bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recolonization of Marginal Coral Reef Flats in Response to Recent Sea‐Level Rise
Authors: Chen Tianran , Roff George , McCook Laurence , Zhao Jianxin , Li Shu 
Published: October 2018

AbstractIn an era of global change and rising sea levels, the capacity for inshore reefs to survive is increasingly unclear. We report on recent colonization of an inshore reef‐flat environment at Sanya Bay, northern South China Sea, in shallow, muddy, eutrophic, and turbid conditions, which are widely viewed as marginal for sustained coral growth. U‐Th dating of fossil Acropora substrate indicated that the reef flat has existed in a dormant state since ~5,400 years BP, with no vertical space available to accommodate coral expansion. Our surveys revealed that populations of free‐living Porites compressa have recolonized the reef flat through asexual fragmentation, covering 13.9 ± 1.3% of reef‐flat substrates. Age‐frequency analysis indicated that the majority (86%) of P. compressa colonies were less than 30 years old. Analysis of long‐term sea‐level data indicated that recent recolonization of the reef flat occurred in response to a sea‐level rise of 16.2 ± 0.6 cm over the past 30 years (1987–2016). Modern sea‐level rise at Sanya Bay appears to have turned on reef growth which has existed in a senescent turned off state for over five millennia. The asexual life history strategy of P. compressa colonies, which involves forming free‐living colonies (coralliths), allows them to overcome turbid environmental conditions that are otherwise adverse to sexual recruitment. Our results provide novel insight into the response of marginal habitats to sea‐level rise, and suggest that coral cover on degraded coral reef flats could increase under future sea‐level rise, albeit with assemblages dominated by a few well‐adapted species.
Generalized Ramsey interferometry explored with a single nuclear spin qudit
Authors: Godfrin Clément , Ballou Rafik , Bonet Edgar , Ruben Mario , Klyatskaya Svetlana , Wernsdorfer Wolfgang , Balestro Franck 
Published: October 2018

AbstractQudits, with their state space of dimension d > 2, open fascinating experimental prospects. The quantum properties of their states provide new potentialities for quantum information, quantum contextuality, expressions of geometric phases, facets of quantum entanglement and many other foundational aspects of the quantum world that are unapproachable via qubits. Here, we have experimentally investigated the quantum dynamics of a qudit (d = 4) that consists of a single 3/2 nuclear spin embedded in a molecular magnet transistor geometry, coherently driven by a microwave electric field. In order to demonstrate the potentialities of molecular magnets for quantum technologies, we implemented three protocols based on a generalization of the Ramsey interferometry to a multilevel system. First, the Ramsey interference is used to measure the accumulation of geometric phases. Then, two distinct transitions of the nuclear spin are addressed to measure the phase of an iSWAP quantum gate. Finally, through a succession of two Hadamard gates, the coherence time of a 3-state superposition is measured.
Imaging of Pseudomonas aeruginosa infection with Ga-68 labelled pyoverdine for positron emission tomography
Authors: Petrik Milos , Umlaufova Eva , Raclavsky Vladislav , Palyzova Andrea , Havlicek Vladimir , Haas Hubertus , Novy Zbynek , Dolezal Dalibor , Hajduch Marian , Decristoforo Clemens 
Published: October 2018

AbstractPseudomonas aeruginosa is an increasingly prevalent opportunistic pathogen that causes a variety of life-threatening nosocomial infections. Novel strategies for the development of new antibacterial treatments as well as diagnostic tools are needed. One of the novel diagnostic strategies for the detection of infection could be the utilization of siderophores. Siderophores are low-molecular-weight chelators produced by microbes to scavenge essential iron. Replacing iron in siderophores by suitable radiometals, such as Ga-68 for positron emission tomography (PET) imaging, opens approaches for targeted imaging of infection. Here we report on pyoverdine PAO1 (PVD-PAO1), a siderophore produced by P. aeruginosa, labelled with Ga-68 for specific imaging of Pseudomonas infections. PVD-PAO1 was labelled with Ga-68 with high radiochemical purity. The resulting complex showed hydrophilic properties, low protein binding and high stability in human serum. In vitro uptake of 68Ga-PVD-PAO1 was highly dependent on the type of microbial culture. In normal mice 68Ga-PVD-PAO1 showed rapid pharmacokinetics with urinary excretion. PET imaging in infected animals displayed specific accumulation of 68Ga-PVD-PAO1 in infected tissues and better distribution than clinically used 18F-fluorodeoxyglucose (18F-FDG) and 68Ga-citrate. Ga-68 labelled pyoverdine PAO1 seems to be a promising agent for imaging of P. aeruginosa infections by means of PET.
Human Bronchial Epithelial Cells Inhibit Aspergillus fumigatus Germination of Extracellular Conidia via FleA Recognition
Authors: Richard Nicolas , Marti Léa , Varrot Annabelle , Guillot Loïc , Guitard Juliette , Hennequin Christophe , Imberty Anne , Corvol Harriet , Chignard Michel , Balloy Viviane 
Published: October 2018

AbstractAspergillus fumigatus is an environmental filamentous fungus that may act as an opportunistic pathogen causing a variety of diseases, including asthma or allergic bronchopulmonary aspergillosis, and infection, ranging from asymptomatic colonization to invasive pulmonary form, especially in immunocompromised patients. This fungus is characterized by different morphotypes including conidia which are the infective propagules able to germinate into hyphae. Due to their small size (2–3 µm), conidia released in the air can reach the lower respiratory tract. The objective of this study was to characterize the interactions between conidia and bronchial epithelial cells. To this end, we studied the role of bronchial epithelial cells, i.e., the BEAS-2B cell line and human primary cells, in conidial germination of a laboratory strain and three clinical strains of A. fumigatus. Microscopic observations and galactomannan measurements demonstrated that contact between epithelial cells and conidia leads to the inhibition of conidia germination. We demonstrated that this fungistatic process is not associated with the release of any soluble components nor internalization by the epithelial cells. We highlight that this antifungal process involves the phosphoinositide 3-kinase pathway on the host cellular side and the lectin FleA on the fungal side. Collectively, our results show that bronchial epithelial cells attenuate fungal virulence by inhibiting germination of extracellular conidia, thus preventing the morphological change from conidia to filaments, which is responsible for tissue invasion.
Effect of natural products on the production and activity of Clostridium difficile toxins in vitro
Authors: Roshan Niloufar , Riley Thomas V. , Knight Daniel R. , Hammer Katherine A. 
Published: October 2018

AbstractClostridium difficile infection is a toxin-mediated disease of the colon. C. difficile virulence is primarily attributed to the production of toxin A and toxin B; thus this study was aimed to investigate the effect of a range of natural products on the production and activity of C. difficile toxins in vitro. Twenty-two natural products were investigated against four C. difficile strains. The activity of products against toxins was determined using Vero and HT-29 cells cytotoxicity and neutral red uptake assays. The indirect effect of products on toxin-mediated cytotoxicity was determined using the same cell lines. The effect of seven products on toxin production by C. difficile was determined using ELISA. Zingerone (0.3 mg/ml) protected both cell lines from C. difficile cytopathic effects, confirmed by the neutral red uptake assay (P < 0.05). Three Leptospermum honeys (4% w/v), fresh onion bulb extract (12.5% v/v) and trans-cinnamaldehyde (0.005% v/v) all reduced toxin production and activity significantly (P ≤ 0.023). Garlic clove powder (4.7 mg/ml) only reduced toxin activity (P ≤ 0.047). Overall, several natural products had activity against C. difficile toxins in vitro encouraging further investigation against C. difficile toxins in vivo.
The yeast GRASP Grh1 displays a high polypeptide backbone mobility along with an amyloidogenic behavior
Authors: Fontana N. A. , Fonseca-Maldonado R. , Mendes L. F. S , Meleiro L. P. , Costa-Filho A. J. 
Published: October 2018

AbstractGRASPs are proteins involved in cell processes that seem paradoxical: responsible for shaping the Golgi cisternae and involved in unconventional secretion mechanisms that bypass the Golgi. Despite its physiological relevance, there is still a considerable lack of studies on full-length GRASPs. Our group has previously reported an unexpected behavior of the full-length GRASP from the fungus C. neoformans: its intrinsically-disordered characteristic. Here, we generalize this finding by showing that it is also observed in the GRASP from S. cerevisae (Grh1), which strongly suggests it might be a general property within the GRASP family. Furthermore, Grh1 is also able to form amyloid-like fibrils either upon heating or when submitted to changes in the dielectric constant of its surroundings, a condition that is experienced by the protein when in close contact with membranes of cell compartments, such as the Golgi apparatus. Intrinsic disorder and fibril formation can thus be two structural properties exploited by GRASP during its functional cycle.
Assessing the suitability of copper thiocyanate as a hole-transport layer in inverted CsSnI3 perovskite photovoltaics
Authors: Wijesekara Anjana , Varagnolo Silvia , Dabera G. Dinesha M. R. , Marshall Kenneth P. , Pereira H. Jessica , Hatton Ross A. 
Published: October 2018

AbstractWe report the findings of a study into the suitability of copper (I) thiocyanate (CuSCN) as a hole-transport layer in inverted photovoltaic (PV) devices based on the black gamma phase (B-γ) of CsSnI3 perovskite. Remarkably, when B-γ-CsSnI3 perovskite is deposited from a dimethylformamide solution onto a 180–190 nm thick CuSCN film supported on an indium-tin oxide (ITO) electrode, the CuSCN layer is completely displaced leaving a perovskite layer with high uniformity and coverage of the underlying ITO electrode. This finding is confirmed by detailed analysis of the thickness and composition of the film that remains after perovskite deposition, together with photovoltaic device studies. The results of this study show that, whilst CuSCN has proved to be an excellent hole-extraction layer for high performance lead-perovskite and organic photovoltaics, it is unsuitable as a hole-transport layer in inverted B-γ-CsSnI3 perovskite photovoltaics processed from solution.
Improving Protein Gamma-Turn Prediction Using Inception Capsule Networks
Authors: Fang Chao , Shang Yi , Xu Dong 
Published: October 2018

AbstractProtein gamma-turn prediction is useful in protein function studies and experimental design. Several methods for gamma-turn prediction have been developed, but the results were unsatisfactory with Matthew correlation coefficients (MCC) around 0.2–0.4. Hence, it is worthwhile exploring new methods for the prediction. A cutting-edge deep neural network, named Capsule Network (CapsuleNet), provides a new opportunity for gamma-turn prediction. Even when the number of input samples is relatively small, the capsules from CapsuleNet are effective to extract high-level features for classification tasks. Here, we propose a deep inception capsule network for gamma-turn prediction. Its performance on the gamma-turn benchmark GT320 achieved an MCC of 0.45, which significantly outperformed the previous best method with an MCC of 0.38. This is the first gamma-turn prediction method utilizing deep neural networks. Also, to our knowledge, it is the first published bioinformatics application utilizing capsule network, which will provide a useful example for the community. Executable and source code can be download at http://dslsrv8.cs.missouri.edu/~cf797/MUFoldGammaTurn/download.html.
Rapid degradation of progressive ankylosis protein (ANKH) in craniometaphyseal dysplasia
Authors: Kanaujiya Jitendra , Bastow Edward , Luxmi Raj , Hao Zhifang , Zattas Dimitrios , Hochstrasser Mark , Reichenberger Ernst J. , Chen I-Ping 
Published: October 2018

AbstractMutations in the progressive ankylosis protein (NP_473368, human ANKH) cause craniometaphyseal dysplasia (CMD), characterized by progressive thickening of craniofacial bones and widened metaphyses in long bones. The pathogenesis of CMD remains largely unknown, and treatment for CMD is limited to surgical intervention. We have reported that knock-in mice (AnkKI/KI) carrying a F377del mutation in ANK (NM_020332, mouse ANK) replicate many features of CMD. Interestingly, ablation of the Ank gene in AnkKO/KO mice also leads to several CMD-like phenotypes. Mutations causing CMD led to decreased steady-state levels of ANK/ANKH protein due to rapid degradation. While wild type (wt) ANK was mostly associated with plasma membranes, endoplasmic reticulum (ER), Golgi apparatus and lysosomes, CMD-linked mutant ANK was aberrantly localized in cytoplasm. Inhibitors of proteasomal degradation significantly restored levels of overexpressed mutant ANK, whereas endogenous CMD-mutant ANK/ANKH levels were more strongly increased by inhibitors of lysosomal degradation. However, these inhibitors do not correct the mislocalization of mutant ANK. Co-expressing wt and CMD-mutant ANK in cells showed that CMD-mutant ANK does not negatively affect wt ANK expression and localization, and vice versa. In conclusion, our finding that CMD mutant ANK/ANKH protein is short-lived and mislocalized in cells may be part of the CMD pathogenesis.
Whole-genome sequencing of esophageal adenocarcinoma in Chinese patients reveals distinct mutational signatures and genomic alterations
Authors: Dai James Y. , Wang Xiaoyu , Buas Matthew F. , Zhang Chengjuan , Ma Jie , Wei Bing , Li Yin , Zhao Baosheng , Hyun Teresa S. , Chen Xueyan , Loeb Keith R. , Odze Robert , Yao Lena , Sun Xin , Self Steve , Vaughan Thomas L. , Guo Yongjun 
Published: October 2018

AbstractWhile the incidence of esophageal adenocarcinoma (EAC) has risen drastically in Western countries over the last 40 years, a similar trend has not been observed for EAC in China. Here, we analyzed mutational spectrum, copy number alterations, and structural variants from whole-genome sequencing of 10 Chinese EAC tumor samples and their matched normal samples, and compared them to previously reported EAC tumor specimens from Western countries. The mutational burden in Chinese EAC was significantly lower than that found in EAC from Western countries. The hallmark A>C mutational signature observed at high frequency in EAC from Western countries, which has been linked to acid reflux, is completely absent in Chinese samples. Furthermore, none of the Chinese samples showed evidence of chromothripsis and genome doubling that are often found in EAC from Western countries. In summary, Chinese EAC tumor samples had distinct genomic profiles and signatures, suggesting that EAC in Chinese individuals may arise from a different etiological pathway.
Repeat bleaching of a central Pacific coral reef over the past six decades (1960–2016)
Authors: Barkley Hannah C. , Cohen Anne L. , Mollica Nathaniel R. , Brainard Russell E. , Rivera Hanny E. , DeCarlo Thomas M. , Lohmann George P. , Drenkard Elizabeth J. , Alpert Alice E. , Young Charles W. , Vargas-Ángel Bernardo , Lino Kevin C. , Oliver Thomas A. , Pietro Kathryn R. , Luu Victoria H. 
Published: October 2018

AbstractThe oceans are warming and coral reefs are bleaching with increased frequency and severity, fueling concerns for their survival through this century. Yet in the central equatorial Pacific, some of the world’s most productive reefs regularly experience extreme heat associated with El Niño. Here we use skeletal signatures preserved in long-lived corals on Jarvis Island to evaluate the coral community response to multiple successive heatwaves since 1960. By tracking skeletal stress band formation through the 2015-16 El Nino, which killed 95% of Jarvis corals, we validate their utility as proxies of bleaching severity and show that 2015-16 was not the first catastrophic bleaching event on Jarvis. Since 1960, eight severe (>30% bleaching) and two moderate (<30% bleaching) events occurred, each coinciding with El Niño. While the frequency and severity of bleaching on Jarvis did not increase over this time period, 2015–16 was unprecedented in magnitude. The trajectory of recovery of this historically resilient ecosystem will provide critical insights into the potential for coral reef resilience in a warming world.
Subdiffusion of loci and cytoplasmic particles are different in compressed Escherichia coli cells
Authors: Yu Shi , Sheats Julian , Cicuta Pietro , Sclavi Bianca , Cosentino Lagomarsino Marco , Dorfman Kevin D. 
Published: October 2018

AbstractThe complex physical nature of the bacterial intracellular environment remains largely unknown, and has relevance for key biochemical and biological processes of the cell. Although recent work has addressed the role of non-equilibrium sources of activity and crowding, the consequences of mechanical perturbations are relatively less explored. Here we use a microfabricated valve system to track both fluorescently labeled chromosomal loci and cytoplasmic particles in Escherichia coli cells shortly after applying a compressive force, observing the response on time scales that are too sudden to allow for biochemical response from the cell. Cytoplasmic diffusion slows markedly on compression but the exponent governing the growth of the ensemble-averaged mean-squared displacement of cytoplasmic particles is unaffected. In contrast, the corresponding exponent for DNA loci changes significantly. These results suggest that DNA elasticity and nucleoid organization play a more important role in loci subdiffusion than cytoplasmic viscoelasticity under such short time scales.
Synkope – Eine praktische Abklärungsstrategie
Authors: Nemeth Blanka , Weber Elisabeth , Huber Lars 
Published: October 2018

AbstractSyncope is defined as a transient, self-limited loss of consciousness due to insufficient cerebral blood perfusion. In a clinical setting, syncopal events usually present a diagnostic dilemma due to its broad differential diagnosis ranging from banal to potentially harmful causes. In the absence of a working hypothesis, multiple tests are ordered that result in high costs but are of questionable diagnostic and therapeutic value. This article provides a practical overview and, based on international guidelines and selected studies, proposes a standardized approach to patients with syncope. Initial evaluation of these patients includes taking a careful medical history, physical examination and ECG. These tests result in an individual risk assessment that supports decision-making whether further analysis should be performed in an outpatient or inpatient setting. Additional tests including echocardiography, laboratory analysis, cardiac monitoring, CT-scans, are ordered according to prior evaluation. This article reviews the most common diagnostic tests, their indications and the clinical relevance for the evaluation of patients with syncopal events. Therapeutic options are not within the focus of this article.
The Excised Appendix Tip—To Send or not to Send, That is the Question
Authors: Tullie Lucinda , Vadgama Bhumita , Anbarasan Ravindar , Stanton Michael , Steinbrecher Henrik 
Published: October 2018

AbstractA 9-year-old boy, with previous anorectal malformation and neuropathic bladder and bowel, underwent ileocystoplasty, Monti–Mitrofanoff and appendix antegrade colonic enema procedure. The tip of the macroscopically normal appendix was sent for routine histopathology. Microscopy demonstrated a 5-mm well-differentiated neuroendocrine tumor extending into muscularis propria. Ki-67 index was <2%. Due to margin involvement, the appendix conduit and surrounding skin were re-excised and a tube cecostomy was created through a separate incision. Microscopy revealed no residual neuroendocrine tumor, and no further treatment was required.
A Case of Inferior Vena Cava Thrombosis Induced by Left Iliac Vein Stents
Authors: Wei Wei , Jiang Xuemei , Xu Bo , Chen Yikuan 
Published: October 2018

AbstractStents have been widely used to restore the patency of the iliac vein in the treatment of its obstruction. However, various complications related to those stents have been reported. This case report covers a 67-year-old male who was diagnosed with left iliofemoral venous post-thrombotic syndrome with recurrent acute deep venous thrombosis. Thrombosis of the inferior vena cava was induced by pronounced extension of left iliac vein stents. Extending stents in this way covers the outlet of the contralateral common iliac vein and may induce thrombosis in the inferior vena cava.
Evaluation of Blood Loss and Implant Alignment after Total Knee Arthroplasty with Inertial Based Extramedullary Femoral Cutting Guide
Authors: Bonanzinga Tommaso , Tanzi Piergiuseppe , Pia Neri Maria , Iacono Francesco , Mazzola Claudio , Belluati Alberto , Colombelli Andrea , Zaffagnini Stefano , Marcacci Maurilio 
Published: October 2018

Purpose The purpose of this study was to compare, in terms of blood loss and implant alignment, a new generation of smart extramedullary (EM) cutting guides with the conventional intramedullary (IM) guide for total knee arthroplasty (TKA). The hypothesis was that the EM system would result in less blood loss and fewer days of hospitalization, while ensuring equal or higher accuracy in the alignment of the femoral implant.
Methods Thirty-six patients were enrolled for the present study: 18 patients underwent TKA using the EM guide and for the other 18 patients the IM guide was used. Preoperative and postoperative X-rays were acquired. The preoperative and postoperative hemoglobin values were compared. Lastly, length of hospital stay was recorded.
Results The hemoglobin difference was significantly lower in the EM group. The alignment of the prosthetic femoral implant in the two groups was comparable but all patients in the EM cohort had a final alignment within 3 degrees of range on the frontal view, while 22% of the patients in the IM cohort had a final alignment exceeding 3 degrees of range. The mean hospitalization duration showed no significant difference between groups, though EM group showed 1.6 days less compared with IM group.
Conclusions The inertial-based EM guide system could be useful for decreasing blood loss compared with conventional guide. This device tended to have better results even in terms of accuracy, but this difference was not significant.
Level of Evidence This is a level II, prospective cohort study.