bluuebunny/crossref_metadata_2025_split huggingface dataset:
Factors explaining the yearly changes in minimum bottom dissolved oxygen concentrations in Lake Biwa, a warm monomictic lake
Authors: Fukushima Takehiko , Inomata Tomohiro , Komatsu Eiji , Matsushita Bunkei 
Published: January 2019

AbstractVertical profiles of dissolved oxygen (DO) and water temperature (WT) measured bi-monthly for 36 years (1980–2015) near the deepest part of a warm monomictic lake were analyzed with special reference to yearly minimum DO at bottom (DOmin). DOmin changed yearly (3.0 ± 1.2 mg l−1) and significant differences in DOmin were not observed between Period I (1980–1993; cooler and worse in water quality) and Period II (1994–2015; warmer and better in water quality). This unclear trend in DOmin was probably due to the offsetting influences between warming induced by global warming and oligotrophication attempted by local governments etc. for the study period. DOmin was positively correlated with disturbance time (timing of last cold water intrusion observed from Mar to Aug), which could be related to the start of DO depletion at bottom. Thus, the linear model using this parameter could predict yearly DOmin fairly well for the entire study period (r2 = 0.60). In addition, DOmin and time of disturbance were correlated negatively with water density at bottom in Jan and positively with water density equilibrated to air temperature (AT) in Mar. Higher lake water density after full depth mixing advances the disturbance time. In contrast, lower AT in Mar and/or higher density of influent water after Mar delays the time likely due to the larger amount of snowfall in the watershed. Further, DOmin was positively correlated with maximum wind velocity in Sep which probably induced the recovery of DO. Multiple-regression models to predict DOmin using these meteorological and water quality parameters were developed (r2 ≥ 0.38, worse performances than the model using disturbance time) to forecast future trends of DOmin through global warming and/or climate change. Significant influences of water or sediment oxygen demands on DOmin were not detected. We also discuss the applicability of the proposed models.
Damage to the right temporoparietal junction, but not lateral prefrontal or insular cortex, amplifies the role of goal-directed attention
Authors: Pedrazzini Elena , Ptak Radek 
Published: January 2019

AbstractWhether an object captures attention depends on the interplay between its saliency and current behavioral predispositions of the observer. Neuroimaging work has implied a ventral attention network, comprising the temporoparietal junction (TPJ), lateral prefrontal cortex (lPFC) and the insula, in attentional orienting toward salient events. Activity of the TPJ is driven by novel and unexpected objects, while the lateral prefrontal cortex is involved in stimulus-driven as well as goal-directed processing. The insula in turn, is part of a saliency network, which has been implicated in detecting biologically salient signals. These roles predict that damage to the TPJ, lPFC, or insula should affect performance in tasks measuring the capture of attention by salient and behaviorally relevant events. Here, we show that patients with lesions to the right TPJ have a characteristic increase of attentional capture by relevant distracters. In contrast, damage to the lPFC or insular cortex only increases reaction times, irrespective of the task-relevant properties of distracters. These findings show that acquired damage to the TPJ pathologically amplifies the capture of attention by task-relevant information, and thus indicate that the TPJ has a decisive role in goal-directed orienting.
Partial depletion of dopaminergic neurons in the substantia nigra impairs olfaction and alters neural activity in the olfactory bulb
Authors: Zhang Wenfeng , Sun Changcheng , Shao Yufeng , Zhou Zheng , Hou Yiping , Li Anan 
Published: January 2019

AbstractOlfactory dysfunction is a major non-motor symptom that appears during the early stages of Parkinson’s Disease (PD), a neurodegenerative disorder characterized by loss of dopaminergic neurons in the substantia nigra (SN). Depletion of SN dopaminergic neurons by 6-hydroxydopamine (6-OHDA) is widely used as a model for PD and ultimately results in motor deficits. However, it is largely unknown whether olfactory behavior and, more importantly, neural activity in the olfactory bulb (OB) are impaired prior to the appearance of motor deficits. We partially depleted the SN dopaminergic population in mice by injection of 6-OHDA. Seven days after injection of 6-OHDA, motor ability was unchanged but olfactory-driven behaviors were significantly impaired. Injection of 6-OHDA into the SN significantly increased the power of the ongoing local field potential in the OB for all frequency bands, and decreased odor-evoked excitatory beta responses and inhibitory high-gamma responses. Moreover, 6-OHDA treatment led to increased odor-evoked calcium responses in the mitral cells in the OB of awake mice. These data suggest that the olfactory deficits caused by depletion of the SN dopaminergic population are likely due to abnormal hyperactivity of the mitral cells in the OB.
Lithography-Free Planar Band-Pass Reflective Color Filter Using A Series Connection of Cavities
Authors: Ghobadi Amir , Hajian Hodjat , Soydan Mahmut Can , Butun Bayram , Ozbay Ekmel 
Published: January 2019

AbstractIn this article, a lithography-free multilayer based color filter is realized using a proper series connection of two cavities that shows relatively high efficiency, high color purity, and a wide view angle. The proposed structure is a metal-insulator-metal-insulator-semiconductor (MIMIS) design. To optimize the device performance, at the first step, transfer matrix method (TMM) modeling is utilized to find the right choices of materials for each layer. Simulations are carried out later on to optimize the geometries of the layers to obtain our desired colors. Finally, the optimized devices are fabricated and experimentally characterized to evaluate our modelling findings. The characterization results of the fabricated samples prove the successful formation of efficient and wide view angle color filters. Unlike previously reported FP based designs that act as a band-stop filter in reflection mode (absorbing a narrow frequency range and reflecting the rest of the spectrum), this design generates a specific color by reflecting a narrow spectral range and absorbing the rest of the spectrum. The findings of this work can be extended to other multilayer structures where an efficient connection of cavities in a tandem scheme can propose functionalities that cannot be realized with conventional FP resonators.
Dynamic colour change and the confusion effect against predation
Authors: Murali Gopal , Kumari Kajal , Kodandaramaiah Ullasa 
Published: January 2019

AbstractThe confusion effect - the decreased attack-to-kill ratio of a predator with increase in prey group size - is thought to be one of the main reasons for the evolution of group living in animals. Despite much interest, the influence of prey coloration on the confusion effect is not well understood. We hypothesized that dynamic colour change in motion (due to interference coloration or flash marks), seen widely in many group living animals, enhances the confusion effect. Utilizing a virtual tracking task with humans, we found targets that dynamically changed colour during motion were more difficult to track than targets with background matching patterns, and this effect was stronger at larger group sizes. The current study thus provides the first empirical evidence for the idea that dynamic colour change can benefit animals in a group and may explain the widespread occurrence of dynamic colorations in group-living animals.
Multipartite state generation in quantum networks with optimal scaling
Authors: Wallnöfer J. , Pirker A. , Zwerger M. , Dür W. 
Published: January 2019

AbstractWe introduce a repeater scheme to efficiently distribute multipartite entangled states in a quantum network with optimal scaling. The scheme allows to generate graph states such as 2D and 3D cluster states of growing size or GHZ states over arbitrary distances, with a constant overhead per node/channel that is independent of the distance. The approach is genuine multipartite, and is based on the measurement-based implementation of multipartite hashing, an entanglement purification protocol that operates on a large ensemble together with local merging/connection of elementary building blocks. We analyze the performance of the scheme in a setting where local or global storage is limited, and compare it to bipartite and hybrid approaches that are based on the distribution of entangled pairs. We find that the multipartite approach offers a storage advantage, which results in higher efficiency and better performance in certain parameter regimes. We generalize our approach to arbitrary network topologies and different target graph states.
Complementary relation of quantum coherence and quantum correlations in multiple measurements
Authors: Fan Zeyang , Peng Yi , Zhang Yu-Ran , Liu Shang , Mu Liang-Zhu , Fan Heng 
Published: January 2019

AbstractQuantum coherence and quantum correlations lie in the center of quantum information science, since they both are considered as fundamental reasons for significant features of quantum mechanics different from classical mechanics. We present a group of complementary relations for quantum coherence and quantum correlations; specifically, we focus on thermal discord and conditional information in scenarios of multiple measurements. We show that the summation of quantum coherence quantified in different bases has a lower bound, resulting from entropic uncertainty relations with multiple measurements. Similar results are also obtained for thermal discord and for post-measurement conditional information with multiple measurements in a multipartite system. These results indicate the general applications of the uncertainty principle to various concepts of quantum information.
Analysis of genetic diversity of Xanthomonas oryzae pv. oryzae populations in Taiwan
Authors: Chien Chih-Cheng , Chou Mei-Yi , Chen Chun-Yi , Shih Ming-Che 
Published: January 2019

AbstractRice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major rice disease. In Taiwan, the tropical indica type of Oryza sativa originally grown in this area is mix-cultivated with the temperate japonica type of O. sativa, and this might have led to adaptive changes of both rice host and Xoo isolates. In order to better understand how Xoo adapts to this unique environment, we collected and analyzed fifty-one Xoo isolates in Taiwan. Three different genetic marker systems consistently identified five groups. Among these groups, two of them had unique sequences in the last acquired ten spacers in the clustered regularly interspaced short palindromic repeats (CRISPR) region, and the other two had sequences that were similar to the Japanese isolate MAFF311018 and the Philippines isolate PXO563, respectively. The genomes of two Taiwanese isolates with unique CRISPR sequence features, XF89b and XM9, were further completely sequenced. Comparison of the genome sequences suggested that XF89b is phylogenetically close to MAFF311018, and XM9 is close to PXO563. Here, documentation of the diversity of groups of Xoo in Taiwan provides evidence of the populations from different sources and hitherto missing information regarding distribution of Xoo populations in East Asia.
Globin E is a myoglobin-related, respiratory protein highly expressed in lungfish oocytes
Authors: Lüdemann Julia , Verissimo Kellen Matos , Dreger Kimberley , Fago Angela , Schneider Igor , Burmester Thorsten 
Published: January 2019

AbstractGlobins are a classical model system for the studies of protein evolution and function. Recent studies have shown that – besides the well-known haemoglobin and myoglobin – additional globin-types occur in vertebrates that serve different functions. Globin E (GbE) was originally identified as an eye-specific protein of birds that is distantly related to myoglobin. GbE is also present in turtles and the coelacanth but appeared to have been lost in other vertebrates. Here, we show that GbE additionally occurs in lungfish, the closest living relatives of the tetrapods. Each lungfish species harbours multiple (≥5) GbE gene copies. Surprisingly, GbE is exclusively and highly expressed in oocytes, with mRNA levels that exceed that of myoglobin in the heart. Thus, GbE is the first known oocyte-specific globin in vertebrates. No GbE transcripts were found in the ovary or egg transcriptomes of other vertebrates, suggesting a lungfish-specific function. Spectroscopic analysis and kinetic studies of recombinant GbE1 of the South American lungfish Lepidosiren paradoxa revealed a typical pentacoordinate globin with myoglobin-like O2-binding kinetics, indicating similar functions. Our findings suggest that the multiple copies of GbE evolved to enhance O2-supply in the developing embryo of lungfish, analogous to the embryonic and fetal haemoglobins of other vertebrates. In evolution, GbE must have changed its expression site from oocytes to eyes, or vice versa.
Long-term outcome of intrastromal corneal ring segments in keratoconus: Five-year follow up
Authors: Kang Min-Ji , Byun Yong-Soo , Yoo Young-Sik , Whang Woong-Joo , Joo Choun-Ki 
Published: January 2019

AbstractTo evaluate the effectiveness of intrastromal corneal ring segment (ICRS) use in keratoconus after five years. ICRS has been widely used to correct astigmatism and improve visual acuity in keratoconus. Although the short-term outcome is well known to be effective, long-term outcome has rarely been reported. A retrospective chart review was done. A total of 30 eyes diagnosed with keratoconus and treated with INTACS (Addition Technology, Sunnyvale, CA, USA) were included. Visual acuity, refraction, indices of corneal irregularity, and higher-order aberration were evaluated at preoperative, two months, one year, three years, and five years postoperatively. Uncorrected distance visual acuity (UDVA) and spherical and spherical equivalent were improved (p < 0.05) for three years. However, they worsened (p < 0.05) at five years to preoperative values. On the other hand, corrected distance visual acuity (CDVA) was improved for five years (p < 0.05). Topographic keratometry was flattened, and corneal irregularity indices were improved at five years (all p < 0.05). Coma RMS was improved (p < 0.05) continuously for five years. ICRS has advantages in improving CDVA with topographic stabilization and decreasing coma in keratoconus for five years.
Saccharomyces cerevisiae ASN1 and ASN2 are asparagine synthetase paralogs that have diverged in their ability to polymerize in response to nutrient stress
Authors: Noree Chalongrat , Sirinonthanawech Naraporn , Wilhelm James E. 
Published: January 2019

AbstractRecent work has found that many metabolic enzymes have the ability to polymerize in response to metabolic changes or environmental stress. This ability to polymerize is well conserved for the few metabolic enzyme paralogs that have been studied in yeast. Here we describe the first set of paralogs, Asn1p and Asn2p, that have differential assembly behavior. Asn1p and Asn2p both co-assemble into filaments in response to nutrient limitation. However, the ability of Asn2p to form filaments is strictly dependent on the presence of Asn1p. Using mutations that block enzyme activity but have differential effects on Asn1p polymerization, we have found that Asn1p polymers are unlikely to have acquired a moonlighting function. Together these results provide a novel system for understanding the regulation and evolution of metabolic enzyme polymerization.
Streamlined procedure for gene knockouts using all-in-one adenoviral CRISPR-Cas9
Authors: Jin Yuan-Hu , Joo Hyunjeong , Lee Kwangjun , Kim Hyeongseok , Didier Ruth , Yang Young , Shin Heungsop , Lee Choogon 
Published: January 2019

AbstractCRISPR-Cas9 is a powerful gene editing technique that can induce mutations in a target gene of interest in almost any mammalian cell line. However, its practicality can be limited if target cell lines are difficult to transfect and do not proliferate. In the current study, we have developed a streamlined approach for CRISPR-based gene knockouts with three key advantages, which allows phenotypic assay of gene knockouts without clonal selection and expansion. First, it integrates into a single, all-in-one vector transgenes for Cas9, sgRNA, and a fluorescence marker. Second, we used the Gateway system to rapidly clone specific sgRNAs into the all-in-one vector through PCR and in vitro recombination, without conventional enzyme digestion and ligation. Third, it uses adenovirus for the capacity to package the all-in-one vector, and for its high efficiency of transduction. We tested the all-in-one adenoviral CRISPR-Cas9 in a circadian clock model cell line U2OS, and demonstrated that essential clock genes such as Bmal1 and Per1 were knocked out so efficiently that functional assays could be performed from the heterogenic population without any clonal selection and expansion. This streamlined approach may prove invaluable for rapid functional assays of candidate genes in diverse biological pathways, including the circadian clock.
Digital Biosensing by Foundry-Fabricated Graphene Sensors
Authors: Goldsmith Brett R. , Locascio Lauren , Gao Yingning , Lerner Mitchell , Walker Amy , Lerner Jeremy , Kyaw Jayla , Shue Angela , Afsahi Savannah , Pan Deng , Nokes Jolie , Barron Francie 
Published: January 2019

AbstractThe prevailing philosophy in biological testing has been to focus on simple tests with easy to interpret information such as ELISA or lateral flow assays. At the same time, there has been a decades long understanding in device physics and nanotechnology that electrical approaches have the potential to drastically improve the quality, speed, and cost of biological testing provided that computational resources are available to analyze the resulting complex data. This concept can be conceived of as “the internet of biology” in the same way miniaturized electronic sensors have enabled “the internet of things.” It is well established in the nanotechnology literature that techniques such as field effect biosensing are capable of rapid and flexible biological testing. Until now, access to this new technology has been limited to academic researchers focused on bioelectronic devices and their collaborators. Here we show that this capability is retained in an industrially manufactured device, opening access to this technology generally. Access to this type of production opens the door for rapid deployment of nanoelectronic sensors outside the research space. The low power and resource usage of these biosensors enables biotech engineers to gain immediate control over precise biological and environmental data.
Characterization of the housekeeping sortase from the human pathogen Propionibacterium acnes: first investigation of a class F sortase
Authors: Di Girolamo Salvatore , Puorger Chasper , Castiglione Mara , Vogel Maren , Gébleux Rémy , Briendl Manfred , Hell Tamara , Beerli Roger R. , Grawunder Ulf , Lipps Georg 
Published: January 2019

Abstract
Sortase enzymes play an important role in Gram-positive bacteria. They are responsible for the covalent attachment of proteins to the surface of the bacteria and perform this task via a highly sequence-specific transpeptidation reaction. Since these immobilized proteins are often involved in pathogenicity of Gram-positive bacteria, characterization of this type of enzyme is also of medical relevance. Different classes of sortases (A–F) have been found, which recognize characteristic recognition sequences present in substrate proteins. Up to date, sortase A from Staphylococcus aureus, a housekeeping class A sortase, is the most thoroughly studied representative of the sortase family of enzymes. Here we report the in-depth characterization of the class F sortase from Propionibacterium acnes, a class of sortases that has not been investigated before. As Sortase F is the only transpeptidase found in the P. acnes genome, it is the housekeeping sortase of this organism. Sortase F from P. acnes shows a behavior similar to sortases from class A in terms of pH dependence, recognition sequence and catalytic activity; furthermore, its activity is independent of bivalent ions, which contrasts to sortase A from S. aureus. We demonstrate that sortase F is useful for protein engineering applications, by producing a site-specifically conjugated homogenous antibody–drug conjugate with a potency similar to that of a conjugate prepared with sortase A. Thus, the detailed characterization presented here will not only enable the development of anti-virulence agents targeting P. acnes but also provides a powerful alternative to sortase A for protein engineering applications.
Group A Streptococcus co-ordinates manganese import and iron efflux in response to hydrogen peroxide stress
Authors: Turner Andrew G. , Djoko Karrera Y. , Ong Cheryl-lynn Y. , Barnett Timothy C. , Walker Mark J. , McEwan Alastair G. 
Published: January 2019

Abstract
Bacterial pathogens encounter a variety of adverse physiological conditions during infection, including metal starvation, metal overload and oxidative stress. Here, we demonstrate that group A Streptococcus (GAS) utilises Mn(II) import via MtsABC during conditions of hydrogen peroxide stress to optimally metallate the superoxide dismutase, SodA, with Mn. MtsABC expression is controlled by the DtxR family metalloregulator MtsR, which also regulates the expression of Fe uptake systems in GAS. Our results indicate that the SodA in GAS requires Mn for full activity and has lower activity when it contains Fe. As a consequence, under conditions of hydrogen peroxide stress where Fe is elevated, we observed that the PerR-regulated Fe(II) efflux system PmtA was required to reduce intracellular Fe, thus protecting SodA from becoming mismetallated. Our findings demonstrate the co-ordinate action of MtsR-regulated Mn(II) import by MtsABC and PerR-regulated Fe(II) efflux by PmtA to ensure appropriate Mn(II) metallation of SodA for optimal superoxide dismutase function.
Two new transformerless high step‐down DC–DC converters
Authors: Saadatizadeh Zahra , Chavoshipour Heris Pedram , Sabahi Mehran , Babaei Ebrahim 
Published: January 2019

In this study, two new high step‐down DC–DC converters are proposed. The proposed converters are designed transformerless and have similar power circuits. For controlling the switches of the proposed converters, two distinct switching patterns are applied. The first switching pattern is interleaved pulse‐width modulation pulses with 180° phase shifts, which are applied for the first proposed converter, therefore, the first converter has an interleaved switching pattern and its structure is symmetrical, the voltage stress on its elements decreased. On the other hand, there will be two conversion ratio equations for the first proposed converter for duty cycles larger and less than 0.5. The second switching pattern is applied to the proposed second converter; therefore, in this case, the constant voltage gain is obtained for the whole ranges of duty cycles. The sum of voltage stress on its switches and diodes are a little more than the first converter. The proposed converters are analysed for all of their operating modes. To verify the theoretical results, a prototype of the first and second proposed converter for 500/26 and 800/20.5 V, respectively, and 430 W is implemented in laboratory and the extracted results are compared with calculated ones.