bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tree height explains mortality risk during an intense drought
Authors: Stovall Atticus E. L. , Shugart Herman , Yang Xi 
Published: September 2019

AbstractForest mortality is accelerating due to climate change and the largest trees may be at the greatest risk, threatening critical ecological, economic, and social benefits. Here, we combine high-resolution airborne LiDAR and optical data to track tree-level mortality rates for ~2 million trees in California over 8 years, showing that tree height is the strongest predictor of mortality during extreme drought. Large trees die at twice the rate of small trees and environmental gradients of temperature, water, and competition control the intensity of the height-mortality relationship. These findings suggest that future persistent drought may cause widespread mortality of the largest trees on Earth.
Distinct transcriptional roles for Histone H3-K56 acetylation during the cell cycle in Yeast
Authors: Topal Salih , Vasseur Pauline , Radman-Livaja Marta , Peterson Craig L. 
Published: September 2019

AbstractDynamic disruption and reassembly of promoter-proximal nucleosomes is a conserved hallmark of transcriptionally active chromatin. Histone H3-K56 acetylation (H3K56Ac) enhances these turnover events and promotes nucleosome assembly during S phase. Here we sequence nascent transcripts to investigate the impact of H3K56Ac on transcription throughout the yeast cell cycle. We find that H3K56Ac is a genome-wide activator of transcription. While H3K56Ac has a major impact on transcription initiation, it also appears to promote elongation and/or termination. In contrast, H3K56Ac represses promiscuous transcription that occurs immediately following replication fork passage, in this case by promoting efficient nucleosome assembly. We also detect a stepwise increase in transcription as cells transit S phase and enter G2, but this response to increased gene dosage does not require H3K56Ac. Thus, a single histone mark can exert both positive and negative impacts on transcription that are coupled to different cell cycle events.
Efficiently measuring a quantum device using machine learning
Authors: Lennon D. T. , Moon H. , Camenzind L. C. , Yu Liuqi , Zumbühl D. M. , Briggs G. A .D. , Osborne M. A. , Laird E. A. , Ares N. 
Published: September 2019

AbstractScalable quantum technologies such as quantum computers will require very large numbers of quantum devices to be characterised and tuned. As the number of devices on chip increases, this task becomes ever more time-consuming, and will be intractable on a large scale without efficient automation. We present measurements on a quantum dot device performed by a machine learning algorithm in real time. The algorithm selects the most informative measurements to perform next by combining information theory with a probabilistic deep-generative model that can generate full-resolution reconstructions from scattered partial measurements. We demonstrate, for two different current map configurations that the algorithm outperforms standard grid scan techniques, reducing the number of measurements required by up to 4 times and the measurement time by 3.7 times. Our contribution goes beyond the use of machine learning for data search and analysis, and instead demonstrates the use of algorithms to automate measurements. This works lays the foundation for learning-based automated measurement of quantum devices.
Osmolyte homeostasis controls single-cell growth rate and maximum cell size of Saccharomyces cerevisiae
Authors: Altenburg Tom , Goldenbogen Björn , Uhlendorf Jannis , Klipp Edda 
Published: September 2019

AbstractCell growth is well described at the population level, but precisely how nutrient and water uptake and cell wall expansion drive the growth of single cells is poorly understood. Supported by measurements of single-cell growth trajectories and cell wall elasticity, we present a single-cell growth model for yeast. The model links the thermodynamic quantities, such as turgor pressure, osmolarity, cell wall elasto-plasticity, and cell size, applying concepts from rheology and thin shell theory. It reproduces cell size dynamics during single-cell growth, budding, and hyper-osmotic or hypo-osmotic stress. We find that single-cell growth rate and final size are primarily governed by osmolyte uptake and consumption, while bud expansion requires additionally different cell wall extensibilities between mother and bud. Based on first principles the model provides a more accurate description of size dynamics than previous attempts and its analytical simplification allows for easy combination with models for other cell processes.
Fabrication of superhydrophobic and ice-repellent surfaces on pure aluminium using single and multiscaled periodic textures
Authors: Milles Stephan , Soldera Marcos , Voisiat Bogdan , Lasagni Andrés F. 
Published: September 2019

AbstractFabricating aluminium surfaces with superhydrophobic and ice-repellent properties present nowadays a challenging task. In this work, multifunctional structures are manufactured by direct laser writing and direct laser interference patterning methods using pulsed infrared laser radiation (1064 nm). Different periodic patterns with feature sizes ranging from 7.0 to 50.0 µm are produced. In addition, hierarchical textures are produced combining both mentioned laser based methods. Water contact angle tests at room temperature showed that all produced patterns reached the superhydrophobic state after 13 to 16 days. In addition, these experiments were repeated at substrate temperatures from −30 °C to 80 °C allowing to determine three wettability behaviours as a function of the temperature. The patterned surfaces also showed ice-repellent properties characterized by a near three-fold increase in the droplets freezing times compared to the untreated samples. Using finite element simulations, it was found that the main reason behind the ice-prevention is the change in the droplet geometrical shape due to the hydrophobic nature of the treated surfaces. Finally, dynamic tests of droplets imping the treated aluminium surfaces cooled down to −20 °C revealed that only on the hierarchically patterned surface, the droplets were able to bounce off the substrate.
Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia)
Authors: Morley Mike W. , Goldberg Paul , Uliyanov Vladimir A. , Kozlikin Maxim B. , Shunkov Michael V. , Derevianko Anatoly P. , Jacobs Zenobia , Roberts Richard G. 
Published: September 2019

AbstractDenisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal–Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.
Characterization of biklf/klf17-deficient zebrafish in posterior lateral line neuromast and hatching gland development
Authors: Suzuki Hiroaki , Ishizaka Tomoe , Yanagi Kanoko , Sone Ryota , Sunaga Yuto , Ohga Rie , Kawahara Atsuo 
Published: September 2019

AbstractKrüpple-like factors (Klfs) are highly conserved zinc-finger transcription factors that regulate various developmental processes, such as haematopoiesis and cardiovascular development. In zebrafish, transient knockdown analysis of biklf/klf17 using antisense morpholino suggests the involvement of biklf/klf17 in primitive erythropoiesis and hatching gland development; however, the continuous physiological importance of klf17 remains uncharacterized under the genetic ablation of the klf17 gene among vertebrates. We established the klf17-disrupted zebrafish lines using the CRISPR/Cas9 technology and performed phenotypic analysis throughout early embryogenesis. We found that the klf17-deficient embryos exhibited abnormal lateral line neuromast deposition, whereas the production of primitive erythrocytes and haemoglobin production were observed in the klf17-deficient embryos. The expression of lateral line neuromast genes, klf17 and s100t, in the klf17-deficient embryos was detected in posterior lateral line neuromasts abnormally positioned at short intervals. Furthermore, the klf17-deficient embryos failed to hatch and died without hatching around 15 days post-fertilization (dpf), whereas the dechorionated klf17-deficient embryos and wild-type embryos were alive at 15 dpf. The klf17-deficient embryos abolished hatching gland cells and Ctsl1b protein expression, and eliminated the expression of polster and hatching gland marker genes, he1.1, ctsl1b and cd63. Thus, the klf17 gene plays important roles in posterior lateral line neuromast and hatching gland development.
Prevalence of Hepatitis B Virus Infection in Shenzhen, China, 2015–2018
Authors: Tao Jian , Zhang Weimin , Yue Huakui , Zhu Guohun , Wu Wenyuan , Gong Wenbo , Fang Honghui , He Guirong , Hu Xiaoyun , Zhao Hongyue , Liu Aiqin 
Published: September 2019

AbstractChina has nearly 10% of the general HBV carrier population in the world; this infection is the most common cause of chronic liver disease. Understanding HBV epidemiology is essential for future infection control, evaluation, and treatment. This study determined the prevalence of HBV infection in Shenzhen by serological testing and analysis in 282,166 HBV screening cases for the following: HBcAb, indicative of previous HBV infection; HBsAg, indicative of chronic (current) infection; HBsAb, indicative of immunity from vaccination; and 34,368 HBV etiological screening cases for HBV-DNA, indicative of virus carriage, in which 1,204 cases were genotyped and mutation analyzed for drug-resistance evaluation. Shenzhen was a highly endemic area of HBV throughout the study period (prevalence 9.69%). HBV infections were almost entirely in the 20 and older age groups with a male-to-female ratio of 1.16:1 which is approximately the same as the male-to-female ratio of the general population in China. However, only 71.25% of the general population retained HBV immune protection. Genotype B and C were identified as the most common agents; recombinant B/C and B/D also existed; some cases, however, could not be genotyped. NAs resistant mutation occurrence patterns were multitudinous; single mutation patterns of rtM204I/V and rtL180M occurrences accounted for majority, followed by the combinational mutation pattern L180M + M204I/V. Drug-resistance was prevalent, mainly occurring in the cross resistance patterns LAM + LdT and LAM + LdT + ETV, and significantly more critical in males. These results demonstrate that all people free from HBV infection should obtain injections of the vaccine or booster shots, and conventional virologic detection in a clinical laboratory center should incorporate genotype and mutation alongside the serological factors for etiology and develop better classification methods, such as sequencing.
Metabolic dependency of chorismate in Plasmodium falciparum suggests an alternative source for the ubiquinone biosynthesis precursor
Authors: Valenciano Ana Lisa , Fernández-Murga Maria L. , Merino Emilio F. , Holderman Nicole R. , Butschek Grant J. , Shaffer Karl J. , Tyler Peter C. , Cassera Maria Belen 
Published: September 2019

AbstractThe shikimate pathway, a metabolic pathway absent in humans, is responsible for the production of chorismate, a branch point metabolite. In the malaria parasite, chorismate is postulated to be a direct precursor in the synthesis of p-aminobenzoic acid (folate biosynthesis), p-hydroxybenzoic acid (ubiquinone biosynthesis), menaquinone, and aromatic amino acids. While the potential value of the shikimate pathway as a drug target is debatable, the metabolic dependency of chorismate in P. falciparum remains unclear. Current evidence suggests that the main role of chorismate is folate biosynthesis despite ubiquinone biosynthesis being active and essential in the malaria parasite. Our goal in the present work was to expand our knowledge of the ubiquinone head group biosynthesis and its potential metabolic dependency on chorismate in P. falciparum. We systematically assessed the development of both asexual and sexual stages of P. falciparum in a defined medium in the absence of an exogenous supply of chorismate end-products and present biochemical evidence suggesting that the benzoquinone ring of ubiquinones in this parasite may be synthesized through a yet unidentified route.
How to copy and paste DNA microarrays
Authors: Krämer Stefan D. , Wöhrle Johannes , Meyer Philipp A. , Urban Gerald A. , Roth Günter 
Published: September 2019

AbstractAnalogous to a photocopier, we developed a DNA microarray copy technique and were able to copy patterned original DNA microarrays. With this process the appearance of the copied DNA microarray can also be altered compared to the original by producing copies of different resolutions. As a homage to the very first photocopy made by Chester Charlson and Otto Kornei, we performed a lookalike DNA microarray copy exactly 80 years later. Those copies were also used for label-free real-time kinetic binding assays of apo-dCas9 to double stranded DNA and of thrombin to single stranded DNA. Since each DNA microarray copy was made with only 5 µl of spPCR mix, the whole process is cost-efficient. Hence, our DNA microarray copier has a great potential for becoming a standard lab tool.
Ability of Saccharomyces cerevisiae MC87-46 to assimilate isomaltose and its effects on sake taste
Authors: Tsutsumi Seitaro , Mochizuki Mai , Sakai Kiyota , Ieda Akane , Ohara Reiji , Mitsui Shun , Ito Akitoshi , Hirano Tatsuya , Shimizu Motoyuki , Kato Masashi 
Published: September 2019

AbstractRecently, wild strains of Saccharomyces cerevisiae isolated from a variety of natural resources have been used to make bread, beer, wine, and sake. In the current study, we isolated wild S. cerevisiae MC strain from the carnation (Dianthus caryophyllus L) flower and produced sake using its cerulenin-resistant mutant strain MC87-46. Then, we characterized the components, including ethanol, amino acids, organic acids, and sugars, in the fermented sake. Sake brewed with MC87-46 is sweet owing to the high content of isomaltose, which was at a concentration of 44.3 mM. The low sake meter value of −19.6 is most likely due to this high isomaltose concentration. The genomic DNA of MC87-46 encodes for isomaltases IMA1, IMA2, IMA3, IMA4 and IMA5, as well as the isomaltose transporter gene, AGT1. However, these genes were not induced in MC87-46 by isomaltose, and the strain did not possess isomaltase activity. These results show that MC87-46 cannot utilize isomaltose, resulting in its accumulation in the fermented sake. Isomaltose concentrations in sake brewed with MC87-46 were 24.6-fold more than in commercial sake. These findings suggest that MC87-46 may be useful for commercial application in Japanese sake production because of its unique flavour and nutrient profile.
On the Large Near-Field Enhancement on Nanocolumnar Gold Substrates
Authors: Díaz-Núñez Pablo , García-Martín José Miguel , González María Ujué , González-Arrabal Raquel , Rivera Antonio , Alonso-González Pablo , Martín-Sánchez Javier , Taboada-Gutiérrez Javier , González-Rubio Guillermo , Guerrero-Martínez Andrés , Bañares Luis , Peña-Rodríguez Ovidio 
Published: September 2019

AbstractOne of the most important and distinctive features of plasmonic nanostructures is their ability to confine large electromagnetic fields on nanometric volumes; i.e., the so-called hot spots. The generation, control and characterization of the hot spots are fundamental for several applications, like surface-enhanced spectroscopies. In this work, we characterize the near-field distribution and enhancement of nanostructured gold thin films fabricated by glancing angle deposition magnetron sputtering. These films are composed of columnar nanostructures with high roughness and high density of inter-columnar gaps, where the electromagnetic radiation can be confined, generating hot spots. As expected, the hot spots are localized in the gaps between adjacent nanocolumns and we use scattering-type scanning near-field optical microscopy to image their distribution over the surface of the samples. The experimental results are compared with finite-difference time-domain simulations, finding an excellent agreement between them. The spectral dependence of the field-enhancement is also studied with the simulations, together with surface-enhanced Raman spectroscopy at different excitation wavelengths in the visible-NIR range, proving a broad-band response of the substrates. These findings may result in interesting applications in the field of surface-enhanced optical spectroscopies or sensing.
Bidirectional in vivo structural dendritic spine plasticity revealed by two-photon glutamate uncaging in the mouse neocortex
Authors: Noguchi Jun , Nagaoka Akira , Hayama Tatsuya , Ucar Hasan , Yagishita Sho , Takahashi Noriko , Kasai Haruo 
Published: September 2019

AbstractMost excitatory synapses in the brain form on dendritic spines. Two-photon uncaging of glutamate is widely utilized to characterize the structural plasticity of dendritic spines in brain slice preparations in vitro. In the present study, glutamate uncaging was used to investigate spine plasticity, for the first time, in vivo. A caged glutamate compound was applied to the surface of the mouse visual cortex in vivo, revealing the successful induction of spine enlargement by repetitive two-photon uncaging in a magnesium free solution. Notably, this induction occurred in a smaller fraction of spines in the neocortex in vivo (22%) than in hippocampal slices (95%). Once induced, the time course and mean long-term enlargement amplitudes were similar to those found in hippocampal slices. However, low-frequency (1–2 Hz) glutamate uncaging in the presence of magnesium caused spine shrinkage in a similar fraction (35%) of spines as in hippocampal slices, though spread to neighboring spines occurred less frequently than it did in hippocampal slices. Thus, the structural plasticity may occur similarly in the neocortex in vivo as in hippocampal slices, although it happened less frequently in our experimental conditions.
Abgehängt?
Authors: Wagner Franz 
Published: September 2019

ZusammenfassungSeit Jahrzehnten hinkt Deutschland dem Rest der Europäischen Union nach –
zumindest was die Pflegeausbildung betrifft. Mit dem neuen Pflegeberufegesetz
soll sich das zumindest in Teilen ändern. Der Präsident des Deutschen
Pflegerats (DPR) Franz Wagner zieht Bilanz.
Verwaist die Altenpflege?
Authors: Halletz Isabell 
Published: September 2019

Zusammenfassung
Altenpfleger und nicht „Generalist“ werden, ist laut neuem
Pflegeberufegesetz weiter möglich, wenn auch auf den ersten Blick wenig
attraktiv. Es drohen Kompetenzverlust und Mitarbeiterschwund. Der
Arbeitgeberverband Pflege (AGVP) wagt einen Ausblick.
Expanding Role of Self Expanding Esophageal Stents
Authors: Dua Kulwinder S 
Published: September 2019

ABSTRACTEsophageal cancer is often diagnosed at a late stage and hence carries a poor prognosis with an overall 5-year survival rate of 10% to 15%. Therefore, palliative treatment primarily aimed at the relieving dysphagia is the only available option. Endoscopic placement of self expanding metal stents (SEMS) has become a widely used method for palliation offering prompt relief of dysphagia and numerous reports have shown it to be safe and effective. Secondary to tissue in-growth into the uncovered segments of the stent, SEMS cannot be removed and hence are not approved for benign indications. With the advent of the removable self expanding plastic stents, the indications for esophageal stent insertion have expanded to as bridge to surgery for patients undergoing neoadjuvant chemotherapy, for refractory benign esophageal strictures, for non- malignant esophageal perforations, leaks and fistulae, and even for variceal hemorrhage. Newer fully covered SEMS that are potentially removable are also being tried for benign indications but await FDA clearance. Similarly biodegradeable stents for benign disorders and radioactive or drug-eluding stents for malignant disease are hoped to improve the management of esophageal diseases. The purpose of this article is to review the expanding role of self expanding stents in the management of esophageal disorders other than palliating malignant dysphagia and fistulae.(J Dig Endos 2011;2(1):9-14)
Intuitions on the Individuation of Musical Works. An Empirical Study
Authors: Mikalonytė Elzė Sigutė , Dranseika Vilius 
Published: September 2019

Abstract
Philosophers often consider better compliance with prevalent pre-theoretical intuitions to be an advantage of a theory of ontology of musical works. However, despite many predictions of what these intuitions on relevant questions might be, so far there is only one experimental philosophy study on the repeatability of musical works by Christopher Bartel. We decided to examine the intuitions concerning the individuation of musical works by creating scenarios reflecting the differences in the positions of musical ontologists: pure and timbral sonicism, instrumentalism, and contextualism. The results show that emotional expressivity, instrument, timbre, and images evoked in the listeners were not considered as properties individuating musical works. However, the musical works were held to be different if the composers were different. In most cases, the participants had clear intuitions. Pure sonicism, complemented with additional stress on significance of the composer’s creativity, seems to be the most intuitive position.