bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermodynamic efficiency in dissipative chemistry
Authors: Penocchio Emanuele , Rao Riccardo , Esposito Massimiliano
Published: August 2019

Chemical processes in closed systems inevitably relax to equilibrium. Living systems avoid this fate and give rise to a much richer diversity of phenomena by operating under nonequilibrium conditions. Recent experiments in dissipative self-assembly also demonstrated that by opening reaction vessels and steering certain concentrations, an ocean of opportunities for artificial synthesis and energy storage emerges. To navigate it, thermodynamic notions of energy, work and dissipation must be established for these open chemical systems. Here, we do so by building upon recent theoretical advances in nonequilibrium statistical physics. As a central outcome, we show how to quantify the efficiency of such chemical operations and lay the foundation for performance analysis of any dissipative chemical process.
ZIKV infection induces robust Th1-like Tfh cell and long-term protective antibody responses in immunocompetent mice
Authors: Liang Huabin , Tang Jinyi , Liu Zhihua , Liu Yuanhua , Huang Yuanyuan , Xu Yongfen , Hao Pei , Yin Zhinan , Zhong Jin , Ye Lilin , Jin Xia , Wang Haikun
Published: August 2019

Induction of long-lived antibody responses during infection or vaccination is often essential for subsequent protection, but the relative contributions of T follicular helper (Tfh) cells and T helper 1 (Th1) cells for induction of antigen specific antibody responses to viruses are unclear. Here, we establish an acute Zika virus (ZIKV) infection model in immunocompetent mice, and show that ZIKV infection elicits robust Th1-like Tfh cell and protective antibody responses. While these Th1-like Tfh cells share phenotypic and transcriptomic profiles with both Tfh and Th1 cells, they also have unique surface markers and gene expression characteristics, and are dependent on T-bet for their development. Th1-like Tfh cells, but not Th1 cells, are essential for class switching of ZIKV-specific IgG2c antibodies and maintenance of long-term neutralizing antibody responses. Our study suggests that specific modulation of the Th1-like Tfh cell response during infection or vaccination may augment the induction of antiviral antibody response to ZIKV and other viruses.
Micro-/nano-voids guided two-stage film cracking on bioinspired assemblies for high-performance electronics
Authors: Miao Weining , Yao Yuxing , Zhang Zhiwei , Ma Chunping , Li Shengzhe , Tang Jiayue , Liu He , Liu Zemin , Wang Dianyu , Camburn Michael A. , Fang Jen-Chun , Hao Ruiran , Fang Xinyu , Zheng Shuang , Hu Nan , Wang Xiaoguang
Published: August 2019

Current metal film-based electronics, while sensitive to external stretching, typically fail via uncontrolled cracking under a relatively small strain (~30%), which restricts their practical applications. To address this, here we report a design approach inspired by the stereocilia bundles of a cochlea that uses a hierarchical assembly of interfacial nanowires to retard penetrating cracking. This structured surface outperforms its flat counterparts in stretchability (130% versus 30% tolerable strain) and maintains high sensitivity (minimum detection of 0.005% strain) in response to external stimuli such as sounds and mechanical forces. The enlarged stretchability is attributed to the two-stage cracking process induced by the synergy of micro-voids and nano-voids. In-situ observation confirms that at low strains micro-voids between nanowire clusters guide the process of crack growth, whereas at large strains new cracks are randomly initiated from nano-voids among individual nanowires.
RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis
Authors: Lange Heike , Ndecky Simon Y. A. , Gomez-Diaz Carlos , Pflieger David , Butel Nicolas , Zumsteg Julie , Kuhn Lauriane , Piermaria Christina , Chicher Johana , Christie Michael , Karaaslan Ezgi S. , Lang Patricia L. M. , Weigel Detlef , Vaucheret Hervé , Hammann Philippe , Gagliardi Dominique
Published: August 2019

The RNA exosome is a key 3’−5’ exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM-repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known Ski subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans.
Cyclin A2 degradation during the spindle assembly checkpoint requires multiple binding modes to the APC/C
Authors: Zhang Suyang , Tischer Thomas , Barford David
Published: August 2019

The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are both targeted for degradation by the APC/C, during the spindle assembly checkpoint (SAC), the mitotic checkpoint complex (MCC) represses APC/C’s activity towards cyclin B1, but not cyclin A2. Through structural, biochemical and in vivo analysis, we identify a non-canonical D box (D2) that is critical for cyclin A2 ubiquitination in vitro and degradation in vivo. During the SAC, cyclin A2 is ubiquitinated by the repressed APC/C-MCC, mediated by the cooperative engagement of its KEN and D2 boxes, ABBA motif, and the cofactor Cks. Once the SAC is satisfied, cyclin A2 binds APC/C-Cdc20 through two mutually exclusive binding modes, resulting in differential ubiquitination efficiency. Our findings reveal that a single substrate can engage an E3 ligase through multiple binding modes, affecting its degradation timing and efficiency.
Dispersion relation of the collective excitations in a resonantly driven polariton fluid
Authors: Stepanov Petr , Amelio Ivan , Rousset Jean-Guy , Bloch Jacqueline , Lemaître Aristide , Amo Alberto , Minguzzi Anna , Carusotto Iacopo , Richard Maxime
Published: August 2019

Exciton-polaritons in semiconductor microcavities constitute the archetypal realization of a quantum fluid of light. Under coherent optical drive, remarkable effects such as superfluidity, dark solitons or the nucleation of vortices have been observed, and can be all understood as specific manifestations of the condensate collective excitations. In this work, we perform a Brillouin scattering experiment to measure their dispersion relation $$\omega ({\bf{k}})$$
ω

(

k

)

directly. The results, such as a speed of sound which is apparently twice too low, cannot be explained upon considering the polariton condensate alone. In a combined theoretical and experimental analysis, we demonstrate that the presence of an excitonic reservoir alongside the polariton condensate has a dramatic influence on the characteristics of the quantum fluid, and explains our measurement quantitatively. This work clarifies the role of such a reservoir in polariton quantum hydrodynamics. It also provides an unambiguous tool to determine the condensate-to-reservoir fraction in the quantum fluid, and sets an accurate framework to approach ideas for polariton-based quantum-optical applications.
Multistep nucleation and growth mechanisms of organic crystals from amorphous solid states
Authors: Chen Hongliang , Li Mingliang , Lu Zheyu , Wang Xiaoge , Yang Junsheng , Wang Zhe , Zhang Fei , Gu Chunhui , Zhang Weining , Sun Yujie , Sun Junliang , Zhu Wenguang , Guo Xuefeng
Published: August 2019

Molecular self-assembly into crystallised films or wires on surfaces produces a big family of motifs exhibiting unique optoelectronic properties. However, little attention has been paid to the fundamental mechanism of molecular crystallisation. Here we report a biomimetic design of phosphonate engineered, amphiphilic organic semiconductors capable of self–assembly, which enables us to use real-time in-situ scanning probe microscopy to monitor the growth trajectories of such organic semiconducting films as they nucleate and crystallise from amorphous solid states. The single-crystal film grows through an evolutionary selection approach in a two-dimensional geometry, with five distinct steps: droplet flattening, film coalescence, spinodal decomposition, Ostwald ripening, and self-reorganised layer growth. These sophisticated processes afford ultralong high-density microwire arrays with high mobilities, thus promoting deep understanding of the mechanism as well as offering important insights into the design and development of functional high-performance organic optoelectronic materials and devices through molecular and crystal engineering.
Biofilm formation inhibition and dispersal of multi-species communities containing ammonia-oxidising bacteria
Authors: Keshvardoust Pejhman , Huron Vanessa A. A. , Clemson Matthew , Constancias Florentin , Barraud Nicolas , Rice Scott A.
Published: August 2019

Despite considerable research, the biofilm-forming capabilities of Nitrosomonas europaea are poorly understood for both mono and mixed-species communities. This study combined biofilm assays and molecular techniques to demonstrate that N. europaea makes very little biofilm on its own, and relies on the activity of associated heterotrophic bacteria to establish a biofilm. However, N. europaea has a vital role in the proliferation of mixed-species communities under carbon-limited conditions, such as in drinking water distribution systems, through the provision of organic carbon via ammonia oxidation. Results show that the addition of nitrification inhibitors to mixed-species nitrifying cultures under carbon-limited conditions disrupted biofilm formation and caused the dispersal of pre-formed biofilms. This dispersal effect was not observed when an organic carbon source, glucose, was included in the medium. Interestingly, inhibition of nitrification activity of these mixed-species biofilms in the presence of added glucose resulted in increased total biofilm formation compared to controls without the addition of nitrification inhibitors, or with only glucose added. This suggests that active AOB partially suppress or limit the overall growth of the heterotrophic bacteria. The experimental model developed here provides evidence that ammonia-oxidising bacteria (AOB) are involved in both the formation and maintenance of multi-species biofilm communities. The results demonstrate that the activity of the AOB not only support the growth and biofilm formation of heterotrophic bacteria by providing organic carbon, but also restrict and limit total biomass in mixed community systems.
Quantum topology identification with deep neural networks and quantum walks
Authors: Ming Yurui , Lin Chin-Teng , Bartlett Stephen D. , Zhang Wei-Wei
Published: August 2019

Topologically ordered materials may serve as a platform for new quantum technologies, such as fault-tolerant quantum computers. To fulfil this promise, efficient and general methods are needed to discover and classify new topological phases of matter. We demonstrate that deep neural networks augmented with external memory can use the density profiles formed in quantum walks to efficiently identify properties of a topological phase as well as phase transitions. On a trial topological ordered model, our method’s accuracy of topological phase identification reaches 97.4%, and is shown to be robust to noise on the data. Furthermore, we demonstrate that our trained DNN is able to identify topological phases of a perturbed model, and predict the corresponding shift of topological phase transitions without learning any information about the perturbations in advance. These results demonstrate that our approach is generally applicable and may be used to identify a variety of quantum topological materials.
Deformed wing virus type A, a major honey bee pathogen, is vectored by the mite Varroa destructor in a non-propagative manner
Authors: Posada-Florez Francisco , Childers Anna K. , Heerman Matthew C. , Egekwu Noble I. , Cook Steven C. , Chen Yanping , Evans Jay D. , Ryabov Eugene V.
Published: August 2019

Honey bees, the primary managed insect pollinator, suffer considerable losses due to Deformed wing virus (DWV), an RNA virus vectored by the mite Varroa destructor. Mite vectoring has resulted in the emergence of virulent DWV variants. The basis for such changes in DWV is poorly understood. Most importantly, it remains unclear whether replication of DWV occurs in the mite. In this study, we exposed Varroa mites to DWV type A via feeding on artificially infected honey bees. A significant, 357-fold increase in DWV load was observed in these mites after 2 days. However, after 8 additional days of passage on honey bee pupae with low viral loads, the DWV load dropped by 29-fold. This decrease significantly reduced the mites’ ability to transmit DWV to honey bees. Notably, negative-strand DWV RNA, which could indicate viral replication, was detected only in mites collected from pupae with high DWV levels but not in the passaged mites. We also found that Varroa mites contain honey bee mRNAs, consistent with the acquisition of honey bee cells which would additionally contain DWV replication complexes with negative-strand DWV RNA. We propose that transmission of DWV type A by Varroa mites occurs in a non-propagative manner.
Production of WW males lacking the masculine Z chromosome and mining the Macrobrachium rosenbergii genome for sex-chromosomes
Authors: Levy Tom , Rosen Ohad , Manor Rivka , Dotan Shahar , Azulay Dudu , Abramov Anna , Sklarz Menachem Y. , Chalifa-Caspi Vered , Baruch Kobi , Shechter Assaf , Sagi Amir
Published: August 2019

The cultivation of monosex populations is common in animal husbandry. However, preselecting the desired gender remains a major biotechnological and ethical challenge. To achieve an efficient biotechnology for all-female aquaculture in the economically important prawn (Macrobrachium rosenbergii), we achieved – for the first time – WW males using androgenic gland cells transplantation which caused full sex-reversal of WW females to functional males. Crossing the WW males with WW females yielded all-female progeny lacking the Z chromosome. We now have the ability to manipulate – by non-genomic means – all possible genotype combinations (ZZ, WZ and WW) to retain either male or female phenotypes and hence to produce monosex populations of either gender. This calls for a study of the genomic basis underlying this striking sexual plasticity, questioning the content of the W and Z chromosomes. Here, we report on the sequencing of a high-quality genome exhibiting distinguishable paternal and maternal sequences. This assembly covers ~ 87.5% of the genome and yielded a remarkable N50 value of ~ 20 × 106 bp. Genomic sex markers were used to initiate the identification and validation of parts of the W and Z chromosomes for the first time in arthropods.
Vimentin regulates Notch signaling strength and arterial remodeling in response to hemodynamic stress
Authors: van Engeland Nicole C. A. , Suarez Rodriguez Freddy , Rivero-Müller Adolfo , Ristori Tommaso , Duran Camille L. , Stassen Oscar M. J. A. , Antfolk Daniel , Driessen Rob C. H. , Ruohonen Saku , Ruohonen Suvi T. , Nuutinen Salla , Savontaus Eriika , Loerakker Sandra , Bayless Kayla J. , Sjöqvist Marika , Bouten Carlijn V. C. , Eriksson John E. , Sahlgren Cecilia M.
Published: August 2019

The intermediate filament (IF) cytoskeleton has been proposed to regulate morphogenic processes by integrating the cell fate signaling machinery with mechanical cues. Signaling between endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) through the Notch pathway regulates arterial remodeling in response to changes in blood flow. Here we show that the IF-protein vimentin regulates Notch signaling strength and arterial remodeling in response to hemodynamic forces. Vimentin is important for Notch transactivation by ECs and vimentin knockout mice (VimKO) display disrupted VSMC differentiation and adverse remodeling in aortic explants and in vivo. Shear stress increases Jagged1 levels and Notch activation in a vimentin-dependent manner. Shear stress induces phosphorylation of vimentin at serine 38 and phosphorylated vimentin interacts with Jagged1 and increases Notch activation potential. Reduced Jagged1-Notch transactivation strength disrupts lateral signal induction through the arterial wall leading to adverse remodeling. Taken together we demonstrate that vimentin forms a central part of a mechanochemical transduction pathway that regulates multilayer communication and structural homeostasis of the arterial wall.
Prevalence, awareness, treatment, and control of hypertension and their determinants: Results from the first cohort of non-communicable diseases in a Kurdish settlement
Authors: Rajati Fatemeh , Hamzeh Behrooz , Pasdar Yahya , Safari Roya , Moradinazar Mehdi , Shakiba Ebrahim , Bazargan-Hejazi Shahrzad , Karim Hossein , Najafi Farid
Published: August 2019

Hypertension is a public health issue in Iran. The study aimed to estimate the prevalence, awareness, treatment, and control of hypertension, and to explore their determinants among 10,040 Kurdish adults from Ravansar Non-Communicable Disease (RaNCD) cohort study in Iran. Univariate, and multivariate analyses were used for statistical analysis. Prevalence of hypertension was 15.7%. Among hypertensive patients, awareness, treatment, and control of hypertension were 80.7%, 73.2%, and 53.3%, respectively. In multivariate analysis, significant associations were found between awareness and female sex, older age, being married rather than being single, literacy, living in rural areas, having family history, and comorbidities, with a higher probability for those who had both diabetes and dyslipidemia. Being married, living in rural areas, being ex-smokers, having less physical activity and individuals who had diabetes and dyslipidemia had higher odds of receiving treatment. Being female had a statistically significant association with the control of hypertension. The Kurdish population had higher awareness, with a greater proportion of treated, and controlled patients compared to populations included in previous studies for the last 20 years in Iran. With the continuing health promotion programs in Iran, it is expected to observe a lower prevalence of hypertension, higher awareness and greater number of treated individuals with controlled hypertension.
The effects of di-butyl phthalate exposure from medications on human sperm RNA among men
Authors: Estill Molly , Hauser Russ , Nassan Feiby L. , Moss Alan , Krawetz Stephen A.
Published: August 2019

Endocrine disruptors, such as phthalates, are suspected of affecting reproductive function. The Mesalamine and Reproductive Health Study (MARS) was designed to address the physiological effect of in vivo phthalate exposure on male reproduction in patients with Inflammatory Bowel Disease (IBD). As part of this effort, the effect on sperm RNAs to DBP exposure were longitudinally assessed using a cross-over cross-back binary design of high or background, exposures to DBP. As the DBP level was altered, numerous sperm RNA elements (REs) were differentially expressed, suggesting that exposure to or removal from high DBP produces effects that require longer than one spermatogenic cycle to resolve. In comparison, small RNAs were minimally affected by DBP exposure. While initial study medication (high or background) implicates different biological pathways, initiation on the high-DBP condition activated oxidative stress and DNA damage pathways. The negative correlation of REs with specific genomic repeats suggests a regulatory role. Using ejaculated sperm, this work provides insight into the male germline’s response to phthalate exposure.
CCM1 and CCM2 variants in patients with cerebral cavernous malformation in an ethnically Chinese population in Taiwan
Authors: Chang Chun-Wei , Hsu Peng-Wei , Wei Kuo-Chen , Chang Chia-Wen , Fung Hon-Chung , Hsih Mo-Song , Hsu Wen-Chuin , Ro Long-Sun , Chang Chen-Nen , Wang Jiun-Jie , Wu Yih-Ru , Chen Sien-Tsong
Published: August 2019

Cerebral cavernous malformation (CCM) is a vascular malformation characterized by clustered enlarged capillary-like channels in the central nervous system. The genes harboring variants in patients with CCM includeCCM1/Krev interaction trapped-1,CCM2/MGC4607, andCCM3/programmed cell death protein 10. We aimed to identify pathogenic variants in an ethnic Chinese population in Taiwan. We recruited 95 patients with multiple CCMs or a single lesion with a relevant family history. Sanger sequencing was performed for 41 patients. Variants were identified using sequence alignment tools, and the clinical significance of these variants was determined using American College of Medical Genetics and Genomics standards and guidelines. Several pathogenic variants were found in six patients, including three unrelated patients and three affected members of one family. Two novel pathogenic variants leading to early truncation comprised a deletion variant in exon 18 ofCCM1(c.1846delA; p.Glu617LysfsTer44) and an insertion variant in exon 4 ofCCM2(c.401_402insGCCC; p.Ile136AlafsTer4). One novel pathogenic splice site variant was c.485 + 1G > C at the beginning of intron 8 ofCCM1. In this study, we identified novel variants related to CCM in an ethnically Chinese population in Taiwan.
Continuous-variable Quantum Phase Estimation based on Machine Learning
Authors: Xiao Tailong , Huang Jingzheng , Fan Jianping , Zeng Guihua
Published: August 2019

Making use of the general physical model of the Mach-Zehnder interferometer with photon loss which is a fundamental physical issue, we investigate the continuous-variable quantum phase estimation based on machine learning approach, and an efficient recursive Bayesian estimation algorithm for Gaussian states phase estimation has been proposed. With the proposed algorithm, the performance of the phase estimation may be improved distinguishably. For example, the physical limits (i.e., the standard quantum limit and Heisenberg limit) for the phase estimation precision may be reached in more efficient ways especially in the situation of the prior information being employed, the range for the estimated phase parameter can be extended from [0, π/2] to [0, 2π] compared with the conventional approach, and influences of the photon losses on the output parameter estimation precision may be suppressed dramatically in terms of saturating the lossy bound. In addition, the proposed algorithm can be extended to the time-variable or multi-parameter estimation framework.
Two-Dimensional Brain Microtubule Structures Behave as Memristive Devices
Authors: Cantero María del Rocío , Perez Paula L. , Scarinci Noelia , Cantiello Horacio F.
Published: August 2019

Microtubules (MTs) are cytoskeletal structures that play a central role in a variety of cell functions including cell division and cargo transfer. MTs are also nonlinear electrical transmission lines that produce and conduct electrical oscillations elicited by changes in either electric field and/or ionic gradients. The oscillatory behavior of MTs requires a voltage-sensitive gating mechanism to enable the electrodiffusional ionic movement through the MT wall. Here we explored the electrical response of non-oscillating rat brain MT sheets to square voltage steps. To ascertain the nature of the possible gating mechanism, the electrical response of non-oscillating rat brain MT sheets (2D arrays of MTs) to square pulses was analyzed under voltage-clamping conditions. A complex voltage-dependent nonlinear charge movement was observed, which represented the summation of two events. The first contribution was a small, saturating, voltage-dependent capacitance with a maximum charge displacement in the range of 4 fC/μm2. A second, major contribution was a non-saturating voltage-dependent charge transfer, consistent with the properties of a multistep memristive device. The memristive capabilities of MTs could drive oscillatory behavior, and enable voltage-driven neuromorphic circuits and architectures within neurons.
Pressure accelerates the circadian clock of cyanobacteria
Authors: Kitahara Ryo , Oyama Katsuaki , Kawamura Takahiro , Mitsuhashi Keita , Kitazawa Soichiro , Yasunaga Kazuhiro , Sagara Natsuno , Fujimoto Megumi , Terauchi Kazuki
Published: August 2019

Although organisms are exposed to various pressure and temperature conditions, information remains limited on how pressure affects biological rhythms. This study investigated how hydrostatic pressure affects the circadian clock (KaiA, KaiB, and KaiC) of cyanobacteria. While the circadian rhythm is inherently robust to temperature change, KaiC phosphorylation cycles that were accelerated from 22 h at 1 bar to 14 h at 200 bars caused the circadian-period length to decline. This decline was caused by the pressure-induced enhancement of KaiC ATPase activity and allosteric effects. Because ATPase activity was elevated in the CI and CII domains of KaiC, while ATP hydrolysis had negative activation volumes (ΔV≠), both domains played key roles in determining the period length of the KaiC phosphorylation cycle. The thermodynamic contraction of the structure of the active site during the transition state might have positioned catalytic residues and lytic water molecules favourably to facilitate ATP hydrolysis. Internal cavities might represent sources of compaction and structural rearrangement in the active site. Overall, the data indicate that pressure differences could alter the circadian rhythms of diverse organisms with evolved thermotolerance, as long as enzymatic reactions defining period length have a specific activation volume.
Photonic scheme of discrete quantum Fourier transform for quantum algorithms via quantum dots
Authors: Heo Jino , Won Kitak , Yang Hyung-Jin , Hong Jong-Phil , Choi Seong-Gon
Published: August 2019

We propose an optical scheme of discrete quantum Fourier transform (DQFT) via ancillary systems using quantum dots (QDs) confined in single-sided cavities (QD-cavity systems). In our DQFT scheme, the main component is a controlled-rotation k (CRk) gate, which utilizes the interactions between photons and QDs, consisting of two QD-cavity systems. Since the proposed CRk gate can be experimentally implemented with high efficiency and reliable performance, the scalability of multi-qubit DQFT scheme can also be realized through the simple composition of the proposed CRk gates via the QD-cavity systems. Subsequently, in order to demonstrate the performance of the CRk gate, we analyze the interaction between a photon and a QD-cavity system, and then indicate the condition to be efficient CRk gate with feasibility under vacuum noise and sideband leakage.
PET/MRI in large-vessel vasculitis: clinical value for diagnosis and assessment of disease activity
Authors: Laurent Charlotte , Ricard Laure , Fain Olivier , Buvat Irene , Adedjouma Amir , Soussan Michael , Mekinian Arsène
Published: August 2019

Diagnosis of large vessel vasculitis (LVV) and evaluation of its inflammatory activity can be challenging. Our aim was to investigate the value of hybrid positron-emission tomography/magnetic resonance imaging (PET/MRI) in LVV. All consecutive patients with LVV from the Department of Internal Medicine who underwent PET/MRI were included. Three PET/MRI patterns were defined: (i) “inflammatory,” with positive PET (>liver uptake) and abnormal MRI (stenosis and/or wall thickening); (ii) “fibrous”, negative PET (≤liver uptake) and abnormal MRI; and (iii) “normal”. Thirteen patients (10 female; median age: 67-years [range: 23–87]) underwent 18 PET/MRI scans. PET/MRI was performed at diagnosis (n = 4), at relapse (n = 7), or during remission (n = 7). Among the 18 scans, eight (44%) showed an inflammatory pattern and three (17%) a fibrous pattern; the other seven were normal. The distribution of the three patterns did not differ between patients with Takayasu arteritis (TA, n = 10 scans) and those with giant cell arteritis (GCA, n = 8 scans). PET/MRI findings were normal in 2/10 (20%) TA scans vs. 5/8 (62%) GCA scans (p = 0.3). Median SUVmax was 4.7 [2.1–8.6] vs. 2 [1.8–2.6] in patients with active disease vs. remission, respectively (p = 0.003). PET/MRI is a new hybrid imaging modality allowing comprehensive and multimodal analysis of vascular wall inflammation and the vascular lumen. This technique offers promising perspectives for the diagnosis and monitoring of LVV.
Albumin evokes Ca2+-induced cell oxidative stress and apoptosis through TRPM2 channel in renal collecting duct cells reduced by curcumin
Authors: Nazıroğlu Mustafa , Çiğ Bilal , Yazğan Yener , Schwaerzer Gerburg K. , Theilig Franziska , Pecze László
Published: August 2019

In proteinuric nephropathies of chronic kidney disease, the epithelial cells of the nephron including the collecting duct are exposed to high concentrations of luminal albumin. Albumin is taken up from collecting duct cells by endocytosis causing excessive reactive oxygen species (ROS) production and a proinflammatory response. Curcumin used in the traditional medicine possesses anti-inflammatory and antioxidant effects. ROS and ADP-ribose (ADPR) activate the cation channel TRPM2. We hypothesize, that albumin-induced cell stress and proinflammatory response are mediated by Ca2+ and can be reduced by curcumin. The cortical collecting duct (CCD) cells mpkCCDc14 exhibit spontaneous and inducible Ca2+ oscillations, which can be blocked by pre-treatment with curcumin. Curcumin accumulates in plasma membrane and intracellular vesicles, where it interferes with TRPM2 and decreases the influx of Ca2+. Albumin reduces cell viability and increases apoptosis, NF-κB activation, and mitochondrial membrane depolarization via Ca2+-dependent signaling, which results in increased ROS production. Albumin-induced cell stress is diminished by the inhibition of TRPM2 after administration of curcumin and ADPR (PARP1) inhibitors. Curcumin did not reduce the Ca2+ elevation induced by thapsigargin in Ca2+-free medium, but it reduced the function of store-operated Ca2+ channels and ATP-evoked Ca2+ response. In conclusion, albumin-induced oxidative stress is mediated by Ca2+-dependent signaling via TRPM2 and leads to cell damage and a proinflammatory response, strengthening the role of CCD cells in the progression of chronic kidney disease.
RETRACTED ARTICLE: Investigating the Heteronjunction between ZnO/Fe2O3 and g-C3N4 for an Enhanced Photocatalytic H2 production under visible-light irradiation
Authors: Mao Na
Published: August 2019

A series of ZnO/Fe2O3/g-C3N4 photocatalysts were synthetized by impregnation of g-C3N4 with Zn(NO3)2·6H2O, and Fe(NO3)2·9H2O followed by calcination. The morphology, chemical composition, and structure of the resulted materials were carefully analyzed by various characterization techniques. The photocatalytic performance of ZnO/Fe2O3/g-C3N4 composites was evaluated based on the H2 evolution from water splitting reaction. The results showed that the ZnO/Fe2O3/g-C3N4 composite can effectively produce more H2 than pure g-C3N4 when irradiated under visible-light. H2 production rate over 3-ZnO/Fe2O3/g-C3N4 composite was of 25 μmol·h−1, which is 4 times higher than that obtained in the presence of pure g-C3N4, clearly showing a significant improvement of the photocatalytic activity of the prepared nanocomposite. This result was attributed to the formation of a heterojunction between g-C3N4 and ZnO/Fe2O3, which delayed the recombination of holes-electrons pairs and resulted in a remarkable increase in photocatalytic performance.
SerpinB2 inhibits migration and promotes a resolution phase signature in large peritoneal macrophages
Authors: Schroder Wayne A. , Hirata Thiago D. , Le Thuy T. , Gardner Joy , Boyle Glen M. , Ellis Jonathan , Nakayama Eri , Pathirana Dilan , Nakaya Helder I. , Suhrbier Andreas
Published: August 2019

SerpinB2 (plasminogen activator inhibitor type 2) has been called the “undecided serpin” with no clear consensus on its physiological role, although it is well described as an inhibitor of urokinase plasminogen activator (uPA). In macrophages, pro-inflammatory stimuli usually induce SerpinB2; however, expression is constitutive in Gata6+ large peritoneal macrophages (LPM). Interrogation of expression data from human macrophages treated with a range of stimuli using a new bioinformatics tool, CEMiTool, suggested that SerpinB2 is most tightly co- and counter-regulated with genes associated with cell movement. Using LPM from SerpinB2−/− and SerpinB2R380A (active site mutant) mice, we show that migration on Matrigel was faster than for their wild-type controls. Confocal microscopy illustrated that SerpinB2 and F-actin staining overlapped in focal adhesions and lamellipodia. Genes associated with migration and extracellular matrix interactions were also identified by RNA-Seq analysis of migrating RPM from wild-type and SerpinB2R380A mice. Subsequent gene set enrichment analyses (GSEA) suggested SerpinB2 counter-regulates many Gata6-regulated genes associated with migration. These data argue that the role of SerpinB2 in macrophages is inhibition of uPA-mediated plasmin generation during cell migration. GSEA also suggested that SerpinB2 expression (likely via ensuing modulation of uPA-receptor/integrin signaling) promotes the adoption of a resolution phase signature.
Euler-Lagrange Prediction of Diesel-Exhaust Polydisperse Particle Transport and Deposition in Lung: Anatomy and Turbulence Effects
Authors: Islam Mohammad S. , Saha Suvash C. , Gemci Tevfik , Yang Ian A. , Sauret Emilie , Ristovski Zoran , Gu Y. T.
Published: August 2019

In clinical assessments, the correlation between atmospheric air pollution and respiratory damage is highly complicated. Epidemiological studies show that atmospheric air pollution is largely responsible for the global proliferation of pulmonary disease. This is particularly significant, since most Computational Fluid Dynamics (CFD) studies to date have used monodisperse particles, which may not accurately reflect realistic inhalation patterns, since atmospheric aerosols are mostly polydisperse. The aim of this study is to investigate the anatomy and turbulent effects on polydisperse particle transport and deposition (TD) in the upper airways. The Euler-Lagrange approach is used for polydisperse particle TD prediction in both laminar and turbulent conditions. Various anatomical models are adopted to investigate the polydisperse particle TD under different flow conditions. Rossin-Rammler diameter distribution is used for the distribution of the initial particle diameter. The numerical results illustrate that airflow rate distribution at the right lung of a realistic model is higher than a non-realistic model. The CFD study also shows that turbulence effects on deposition are higher for larger diameter particles than with particles of smaller diameter. A significant amount of polydisperse particles are also shown to be deposited at the tracheal wall for CT-based model, whereas particles are mostly deposited at the carinal angle for the non-realistic model. A comprehensive, polydisperse particle TD analysis would enhance understanding of the realistic deposition pattern and decrease unwanted therapeutic aerosol deposition at the extrathoracic airways.
Prediction of future gastric cancer risk using a machine learning algorithm and comprehensive medical check-up data: A case-control study
Authors: Taninaga Junichi , Nishiyama Yu , Fujibayashi Kazutoshi , Gunji Toshiaki , Sasabe Noriko , Iijima Kimiko , Naito Toshio
Published: August 2019

A comprehensive screening method using machine learning and many factors (biological characteristics, Helicobacter pylori infection status, endoscopic findings and blood test results), accumulated daily as data in hospitals, could improve the accuracy of screening to classify patients at high or low risk of developing gastric cancer. We used XGBoost, a classification method known for achieving numerous winning solutions in data analysis competitions, to capture nonlinear relations among many input variables and outcomes using the boosting approach to machine learning. Longitudinal and comprehensive medical check-up data were collected from 25,942 participants who underwent multiple endoscopies from 2006 to 2017 at a single facility in Japan. The participants were classified into a case group (y = 1) or a control group (y = 0) if gastric cancer was or was not detected, respectively, during a 122-month period. Among 1,431 total participants (89 cases and 1,342 controls), 1,144 (80%) were randomly selected for use in training 10 classification models; the remaining 287 (20%) were used to evaluate the models. The results showed that XGBoost outperformed logistic regression and showed the highest area under the curve value (0.899). Accumulating more data in the facility and performing further analyses including other input variables may help expand the clinical utility.
Homogeneous sulfur isotope signature in East Antarctica and implication for sulfur source shifts through the last glacial-interglacial cycle
Authors: Ishino Sakiko , Hattori Shohei , Savarino Joel , Legrand Michel , Albalat Emmanuelle , Albarede Francis , Preunkert Susanne , Jourdain Bruno , Yoshida Naohiro
Published: August 2019

Sulfate aerosol (SO42−) preserved in Antarctic ice cores is discussed in the light of interactions between marine biological activity and climate since it is mainly sourced from biogenic emissions from the surface ocean and scatters solar radiation during traveling in the atmosphere. However, there has been a paradox between the ice core record and the marine sediment record; the former shows constant non-sea-salt (nss-) SO42− flux throughout the glacial-interglacial changes, and the latter shows a decrease in biogenic productivity during glacial periods compared to interglacial periods. Here, by ensuring the homogeneity of sulfur isotopic compositions of atmospheric nss-SO42− (δ34Snss) over East Antarctica, we established the applicability of the signature as a robust tool for distinguishing marine biogenic and nonmarine biogenic SO42−. Our findings, in conjunction with existing records of nss-SO42− flux and δ34Snss in Antarctic ice cores, provide an estimate of the relative importance of marine biogenic SO42− during the last glacial period to be 48 ± 10% of nss-SO42−, slightly lower than 59 ± 11% during the interglacial periods. Thus, our results tend to reconcile the ice core and sediment records, with both suggesting the decrease in marine productivity around Southern Ocean under the cold climate.
Non-diagnostic Results of Percutaneous Transthoracic Needle Biopsy: A Meta-analysis
Authors: Chae Kum Ju , Hong Hyunsook , Yoon Soon Ho , Hahn Seokyung , Jin Gong Yong , Park Chang Min , Goo Jin Mo
Published: August 2019

Non-diagnostic results can affect the diagnostic performance of percutaneous transthoracic needle biopsy (PTNB) but have not been critically meta-analyzed yet. To meta-analyze the incidence and malignancy rate of non-diagnostic results, 3-by-2 table approaches rather than the conventional 2-by-2 approaches are needed to know its impact on the diagnostic performance of PTNB. A systematic literature search identified studies evaluating the diagnostic performance of PTNB with extractable outcomes. A total of 143 studies with 35,059 biopsies were included. The pooled incidence of non-diagnostic results was 6.8% (95% CI, 6.0–7.6%; I2 = 0.91). The pooled malignancy rate of non-diagnostic results was 59.3% (95% CI, 51.7–66.8%; I2 = 0.80), and was correlated with the prevalence of malignancy (correlation coefficient, 0.66; 95% CI, 0.42–0.91). Pooled percentage decrease of sensitivity and specificity due to non-diagnostic results were 4.5% (95% CI, 3.2–5.7%; I2 = 0.64) and 10.7% (95% CI, 7.7–13.7%; I2 = 0.70), respectively, and the pooled incidence of non-diagnostic results was 4.4% (95% CI, 3.2–5.8%; I2 = 0.83) in lesions ultimately diagnosed as malignancies and 10.4% (95% CI, 7.5–13.8%; I2 = 0.74) in benign disease. In conclusion, non-diagnostic results averagely occurred in 6.8% of PTNB and more than half of the results were malignancies. The non-diagnostic results decreased specificity and sensitivity by 10.7% and 4.5%, respectively, demanding efforts to minimize the non-diagnostic results in PTNB.
Principles of open source bioinstrumentation applied to the poseidon syringe pump system
Authors: Booeshaghi A. Sina , Beltrame Eduardo da Veiga , Bannon Dylan , Gehring Jase , Pachter Lior
Published: August 2019

The poseidon syringe pump and microscope system is an open source alternative to commercial systems. It costs less than $400 and can be assembled in under an hour using the instructions and source files available at https://pachterlab.github.io/poseidon. We describe the poseidon system and use it to illustrate design principles that can facilitate the adoption and development of open source bioinstruments. The principles are functionality, robustness, safety, simplicity, modularity, benchmarking, and documentation.
Association between visual function and the integrity of residual ellipsoid zone in resolved central serous chorioretinopathy
Authors: Fujita Asahi , Aoyama Yurika , Tsuneyoshi Saori , Sugiura Aya , Azuma Keiko , Asano-Shimizu Kimiko , Soga Hirotsugu , Hashimoto Yohei , Asaoka Ryo , Inoue Tatsuya , Obata Ryo
Published: August 2019

Central serous chorioretinopathy (CSC) usually resolves spontaneously; however, in some patients, it can be chronic and visual impairment remains even after resolution of the serous retinal detachment. The impaired photoreceptor cells often present with disrupted ellipsoid zone (EZ) on optical coherence tomography (OCT). In this study, the integrity of EZ was quantified by calculating the index of residual EZ, identified on binarized OCT images from 25 eyes of 23 patients with resolved CSC. To estimate residual EZ, integrity of residual EZ with the central horizontal line on the fovea (rEZc) and average integrity of residual EZ within 3 × 3-mm macular area (rEZave) were investigated. The interrater reliability of the method was assessed using the intraclass correlation coefficient (ICC). The relationship between LogMAR VA and age, central retinal thickness, central choroidal thickness, rEZc, and rEZave were evaluated using the linear mixed model. Retinal sensitivity was measured with the MP-3 microperimeter and similar analyses were iterated for mean retinal sensitivity (MS). ICC values were 0.938 with rEZc and 0.979 with rEZave. rEZc was significantly related to LogMAR VA (p = 0.039). rEZave was significantly related to MS (p < 0.001). These results suggested potential usefulness of residual EZ to predict visual function in resolved CSC.
SQUID-based ultralow-field MRI of a hyperpolarized material using signal amplification by reversible exchange
Authors: Lee Seong-Joo , Jeong Keunhong , Shim Jeong Hyun , Lee Hyun Joon , Min Sein , Chae Heelim , Namgoong Sung Keon , Kim Kiwoong
Published: August 2019

The signal amplification by reversible exchange (SABRE) technique is a very promising method for increasing magnetic resonance (MR) signals. SABRE can play a particularly large role in studies with a low or ultralow magnetic field because they suffer from a low signal-to-noise ratio. In this work, we conducted real-time superconducting quantum interference device (SQUID)-based nuclear magnetic resonance (NMR)/magnetic resonance imaging (MRI) studies in a microtesla-range magnetic field using the SABRE technique after designing a bubble-separated phantom. A maximum enhancement of 2658 for 1H was obtained for pyridine in the SABRE-NMR experiment. A clear SABRE-enhanced MR image of the bubble-separated phantom, in which the para-hydrogen gas was bubbling at only the margin, was successfully obtained at 34.3 μT. The results show that SABRE can be successfully incorporated into an ultralow-field MRI system, which enables new SQUID-based MRI applications. SABRE can shorten the MRI operation time by more than 6 orders of magnitude and establish a firm basis for future low-field MRI applications.
Spontaneous mutations of the Zpld1 gene in mice cause semicircular canal dysfunction but do not impair gravity receptor or hearing functions
Authors: Vijayakumar Sarath , Jones Sherri M. , Jones Timothy A. , Tian Cong , Johnson Kenneth R.
Published: August 2019

The cupula is a gelatinous membrane overlying the crista ampullaris of the semicircular canal, important for sensing rotation of the head and critical for normal balance. Recently the zona pellucida like domain containing 1 protein (ZPLD1, also known as cupulin) was identified in the cupula of fish. Here, we describe two new spontaneous mutations in the mouse Zpld1 gene, which were discovered by the circling behavior of mutant mice, an indicator of balance dysfunction. The Zpld1 mutant mice exhibited normal hearing function as assessed by auditory brainstem response (ABR) measurements, and their otolithic organs appeared normal. In the inner ear, Zpld1 mRNA expression was detected only in the hair cells and supporting cells of the crista ampullaris. Normal vestibular sensory evoked potential (VsEP) responses and abnormal vestibulo-ocular reflex (VOR) responses demonstrated that the vestibular dysfunction of the Zpld1 mutant mice is caused by loss of sensory input for rotary head movements (detected by cristae ampullaris) and not by loss of input for linear head translations (detected by maculae of the utricle and saccule). Taken together, these results are consistent with ZPLD1 being an important functional component of the cupula, but not tectorial or otoconial membranes.
Live-cell STED nanoscopy of mitochondrial cristae
Authors: Stephan Till , Roesch Axel , Riedel Dietmar , Jakobs Stefan
Published: August 2019

Mitochondria are highly dynamic organelles that exhibit a complex inner architecture. They exhibit a smooth outer membrane and a highly convoluted inner membrane that forms invaginations called cristae. Imaging cristae in living cells poses a formidable challenge for super-resolution light microscopy. Relying on a cell line stably expressing the mitochondrial protein COX8A fused to the SNAP-tag and using STED (stimulated emission depletion) nanoscopy, we demonstrate the visualization of cristae dynamics in cultivated human cells. We show that in human HeLa cells lamellar cristae are often arranged in groups separated by voids that are generally occupied by mitochondrial nucleoids.