bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mantle Source and Magmatic Evolution of the Dying Spreading Ridge in the South China Sea
Authors: Zhang Guo‐Liang , Sun Wei‐Dong , Seward Gareth 
Published: October 2018

AbstractThe genesis of seamount chains along fossil spreading ridges reflects the mantle melting dynamics of dying spreading center. The South China Sea developed a seamount chain along its fossil ridge shortly after cessation of spreading. International Ocean Discovery Program Expedition 349 has recovered three volcanic layers, a shallow volcanic breccia layer and two deeper (upper and lower sections) basalt layers, at Site U1431 near the fossil ridge of the South China Sea. Despite the mid‐ocean ridge basalt (MORB)‐like geochemistry of the lower and upper section basalts, they show distinct geochemical differences that indicate a change of mantle source and a transition from spreading to intraplate volcanism. While the lower section basalts could reflect the last stage volcanism before the cessation of ridge spreading, the upper section basalts with whole‐rock MgO up to ~20 wt.% were formed by intraplate volcanism with significant olivine accumulation once the spreading center had become inactive. The MORB type basalts at Site U1431 have Hawaii‐like high olivine Ni and Fe/Mn and low olivine Ca and Mn and bulk‐rock low CaO that are distinctly different from normal global MORBs, suggesting an anomalous mantle source in lithology. We suggest that an eclogite‐/pyroxenite‐rich component, possibly sourced from the Hainan hot spot, played a fundamental role in the transition from spreading to intraplate volcanism of the dying spreading ridge of the South China Sea.
Spatial Extent and Temporal Correlation of Chorus and Hiss: Statistical Results From Multipoint THEMIS Observations
Authors: Agapitov O. , Mourenas D. , Artemyev A. , Mozer F. S. , Bonnell J. W. , Angelopoulos V. , Shastun V. , Krasnoselskikh V. 
Published: October 2018

AbstractThe spatial localization of whistler mode waves, determined by their generation process, propagation, and damping, is important for assessing the efficiency of wave‐particle interactions and the dynamics of the radiation belts. We use 11 years of multipoint wave measurements in 2007–2017 from five Time History of Events and Macroscale Interactions during Substorms (THEMIS) spacecraft covering L = 2–10 at low magnetic latitudes over all magnetic local times (MLTs) to characterize both the instantaneous spatial extent of chorus and hiss active regions and their wave amplitude distribution in the vicinity of their respective generation regions, making use of the time domain correlation technique. The correlation of lower band chorus wave power dynamics from two spacecraft measurements remains significant up to 250–800 km transverse to the background magnetic field, in agreement with the typical scale of a chorus element, with a shorter correlation length for higher peak wave power. Additionally, a coordinated analysis of average chorus amplitudes at separate locations shows that the radial extent of the chorus active region varies from 0.2 RE on the nightside to 1 RE on the dayside, with an azimuthal width of 1 MLT. The wave power correlation scale of hiss has no fine structure and is generally larger (1,500–3,000 km); its correlation remains nonnegligible up to 1.5 RE. Such observations are consistent with chorus generation by localized electron injections and subsequent hiss amplification at lower L shells from seed chorus waves having propagated and spread over a wider region inside the plasmasphere. The connection between hiss and chorus is further explored statistically through the correlation between their respective wave power variations, suggesting a significant link between them.
Wave Generation, Dissipation, and Disequilibrium in an Embayment With Complex Bathymetry
Authors: Chen Jia‐Lin , Ralston David K. , Geyer W. Rockwell , Sommerfield Christopher K. , Chant Robert J. 
Published: October 2018

AbstractHeterogeneous, sharply varying bathymetry is common in estuaries and embayments, and complex interactions between the bathymetry and wave processes fundamentally alter the distribution of wave energy. The mechanisms that control the generation and dissipation of wind waves in an embayment with heterogeneous, sharply varying bathymetry are evaluated with an observational and numerical study of the Delaware Estuary. Waves in the lower bay depend on both local wind forcing and remote wave forcing from offshore, but elsewhere in the estuary waves are controlled by the local winds and the response of the wavefield to bathymetric variability. Differences in the wavefield with wind direction highlight the impacts of heterogeneous bathymetry and limited fetch. Under the typical winter northwest wind conditions waves are fetch‐limited in the middle estuary and reach equilibrium with local water depth only in the lower bay. During southerly wind conditions typical of storms, wave energy is near equilibrium in the lower bay, and midestuary waves are attenuated by the combination of whitecapping and bottom friction, particularly over the steep, longitudinal shoals. Although the energy dissipation due to bottom friction is generally small relative to whitecapping, it becomes significant where the waves shoal abruptly due to steep bottom topography. In contrast, directional spreading keeps wave heights in the main channel significantly less than local equilibrium. The wave disequilibrium in the deep navigational channel explains why the marked increase in depth by dredging of the modern channel has had little impact on wave conditions.
Anthropogenic Aerosol Indirect Effects in Cirrus Clouds
Authors: Penner Joyce E. , Zhou Cheng , Garnier Anne , Mitchell David L. 
Published: October 2018

AbstractWe have implemented a parameterization for forming ice in large‐scale cirrus clouds that accounts for the changes in updrafts associated with a spectrum of waves acting within each time step in the model. This allows us to account for the frequency of homogeneous and heterogeneous freezing events that occur within each time step of the model and helps to determine more realistic ice number concentrations as well as changes to ice number concentrations. The model is able to fit observations of ice number at the lowest temperatures in the tropical tropopause but is still somewhat high in tropical latitudes with temperatures between 195°K and 215°K. The climate forcings associated with different representations of heterogeneous ice nuclei (IN or INPs) are primarily negative unless large additions of IN are made, such as when we assumed that all aircraft soot acts as an IN. However, they can be close to zero if it is assumed that all background dust can act as an INP irrespective of how much sulfate is deposited on these particles. Our best estimate for the forcing of anthropogenic aircraft soot in this model is −0.2 ± 0.06 W/m2, while that from anthropogenic fossil/biofuel soot is −0.093 ± 0.033 W/m2. Natural and anthropogenic open biomass burning leads to a net forcing of −0.057 ± 0.05 W/m2.
Glucose homeostasis dependency on acini–islet–acinar (AIA) axis communication: a new possible pathophysiological hypothesis regarding diabetes mellitus
Authors: Pierzynowski Stefan G. , Gregory Peter C. , Filip Rafał , Woliński Jarosław , Pierzynowska Kateryna Goncharova 
Published: October 2018

AbstractStudies have highlighted the existence of two intra-pancreatic axes of communication: one involved in the regulation of enzyme production by insulin—the insular–acinar axis; and another involved in the regulation of insulin release by pancreatic enzymes—the acini–insular axis. Previous studies by our laboratory show that pancreatic enzymes can affect blood glucose homeostasis and insulin secretion independently of their digestive functions, both from the gut lumen and probably from the blood. As a result we would like to introduce here the concept of acini–islet–acinar (AIA) axis communication (feedback), which could play an important role in the development of obesity and diabetes type 2. The AIA feedback links the endocrine and exocrine parts of the pancreas and emphasizes the essential role that the pancreas plays, as a single organ, in the regulation of glucose homeostasis by amylase most probably in gut epithelium and by insulin and glucagon in peripheral blood.
Gut dysbiosis is associated with the reduced exercise capacity of elderly patients with hypertension
Authors: Yu Yanbo , Mao Genxiang , Wang Jirong , Zhu Liyue , Lv Xiaoling , Tong Qian , Fang Yefei , Lv Yinxiang , Wang Guofu 
Published: October 2018

AbstractHypertension is a global health issue, and a reduced exercise capacity is unavoidable for older people. According to recent clinical studies, the intestinal microbiota play a crucial role in the pathogenesis of many human diseases. We investigated whether specific alterations in the gut microbiota contribute to the reduced exercise capacity of elderly patients with hypertension. This study enrolled 56 subjects, and all patients performed a cardiopulmonary exercise test and underwent fecal bacteria sequencing (16 s ribosomal RNA V4 region). According to peak oxygen uptake values, patients were divided into three groups (Weber A = 19, Weber B = 20, and Weber C = 17). The alpha diversity was not significantly different among the three groups. Regarding the beta diversity, Weber A samples were separate from the other two groups in the nonmetric multidimensional scaling ordination plot (ANOSIM pairwise comparisons generated an R > 0.5; p < 0.05). The abundance of Betaproteobacteria, Burkholderiales, Alcaligenaceae, Faecalibacterium and Ruminococcaceae was diminished in subjects with a reduced exercise capacity (LDA score > 4.0). Escherichia coli are a primary producer of trimethylamine and inflammation in the human gut, and the abundance of this bacteria was increased in patients with a reduced exercise capacity (LDA score > 4.0). On the other hand, Lachnospiraceae-Eubacterium_hallii_group, Lachnospiraceae-Lachnoclostridium, Lachnospiraceae-Blautia-Ruminococcus_sp__5_1_39BFAA, and Ruminococcaceae-Faecalibacterium belong to the order Clostridiales that are likely to produce short-chain fatty acids (LDA score > 4.0), and some of these species were enriched in the Weber B or Weber C group in multiple comparisons. Our data pointed to an altered gut microbiota as a potential contributor to the pathogenesis and progression of the reduced exercise capacity of elderly patients with hypertension.
A cysteine-based molecular code informs collagen C-propeptide assembly
Authors: DiChiara Andrew S. , Li Rasia C. , Suen Patreece H. , Hosseini Azade S. , Taylor Rebecca J. , Weickhardt Alexander F. , Malhotra Diya , McCaslin Darrell R. , Shoulders Matthew D. 
Published: October 2018

AbstractFundamental questions regarding collagen biosynthesis, especially with respect to the molecular origins of homotrimeric versus heterotrimeric assembly, remain unanswered. Here, we demonstrate that the presence or absence of a single cysteine in type-I collagen’s C-propeptide domain is a key factor governing the ability of a given collagen polypeptide to stably homotrimerize. We also identify a critical role for Ca2+ in non-covalent collagen C-propeptide trimerization, thereby priming the protein for disulfide-mediated covalent immortalization. The resulting cysteine-based code for stable assembly provides a molecular model that can be used to predict, a priori, the identity of not just collagen homotrimers, but also naturally occurring 2:1 and 1:1:1 heterotrimers. Moreover, the code applies across all of the sequence-diverse fibrillar collagens. These results provide new insight into how evolution leverages disulfide networks to fine-tune protein assembly, and will inform the ongoing development of designer proteins that assemble into specific oligomeric forms.
Generation of orthotopically functional salivary gland from embryonic stem cells
Authors: Tanaka Junichi , Ogawa Miho , Hojo Hironori , Kawashima Yusuke , Mabuchi Yo , Hata Kenji , Nakamura Shiro , Yasuhara Rika , Takamatsu Koki , Irié Tarou , Fukada Toshiyuki , Sakai Takayoshi , Inoue Tomio , Nishimura Riko , Ohara Osamu , Saito Ichiro , Ohba Shinsuke , Tsuji Takashi , Mishima Kenji 
Published: October 2018

AbstractOrganoids generated from pluripotent stem cells are used in the development of organ replacement regenerative therapy by recapitulating the process of organogenesis. These processes are strictly regulated by morphogen signalling and transcriptional networks. However, the precise transcription factors involved in the organogenesis of exocrine glands, including salivary glands, remain unknown. Here, we identify a specific combination of two transcription factors (Sox9 and Foxc1) responsible for the differentiation of mouse embryonic stem cell-derived oral ectoderm into the salivary gland rudiment in an organoid culture system. Following orthotopic transplantation into mice whose salivary glands had been removed, the induced salivary gland rudiment not only showed a similar morphology and gene expression profile to those of the embryonic salivary gland rudiment of normal mice but also exhibited characteristics of mature salivary glands, including saliva secretion. This study suggests that exocrine glands can be induced from pluripotent stem cells for organ replacement regenerative therapy.
Patient-derived frontotemporal lobar degeneration brain extracts induce formation and spreading of TDP-43 pathology in vivo
Authors: Porta Sílvia , Xu Yan , Restrepo Clark R. , Kwong Linda K. , Zhang Bin , Brown Hannah J. , Lee Edward B. , Trojanowski John Q. , Lee Virginia M.-Y. 
Published: October 2018

AbstractThe stereotypical distribution of TAR DNA-binding 43 protein (TDP-43) aggregates in frontotemporal lobar degeneration (FTLD-TDP) suggests that pathological TDP-43 spreads throughout the brain via cell-to-cell transmission and correlates with disease progression, but no in vivo experimental data support this hypothesis. We first develop a doxycycline-inducible cell line expressing GFP-tagged cytoplasmic TDP-43 protein (iGFP-NLSm) as a cell-based system to screen and identify seeding activity of human brain-derived pathological TDP-43 isolated from sporadic FTLD-TDP and familial cases with Granulin (FTLD-TDP-GRN) or C9orf72 repeat expansion mutations (FTLD-TDP-C9+). We demonstrate that intracerebral injections of biologically active pathogenic FTLD-TDP seeds into transgenic mice expressing cytoplasmic human TDP-43 (lines CamKIIa-hTDP-43NLSm, rNLS8, and CamKIIa-208) and non-transgenic mice led to the induction of de-novo TDP-43 pathology. Moreover, TDP-43 pathology progressively spreads throughout the brain in a time-dependent manner via the neuroanatomic connectome. Our study suggests that the progression of FTLD-TDP reflects the templated cell-to-cell transneuronal spread of pathological TDP-43.
Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole
Authors: Liu Dazhi , Wei Yifeng , Liu Xuyang , Zhou Yan , Jiang Li , Yin Jinyu , Wang Feifei , Hu Yiling , Nanjaraj Urs Ankanahalli N. , Liu Yanhong , Ang Ee Lui , Zhao Suwen , Zhao Huimin , Zhang Yan 
Published: October 2018

AbstractSkatole is a malodorous compound that contributes to the characteristic smell of animal faeces. Although skatole has long been known to originate from bacterial tryptophan fermentation, the enzyme catalysing its formation has so far remained elusive. Here we report the use of comparative genomics for the discovery of indoleacetate decarboxylase, an O2-sensitive glycyl radical enzyme catalysing the decarboxylation of indoleacetate to form skatole as the terminal step of tryptophan fermentation in certain anaerobic bacteria. We describe its biochemical characterization and compare it to other glycyl radical decarboxylases. Indoleacetate decarboxylase may serve as a genetic marker for the identification of skatole-producing environmental and human-associated bacteria, with impacts on human health and the livestock industry.
Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters
Authors: de Lorgeril Julien , Lucasson Aude , Petton Bruno , Toulza Eve , Montagnani Caroline , Clerissi Camille , Vidal-Dupiol Jeremie , Chaparro Cristian , Galinier Richard , Escoubas Jean-Michel , Haffner Philippe , Dégremont Lionel , Charrière Guillaume M. , Lafont Maxime , Delort Abigaïl , Vergnes Agnès , Chiarello Marlène , Faury Nicole , Rubio Tristan , Leroy Marc A. , Pérignon Adeline , Régler Denis , Morga Benjamin , Alunno-Bruscia Marianne , Boudry Pierre , Le Roux Frédérique , Destoumieux-Garzόn Delphine , Gueguen Yannick , Mitta Guillaume 
Published: October 2018

AbstractInfectious diseases are mostly explored using reductionist approaches despite repeated evidence showing them to be strongly influenced by numerous interacting host and environmental factors. Many diseases with a complex aetiology therefore remain misunderstood. By developing a holistic approach to tackle the complexity of interactions, we decipher the complex intra-host interactions underlying Pacific oyster mortality syndrome affecting juveniles of Crassostrea gigas, the main oyster species exploited worldwide. Using experimental infections reproducing the natural route of infection and combining thorough molecular analyses of oyster families with contrasted susceptibilities, we demonstrate that the disease is caused by multiple infection with an initial and necessary step of infection of oyster haemocytes by the Ostreid herpesvirus OsHV-1 µVar. Viral replication leads to the host entering an immune-compromised state, evolving towards subsequent bacteraemia by opportunistic bacteria. We propose the application of our integrative approach to decipher other multifactorial diseases that affect non-model species worldwide.
Predicting CTCF-mediated chromatin interactions by integrating genomic and epigenomic features
Authors: Kai Yan , Andricovich Jaclyn , Zeng Zhouhao , Zhu Jun , Tzatsos Alexandros , Peng Weiqun 
Published: October 2018

AbstractThe CCCTC-binding zinc-finger protein (CTCF)-mediated network of long-range chromatin interactions is important for genome organization and function. Although this network has been considered largely invariant, we find that it exhibits extensive cell-type-specific interactions that contribute to cell identity. Here, we present Lollipop, a machine-learning framework, which predicts CTCF-mediated long-range interactions using genomic and epigenomic features. Using ChIA-PET data as benchmark, we demonstrate that Lollipop accurately predicts CTCF-mediated chromatin interactions both within and across cell types, and outperforms other methods based only on CTCF motif orientation. Predictions are confirmed computationally and experimentally by Chromatin Conformation Capture (3C). Moreover, our approach identifies other determinants of CTCF-mediated chromatin wiring, such as gene expression within the loops. Our study contributes to a better understanding about the underlying principles of CTCF-mediated chromatin interactions and their impact on gene expression.
Unbiased biocatalytic solar-to-chemical conversion by FeOOH/BiVO4/perovskite tandem structure
Authors: Lee Yang Woo , Boonmongkolras Passarut , Son Eun Jin , Kim Jinhyun , Lee Sahng Ha , Kuk Su Keun , Ko Jong Wan , Shin Byungha , Park Chan Beum 
Published: October 2018

AbstractRedox enzymes catalyze fascinating chemical reactions with excellent regio- and stereo-specificity. Nicotinamide adenine dinucleotide cofactor is essential in numerous redox biocatalytic reactions and needs to be regenerated because it is consumed as an equivalent during the enzymatic turnover. Here we report on unbiased photoelectrochemical tandem assembly of a photoanode (FeOOH/BiVO4) and a perovskite photovoltaic to provide sufficient potential for cofactor-dependent biocatalytic reactions. We obtain a high faradaic efficiency of 96.2% and an initial conversion rate of 2.4 mM h−1 without an external applied bias for the photoelectrochemical enzymatic conversion of α-ketoglutarate to l-glutamate via l-glutamate dehydrogenase. In addition, we achieve a total turnover number and a turnover frequency of the enzyme of 108,800 and 6200 h−1, respectively, demonstrating that the tandem configuration facilitates redox biocatalysis using light as the only energy source.
Space- and time-resolved small angle X-ray scattering to probe assembly of silver nanocrystal superlattices
Authors: Yu Yixuan , Yu Dian , Sadigh Babak , Orme Christine A. 
Published: October 2018

AbstractThe structure of nanocrystal superlattices has been extensively studied and well documented, however, their assembly process is poorly understood. In this work, we demonstrate an in situ space- and time-resolved small angle X-ray scattering measurement that we use to probe the assembly of silver nanocrystal superlattices driven by electric fields. The electric field creates a nanocrystal flux to the surface, providing a systematic means to vary the nanocrystal concentration near the electrode and thereby to initiate nucleation and growth of superlattices in several minutes. Using this approach, we measure the space- and time-resolved concentration and polydispersity gradients during deposition and show how they affect the superlattice constant and degree of order. We find that the field induces a size-selection effect that can reduce the polydispersity near the substrate by 21% leading to better quality crystals and resulting in field strength-dependent superlattice lattice constants.
Mechanochemical feedback control of dynamin independent endocytosis modulates membrane tension in adherent cells
Authors: Thottacherry Joseph Jose , Kosmalska Anita Joanna , Kumar Amit , Vishen Amit Singh , Elosegui-Artola Alberto , Pradhan Susav , Sharma Sumit , Singh Parvinder P. , Guadamillas Marta C. , Chaudhary Natasha , Vishwakarma Ram , Trepat Xavier , del Pozo Miguel A. , Parton Robert G. , Rao Madan , Pullarkat Pramod , Roca-Cusachs Pere , Mayor Satyajit 
Published: October 2018

AbstractPlasma membrane tension regulates many key cellular processes. It is modulated by, and can modulate, membrane trafficking. However, the cellular pathway(s) involved in this interplay is poorly understood. Here we find that, among a number of endocytic processes operating simultaneously at the cell surface, a dynamin independent pathway, the CLIC/GEEC (CG) pathway, is rapidly and specifically upregulated upon a sudden reduction of tension. Moreover, inhibition (activation) of the CG pathway results in lower (higher) membrane tension. However, alteration in membrane tension does not directly modulate CG endocytosis. This requires vinculin, a mechano-transducer recruited to focal adhesion in adherent cells. Vinculin acts by controlling the levels of a key regulator of the CG pathway, GBF1, at the plasma membrane. Thus, the CG pathway directly regulates membrane tension and is in turn controlled via a mechano-chemical feedback inhibition, potentially leading to homeostatic regulation of membrane tension in adherent cells.