the 87 VUS were tested, and 4/11 were found to have an impact on splicing by using a minigene splicing assay. We here report for the first time the splicing anomalies using this assay for the variants ATM c.3806A > G and BUB1 c.677C > T, whereas CHEK1 c.61G > A did not result in any detectable splicing anomaly. Our study confirms the presence of pathogenic or likely pathogenic variants in genes that are not routinely tested in the context of the above-mentioned clinical phenotypes. Interestingly, more than half of the pathogenic germline variants were found in the moderately penetrant ATM and CHEK2 genes, where only truncating variants from these genes are recommended to be reported in clinical genetic testing practice.
Field-induced p-n transition in yttria-stabilized zirconia
Authors: Jovaní Marc , Beltrán-Mir Héctor , Cordoncillo Eloísa , West Anthony R.
Published: December 2019

Oxide ion conducting yttria-stabilised zirconia ceramics show the onset of electronic conduction under a small bias voltage. Compositions with a high yttria content undergo a transition from p-type to n-type behavior at voltages in the range 2.4 to 10 V, which also depends on oxygen partial pressure. Surface reactions have a direct influence on bulk electronic conductivities, with possible implications for voltage-induced flash phenomena and resistive switching.
Author Correction: Annihilation of the Somali upwelling system during summer monsoon
Authors: Chatterjee Abhisek , Kumar B. Praveen , Prakash Satya , Singh Prerna
Published: December 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Visualization of the Stimuli-responsive Surface Behavior of Functionalized Wood Material by Chemical Force Microscopy
Authors: Gusenbauer Claudia , Cabane Etienne , Gierlinger Notburga , Colson Jérôme , Konnerth Johannes
Published: December 2019

The hierarchical and porous wood structure provides a stable scaffold to design functionalized lignocellulosic materials with extended properties by chemical modification techniques. However, proper nanoscale characterization methods for these novel materials are needed to confirm the presence of the added functionality and to locate the introduced functional groups with high spatial resolution. Chemical force microscopy is a suitable characterization method to distinguish chemical surface characteristics by scanning the samples surface with a functionalized tip. We report the application of this nanotechnology method on both, unmodified and functionalized wood samples to confirm the thermo-responsive behavior of poly(N-isopropylacrylamide) (PNIPAM) modified spruce wood. By performing force measurements on ultra-microtomed surfaces, adhesion force differences on the analysed structure are monitored and reveal the location and functionality of introduced functional groups. The modified samples are scanned below and above their lower critical solution temperature with a hydrophobic tip in aqueous media to observe adhesion changes. Additionally, confocal Raman microscopy support the chemical force microscopy measurements by revealing the success of the modification and the distribution of PNIPAM across the sample cross-sections. The results show that PNIPAM is mainly located in wood cell wall areas close to the lumen in early- and transitionwood.
Particle-size dependent bactericidal activity of magnesium oxide against Xanthomonas perforans and bacterial spot of tomato
Authors: Liao Y. Y. , Strayer-Scherer A. , White J. C. , De La Torre-Roche R. , Ritchie L. , Colee J. , Vallad G. E. , Freeman J. , Jones J. B. , Paret M. L.
Published: December 2019

Bacterial spot, caused by Xanthomonas spp., is a highly destructive disease of tomatoes worldwide. Copper (Cu) bactericides are often ineffective due to the presence of Cu-tolerant strains. Magnesium oxide (MgO) is an effective alternative to Cu bactericides against Xanthomonas spp. However, the effects of particle size on bactericidal activity and fruit elemental levels are unknown. In this study, nano (20 nm) and micron (0.3 and 0.6 µm) size MgO particles were compared for efficacy. Nano MgO had significantly greater in vitro bactericidal activity against Cu-tolerant X. perforans than micron MgO at 25–50 µg/ml. In field experiments nano and micron MgO applied at 200 and 1,000 µg/ml were evaluated for disease control. Nano MgO at 200 µg/ml was the only treatment that consistently reduced disease severity compared to the untreated control. Inductively Coupled Plasma Optical Emission Spectroscopy revealed that nano MgO applications did not significantly alter Mg, Cu, Ca, K, Mn, P and S accumulation compared to fruits from the untreated plots. We demonstrated that although both nano MgO and micron MgO had bactericidal activity against Cu-tolerant strains in vitro, only nano MgO was effective in bacterial spot disease management under field conditions.
Variations in tetrodotoxin levels in populations of Taricha granulosa are expressed in the morphology of their cutaneous glands
Authors: Mailho-Fontana Pedro Luiz , Jared Carlos , Antoniazzi Marta Maria , Sciani Juliana Mozer , Pimenta Daniel Carvalho , Stokes Amber N. , Grant Taran , Brodie Edmund D. , Brodie Edmund D.
Published: December 2019

Tetrodotoxin (TTX), one of the most toxic substances in nature, is present in bacteria, invertebrates, fishes, and amphibians. Marine organisms seem to bioaccumulate TTX from their food or acquire it from symbiotic bacteria, but its origin in amphibians is unclear.Taricha granulosacan exhibit high TTX levels, presumably concentrated in skin poison glands, acting as an agent of selection upon predatory garter snakes (Thamnophis). This co-evolutionary arms race induces variation inT. granulosaTTX levels, from very high to undetectable. Using morphology and biochemistry, we investigated differences in toxin localization and quality between two populations at the extremes of toxicity. TTX concentration within poison glands is related to the volume of a single cell type in which TTX occurs exclusively in distinctive secretory granules, suggesting a relationship between granule structure and chemical composition. TTX was detected in mucous glands in both populations, contradicting the general understanding that these glands do not secrete defensive chemicals and expanding currently held interpretations of amphibian skin gland functionality. Skin secretions of the two populations differed in low-mass molecules and proteins. Our results demonstrate that interpopulation variation in TTX levels is related to poison gland morphology.
Estimating Visual Field Mean Deviation using Optical Coherence Tomographic Nerve Fiber Layer Measurements in Glaucoma Patients
Authors: Tan Ou , Greenfield David S. , Francis Brian A. , Varma Rohit , Schuman Joel S. , Huang David
Published: December 2019

To construct an optical coherence tomography (OCT) nerve fiber layer (NFL) parameter that has maximal correlation and agreement with visual field (VF) mean deviation (MD). The NFL_MD parameter in dB scale was calculated from the peripapillary NFL thickness profile nonlinear transformation and VF area-weighted averaging. From the Advanced Imaging for Glaucoma study, 245 normal, 420 pre-perimetric glaucoma (PPG), and 289 perimetric glaucoma (PG) eyes were selected. NFL_MD had significantly higher correlation (Pearson R: 0.68 vs 0.55, p < 0.001) with VF_MD than the overall NFL thickness. NFL_MD also had significantly higher sensitivity in detecting PPG (0.14 vs 0.08) and PG (0.60 vs 0.43) at the 99% specificity level. NFL_MD had better reproducibility than VF_MD (0.35 vs 0.69 dB, p < 0.001). The differences between NFL_MD and VF_MD were −0.34 ± 1.71 dB, −0.01 ± 2.08 dB and 3.54 ± 3.18 dB and 7.17 ± 2.68 dB for PPG, early PG, moderate PG, and severe PG subgroups, respectively. In summary, OCT-based NFL_MD has better correlation with VF_MD and greater diagnostic sensitivity than the average NFL thickness. It has better reproducibility than VF_MD, which may be advantageous in detecting progression. It agrees well with VF_MD in early glaucoma but underestimates damage in moderate~advanced stages.
Development and performance verification of a 3-D position-sensitive Compton camera for imaging MeV gamma rays
Authors: Hosokoshi Hiroki , Kataoka Jun , Mochizuki Saku , Yoneyama Masaki , Ito Soichiro , Kiji Hiroaki , Nishi Fumiya , Miyamoto Shuji , Shima Tatsushi
Published: December 2019

In gamma-ray astronomy, the 1–10 MeV range is one of the most challenging energy bands to observe owing to low photon signals and a considerable amount of background contamination. This energy band, however, comprises a substantial number of nuclear gamma-ray lines that may hold the key to understanding the nucleosynthesis at the core of stars, spatial distribution of cosmic rays, and interstellar medium. Although several studies have attempted to improve observation of this energy window, development of a detector for astronomy has not progressed since NASA launched the Compton Gamma Ray Observatory (CGRO) in 1991. In this work, we first developed a prototype 3-D position-sensitive Compton camera (3D-PSCC), and then conducted a performance verification at NewSUBARU, Hyogo in Japan. To mimic the situation of astronomical observation, we used a MeV gamma-ray beam produced by laser inverse Compton scattering. As a result, we obtained sharp peak images of incident gamma rays irradiating from incident angles of 0° and 20°. The angular resolution of the prototype 3D-PSCC was measured by the Angular Resolution Measure and estimated to be 3.4° ± 0.1° (full width at half maximum (FWHM)) at 1.7 MeV and 4.0° ± 0.5° (FWHM) at 3.9 MeV. Subsequently, we conceived a new geometry of the 3D-PSCC optimized for future astronomical observations, assuming a 50-kg class small satellite mission. The SΩ of the 3D-PSCC is 11 cm2sr, anticipated at 1 MeV, which is small but provides an interesting possibility to observe bright gamma-ray sources owing to the high intrinsic efficiency and large field of view (FoV).
Association between peripapillary scleral deformation and choroidal microvascular circulation in glaucoma
Authors: Shin Da Young , Jeon Soo Ji , Kim Eun Kyoung , Jung Kyoung In , Park Hae Young Lopilly , Park Chan Kee
Published: December 2019

Peripapillary vessel density, which is reduced in eyes with glaucoma, has been proposed as a diagnostic tool for the desease and peripapillary choroidal microvasculature dropout(MvD) is considered one of pathophysiological manifestation of glaucomatous damage. However, little is known about the underlying pathogenic mechanism of dropout. According to recent studies, MvD is associated with structural changes in ONH structures. Therefore, we investigated the association between peripapillary scleral deformation and MvD. Data from 62 open-angle glaucoma (OAG) eyes with MvD and 36 eyes without MvD were analyzed in this study. And eyes with MvD were classified into two groups based on location: a juxtapapillary group and a non-juxtapapillary group for further analysis. More eyes with MvD had focal scleral deformation than did those without MvD (64.5% versus 2.8%; P < 0.001). Peripapillary choroidal thickness and focal scleral deformation were significantly associated with MvD. And juxtapapillary group was more associated with focal scleral deformation and coincidental RNFL defects than non-juxtapapillary groups. Peripapillary choroidal MvD was associated with the presence of scleral deformation, especially with juxtapapillary MvD, which was related to corresponding RNFL defects.
Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab
Authors: Yokoyama Hideshi , Mizutani Ryuta , Noguchi Shuji , Hayashida Naoki
Published: December 2019

The formation of the isoaspartate (isoAsp) is one of spontaneous degradation processes of proteins, affecting their stability and activity. Here, we report for the first time the crystal structures of an antibody Fab that contains isoAsp in the complementarity-determining region (CDR), along with biochemical studies to detect isoAsp. By comparing the elution profiles of cation-exchange chromatography, it was clarified that the antibody 64M-5 Fab is converted from the normal form to isoAsp form spontaneously and time-dependently under physiological conditions. The isoAsp residue was identified with tryptic peptide mapping, N-terminal sequencing, and the protein isoaspartyl methyltransferase assay. Based on the fluorescence quenching method, the isoAsp form of 64M-5 Fab shows a one order of magnitude lower binding constant for its dinucleotide ligand dT(6–4)T than the normal form. According to the structure of the isoAsp form, the conformation of CDR L1 is changed from the normal form to isoAsp form; the loss of hydrogen bonds involving the Asn28L side-chain, and structural conversion of the β-turn from type I to type II’. The formation of isoAsp leads to a large displacement of the side chain of His27dL, and decreased electrostatic interactions with the phosphate group of dT(6–4)T. Such structural changes should be responsible for the lower affinity of the isoAsp form for dT(6–4)T than the normal form. These findings may provide insight into neurodegenerative diseases (NDDs) and related diseases caused by misfolded proteins.
Early postnatal cardiac manifestations are associated with perinatal brain injury in preterm infants with twin to twin transfusion syndrome
Authors: Cho Hannah , Shin Seung Han , Jun Jong Kwan , Shin Seung Hyun , Kim Yoo-Jin , Kim Seh Hyun , Kim Ee-Kyung , Kim Han-Suk
Published: December 2019

Altered hemodynamics associated with twin to twin transfusion syndrome (TTTS) can be manifested in the fetal and neonatal heart. This study evaluated the association between cardiac manifestations immediately after birth and brain injury in preterm infants with TTTS. Medical records of preterm infants who were born at <35 weeks of gestation with TTTS and admitted to the neonatal intensive care unit at Seoul National University Children’s Hospital between January 2011 and January 2018 were reviewed. TTTS was prenatally diagnosed and staged according to the Quintero criteria. Echocardiographic findings, brain ultrasound and MRI imaging findings were analyzed. Fifty-three infants were enrolled in this study. Thirty-two infants (60.3%) were treated by fetoscopic laser coagulation. Brain injury developed in 15 infants (28.3%). Hypotension within the first week and immediate postnatal cardiac manifestations were more prevalent in the brain injury group. In the multivariate analysis, acute kidney injury and cardiac manifestations, such as ventricular dysfunction and tricuspid regurgitation, were statistically associated with brain injury in the study population. Immediate postnatal cardiac manifestations, such as ventricular dysfunction and tricuspid regurgitation, can serve as surrogate markers for perinatal hemodynamic disturbance, which are associated with early neonatal brain injury in preterm infants with TTTS.
Chronic Disease Onset Among People Living with HIV and AIDS in a Large Private Insurance Claims Dataset
Authors: Yang Hsin-Yun , Beymer Matthew R. , Suen Sze-chuan
Published: December 2019

People living with HIV/AIDS (PLWHA) have a growing life expectancy in the US due to early provision of effective antiretroviral treatment. This has resulted in increasing exposure to age-related chronic illness that may be exacerbated by HIV/AIDS or antiretroviral treatment. Prior work has suggested that PLWHA may be subject to accelerated aging, with earlier onset and higher risk of acquiring many chronic illnesses. However, the magnitude of these effects, controlling for chronic co-morbidities, has not been fully quantified. We evaluate the magnitude of association of HIV infection on developing chronic conditions while controlling for demographics, behavioral risk factors, and chronic comorbidities. We compare chronic disease risks of diabetes, hypertension, stroke, cancers, lung diseases, cardiovascular diseases, and cognitive impairment between PLWHA and HIV- individuals in a large, de-identified private insurance claims dataset (~24,000 PLWHA) using logistic regressions. HIV status is statistically significantly associated with higher levels for all chronic illnesses examined, a result which is robust to multiple model specifications and duration of analysis (2, 5, and 10 years from enrollment). Our results suggest that PLWHA may be at elevated risk for a wide variety of chronic illnesses and may require additional care as the aging PLWHA population grows.
Author Correction: Risk factors for serious morbidity, prolonged length of stay and hospital readmission after laparoscopic appendectomy - results from Pol-LA (Polish Laparoscopic Appendectomy) multicenter large cohort study
Authors: Walędziak Maciej , Lasek Anna , Wysocki Michał , Su Michael , Bobowicz Maciej , Myśliwiec Piotr , Astapczyk Kamil , Burdzel Mateusz , Chruściel Karolina , Cygan Rafał , Czubek Wojciech , Dowgiałło-Wnukiewicz Natalia , Droś Jakub , Franczak Paula , Hołówko Wacław , Kacprzyk Artur , Karcz Wojciech Konrad , Kenig Jakub , Konrad Paweł , Kopiejć Arkadiusz , Kot Adam , Krakowska Karolina , Kukla Maciej , Leszko Agnieszka , Łozowski Leszek , Major Piotr , Makarewicz Wojciech , Malinowska-Torbicz Paulina , Matyja Maciej , Michalik Maciej , Niekurzak Adam , Nowiński Damian , Ostaszewski Radomir , Pabis Małgorzata , Polańska-Płachta Małgorzata , Rubinkiewicz Mateusz , Stefura Tomasz , Stępień Anna , Szabat Paweł , Śmiechowski Rafał , Tomaszewski Sebastian , von Ehrlich-Treuenstätt Viktor , Wasilczuk Maciej , Wierdak Mateusz , Wojdyła Anna , Wroński Jan Wojciech , Zwolakiewicz Leszek , Pędziwiatr Michał
Published: December 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Author Correction: Modeling Snyder-Robinson Syndrome in multipotent stromal cells reveals impaired mitochondrial function as a potential cause for deficient osteogenesis
Authors: Ramsay Ashley L. , Alonso-Garcia Vivian , Chaboya Cutter , Radut Brian , Le Bryan , Florez Jose , Schumacher Cameron , Fierro Fernando A.
Published: December 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Improved Visualization of the Necrotic Zone after Microwave Ablation Using Computed Tomography Volume Perfusion in an In Vivo Porcine Model
Authors: Bressem Keno K. , Vahldiek Janis L. , Erxleben Christoph , Shnayien Seyd , Poch Franz , Geyer Beatrice , Lehmann Kai S. , Hamm B. , Niehues Stefan M.
Published: December 2019

After hepatic microwave ablation, the differentiation between fully necrotic and persistent vital tissue through contrast enhanced CT remains a clinical challenge. Therefore, there is a need to evaluate new imaging modalities, such as CT perfusion (CTP) to improve the visualization of coagulation necrosis. MWA and CTP were prospectively performed in five healthy pigs. After the procedure, the pigs were euthanized, and the livers explanted. Orthogonal histological slices of the ablations were stained with a vital stain, digitalized and the necrotic core was segmented. CTP maps were calculated using a dual-input deconvolution algorithm. The segmented necrotic zones were overlaid on the DICOM images to calculate the accuracy of depiction by CECT/CTP compared to the histological reference standard. A receiver operating characteristic analysis was performed to determine the agreement/true positive rate and disagreement/false discovery rate between CECT/CTP and histology. Standard CECT showed a true positive rate of 81% and a false discovery rate of 52% for display of the coagulation necrosis. Using CTP, delineation of the coagulation necrosis could be improved significantly through the display of hepatic blood volume and hepatic arterial blood flow (p < 0.001). The ratios of true positive rate/false discovery rate were 89%/25% and 90%/50% respectively. Other parameter maps showed an inferior performance compared to CECT.
Polypyrrole-multi walled carbon nanotube hybrid material
supported Pt NPs for hydrogen evolution from the hydrolysis of MeAB at mild
conditions
Authors: Karatas Yasar , Kuyuldar Esra , Acidereli Hilal , Gulcan Mehmet , Sen Fatih
Published: December 2019

Herein, we report a facile method for the preparation of
polypyrrole-multi walled carbon nanotube hybrid material including Pt nanoparticles
(Pt@PPy-MWCNT NPs) and the use in methylamine borane (MeAB) for hydrolysis reaction
at mild conditions. The prepared catalyst of Pt@PPy-MWCNT NPs was characterized by
some advanced analytical methods. The catalytic experiments showed the Pt@PPy-MWCNT
NPs can catalyze MeAB in aquatic solution with high catalytical performance at mild
conditions. The reaction rate of catalytic hydrolysis with Pt@PPy-MWCNT NPs was
found to be
-d[CH3NH2BH3]/dt = + d[H2]/3dt = kobs[Pt@PPy-MWCNT]1.19
[MeAB]0.88. The TOF value for the hydrolysis of MeAB
catalyzed with Pt@PPy-MWCNT NPs was detected to be 10234.2 1/h (170.57 1/min) which
is very high compared with TOF values found for other catalysts. Enthalpy, entropy
and activation energy for the hydrolysis of MeAB were calculated to be
31.57 kJ mol−1,
−119.97 J mol−1 K and
34.27 kJ mol−1, respectively.
Estimating non-additive within-season temperature effects on maize yields using Bayesian approaches
Authors: Yu Jisang , Goh Gyuhyeong
Published: December 2019

Detrimental impacts of extreme heats on the U.S. crop yields have been well-documented by a number of empirical studies. However, less have focused on within-growing season weather variation and the interaction between temperature and precipitation. The objective of this study is to emphasize the importance of disaggregating temperature exposures within growing season. To achieve our objective, we estimate the impact of within-season monthly temperature and precipitation variations on maize yields in the U.S. corn belt region. We provide a discussion on variable selection methods in the context of estimating crop yield responses to climate variables. We find that the models that utilize within-growing season monthly variations performs better compared to the models with growing season aggregated weather variables and show the strength of Bayesian estimations. We also find that the warming impacts predicted by the models that utilize within-growing season variations are smaller than the predicted impacts of the models with aggregated weather variables. The findings indicate that the temperature effects are not additive across months within growing season.
Eugenol prevents fMLF-induced superoxide anion production in human neutrophils by inhibiting ERK1/2 signaling pathway and p47phox phosphorylation
Authors: Chniguir Amina , Pintard Coralie , Liu Dan , Dang Pham My-Chan , El-Benna Jamel , Bachoual Rafik
Published: December 2019

Eugenol is a polyphenol extracted from Syzygium aromaticum essential oil. It is known to have anti-inflammatory and chemoprotective properties as well as a potent anti-oxidant activity due the presence of its phenolic group. In this study, we examined the effects of eugenol on neutrophil superoxide production, a key process involved in innate immunity and inflammation. Superoxide anion generationin human neutrophils was measured by cytochrome c reduction assay. Western blotting was used to analyze the phosphorylation of, p47phox, MAPKinases (p38 and ERK1/2), MEK1/2 and Raf, key proteins involved in the activation of NADPH oxidase. Pretreatment of neutrophils by increasing concentrations (2.5 µg/mL–20 µg/mL) of eugenol for 30 min, inhibited significantly (p < 0.001) superoxide anion generation induced by the chemotactic peptide formyl-Met-Leu-Phe (fMLF) with an IC50 of 5 µg/mL. Phorbolmyristate acetate (PMA)-stimulated O2− production was affected only at the highest eugenol concentration (20 µg/mL). Results showed that eugenol decreased the phosphorylation of p47phox onSer-345 and Ser-328, the translocation of p47phox to the membranesand the phosphorylation of Raf, MEK1/2 and ERK1/2 proteins. Taken together, our results suggest that eugenol inhibits the generation of superoxide anion by neutrophils via the inhibition of Raf/MEK/ERK1/2/p47phox-phosphorylation pathway.
Polymorphisms of MFGE8 are associated with susceptibility and clinical manifestations through gene expression modulation in Koreans with systemic lupus erythematosus
Authors: Baek Wook-Young , Woo Ji-Min , Kim Hyoun-Ah , Jung Ju-Yang , Suh Chang-Hee
Published: December 2019

Systemic lupus erythematosus (SLE) is characterized by impaired clearance of apoptotic cells. Milk fat globule epidermal growth factor 8 (MFGE8) is a protein that connects αvβ3 integrin on phagocytic macrophages with phosphatidylserine on apoptotic cells. We investigated whether genetic variation of the MFGE8 gene and serum MFGE8 concentration are associated with SLE. Single nucleotide polymorphisms (SNPs) were genotyped and serum concentrations were analyzed. The rs2271715 C allele and rs3743388 G allele showed higher frequency in SLE than in healthy subjects (HSs). Three haplotypes were found among 4 SNPs (rs4945, rs1878327, rs2271715, and rs3743388): AACG, CGCG, and CGTC. CGCG haplotype was significantly more common in SLE than in HSs. rs4945 was associated with the erythrocyte sedimentation rate and rs1878327 was associated with alopecia, C-reactive protein, complement 3, anti-dsDNA antibody, and high disease activity. rs2271715 and rs3743388 were associated with renal disease, cumulative glucocorticoid dose, and cyclophosphamide and mycophenolate mofetil use. Serum MFGE8 concentrations were significantly higher in SLE than in HSs. Furthermore, the levels of MFGE8 were significantly higher in SLE than HSs of the rs2271715 CC genotype. In conclusion, MFGE8 genetic polymorphisms are associated not only with susceptibility to SLE but also with disease activity through modulation of gene expression.
Land use change effects on diversity of soil bacterial, Acidobacterial and fungal communities in wetlands of the Sanjiang Plain, northeastern China
Authors: Sui Xin , Zhang Rongtao , Frey Beat , Yang Libin , Li Mai-He , Ni Hongwei
Published: December 2019

The bacterial, acidobacterial, and fungal communities in wetlands can undergo perturbations by various human activities, such as disturbances caused by cultivation and during the process of system restoration. In this study, we investigated the relationships between the composition of the soil bacterial, acidobacterial, and fungal communities and the transformation of wetlands by human activities in the Sanjiang Plain. Soil microbial communities were assessed in wetland soils collected from pristine marsh, neighboring cropland (wetland turned into arable land), and land that had been reforested with Larix gmelinii. The alpha-diversities of bacteria, Acidobacteria, and fungi were affected by land-use change and were highest in the arable land and lowest in the wetland soils. The soil microbial community structures were also altered with changing land-use. Canonical correlation analyses showed that beta-diversity was significantly affected by soil pH, available phosphorus, soil nitrogen, and total organic carbon. Overall, our results showed that the agricultural cultivation of wetlands changes the available soil carbon, nitrogen, and phosphorus pools, thereby influencing the bacterial, acidobacterial, and fungal diversity and community structure. Once the soil microbial community has been altered by human activity, it might be difficult to restore it to its original state. These findings highlight the importance of effectively maintaining the diversity of soil bacterial, Acidobacterial, and fungal communities despite land use change in order to sustain a microbial community diversity and ecosystem function.
Genetic evidence against monophyly of Oniscidea implies a need to revise scenarios for the origin of terrestrial isopods
Authors: Dimitriou Andreas C. , Taiti Stefano , Sfenthourakis Spyros
Published: December 2019

Among the few crustacean taxa that managed to inhabit terrestrial environments, Oniscidea includes the most successful colonizers in terms of species richness and abundance. However, neither morphological traits nor molecular markers have definitively resolved phylogenetic relationships among major Oniscidea clades or established the monophyly of the taxon. Herein, we employed the highly conserved, nuclear protein-coding genes Sodium-Potassium Pump (NAK) and Phosphoenolpyruvate Carboxykinase (PEPCK), along with the traditionally used 18 s and 28 s ribosomal RNA genes, in an attempt to clarify these questions. Our dataset included sequences representing all major Oniscidea clades and closely related aquatic taxa, as suggested by previous studies. We applied Bayesian Inference and Maximum Likelihood methods and produced a robust and fully resolved phylogenetic tree that offers strong evidence against the monophyly of Oniscidea. The amphibious genusLigiaappears to be more closely related to representatives of marine suborders, while the phylogenetic pattern of the remaining Oniscidea implies a complex history of the transition from the marine environment to land. With the exception of the basal clade, all other established major clades have been recovered as monophyletic, even though relationships within these clades call for a revised interpretation of morphological characters used in terrestrial isopod taxonomy.
The origins and implications of glycerol ether lipids in China coastal wetland sediments
Authors: Lü Xiaoxia , Liu Xiaolei , Xu Changgui , Song Jinming , Li Xuegang , Yuan Huamao , Li Ning , Wang Deying , Yuan Hongming , Ye Siyuan
Published: December 2019

Coastal wetlands are terrestrial-marine transition zones harboring diverse active microbial communities. The origins of diverse glycerol ether lipids preserved in coastal wetlands are rarely investigated. 16 surface sediments were collected from the coastal wetland at Guangrao (GR), Changyi (CY) and Xiamen (XM), where both climate and sedimentary environment show significant differences. Ten groups of glycerol ether lipids, including isoprenoidal and branched glycerol dialkyl glycerol tetraethers (iGDGTs and bGDGTs), isoprenoidal and branched glycerol dialkanol diethers (iGDDs and bGDDs), hydroxylated isoprenoidal GDGTs and GDDs (OH-GDGTs and OH-GDDs), overly branched GDGTs (OB-GDGTs), sparsely branched GDGTs (SB-GDGTs), hybrid isoprenoid/branched GDGTs (IB-GDGTs) and a tentatively assigned H-shaped branched GDGTs (H-B-GDGTs) were detected and quantified. Sediments collected in the north (Guangrao and Changyi) contain, in general, a lower abundance of GDGT (3.7–55.9 ng/g sed) than samples from south (Xiamen; 251–1020 ng/g sed). iGDGTs and bGDGTs are the predominant components at all sites and account for 17.2–74.3% and 16.1–75.1% of total ether lipids, respectively. The relative abundance of iGDGTs decreases but that of bGDGTs increases with the distance from sea, suggesting a marine vs. terrestrial origin of iGDGT and bGDGTs, respectively. In addition, the methylation index (MIOB/B/SB) of branched GDGTs shows a significant inverse correlation with water content, suggesting that marine waters have a major influence on the microbial communities inhabiting wetland sediment. Such an assumption was confirmed by the distinct lipid pattern of three low water content (<5%) samples collected in an area isolated from tidal flushing. The other isoprenoidal ether lipids, such as iGDDs, OH-GDGTs and OH-GDGTs, have a similar distribution as iGDGTs, indicating a common biological source, so do the corresponding non-isoprenoidal ether lipid series with bGDGTs. The BIT value increases with increasing distance from the sea, which implies that the BIT index can be probably applied to trace past sea level change in costal wetland settings. The reconstructed temperature from TEX86 shows significant offset from observed data, but only little deviation for the MBT/CBT calculated temperature. This suggests that the MBT/CBT has the potential to reconstruct past temperatures in coastal wetland settings.
Serum levels of gamma-glutamyltransferase predict outcome in heart failure with preserved ejection fraction
Authors: Dalos Daniel , Binder Christina , Duca Franz , Aschauer Stefan , Kammerlander Andreas , Hengstenberg Christian , Mascherbauer Julia , Reiberger Thomas , Bonderman Diana
Published: December 2019

Previous studies suggested an association between heart failure (HF) and hepatic disorders. Liver function parameters have been shown to predict outcome in HF with reduced ejection fraction, but their impact in HF with preserved ejection fraction (HFpEF) has not yet been investigated. Between January 2011 and February 2017, 274 patients with confirmed HFpEF were enrolled (age 71.3 ± 8.4 years, 69.3% female) in a prospective registry. During a median follow-up of 21.5 ± 18.6 months, 97 patients (35.4%) reached the combined endpoint defined as hospitalization due to HF and/ or death from any cause. By multivariable cox regression, serum gamma-glutamyltransferase (GT) was independently associated with outcome (Hazard Ratio (HR) 1.002, p = 0.004) along with N-terminal pro brain natriuretic peptide (HR 2.213, p = 0.001) and hemoglobin (HR 0.840, p = 0.006). Kaplan-Meier analysis showed that patients with serum gamma-GT levels above a median of 36 U/L had significantly more events as compared to the remainder of the group (log-rank p = 0.012). By multivariable logistic regression, higher early mitral inflow velocity/ mitral peak velocity of late filling (Odds Ratio (OR) 2.173, p = 0.024), higher right atrial (RA) pressure (OR 1.139, p < 0.001) and larger RA diameter (OR 1.070, p = 0.001) were independently associated with serum gamma-GT > 36 U/L. Serum levels of gamma-GT are associated with both left and right-sided cardiac alterations and may serve as a simple tool for risk prediction in HFpEF, especially when further diagnostic modalities are not available.