bluuebunny/crossref_metadata_2025 huggingface dataset:
Different Influences of Mesoscale Oceanic Eddies on the North Pacific Subsurface Low Potential Vorticity Water Mass Between Winter and Summer
Authors: Wen Zhibin , Hu Haibo , Song Zhenya , Bai Haokun , Wang Ziyi
Published: December 2019

The generation and dissipation of North Pacific subsurface low potential vorticity water mass (SLPVW) affect various ocean‐atmosphere dynamic and thermodynamic processes on a wide range of time scales. Mesoscale oceanic eddies are believed to play an important role in the variation of SLPVW. National Centers for Environmental Prediction (NCEP)/NCEP‐Climate Forecast System Reanalysis coupled data set during 1979–2010 has been analyzed to investigate the different influences of mesoscale oceanic eddies on the SLPVW between winter and summer. It is found that the correlation between the sea surface height and SLPVW volume in winter is positive on the north of 30°N but negative on the south of 30°N, which is mainly caused by the eddy vorticity strength. The negative correlation value region has more strong anticyclones than the positive correlation value region, so the mixed layer depth in the negative (positive) correlation value region tends to be deeper (shallower) caused by stronger (weaker) anticyclones, which leads to the decreasing (increasing) of the low PV water mass under mixed layer depth (namely, SLPVW). Eddies also have obvious impacts on the subduction rate. The climatological eddy subduction rate can reach to 1.88 Sv in the NCEP‐Climate Forecast System Reanalysis, which accounts for 36.4% of the total subduction rate. In summer, the correlation between the sea surface height and SLPVW volume is remarkably negative. It is found that water diverges (converges) in the composite anticyclone (cyclone), which leads to the increasing (decreasing) of PV value in the composite anticyclone (cyclone), finally accelerates (hinders) the dissipation of SLPVW.
Eddy‐Induced Chlorophyll Anomalies in the Western South China Sea
Authors: He Qingyou , Zhan Haigang , Xu Jie , Cai Shuqun , Zhan Weikang , Zhou Linbin , Zha Guozhen
Published: December 2019

The western South China Sea (WSCS) exhibits intense mesoscale eddy activity, especially in summer. However, the influence of the eddies on regional ecosystems is not well understood. By analyzing historical in situ observations, satellite‐derived near‐surface chlorophyll (CHL) data and eddy data, we investigated the composite response of CHL to eddies in the WSCS. The results show that eddies decrease CHL in the WSCS and that nearly half of this decrease is attributed to the activity of anticyclonic eddies during summer when they are much more energetic than cyclonic eddies. A comparison between local and nonlocal eddies suggests that the CHL response to the eddies is dominated by local dynamics rather than being trapped and transported from neighboring regions. In situ observations provide evidence that intense convergence and downwelling in anticyclonic eddies deepen the mixed layer depth and subsurface CHL maximum depth. The decreased nutrients in the euphotic layer inhibits the growth of phytoplankton, resulting in a weakened subsurface CHL maximum (by 54%) and decreased CHL in the entire euphotic layer (by 41% for the upper 100 m). Considering the greater number and area of anticyclonic eddies compared with cyclonic eddies, eddy activity might cause an upper ocean CHL decrease of ~7% in the WSCS in summer. This study demonstrated that the response of CHL to eddies in the WSCS differs in both spatial distribution and seasonal variation from those in other subregions of the SCS, emphasizing the importance of considering regional variability in eddies and large‐scale environments when evaluating the biogeochemical influences of eddies.
High‐Frequency Tide‐Surge‐River Interaction in Estuaries: Causes and Implications for Coastal Flooding
Authors: Spicer Preston , Huguenard Kimberly , Ross Lauren , Rickard Laura N.
Published: December 2019

Tide‐surge interaction creates perturbations to storm surge at tidal frequencies and can affect the timing and magnitude of surge in tidally energetic regions. To date, limited research has identified high‐frequency tide‐surge interaction (>4 cycles per day) in coastal areas, and its significance in fluvial estuaries (where we consider it tide‐surge‐river interaction) is not well documented. Water level and current velocity observations were used to analyze tide‐surge‐river interaction at multiple tidal and overtide frequencies inside of a shallow estuary. Near the head of the estuary, higher frequency harmonics dominate tide‐surge‐river interaction and produce amplitudes more than double that of wind and pressure‐driven surge. Bottom friction enhanced by storm‐induced currents is the primary mechanism behind the interaction, which is further amplified by within‐estuary resonance. High‐frequency tide‐surge‐river interactions in estuaries present a significant threat to human life, as the onset of flooding (in <1.5 hr) is more rapid than coastal storm surge flooding. Commonly used storm surge forecasting models neglect high‐frequency tide‐surge‐river interaction and thus can markedly underestimate the magnitude and timing of inland storm surge flooding.
Enhanced Light‐Absorption of Black Carbon in Rainwater Compared With Aerosols Over the Northern Indian Ocean
Authors: Budhavant Krishnakant , Andersson August , Holmstrand Henry , Bikkina Poonam , Bikkina Srinivas , Satheesh S. K. , Gustafsson Örjan
Published: December 2019

Black carbon (BC) aerosols affect climate, especially in high aerosol loading regions such as South Asia. A key uncertainty for the climate effects of BC is the evolution of light‐absorbing properties in the atmosphere. Here, we present a year‐round comparison of the mass absorption cross section (MAC; 678 nm) of BC in air (PM10) and rain, for samples collected at the Maldives Climate Observatory at Hanimaadhoo. We develop a filter‐loading correction scheme for estimating BC absorption on filters used in high‐volume samplers. The year‐round average MAC678 of BC in the rain is almost twice (13.3 ± 4.2 m2/g) compared to the PM10 aerosol (7.2 ± 2.6 m2/g). A possible explanation is the elevated ratio of organic carbon (OC) to BC observed in rain particulate matter (9.4 ± 6.3) compared to in the aerosols (OC/BC 2.6 ± 1.4 and water‐insoluble organic carbon/BC 1.2 ± 0.8), indicating a coating‐enhancement effect. In addition to BC, we also investigated the MAC365 of water‐soluble brown carbon in PM10 (0.4 ± 0.4 m2/g, at 365 nm). In contrast to BC, MAC365brown carbon relates to air mass history, showing higher values for samples from air originating over the South Asian landmass. Furthermore, calculated washout ratios are much lower for BC compared to OC and inorganic ions such as sulfate, implying a longer atmospheric lifetime for BC. The wet deposition flux for BC during the high loading winter was 3 times higher than during the wet summer, despite much less precipitation in the winter.
Inertial Effects During the Process of Supercritical CO2 Displacing Brine in a Sandstone: Lattice Boltzmann Simulations Based on the Continuum‐Surface‐Force and Geometrical Wetting Models
Authors: Chen Yu , Valocchi Albert J. , Kang Qinjun , Viswanathan Hari S.
Published: December 2019

Inertial effects during the process of supercritical CO2 displacing brine in porous media may not be negligible according to recent studies. Capturing the inertial effects of the physical CO2‐brine system imposes a requirement on the grid resolution and viscosity to surface tension ratio for pore‐scale simulations, which some commonly used simulators may not be able to meet. To fulfill the parameter requirement, we combine the continuum‐surface‐force based color‐gradient lattice Boltzmann (LB) multiphase model and the geometrical wetting model and extend the model to 3D under the multiple‐relaxation‐time framework. We validate the model via simple benchmarks which show significant improvement over the traditional models. We then perform 3D drainage simulations in a heterogeneous micromodel where the simulation result agrees well with experimental data, while our previous work fails to reproduce certain displacement patterns in the experiment due to the use of a traditional LB model that cannot fulfill the parameter requirement. Finally, we perform high‐fidelity 3D drainage simulations to study the inertial effects in a Bentheimer sandstone sample. Our results show that stronger inertial effects generally help develop more CO2 flow pathways for the same capillary number which results in higher CO2 saturation, consistent with the micromodel results. The phenomena can be found in both low and high capillary number cases, indicating that the inertial effects are not dependent on the mean velocity. In addition, the change of the invasion patterns is not proportional to the change of inertial effects, thus exhibiting threshold behavior.
Syncope as a sign of occult cancers: a population-based cohort study
Authors: Lorenzen Mads Okkels Birk , Farkas Dóra Körmendiné , Adelborg Kasper , Sundbøll Jens , Sørensen Henrik Toft
Published: December 2019

Background

We examined if syncope was a marker of an occult cancer by comparing the risk in patients with a syncope episode with that of the general population.

Methods

Using Danish population-based medical registries, we identified all patients diagnosed with syncope during 1994–2013 and followed them until a cancer diagnosis, emigration, death or end of follow-up, whichever came first. We computed cumulative risks and standardised incidence ratios (SIR) with 95% confidence intervals (CI).

Results

Among 208,361 patients with syncope, 20,278 subsequent cancers were observed. The 6-month cumulative risk of any cancer was 1.2%, increasing to 17.9 % for 1–20 years of follow-up. The highest cumulative risks after 6 months of follow-up were lung cancer (0.2%), colorectal cancer (0.2%), prostate cancer (0.1%) and brain cancer (0.1%). The 6-month SIR were 2.7 (95% CI: 2.4–3.0) for lung cancer, 2.0 (95% CI: 1.8–2.2) for colorectal cancer, 1.7 (95% CI: 1.5–1.9) for prostate cancer and 10.0 (95% CI: 8.6–11.4) for brain cancer.

Conclusions

Syncope was a weak marker of an occult cancer. In short-term the highest cumulative risks were observed for lung, colorectal, prostate and brain cancers. An aggressive search for occult cancer in a patient with syncope is probably not warranted.
Development of PancRISK, a urine biomarker-based risk score for stratified screening of pancreatic cancer patients
Authors: Blyuss Oleg , Zaikin Alexey , Cherepanova Valeriia , Munblit Daniel , Kiseleva Elena M. , Prytomanova Olga M. , Duffy Stephen W. , Crnogorac-Jurcevic Tatjana
Published: December 2019

Background

An accurate and simple risk prediction model that would facilitate earlier detection of pancreatic adenocarcinoma (PDAC) is not available at present. In this study, we compare different algorithms of risk prediction in order to select the best one for constructing a biomarker-based risk score, PancRISK.

Methods

Three hundred and seventy-nine patients with available measurements of three urine biomarkers, (LYVE1, REG1B and TFF1) using retrospectively collected samples, as well as creatinine and age, were randomly split into training and validation sets, following stratification into cases (PDAC) and controls (healthy patients). Several machine learning algorithms were used, and their performance characteristics were compared. The latter included AUC (area under ROC curve) and sensitivity at clinically relevant specificity.

Results

None of the algorithms significantly outperformed all others. A logistic regression model, the easiest to interpret, was incorporated into a PancRISK score and subsequently evaluated on the whole data set. The PancRISK performance could be even further improved when CA19-9, commonly used PDAC biomarker, is added to the model.

Conclusion

PancRISK score enables easy interpretation of the biomarker panel data and is currently being tested to confirm that it can be used for stratification of patients at risk of developing pancreatic cancer completely non-invasively, using urine samples.
Drug responses are conserved across patient-derived xenograft models of melanoma leading to identification of novel drug combination therapies
Authors: Ice Ryan J. , Chen Michelle , Sidorov Max , Le Ho Tam , Woo Rinette W. L. , Rodriguez-Brotons Aida , Luu Tri , Jian Damon , Kim Kevin B. , Leong Stanley P. , Kim HanKyul , Kim Angela , Stone Des , Nazarian Ari , Oh Alyssia , Tranah Gregory J. , Nosrati Mehdi , de Semir David , Dar Altaf A. , Chang Stephen , Desprez Pierre-Yves , Kashani-Sabet Mohammed , Soroceanu Liliana , McAllister Sean D.
Published: December 2019

Background

Patient-derived xenograft (PDX) mouse tumour models can predict response to therapy in patients. Predictions made from PDX cultures (PDXC) would allow for more rapid and comprehensive evaluation of potential treatment options for patients, including drug combinations.

Methods

We developed a PDX library of BRAF-mutant metastatic melanoma, and a high-throughput drug-screening (HTDS) platform utilising clinically relevant drug exposures. We then evaluated 34 antitumor agents across eight melanoma PDXCs, compared drug response to BRAF and MEK inhibitors alone or in combination with PDXC and the corresponding PDX, and investigated novel drug combinations targeting BRAF inhibitor-resistant melanoma.

Results

The concordance of cancer-driving mutations across patient, matched PDX and subsequent PDX generations increases as variant allele frequency (VAF) increases. There was a high correlation in the magnitude of response to BRAF and MEK inhibitors between PDXCs and corresponding PDXs. PDXCs and corresponding PDXs from metastatic melanoma patients that progressed on standard-of-care therapy demonstrated similar resistance patterns to BRAF and MEK inhibitor therapy. Importantly, HTDS identified novel drug combinations to target BRAF-resistant melanoma.

Conclusions

The biological consistency observed between PDXCs and PDXs suggests that PDXCs may allow for a rapid and comprehensive identification of treatments for aggressive cancers, including combination therapies.
TIPRL potentiates survival of lung cancer by inducing autophagy through the eIF2α-ATF4 pathway
Authors: Jeon Su-Jin , Ahn Jun-Ho , Halder Debasish , Cho Hyun-Soo , Lim Jung-Hwa , Jun Soo Young , Lee Jeong-Ju , Yoon Ji-Yong , Choi Min-Hyuk , Jung Cho-Rok , Kim Jin-Man , Kim Nam-Soon
Published: December 2019

Autophagy, an intracellular system of degrading damaged organelles and misfolded proteins, is essential for cancer cell survival. Despite the progress made towards understanding the mechanism, identification of novel autophagy regulators presents a major obstacle in developing anticancer therapies. Here, we examine the association between the TOR signaling pathway regulator-like (TIPRL) protein and autophagy in malignant transformation of tumors. We show that TIPRL upregulation in non-small cell lung cancer (NSCLC) potentiated autophagy activity and enabled autophagic clearance of metabolic and cellular stress, conferring a survival advantage to cancer cells. Importantly, the interaction of TIPRL with eukaryotic initiation factor 2α (eIF2α) led to eIF2α phosphorylation and activation of the eIF2α-ATF4 pathway, thereby inducing autophagy. Conversely, TIPRL depletion increased apoptosis by reducing autophagic clearance, which was markedly enhanced in TIPRL-depleted A549 xenografts treated with 2-deoxy-D-glucose. Overall, the study indicated that TIPRL is a potential regulator of autophagy and an important drug target for lung cancer therapy.
Biosynthetic CircRNA_001160 induced by PTBP1 regulates the permeability of BTB via the CircRNA_001160/miR-195-5p/ETV1 axis
Authors: Li Hua , Shen Shuyuan , Ruan Xuelei , Liu Xiaobai , Zheng Jian , Liu Yunhui , Yang Chunqing , Wang Di , Liu Libo , Ma Jun , Ma Teng , Wang Ping , Cai Heng , Li Zhen , Zhao Lini , Xue Yixue
Published: December 2019

The presence of the blood-tumor barrier (BTB) severely impedes the transport of anti-neoplasm drugs to the central nervous system, affecting the therapeutic effects of glioma. Glioma endothelial cells (GECs) are the main structural basis of the BTB. Circular RNA is considered to be an important regulator of endothelial cell growth. In this study, we found that polypyrimidine tract binding protein 1 (PTBP1) and circRNA_001160 were remarkably upregulated in GECs. Knockdown of PTBP1 or circRNA_001160 significantly increased BTB permeability, respectively. As a molecular sponge of miR-195-5p, circRNA_001160 attenuated its negative regulation of the target gene ETV1 by adsorbing miR-195-5p. In addition, ETV1 was overexpression in GECs. ETV1 bounded to the promoter regions of tight junction-related proteins and increased the promoter activities, which significantly promoted the expression levels of tight junction-related proteins. The present study showed that the combined application of PTBP1, circRNA_001160, and miR-195-5p with the anti-tumor drug Dox effectively promoted Dox through BTB and extremely induced the apoptosis of glioma cells. Our results demonstrated that the PTBP1/circRNA_001160/miR-195-5p/ETV1 axis was critical in the regulation of BTB permeability and provided new targets for the treatment of glioma.
Inhibition of AIM2 inflammasome-mediated pyroptosis by Andrographolide contributes to amelioration of radiation-induced lung inflammation and fibrosis
Authors: Gao Jian , Peng Shuang , Shan Xinni , Deng Guoliang , Shen Lihong , Sun Jian , Jiang Chunhong , Yang Xiaoling , Chang Zhigang , Sun Xinchen , Feng Fude , Kong Lingdong , Gu Yanhong , Guo Wenjie , Xu Qiang , Sun Yang
Published: December 2019

Radiation-induced lung injury (RILI) is one of the most common and fatal complications of thoracic radiotherapy, whereas no effective interventions are available. Andrographolide, an active component extracted from Andrographis paniculate, is prescribed as a treatment for upper respiratory tract infection. Here we report the potential radioprotective effect and mechanism of Andrographolide on RILI. C57BL/6 mice were exposed to 18 Gy of whole thorax irradiation, followed by intraperitoneal injection of Andrographolide every other day for 4 weeks. Andrographolide significantly ameliorated radiation-induced lung tissue damage, inflammatory cell infiltration, and pro-inflammatory cytokine release in the early phase and progressive fibrosis in the late phase. Moreover, Andrographolide markedly hampered radiation-induced activation of the AIM2 inflammasome and pyroptosis in vivo. Furthermore, bone marrow-derived macrophages (BMDMs) were exposed to 8 Gy of X-ray radiation in vitro and Andrographolide significantly inhibited AIM2 inflammasome mediated-pyroptosis in BMDMs. Mechanistically, Andrographolide effectively prevented AIM2 from translocating into the nucleus to sense DNA damage induced by radiation or chemotherapeutic agents in BMDMs. Taken together, Andrographolide ameliorates RILI by suppressing AIM2 inflammasome mediated-pyroptosis in macrophage, identifying Andrographolide as a novel potential protective agent for RILI.
Adhesive liposomes loaded onto an injectable, self-healing and antibacterial hydrogel for promoting bone reconstruction
Authors: Liu Lili , Xiang Yi , Wang Zhen , Yang Xiaonan , Yu Xiaohua , Lu Yong , Deng Lianfu , Cui Wenguo
Published: December 2019

Loading hydrogels with bioactive agents is an important method for expanding the functional application of hydrogels. However, how to improve the local administration and slow release of drugs from a hydrogel is a challenge when using hydrogels loaded with drugs. In this paper, we first developed adhesive liposomes (A-LIP) loaded with BMP-2. Then, we incorporated the A-LIP into PEG hydrogels based on the coordinated cross-linking principle of SH-PEG and Ag+, fabricating an injectable, antibacterial and self-healing multifunctional drug delivery system. The adhesive lipo-hydrogel (A-LIP-PEG) fabricated by mixing PEG hydrogels and adhesive liposomes can be locally injected into an osteoporotic fracture and bone marrow cavity, where A-LIP-PEG can release adhesive liposomes that adhere to the bone injury area and promote bone reconstruction. Based on the principle of electrostatic attraction, tissue nonspecific A-LIP were fabricated by grafting octadecylamine onto liposomes. Because of the coordination and cross-linking of thiolated polyethylene (SH-PEG) and Ag+, the A-LIP-PEG showed excellent injectability and self-healing properties; further, because of the presence of Ag+, the A-LIP-PEG showed effective inhibition of S. aureus and Escherichia coli. The liposomes released by the A-LIP-PEG were able to adhere to tissue. In vitro studies showed that A-LIP-PEG significantly promoted osteogenic differentiation and had no significant effect on cell proliferation. Compared with common lipo-hydrogel (LIP-PEG), the A-LIP-PEG had better tissue adhesion in vivo, which led to better osteogenic differentiation and faster local bone remodeling of osteoporotic fractures in rats. This research developed a novel hydrogel system with adhesive liposomes to expand the application of hydrogels.
Profiling of the plasma proteome across different stages of human heart failure
Authors: Egerstedt Anna , Berntsson John , Smith Maya Landenhed , Gidlöf Olof , Nilsson Roland , Benson Mark , Wells Quinn S. , Celik Selvi , Lejonberg Carl , Farrell Laurie , Sinha Sumita , Shen Dongxiao , Lundgren Jakob , Rådegran Göran , Ngo Debby , Engström Gunnar , Yang Qiong , Wang Thomas J. , Gerszten Robert E. , Smith J. Gustav
Published: December 2019

Heart failure (HF) is a major public health problem characterized by inability of the heart to maintain sufficient output of blood. The systematic characterization of circulating proteins across different stages of HF may provide pathophysiological insights and identify therapeutic targets. Here we report application of aptamer-based proteomics to identify proteins associated with prospective HF incidence in a population-based cohort, implicating modulation of immunological, complement, coagulation, natriuretic and matrix remodeling pathways up to two decades prior to overt disease onset. We observe further divergence of these proteins from the general population in advanced HF, and regression after heart transplantation. By leveraging coronary sinus samples and transcriptomic tools, we describe likely cardiac and specific cellular origins for several of the proteins, including Nt-proBNP, thrombospondin-2, interleukin-18 receptor, gelsolin, and activated C5. Our findings provide a broad perspective on both cardiac and systemic factors associated with HF development.
Crystal scavenging from mush piles recorded by melt inclusions
Authors: Wieser Penny E. , Edmonds Marie , Maclennan John , Jenner Frances E. , Kunz Barbara E.
Published: December 2019

Olivine-hosted melt inclusions are commonly used to determine pre-eruptive storage conditions. However, this approach relies on the assumption that co-erupted olivines have a simple association with their carrier melts. We show that primitive olivine crystal cargoes and their melt inclusions display a high degree of geochemical disequilibrium with their carrier melts at Kīlauea Volcano, Hawai’i. Within a given eruption, melt inclusions trapped in primitive olivine crystals exhibit compositional diversity exceeding that in erupted lava compositions since 1790 CE. This demonstrates that erupting liquids scavenge crystal cargoes from mush piles accumulating diverse melt inclusion populations over timescales of centuries or longer. Entrainment of hot primitive olivines into cooler, evolved carrier melts drives post-entrapment crystallization and sequestration of CO2 into vapour bubbles, producing spurious barometric estimates. While scavenged melt inclusion records may not be suitable for the investigation of eruption-specific processes, they record timescales of crystal storage and remobilization within magmatic mush piles.
Forty-five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor
Authors: Murphy Andrew J. , Chen Xiang , Pinto Emilia M. , Williams Justin S. , Clay Michael R. , Pounds Stanley B. , Cao Xueyuan , Shi Lei , Lin Tong , Neale Geoffrey , Morton Christopher L. , Woolard Mary A. , Mulder Heather L. , Gil Hyea Jin , Rehg Jerold E. , Billups Catherine A. , Harlow Matthew L. , Dome Jeffrey S. , Houghton Peter J. , Easton John , Zhang Jinghui , George Rani E. , Zambetti Gerard P. , Davidoff Andrew M.
Published: December 2019

The lack of model systems has limited the preclinical discovery and testing of therapies for Wilms tumor (WT) patients who have poor outcomes. Herein, we establish 45 heterotopic WT patient-derived xenografts (WTPDX) in CB17 scid-/- mice that capture the biological heterogeneity of Wilms tumor (WT). Among these 45 total WTPDX, 6 from patients with diffuse anaplastic tumors, 9 from patients who experienced disease relapse, and 13 from patients with bilateral disease are included. Early passage WTPDX show evidence of clonal selection, clonal evolution and enrichment of blastemal gene expression. Favorable histology WTPDX are sensitive, whereas unfavorable histology WTPDX are resistant to conventional chemotherapy with vincristine, actinomycin-D, and doxorubicin given singly or in combination. This WTPDX library is a unique scientific resource that retains the spectrum of biological heterogeneity present in WT and provides an essential tool to test targeted therapies for WT patient groups with poor outcomes.
Relationship between gut microbiota and circulating metabolites in population-based cohorts
Authors: Vojinovic Dina , Radjabzadeh Djawad , Kurilshikov Alexander , Amin Najaf , Wijmenga Cisca , Franke Lude , Ikram M. Arfan , Uitterlinden Andre G. , Zhernakova Alexandra , Fu Jingyuan , Kraaij Robert , van Duijn Cornelia M.
Published: December 2019

Gut microbiota has been implicated in major diseases affecting the human population and has also been linked to triglycerides and high-density lipoprotein levels in the circulation. Recent development in metabolomics allows classifying the lipoprotein particles into more details. Here, we examine the impact of gut microbiota on circulating metabolites measured by Nuclear Magnetic Resonance technology in 2309 individuals from the Rotterdam Study and the LifeLines-DEEP cohort. We assess the relationship between gut microbiota and metabolites by linear regression analysis while adjusting for age, sex, body-mass index, technical covariates, medication use, and multiple testing. We report an association of 32 microbial families and genera with very-low-density and high-density subfractions, serum lipid measures, glycolysis-related metabolites, ketone bodies, amino acids, and acute-phase reaction markers. These observations provide insights into the role of microbiota in host metabolism and support the potential of gut microbiota as a target for therapeutic and preventive interventions.
Perfect secrecy cryptography via mixing of chaotic waves in irreversible time-varying silicon chips
Authors: Di Falco A. , Mazzone V. , Cruz A. , Fratalocchi A.
Published: December 2019

Protecting confidential data is a major worldwide challenge. Classical cryptography is fast and scalable, but is broken by quantum algorithms. Quantum cryptography is unclonable, but requires quantum installations that are more expensive, slower, and less scalable than classical optical networks. Here we show a perfect secrecy cryptography in classical optical channels. The system exploits correlated chaotic wavepackets, which are mixed in inexpensive and CMOS compatible silicon chips. The chips can generate 0.1 Tbit of different keys for every mm of length of the input channel, and require the transmission of an amount of data that can be as small as 1/1000 of the message’s length. We discuss the security of this protocol for an attacker with unlimited technological power, and who can access the system copying any of its part, including the chips. The second law of thermodynamics and the exponential sensitivity of chaos unconditionally protect this scheme against any possible attack.
A mitochondrial megachannel resides in monomeric F1FO ATP synthase
Authors: Mnatsakanyan Nelli , Llaguno Marc C. , Yang Youshan , Yan Yangyang , Weber Joachim , Sigworth Fred J. , Jonas Elizabeth A.
Published: December 2019

Purified mitochondrial ATP synthase has been shown to form Ca2+-activated, large conductance channel activity similar to that of mitochondrial megachannel (MMC) or mitochondrial permeability transition pore (mPTP) but the oligomeric state required for channel formation is being debated. We reconstitute purified monomeric ATP synthase from porcine heart mitochondria into small unilamellar vesicles (SUVs) with the lipid composition of mitochondrial inner membrane and analyze its oligomeric state by electron cryomicroscopy. The cryo-EM density map reveals the presence of a single ATP synthase monomer with no density seen for a second molecule tilted at an 86o angle relative to the first. We show that this preparation of SUV-reconstituted ATP synthase monomers, when fused into giant unilamellar vesicles (GUVs), forms voltage-gated and Ca2+-activated channels with the key features of mPTP. Based on our findings we conclude that the ATP synthase monomer is sufficient, and dimer formation is not required, for mPTP activity.
An ultrathin ionomer interphase for high efficiency lithium anode in carbonate based electrolyte
Authors: Weng Yu-Ting , Liu Hao-Wen , Pei Allen , Shi FeiFei , Wang Hansen , Lin Chih-Yuan , Huang Sheng-Siang , Su Lin-Ya , Hsu Jyh-Ping , Fang Chia-Chen , Cui Yi , Wu Nae-Lih
Published: December 2019

High coulombic efficiency and dendrite suppression in carbonate electrolytes remain challenges to the development of high-energy lithium ion batteries containing lithium metal anodes. Here we demonstrate an ultrathin (≤100 nm) lithium-ion ionomer membrane consisting of lithium-exchanged sulfonated polyether ether ketone embedded with polyhedral oligosilsesquioxane as a coating layer on copper or lithium for achieving efficient and stable lithium plating-stripping cycles in a carbonate-based electrolyte. Operando analyses and theoretical simulation reveal the remarkable ability of the ionomer coating to enable electric field homogenization over a considerably large lithium-plating surface. The membrane coating, serving as an artificial solid-electrolyte interphase filter in minimizing parasitic reactions at the electrolyte-electrode interface, enables dendrite-free lithium plating on copper with outstanding coulombic efficiencies at room and elevated (50 °C) temperatures. The membrane coated copper demonstrates itself as a promising current collector for manufacturing high-quality pre-plated lithium thin-film anode.
Ultrafast valence to non-valence excited state dynamics in a common anionic chromophore
Authors: Bull James N. , Anstöter Cate S. , Verlet Jan R. R.
Published: December 2019

Non-valence states in neutral molecules (Rydberg states) have well-established roles and importance in photochemistry, however, considerably less is known about the role of non-valence states in photo-induced processes in anions. Here, femtosecond time-resolved photoelectron imaging is used to show that photoexcitation of the S1(ππ*) state of the methyl ester of deprotonated para-coumaric acid – a model chromophore for photoactive yellow protein (PYP) – leads to a bifurcation of the excited state wavepacket. One part remains on the S1(ππ*) state forming a twisted intermediate, whilst a second part leads to the formation of a non-valence (dipole-bound) state. Both populations eventually decay independently by vibrational autodetachment. Valence-to-non-valence internal conversion has hitherto not been observed in the intramolecular photophysics of an isolated anion, raising questions into how common such processes might be, given that many anionic chromophores have bright valence states near the detachment threshold.
The anticipation of events in time
Authors: Grabenhorst Matthias , Michalareas Georgios , Maloney Laurence T. , Poeppel David
Published: December 2019

Humans anticipate events signaled by sensory cues. It is commonly assumed that two uncertainty parameters modulate the brain's capacity to predict: the hazard rate (HR) of event probability and the uncertainty in time estimation which increases with elapsed time. We investigate both assumptions by presenting event probability density functions (PDFs) in each of three sensory modalities. We show that perceptual systems use the reciprocal PDF and not the HR to model event probability density. We also demonstrate that temporal uncertainty does not necessarily grow with elapsed time but can also diminish, depending on the event PDF. Previous research identified neuronal activity related to event probability in multiple levels of the cortical hierarchy (sensory (V4), association (LIP), motor and other areas) proposing the HR as an elementary neuronal computation. Our results—consistent across vision, audition, and somatosensation—suggest that the neurobiological implementation of event anticipation is based on a different, simpler and more stable computation than HR: the reciprocal PDF of events in time.
Photorealistic modelling of metals from first principles
Authors: Prandini Gianluca , Rignanese Gian-Marco , Marzari Nicola
Published: December 2019

The colours of metals have attracted the attention of humanity since ancient times, and coloured metals, in particular gold compounds, have been employed for tools and objects symbolizing the aesthetics of power. In this work, we develop a comprehensive framework to obtain the reflectivity and colour of metals, and show that the trends in optical properties and the colours can be predicted by straightforward first-principles techniques based on standard approximations. We apply this to predict reflectivity and colour of several elemental metals and of different types of metallic compounds (intermetallics, solid solutions and heterogeneous alloys), considering mainly binary alloys based on noble metals. We validate the numerical approach through an extensive comparison with experimental data and the photorealistic rendering of known coloured metals.
Scalable repeater architectures for multi-party states
Authors: Kuzmin V. V. , Vasilyev D. V. , Sangouard N. , Dür W. , Muschik C. A.
Published: December 2019

The vision to develop quantum networks entails multi-user applications, which require the generation of long-distance multi-party entangled states. The current rapid experimental progress in building prototype-networks calls for new design concepts to guide future developments. Here we describe an experimentally feasible scheme implementing a two-dimensional repeater network for robust distribution of three-party entangled states of GHZ type in the presence of excitation losses and detector dark counts — the main sources of errors in real-world hardware. Our approach is based on atomic or solid state ensembles and employs built-in error filtering mechanisms peculiar to intrinsically two-dimensional networks. This allows us to overcome the performance limitation of conventional one-dimensional ensemble-based networks distributing multi-party entangled states and provides an efficient design for future experiments with a clear perspective in terms of scalability.
A longitudinal neuroimaging dataset on multisensory lexical processing in school-aged children
Authors: Lytle Marisa N. , McNorgan Chris , Booth James R.
Published: December 2019

Here we describe the open access dataset entitled “Longitudinal Brain Correlates of Multisensory Lexical Processing in Children” hosted on OpenNeuro.org. This dataset examines reading development through a longitudinal multimodal neuroimaging and behavioral approach, including diffusion-weighted and T1-weighted structural magnetic resonance imaging (MRI), task based functional MRI, and a battery of psycho-educational assessments and parental questionnaires. Neuroimaging, psycho-educational testing, and functional task behavioral data were collected from 188 typically developing children when they were approximately 10.5 years old (session T1). Seventy children returned approximately 2.5 years later (session T2), of which all completed longitudinal follow-ups of psycho-educational testing, and 49 completed neuroimaging and functional tasks. At session T1 participants completed auditory, visual, and audio-visual word and pseudo-word rhyming judgment tasks in the scanner. At session T2 participants completed visual word and pseudo-word rhyming judgement tasks in the scanner.
Multi-Locus Genome Wide Association Mapping for Yield and Its Contributing Traits in Hexaploid Wheat under Different Water Regimes
Authors: Gahlaut Vijay , Jaiswal Vandana , Singh Sukhwinder , Balyan H. S. , Gupta P. K.
Published: December 2019

Multi-locus genome wide association study was undertaken using a set of 320 diverse spring wheat accessions, which were each genotyped for 9,626 SNPs. The association panel was grown in replicated trials in four environments [two each in irrigated (IR) and rainfed (RF) environments], and phenotypic data were recorded for five traits including days to heading, days to maturity, plant height, thousand grain weight and grain yield. Forty-six significant marker-trait associations (MTAs) were identified for five traits. These included 20 MTAs in IR and 19 MTAs in RF environments; seven additional MTAs were common to both the environments. Five of these MTAs were co-localized with previously known QTL/MTAs and the remaining MTAs were novel and add to the existing knowledge. Three desirable haplotypes for agronomic traits, one for improvement in RF environment and two for improvement in IR environment were identified. Eighteen (18) promising candidate genes (CGs) involved in seven different biological activities were also identified. The expression profiles of four (Trehalose-6-Phosphate, APETALA2/Ethylene-responsive factor, DNA-binding One Zinc Finger and Gibberellin-dioxygenases) of the 18 genes showed that they were induced by drought stress in the wheat seedlings. The MTAs, haplotypes and CG-based markers may be used in marker-assisted breeding for drought tolerance in wheat.
Boson peak, elasticity, and glass transition temperature in polymer glasses: Effects of the rigidity of chain bending
Authors: Tomoshige Naoya , Mizuno Hideyuki , Mori Tatsuya , Kim Kang , Matubayasi Nobuyuki
Published: December 2019

The excess low-frequency vibrational spectrum, called boson peak, and non-affine elastic response are the most important particularities of glasses. Herein, the vibrational and mechanical properties of polymeric glasses are examined by using coarse-grained molecular dynamics simulations, with particular attention to the effects of the bending rigidity of the polymer chains. As the rigidity increases, the system undergoes a glass transition at a higher temperature (under a constant pressure), which decreases the density of the glass phase. The elastic moduli, which are controlled by the decrease of the density and the increase of the rigidity, show a non-monotonic dependence on the rigidity of the polymer chain that arises from the non-affine component. Moreover, a clear boson peak is observed in the vibrational density of states, which depends on the macroscopic shear modulusG. In particular, the boson peak frequency ωBPis proportional to$$\sqrt{G}$$G. These results provide a positive correlation between the boson peak, shear elasticity, and the glass transition temperature.
Data-mining Techniques for Image-based Plant Phenotypic Traits Identification and Classification
Authors: Rahaman Md. Matiur , Ahsan Md. Asif , Chen Ming
Published: December 2019

Statistical data-mining (DM) and machine learning (ML) are promising tools to assist in the analysis of complex dataset. In recent decades, in the precision of agricultural development, plant phenomics study is crucial for high-throughput phenotyping of local crop cultivars. Therefore, integrated or a new analytical approach is needed to deal with these phenomics data. We proposed a statistical framework for the analysis of phenomics data by integrating DM and ML methods. The most popular supervised ML methods; Linear Discriminant Analysis (LDA), Random Forest (RF), Support Vector Machine with linear (SVM-l) and radial basis (SVM-r) kernel are used for classification/prediction plant status (stress/non-stress) to validate our proposed approach. Several simulated and real plant phenotype datasets were analyzed. The results described the significant contribution of the features (selected by our proposed approach) throughout the analysis. In this study, we showed that the proposed approach removed phenotype data analysis complexity, reduced computational time of ML algorithms, and increased prediction accuracy.
Signatures of Molecular Unification and Progressive Oxidation Unfold in Dissolved Organic Matter of the Ob-Irtysh River System along Its Path to the Arctic Ocean
Authors: Perminova I. V. , Shirshin E. A. , Zherebker A. , Pipko I. I. , Pugach S. P. , Dudarev O. V. , Nikolaev E. N. , Grigoryev A. S. , Shakhova N. , Semiletov I. P.
Published: December 2019

The Ob-Irtysh River system is the seventh-longest one in the world. Unlike the other Great Siberian rivers, it is only slightly impacted by the continuous permafrost in its low flow. Instead, it drains the Great Vasyugan mire, which is the world largest swamp, and receives huge load of the Irtysh waters which drain the populated lowlands of the East Siberian Plain. The central challenge of this paper is to understand the processes responsible for molecular transformations of natural organic matter (NOM) in the Ob-Irtysh river system along the South-North transect. For solving this task, the NOM was isolated from the water samples collected along the 3,000 km transect using solid-phase extraction. The NOM samples were further analyzed using high resolution mass spectrometry and optical spectroscopy. The obtained results have shown a distinct trend both in molecular composition and diversity of the NOM along the South-North transect: the largest diversity was observed in the Southern “swamp-wetland” stations. The samples were dominated with humic and lignin-like components, and enriched with aminosugars. After the Irtysh confluence, the molecular nature of NOM has changed drastically: it became much more oxidized and enriched with heterocyclic N-containing compounds. These molecular features are very different from the aliphatics-rich permafrost NOM. They witnesses much more conservative nature of the NOM discharged into the Arctic by the Ob-Irtysh river system. In general, drastic reduction in molecular diversity was observed in the northern stations located in the lower Ob flow.
Transcriptome-wide analysis associates ID2 expression with combined pre- and post-capillary pulmonary hypertension
Authors: Arwood Meghan J. , Vahabi Nasim , Lteif Christelle , Sharma Ravindra K. , Machado Roberto F. , Duarte Julio D.
Published: December 2019

Heart failure with preserved ejection fraction (HFpEF) patients who develop pulmonary hypertension (PH) have an increased risk of death, with combined pre- and post-capillary PH (CpcPH) having the highest risk. However, the mechanism behind PH development in HFpEF is poorly understood. We aimed to identify transcriptomic associations with PH development in HFpEF. Blood was collected from 30 HFpEF patients: 10 without PH, 10 with isolated post-capillary PH, and 10 with CpcPH. Gene expression measurements were completed using transcriptome-wide RNA sequencing. Gene expression differences were compared using a quasi-likelihood method adjusting for age, sex, race, and smoking-status. Biological pathways were compared using global gene expression differences. A replication in 34 additional heart failure patients and a validation in lung tissue from a representative mouse model were completed using quantitative PCR. Six differentially expressed genes were identified when comparing transcriptomics between subjects with CpcPH and those without PH. When tested in additional subjects, only the association with ID2 replicated. Consistent with clinical findings, Id2 expression was also upregulated in mice with HFpEF and PH. Pathway analysis identified proliferative and mitochondrial pathways associated with CpcPH. Thus, these patients may possess systemic pathophysiological differences similar to those observed in pulmonary arterial hypertension patients.
Minimal Linear Networks for Magnetic Resonance Image Reconstruction
Authors: Liberman Gilad , Poser Benedikt A.
Published: December 2019

Modern sequences for Magnetic Resonance Imaging (MRI) trade off scan time with computational challenges, resulting in ill-posed inverse problems and the requirement to account for more elaborated signal models. Various deep learning techniques have shown potential for image reconstruction from reduced data, outperforming compressed sensing, dictionary learning and other advanced techniques based on regularization, by characterization of the image manifold. In this work we suggest a framework for reducing a “neural” network to the bare minimum required by the MR physics, reducing the network depth and removing all non-linearities. The networks performed well both on benchmark simulated data and on arterial spin labeling perfusion imaging, showing clear images while preserving sensitivity to the minute signal changes. The results indicate that the deep learning framework plays a major role in MR image reconstruction, and suggest a concrete approach for probing into the contribution of additional elements.
Not all birds have a single dominantly expressed MHC-I gene: Transcription suggests that siskins have many highly expressed MHC-I genes
Authors: Drews Anna , Westerdahl Helena
Published: December 2019

Passerine birds belong to the most species rich bird order and are found in a wide range of habitats. The extremely polymorphic adaptive immune system of passerines, identified through their major histocompatibility complex class I genes (MHC-I), may explain some of this extreme radiation. Recent work has shown that passerines have higher numbers of MHC-I gene copies than other birds, but little is currently known about expression and function of these gene copies. Non-passerine birds have a single highly expressed MHC-I gene copy, a pattern that seems unlikely in passerines. We used high-throughput sequencing to study MHC-I alleles in siskins (Spinus spinus) and determined gene expression, phylogenetic relationships and sequence divergence. We verified between six and 16 MHC-I alleles per individual and 97% of these were expressed. Strikingly, up to five alleles per individual had high expression. Out of 88 alleles 18 were putatively non-classical with low sequence divergence and expression, and found in a single phylogenetic cluster. The remaining 70 alleles were classical, with high sequence divergence and variable degrees of expression. Our results contradict the suggestion that birds only have a single dominantly expressed MHC-I gene by demonstrating several highly expressed MHC-I gene copies in a passerine.