bluuebunny/crossref_metadata_2025_split huggingface dataset:
Track Structure Study for Energy Dependency of Electrons and X-rays on DNA Double-Strand Break Induction
Authors: Yachi Yoshie , Yoshii Yuji , Matsuya Yusuke , Mori Ryosuke , Oikawa Joma , Date Hiroyuki 
Published: November 2019

AbstractRadiation weighting factor wR for photons and electrons has been defined as unity independently of the energy of the particles. However, the biological effects depend on the incident energies according to in vitro experimental data. In this study, we have quantified the energy concentration along electron tracks in terms of dose-mean lineal energy (yD) on chromosome (micro-meter) and DNA (nano-meter) order scales by Monte Carlo simulations, and evaluated the impact of photon energies on DNA double-strand break (DNA-DSB) induction from an experimental study of irradiated cells. Our simulation result shows that the yD values for diagnostic X-rays (60–250 kVp) are higher than that for therapeutic X-rays (linac 6 MV), which agrees well with the tissue equivalent proportional counter (TEPC) measurements. The relation between the yD values and the numbers of γ-H2AX foci for various photon energy spectra suggests that low energy X-rays induce DNA-DSB more efficiently than higher energy X-rays even at the same absorbed dose (e.g., 1.0 Gy). The relative biological effectiveness based on DNA-DSBs number (RBEDSB) is proportionally enhanced as the yD value increases, demonstrating that the biological impact of the photon irradiation depends on energy concentration along radiation tracks of electrons produced in the bio-tissues. Ultimately, our study implies that the value of wR for photons varies depending on their energies.
Subtype I (intrinsic) adenomyosis is an independent risk factor for dienogest-related serious unpredictable bleeding in patients with symptomatic adenomyosis
Authors: Matsubara Sho , Kawaguchi Ryuji , Akinishi Mika , Nagayasu Mika , Iwai Kana , Niiro Emiko , Yamada Yuki , Tanase Yasuhito , Kobayashi Hiroshi 
Published: November 2019

AbstractWe aimed to retrospectively analyze the risk factors of a continuous dienogest (DNG) therapy for serious unpredictable bleeding in patients with symptomatic adenomyosis. This is a retrospective study based on data extracted from medical records of 84 women treated with 2 mg of DNG orally each day between 2008 and 2017. 47 subjects were excluded from the original analyses due to an inadequate subcategorization into subtype I and subtype II and a lack of hemoglobin levels. The influence of various independent variables on serious unpredictable bleeding was assessed. Of the 37 eligible patients who received the continuous DNG therapy, 14 patients experienced serious unpredictable bleeding. Univariate analysis revealed that the serious bleeding group had subtype I adenomyosis (P = 0.027). There was no correlation between age, parity, minimum hemoglobin level before treatment, previous endometrial curettage, and duration of DNG administration, or uterine or adenomyosis size and the serious bleeding. A DNG-related serious unpredictable bleeding is associated with the structural type of adenomyosis (subtype I) in patients with symptomatic adenomyosis.
Bacterial cellulose films with ZnO nanoparticles and propolis extracts: Synergistic antimicrobial effect
Authors: Mocanu Alexandra , Isopencu Gabriela , Busuioc Cristina , Popa Oana-Maria , Dietrich Paul , Socaciu-Siebert Liana 
Published: November 2019

AbstractThis study aimed to obtain possible materials for future antimicrobial food packaging applications based on biodegradable bacterial cellulose (BC). BC is a fermentation product obtained by Gluconacetobacter xylinum using food or agricultural wastes as substrate. In this work we investigated the synergistic effect of zinc oxide nanoparticles (ZnO NPs) and propolis extracts deposited on BC. ZnO NPs were generated in the presence of ultrasounds directly on the surface of BC films. The BC-ZnO composites were further impregnated with ethanolic propolis extracts (EEP) with different concentrations.The composition of raw propolis and EEP were previously determined by gas-chromatography mass-spectrometry (GC-MS), while the antioxidant activity was evaluated by TEAC (Trolox equivalent antioxidant capacity). The analysis methods performed on BC-ZnO composites such as scanning electron microscopy (SEM), thermo-gravimetrically analysis (TGA), and energy-dispersive X-ray spectroscopy (EDX) proved that ZnO NPs were formed and embedded in the whole structure of BC films. The BC-ZnO-propolis films were characterized by SEM and X-ray photon spectroscopy (XPS) in order to investigate the surface modifications. The antimicrobial synergistic effect of the BC-ZnO-propolis films were evaluated against Escherichia coli, Bacillus subtilis, and Candida albicans. The experimental results revealed that BC-ZnO had no influence on Gram-negative and eukaryotic cells.
Increase in negative charge of 68Ga/chelator complex reduces unspecific hepatic uptake but does not improve imaging properties of HER3-targeting affibody molecules
Authors: Rinne Sara S. , Dahlsson Leitao Charles , Gentry Joshua , Mitran Bogdan , Abouzayed Ayman , Tolmachev Vladimir , Ståhl Stefan , Löfblom John , Orlova Anna 
Published: November 2019

AbstractUpregulation of the human epidermal growth factor receptor type 3 (HER3) is a common mechanism to bypass HER-targeted cancer therapy. Affibody-based molecular imaging has the potential for detecting and monitoring HER3 expression during treatment. In this study, we compared the imaging properties of newly generated 68Ga-labeled anti-HER3 affibody molecules (HE)3-ZHER3-DOTA and (HE)3-ZHER3-DOTAGA with previously reported [68Ga]Ga-(HE)3-ZHER3-NODAGA. We hypothesized that increasing the negative charge of the gallium-68/chelator complex would reduce hepatic uptake, which could lead to improved contrast of anti-HER3 affibody-based PET-imaging of HER3 expression. (HE)3-ZHER3-X (X = DOTA, DOTAGA) were produced and labeled with gallium-68. Binding of the new conjugates was specific in HER3 expressing BxPC-3 and DU145 human cancer cells. Biodistribution and in vivo specificity was studied in BxPC-3 xenograft bearing Balb/c nu/nu mice 3 h pi. DOTA- and DOTAGA-containing conjugates had significantly higher concentration in blood than [68Ga]Ga-(HE)3-ZHER3-NODAGA. Presence of the negatively charged 68Ga-DOTAGA complex reduced the unspecific hepatic uptake, but did not improve overall biodistribution of the conjugate. [68Ga]Ga-(HE)3-ZHER3-DOTAGA and [68Ga]Ga-(HE)3-ZHER3-NODAGA had similar tumor-to-liver ratios, but [68Ga]Ga-(HE)3-ZHER3-NODAGA had the highest tumor uptake and tumor-to-blood ratio among the tested conjugates. In conclusion, [68Ga]Ga-(HE)3-ZHER3-NODAGA remains the favorable variant for PET imaging of HER3 expression.
Using long and linked reads to improve an Atlantic herring (Clupea harengus) genome assembly
Authors: í Kongsstovu Sunnvør , Mikalsen Svein-Ole , Homrum Eydna í , Jacobsen Jan Arge , Flicek Paul , Dahl Hans Atli 
Published: November 2019

AbstractAtlantic herring (Clupea harengus) is one of the most abundant fish species in the world. It is an important economical and nutritional resource, as well as a crucial part of the North Atlantic ecosystem. In 2016, a draft herring genome assembly was published. Being a species of such importance, we sought to independently verify and potentially improve the herring genome assembly. We sequenced the herring genome generating paired-end, mate-pair, linked and long reads. Three assembly versions of the herring genome were generated based on a de novo assembly (A1), which was scaffolded using linked and long reads (A2) and then merged with the previously published assembly (A3). The resulting assemblies were compared using parameters describing the size, fragmentation, correctness, and completeness of the assemblies. Results showed that the A2 assembly was less fragmented, more complete and more correct than A1. A3 showed improvement in fragmentation and correctness compared with A2 and the published assembly but was slightly less complete than the published assembly. Thus, we here confirmed the previously published herring assembly, and made improvements by further scaffolding the assembly and removing low-quality sequences using linked and long reads and merging of assemblies.
Crustal growth and reworking: A case study from the Erguna Massif, eastern Central Asian Orogenic Belt
Authors: Sun Chenyang , Xu Wenliang , Cawood Peter A. , Tang Jie , Zhao Shuo , Li Yu , Zhang Xiaoming 
Published: November 2019

AbstractDespite being the largest accretionary orogen on Earth, the record of crustal growth and reworking of individual microcontinental massifs within the Central Asian Orogenic Belt (CAOB) remain poorly constrained. Here, we focus on zircon records from granitoids in the Erguna Massif to discuss its crustal evolution through time. Proterozoic–Mesozoic granitoids are widespread in the Erguna Massif, and spatiotemporal variations in their zircon εHf(t) values and TDM2(Hf) ages reveal the crustal heterogeneity of the massif. Crustal growth curve demonstrates that the initial crust formed in the Mesoarchean, and shows a step-like pattern with three growth periods: 2.9–2.7, 2.1–1.9, and 1.7–0.5 Ga. This suggests that microcontinental massifs in the eastern CAOB have Precambrian basement, contradicting the hypothesis of significant crustal growth during the Phanerozoic. Phases of growth are constrained by multiple tectonic settings related to supercontinent development. Calculated reworked crustal proportions and the reworking curve indicate four reworking periods at 1.86–1.78 Ga, 860–720 Ma, 500–440 Ma, and 300–120 Ma, which limited the growth rate. These periods of reworking account for the crustal heterogeneity of the Erguna Massif.
Aktina Vision: Full-parallax three-dimensional display with 100 million light rays
Authors: Watanabe Hayato , Okaichi Naoto , Omura Takuya , Kano Masanori , Sasaki Hisayuki , Kawakita Masahiro 
Published: November 2019

AbstractNatural three-dimensional (3D) images, perceived as real objects in front of the viewer, can be displayed by faithfully reproducing light ray information. However, 3D images with sufficient characteristics for practical use cannot be displayed using conventional technologies because highly accurate reproduction of numerous light rays is required. We propose a novel full-parallax light field 3D display method named ‘Aktina Vision’, which includes a special top-hat diffusing screen with a narrow diffusion angle and an optical system for reproducing high-density light rays. Our prototype system reproduces over 100,000,000 light rays at angle intervals of less than 1° and optimally diffuses light rays with the top-hat diffusing screen. Thus, for the first time, light field 3D image reproduction with a maximum spatial resolution of approximately 330,000 pixels, which is near standard-definition television resolution and three times that of conventional light field display using a lens array, is achieved.
Direct visualization of human myosin II force generation using DNA origami-based thick filaments
Authors: Fujita Keisuke , Ohmachi Masashi , Ikezaki Keigo , Yanagida Toshio , Iwaki Mitsuhiro 
Published: November 2019

AbstractThe sarcomere, the minimal mechanical unit of muscle, is composed of myosins, which self-assemble into thick filaments that interact with actin-based thin filaments in a highly-structured lattice. This complex imposes a geometric restriction on myosin in force generation. However, how single myosins generate force within the restriction remains elusive and conventional synthetic filaments do not recapitulate the symmetric bipolar filaments in sarcomeres. Here we engineered thick filaments using DNA origami that incorporate human muscle myosin to directly visualize the motion of the heads during force generation in a restricted space. We found that when the head diffuses, it weakly interacts with actin filaments and then strongly binds preferentially to the forward region as a Brownian ratchet. Upon strong binding, the two-step lever-arm swing dominantly halts at the first step and occasionally reverses direction. Our results illustrate the usefulness of our DNA origami-based assay system to dissect the mechanistic details of motor proteins.
Sekundäre Neuroprotektion beim Glaukom durch Augendrucksenkung
Authors: Unterlauft Jan Darius 
Published: November 2019

ZusammenfassungDas bisherige zentrale Ziel der Glaukombehandlung liegt darin, den intraokularen Druck (IOD) auf medikamentösem und/oder chirurgischem Weg zu senken, um ein weiteres Voranschreiten der Erkrankung über einen möglichst langen Zeitraum hin suffizient zu verhindern. Eine Stabilisierung des Gesichtsfeldes und des Nervenfasersaums der Papille wurden bisher als bestenfalls zu erreichende Ziele der Therapie des Glaukoms angesehen. Mittels einer systematischen Literaturrecherche und Analyse der bisher zum Thema Neuroprotektion und funktionelle Verbesserung durch Augendrucksenkung bei Glaukom veröffentlichten Untersuchungen sollen die bisher beschriebenen Möglichkeiten der anatomischen und funktionellen Wiederherstellung von vormals verloren gegangenen Strukturen und Funktionen beleuchtet werden. Im Rahmen verschiedener, teils groß angelegter Studien konnten bereits Hinweise für eine anatomische Befundverbesserung am Sehnervenkopf und funktionelle Verbesserungen in den Ergebnissen der Perimetrie gefunden werden. Anatomische sowie funktionelle Befundverbesserungen bei der Behandlung des Glaukoms scheinen in einigen Fällen tatsächlich vorzuliegen. Allerdings finden sich solche Befunde häufig in solchen Fällen, in denen der IOD sehr stark im Vergleich zum Ausgangsbefund gesenkt wurde.
Evaluation of Different Types of Natural Surfactants by Lung Ultrasound in Respiratory Distress Syndrome
Authors: Bozkaya Davut , Dizdar Evrim Alyamaç , Korkut Sabriye , Ceran Burak , Alkan Mihriban , Oğuz Şerife Suna 
Published: November 2019

Abstract
Objective This study aimed to compare the lung ultrasonography (LUS) scores after two different natural surfactant administration as a parameter reflecting lung inflation.
Study Design Preterm infants of 32 gestational weeks and below who were diagnosed with respiratory distress syndrome (RDS) were randomly assigned to be administered either poractant alfa or beractant, prospectively. Serial LUS scans were obtained by an experienced neonatologist in a standardized manner before and after (2 and 6 hours) surfactant administration. The LUS scans were evaluated by protocols based on scores and lung profiles.
Results Thirty-seven infants received poractant alfa and 36 received beractant. The baseline characteristics and presurfactant LUS scores were similar in groups. The scores were significantly decreased after surfactant administration in both groups (2 hours, p = < 0.001; 6 hours, p = < 0.001). LUS scores in poractant group were significantly lower than beractant group when compared at each time point. At the end of 6 hours, the number of infants with the normal profile was significantly higher in the poractant group (∼65%) than the beractant group (22%).
Conclusion LUS is beneficial for evaluating lung aeration after surfactant treatment in preterm infants with RDS. A better lung aeration can be achieved in the early period with the use of poractant alfa.
Large and small extracellular vesicles released by glioma cells in vitro and in vivo
Authors: Yekula Anudeep , Minciacchi Valentina R. , Morello Matteo , Shao Huilin , Park Yongil , Zhang Xuan , Muralidharan Koushik , Freeman Michael R. , Weissleder Ralph , Lee Hakho , Carter Bob , Breakefield Xandra O. , Di Vizio Dolores , Balaj Leonora 
Published: November 2019

ABSTRACTTumour cells release diverse populations of extracellular vesicles (EVs) ranging in size, molecular cargo, and function. We sought to characterize mRNA and protein content of EV subpopulations released by human glioblastoma (GBM) cells expressing a mutant form of epidermal growth factor receptor (U87EGFRvIII) in vitro and in vivo with respect to size, morphology and the presence of tumour cargo. The two EV subpopulations purified from GBM U87EGFRvIII cancer cells, non‐cancer human umbilical vein endothelial cells (HUVEC; control) and serum of U87EGFRvIII glioma‐bearing mice using differential centrifugation (EVs that sediment at 10,000 × g or 100,000 × g are termed large EVs and small EVs, respectively) were characterized using transmission electron microscopy (TEM), confocal microscopy, nanoparticle tracking analysis (NTA), flow cytometry, immunofluorescence (IF), quantitative‐polymerase chain reaction (qPCR), droplet digital polymerase chain reaction (ddPCR) and micro‐nuclear magnetic resonance (μNMR). We report that both U87EGFRvIII and HUVEC release a similar number of small EVs, but U87EGFRvIII glioma cells alone release a higher number of large EVs compared to non‐cancer HUVEC. The EGFRvIII mRNA from the two EV subpopulations from U87EGFRvIII glioma cells was comparable, while the EGFR protein (wild type + vIII) levels are significantly higher in large EVs. Similarly, EGFRvIII mRNA in large and small EVs isolated from the serum of U87EGFRvIII glioma‐bearing mice is comparable, while the EGFR protein (wild type + vIII) levels are significantly higher in large EVs. Here we report for the first time a direct comparison of large and small EVs released by glioma U87EGFRvIII cells and from serum of U87EGFRvIII glioma‐bearing mice. Both large and small EVs contain tumour‐specific EGFRvIII mRNA and proteins and combining these platforms may be beneficial in detecting rare mutant events in circulating biofluids.
Modification of egg shell powder with in situ generated copper and cuprous oxide nanoparticles by hydrothermal method*
Authors: Phuthotham Matuphum , Siengchin Suchart , Ashok Basa , Varada Rajulu Anumakonda 
Published: November 2019

Abstract
The poultry waste of egg shells was cleaned and finely powdered which was subsequently modified with in situ generated copper nanoparticles (CuNPs) and cuprous oxide nanoparticles (Cu2ONPs) by one step hydrothermal method. The modified egg shell powder (MESP) was characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, x-ray diffraction, thermogravimetric analysis and antibacterial tests. The MESP had in situ generated spherical CuNPs and Cu2ONPs in the size range of 50 nm to 120 nm. The spectral analysis indicated lowering of intensity of the peaks of MESP indicating the involvement of the functional groups of the protein component of ESP in the generation and stabilization of the nanoparticles. X-ray analysis indicated the generation of both CuNPs and Cu2ONPs in MSEP. The thermal analysis indicated lowering of the thermal stability for MESP. The MESP exhibited excellent antibacterial activity against both the Gram negative and Gram positive bacteria. Hence the low cost MESP with in situ generated CuNPs and Cu2ONPs can be used as antibacterial cleaning powder for houseware and also as antibacterial filler in the preparation of polymer composites.
Genome size and endopolyploidy evolution across the moss phylogeny
Authors: Bainard Jillian D , Newmaster Steven G , Budke Jessica M 
Published: November 2019

AbstractBackground and AimsCompared with other plant lineages, bryophytes have very small genomes with little variation across species, and high levels of endopolyploid nuclei. This study is the first analysis of moss genome evolution over a broad taxonomic sampling using phylogenetic comparative methods. We aim to determine whether genome size evolution is unidirectional as well as examine whether genome size and endopolyploidy are correlated in mosses.MethodsGenome size and endoreduplication index (EI) estimates were newly generated using flow cytometry from moss samples collected in Canada. Phylogenetic relationships between moss species were reconstructed using GenBank sequence data and maximum likelihood methods. Additional 1C-values were compiled from the literature and genome size and EI were mapped onto the phylogeny to reconstruct ancestral character states, test for phylogenetic signal and perform phylogenetic independent contrasts.Key ResultsGenome size and EI were obtained for over 50 moss taxa. New genome size estimates are reported for 33 moss species and new EIs are reported for 20 species. In combination with data from the literature, genome sizes were mapped onto a phylogeny for 173 moss species with this analysis, indicating that genome size evolution in mosses does not appear to be unidirectional. Significant phylogenetic signal was detected for genome size when evaluated across the phylogeny, whereas phylogenetic signal was not detected for EI. Genome size and EI were not found to be significantly correlated when using phylogenetically corrected values.ConclusionsSignificant phylogenetic signal indicates closely related mosses have more similar genome sizes and EI values. This study supports that DNA content in mosses is defined by small genomes that are highly endopolyploid, suggesting strong selective pressure to maintain these features. Further research is needed to understand the functional significance of DNA content evolution in mosses.
Early Cutoff Criteria for Strong Performance on the Test of Memory Malingering
Authors: Polsinelli Angelina J , Cerhan Jane H 
Published: November 2019

Abstract

Objective
The Test of Memory Malingering (TOMM) is widely used to assess performance validity. To improve efficiency, we investigated whether abbreviated administration (i.e., only the first 25 items of Trial 1 [T1]) is possible when effort is very strong (≥49/50 on T1 or T2).

Method
We collected TOMM scores of 501 consecutive adult patients ranging in cognitive status who underwent standard neuropsychological evaluation at Mayo Clinic, Rochester, MN.

Results
Receiver Operating Characteristic (ROC) analysis showed excellent area under the curve (AUC) (0.94; CI95% [0.92, 0.97]) and a cutoff of 25/25 had 100% specificity for identifying strong performance. Of the 224 patients who obtained a perfect score on the first 25 items, 197 (88%) obtained ≥49 on T1 and the remaining patients (n = 27) obtained ≥49 on T2.

Conclusion
A perfect score on the first 25 items of the TOMM predicted overall strong performance 100% of the time, supporting abbreviated administration in select cases in a general outpatient clinical setting.
genBaRcode: a comprehensive R-package for genetic barcode analysis
Authors: Thielecke Lars , Cornils Kerstin , Glauche Ingmar 
Published: November 2019

Abstract

Motivation
Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance.

Results
We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies.

Availability and implementation
The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).