bluuebunny/crossref_metadata_2025 huggingface dataset:
POTTERY TRADE AND THE FORMATION OF EARLY AND MIDDLE FORMATIVE STYLE HORIZONS AS SEEN FROM CENTRAL MEXICO
Authors: Stoner Wesley D. , Nichols Deborah L.
Published: August 2019

We explore the relationship between long-distance pottery trade and the formation of Early and Middle Formative style horizons in Mesoamerica. A sample of 1,154 ceramics mostly from Early and Middle Formative contexts in the central Mexican highlands was irradiated at the University of Missouri Research Reactor with a subsample (n = 313) for petrographic analysis. We conclude that: (1) most sites and regions display more than one process for making pottery; (2) there is a small amount of intraregional exchange among central Mexican sites, with the southeastern Basin of Mexico making the largest portion of pottery intended for trade within the region; and (3) interregional imports found at several sites likely come from the metamorphic region of southwestern Puebla with smaller numbers imported from the southern Gulf Coast, Morelos, and possibly Oaxaca. The trend over time from Early Formative to the end of the Middle Formative is one of decreasing intensity of long-distance interaction and decreasing geographic range of trade. These two trends contribute to the regional divergence of ceramic styles that peaks by the Late Formative in Mesoamerica.
GEOPHYSICAL PROSPECTION AT THE FORMATIVE SITE OF ALTICA IN THE TEOTIHUACAN VALLEY PIEDMONT
Authors: Mejía Ramón Andrés G. , Barba Luis , Ortiz Agustín , Blancas Jorge
Published: August 2019

The Formative-period site of Altica in the Patlachique Range poses many methodological problems when designing an excavation strategy. Three millennia of erosion, twentieth-century chisel plowing, and modern reforestation efforts have destroyed or disturbed most surface architecture above the local tepetate bedrock. As such, in the early stages of the Altica Project, the primary concern was the detection and identification of subsurface features, especially deep pits as found at other Formative sites. Although Altica is located at the top of a low, flat ridge, strong localized rain frequently flooded the terraces of interest for days, making it impossible to detect subsurface features using the most common prospection techniques. Because of these practical and taphonomic limitations, we relied on magnetic gradient prospection. This technique had never been applied to an early village site in the Basin of Mexico. This paper presents the methods used, discusses various difficulties encountered during prospection, applies interprets the results of the magnetic gradient study using results from excavation and aerial multispectral remote sensing. We discuss how the method might be applied to similar Formative sites to remotely detect indicators of anthropogenic activity, including subsurface features.
Peer-to-peer lending in pre-industrial France
Authors: Dermineur Elise M.
Published: August 2019

This article explores the world of informal financial transactions and informal networks in pre-industrial France. Often considered merely as simple daily transactions made to palliate a lack of cash in circulation and to smooth consumption, the examination of private transactions reveals not only that they served various purposes, including productive investments, but also that they proved to be dynamic. The debts they incurred helped to smooth consumption but also helped to make investments. Some lenders were more prominent than others, although no one really dominated the informal market. This article also compares informal transactions with formal ones through the study of probate inventories and notarial records respectively. It compares these two credit circuits, their similarities and different characteristics, and their various networks features. The debts incurred in the notarial credit market were more substantial but did not serve a different purpose than in the informal market. Here too, the biggest lenders did not monopolise the extension of capital. Perhaps the most striking result lies in the fact that the total volume of exchange between the informal credit market and the notarial credit market (after projection) was similar.
Feasibility of a farm-to-WIC intervention
Authors: Di Noia Jennifer , Monica Dorothy , Sikorskii Alla , Gonzalez Karinna , Abuhadba Lina
Published: August 2019

Objective:

To examine whether an intervention consisting of a WIC-based farmers’ market, nutrition education, recipe demonstrations and tastings, and handouts could be implemented as intended and the acceptability of the programme to recipients. The availability, variety and prices of fruits and vegetables (F&V) and the Farmers’ Market Nutrition Program voucher redemption rate at the site with market (relative to the rate among fourteen other WIC agency sites) also were examined.

Design:

Site-level data were used to evaluate programme implementation. Acceptability was assessed with participant data.

Setting:

A large, New Jersey-based, urban WIC (Special Supplemental Nutrition Program for Women, Infants, and Children) agency.

Participants:

Fifty-four women who purchased F&V at the market.

Results:

Gaps in stakeholder communication and coordination, F&V selling out by midday and staffing levels affected implementation fidelity. On average, 12 (sd3) F&V were available daily at the market (twenty-five unique F&V in total). For thirteen of nineteen items, prices were lower at the WIC-based market than area farmers’ markets. The voucher redemption rate at the site with the market (46 %) was higher than the rate among the fourteen other sites (39 %;P< 0·01). The mean rating of satisfaction with the programme was 6·9 (sd0·6) on a 7-point scale. All participants reported intending to purchase F&V again at the market, owing to the convenient location, quality of the F&V and helpfulness of the staff. Improving F&V availability and variety were recommended.

Conclusions:

The intervention is feasible with improved stakeholder communication and coordination, F&V availability and variety, and staffing.
Relationship between perception of emotional home atmosphere and fruit and vegetable consumption in European adolescents: results from the I.Family survey
Authors: Ghazy Elsayed Hadil A , Lissner Lauren , Mehlig Kirsten , Thumann Barbara Franziska , Hebestreit Antje , Pala Valeria , Veidebaum Toomas , Solea Tonia , Moreno Luis , Molnár Dénes , Wisnuwardani Ratih Wirapuspita , Lauria Fabio , Hunsberger Monica ,   on behalf of the IDEFICS and I.Family consortia
Published: August 2019

Objective:

Consumption of fruits and vegetables (F&V) among adolescents falls below recommendations in many Western countries. The impact of social and emotional aspects of family life on adolescent dietary behaviour may contribute to this, yet remains under-investigated. The present study examines the association between adolescents’ perceptions of emotional home atmosphere (EHA) and their F&V consumption frequency.

Design:

An FFQ was used to assess F&V consumption frequency. EHA was assessed by an eight-item measure with three subscales: perceived home warmth, strictness and relational tension. EHA subscales were used as binary variables: a score equal to or above the median value was considered as a higher perception, while a score below the median was considered as a lower perception of the EHA in question. Country differences in meeting the European 5-a-day recommendations were described. Further, the association between EHA and F&V consumption frequency was investigated using multiple linear regression.

Setting:

Regional examination centres in eight European countries.

Participants:

Adolescents (n 3196) aged 12–18 years.

Results:

The mean F&V consumption frequency was 3·27 (sd 2·84) times/d. Only 16·1 % of boys and 18 % of girls in our study sample met the recommendation of five F&V daily. After controlling for age, sex, education level of the parents and country of origin, perceived home warmth was associated with a 16 (95 % CI 9, 22) % higher F&V consumption frequency (P < 0·001).

Conclusions:

F&V consumption frequency was suboptimal in the survey areas. Interventions targeting perceived warmth as a component of EHA could potentially have a positive effect on adolescents’ dietary behaviour.
Investigation on the Dependency of Phase Retrieval Accuracy Versus Edge Enhancement to the Noise Ratio of X-ray Propagation-Based Phase-Contrast Imaging
Authors: Zhang Lin , Zhao Huijuan , Jiang Jingying , Zhang Limin , Li Jiao , Gao Feng , Zhou Zhongxing
Published: August 2019

Phase retrieval is necessary for propagation-based phase-contrast imaging (PB-PCI). Arhatari established a model for predicting the impact of the sample-to-detector distance and the system noise on the phase retrieval performance. We have extended Arhatari's model to account for the parameters of excessive source size, finite detector resolution, and geometrical magnification for more practical cases. However, there exist interaction effects among these parameters resulting in difficulty of predicting the phase retrieval performance. In this study, we found that optimizing the trade-off among these parameters for phase retrieval is consistent with the improvement of edge enhancement to noise ratio (EE/N) in the “forward problem” of the PB-PCI. Hence, we engaged in establishing a relationship between EE/N and phase retrieval performance in terms of the “forward problem” and “inverse problem” of the PB-PCI, respectively. Our results showed that, at fixed detector resolution, phase retrieval from the phase-contrast projections at the same EE/N level resulted in the consistent phase retrieval performance. Therefore, the performance of phase retrieval can be predicted based on the EE/N level and be quantitatively optimized by increasing EE/N.
ON MORITA EQUIVALENCE AND INTERPRETABILITY
Authors: MCELDOWNEY PAUL ANH
Published: August 2019

In a recent article, Barrett & Halvorson (2016) define a notion of equivalence for first-order theories, which they call “Morita equivalence.” To argue that Morita equivalence is a reasonable measure of “theoretical equivalence,” they make use of the claim that Morita extensions “say no more” than the theories they are extending. The goal of this article is to challenge this central claim by raising objections to their argument for it and by showing why there is good reason to think that the claim itself is false. In light of these criticisms, this article develops a natural way for the advocate of Morita equivalence to respond. I prove that this response makes her criterion a special case of bi-interpretability, an already well-established barometer of theoretical equivalence. I conclude by providing reasons why the advocate of Morita equivalence should opt for a notion of theoretical equivalence that is defined in terms of interpretability rather than Morita extensions.
Flexible biomedical RF sensors to quantify the purity of medical grade glycerol and glucose concentrations
Authors: Tiwari N. K. , Singh S. P. , Mondal D. , Akhtar M. Jaleel
Published: August 2019

A novel flexible radio frequency (RF) sensor is designed to facilitate the accurate testing of various samples used in the biomedical industry at the industrial, scientific and medical (ISM) frequency band. The proposed RF biosensor comprises a liquid channel-loaded interdigitated capacitor, which is integrated on a coplanar waveguide structure. The prototype of the sensor is fabricated on a 0.13 mm thin biodegradable polyethylene terephthalate polyester film to perform the testing of various bio-graded samples by recording the corresponding resonant frequency. It is observed that there is a noticeable change between the measured resonant frequencies of these samples, which primarily occurs due to the difference in their dielectric properties. The designed sensor was used to monitor and investigate the quality of glycerol, which is the most commonly used raw ingredient in the biomedical and food industry. The determination of glucose concentration in base fluids is considered to ease the challenges faced by doctors and biochemists regarding the monitoring of glucose concentration. It is found that the proposed sensor can quantify the glycerol purity up to the minimum specified adulteration level of 2 and 1% corresponding to toxic contaminants diethylene glycol and ethylene glycol, respectively, and the glucose concentration of 0.5 mg/ml.
Imaging the Shallow Subsurface Structure of the North Hikurangi Subduction Zone, New Zealand, Using 2‐D Full‐Waveform Inversion
Authors: Gray Melissa , Bell Rebecca E. , Morgan Joanna V. , Henrys Stuart , Barker Daniel H. N. ,   the IODP Expedition 372 and 375 science parties
Published: August 2019

The northern Hikurangi plate boundary fault hosts a range of seismic behaviors, of which the physical mechanisms controlling seismicity are poorly understood, but often related to high pore fluid pressures and conditionally stable frictional conditions. Using 2‐D marine seismic streamer data, we employ full‐waveform inversion (FWI) to obtain a high‐resolution 2‐D P wave velocity model across the Hikurangi margin down to depths of ~2 km. The validity of the FWI velocity model is investigated through comparison with the prestack depth‐migrated seismic reflection image, sonic well data, and the match between observed and synthetic waveforms. Our model reveals the shallow structure of the overriding plate, including the fault plumbing system above the zone of slow‐slip events to theoretical resolution of a half seismic wavelength. We find that the hanging walls of thrust faults often have substantially higher velocities than footwalls, consistent with higher compaction. In some cases, intrawedge faults identified from reflection data are associated with low‐velocity anomalies, which may suggest that they are high‐porosity zones acting as conduits for fluid flow. The continuity of velocity structure away from International Ocean Discovery Program drill site U1520 suggests that lithological variations in the incoming sedimentary stratigraphy observed at this site continue to the deformation front and are likely important in controlling seismic behavior. This investigation provides a high‐resolution insight into the shallow parts of subduction zones, which shows promise for the extension of modeling to 3‐D using a recently acquired, longer‐offset, seismic data set.
On the Origin of Aged Sedimentary Organic Matter Along a River‐Shelf‐Deep Ocean Transect
Authors: Bao Rui , Zhao Meixun , McNichol Ann , Wu Ying , Guo Xinyu , Haghipour Negar , Eglinton Timothy I.
Published: August 2019

To assess the influences of carbon sources and transport processes on the 14C age of organic matter (OM) in continental margin sediments, we examined a suite of samples collected along a river‐shelf‐deep ocean transect in the East China Sea (ECS). Ramped pyrolysis‐oxidiation was conducted on suspended particulate matter in the Yangtze River and on surface sediments from the ECS shelf and northern Okinawa Trough. 14C ages were determined on OM decomposition products within different temperature windows. These measurements suggest that extensive amounts of pre‐old (i.e., millennial age) organic carbon (OC) are subject to degradation within and beyond the Yangtze River Delta, and this process is accompanied by an exchange of terrestrial and marine OM. These results, combined with fatty acid concentration data, suggest that both the nature and extent of OM preservation/degradation as well as the modes of transport influence the 14C ages of sedimentary OM. Additionally, we find that the age of (thermally) refractory OC increases during across‐shelf transport and that the age offset between the lowest and highest temperature OC decomposition fractions also increases along the shelf‐to‐trough transect. Amplified interfraction spread or 14C heterogeneity is the greatest in the Okinawa Trough. Aged sedimentary OM across the transect may be a consequence of several reasons including fossil OC input, selective degradation of younger OC, hydrodynamic sorting processes, and aging during lateral transport. Consequently, each of them should be considered in assessing the 14C results of sedimentary OM and its implications for the carbon cycle and interpretation of sedimentary records.
Sensitivity of Methane Emissions to Later Soil Freezing in Arctic Tundra Ecosystems
Authors: Arndt Kyle A. , Oechel Walter C. , Goodrich Jordan P. , Bailey Barbara A. , Kalhori Aram , Hashemi Josh , Sweeney Colm , Zona Donatella
Published: August 2019

The atmospheric methane (CH4) concentration, a potent greenhouse gas, is on the rise once again, making it critical to understand the controls on CH4 emissions. In Arctic tundra ecosystems, a substantial part of the CH4 budget originates from the cold season, particularly during the “zero curtain” (ZC), when soil remains unfrozen around 0 °C. Due to the sparse data available at this time, the controls on cold season CH4 emissions are poorly understood. This study investigates the relationship between the fall ZC and CH4 emissions using long‐term soil temperature measurements and CH4 fluxes from four eddy covariance (EC) towers in northern Alaska. To identify the large‐scale implication of the EC results, we investigated the temporal change of terrestrial CH4 enhancements from the National Oceanic and Atmospheric Administration monitoring station in Utqiaġvik, AK, from 2001 to 2017 and their association with the ZC. We found that the ZC is extending later into winter (2.6 ± 0.5 days/year from 2001 to 2017) and that terrestrial fall CH4 enhancements are correlated with later soil freezing (0.79 ± 0.18‐ppb CH4 day−1 unfrozen soil). ZC conditions were associated with consistently higher CH4 fluxes than after soil freezing across all EC towers during the measuring period (2013–2017). Unfrozen soil persisted after air temperature was well below 0 °C suggesting that air temperature has poor predictive power on CH4 fluxes relative to soil temperature. These results imply that later soil freezing can increase CH4 loss and that soil temperature should be used to model CH4 emissions during the fall.
Whole Atmosphere Coupling on Intraseasonal and Interseasonal Time Scales: A Potential Source of Increased Predictive Capability
Authors: Sassi F. , McCormack J. P. , McDonald S. E.
Published: August 2019

Recent advances in developing accurate, physics‐based models of the coupled ionosphere‐thermosphere (CIT) system have now made these models an integral part of next‐generation space weather prediction capabilities. These advances have produced a better understanding of how the CIT is affected by variability in the neutral lower atmosphere. However, the impacts on the CIT of lower atmospheric variability over time scales with characteristic periods longer than ~10 days have received little attention, despite clear evidence of this variability in atmospheric circulation patterns throughout the stratosphere, mesosphere, and lower thermosphere. This review synthesizes the state of knowledge on long‐term variability (>10 days) originating in the lower atmosphere and its impacts on the CIT, highlighting the following critical points and challenges: (a) planetary wave oscillations are likely to couple the lower and upper atmospheres, especially those corresponding to normal modes of the atmosphere, but it remains unclear whether they impact the ionosphere directly via wind‐dynamo coupling, or indirectly via modulation of solar and lunar tides; (b) while fast moving planetary wave oscillations are ubiquitous in the CIT especially during solstices, there is only sporadic evidence that the slowest moving modes are also present in the upper atmosphere; (c) there is abundant evidence of long‐term variations of tidal amplitudes in the CIT, but how and why such variations occur still remain; (d) interseasonal variations associated with major tropospheric and stratospheric variability have been observed, but the physical pathways are still poorly understood.
Targeting HIBCH to reprogram valine metabolism for the treatment of colorectal cancer
Authors: Shan Yunlong , Gao Yuan , Jin Wei , Fan Minmin , Wang Ying , Gu Yanhong , Shan Chenxiao , Sun Lijun , Li Xin , Yu Biao , Luo Qiong , Xu Qiang
Published: August 2019

Valine catabolism is known to be essential for cancer cells but the detailed mechanism remains unclear. This study is to explore the critical roles of 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) in colorectal cancers (CRC) and to develop a new therapy returning valine metabolism homeostasis. High HIBCH expression was first confirmed to correlate with poor survival in patients with CRC, which was then linked to the increased cell growth, resistant apoptosis, and decreased autophagy in CRC cells. The functions of HIBCH in CRC were dependent on its mitochondrial localization. High HIBCH level was further demonstrated to promote the metabolism of tricarboxylic acid cycle as well as oxidative phosphorylation in CRC cells. Based on above findings, we further discovered a novel valine catabolism inhibitor SBF-1. The pharmacological blockade of HIBCH mitochondrial localization with SBF-1 resulted in decreased cancer cell growth and increased autophagy, collectively contributing to the antitumor effect both in vitro and in vivo. Moreover, anti-VEGF therapy with bevacizumab increased HIBCH level in CRC cells, which in turn caused the resistance to the therapy. The interference with HIBCH function by SBF-1 significantly increased the antitumor efficacy of bevacizumab and led to a robust survival benefit. The present study identified HIBCH as a critical enzyme of valine catabolism in CRC progression and resistance to anti-VEGF therapy. We also provided a novel HIBCH inhibitor SBF-1, which highlighted the combined therapy using valine catabolic inhibitor along with anti-VEGF drugs, to control progression of CRC.
MCT1 relieves osimertinib-induced CRC suppression by promoting autophagy through the LKB1/AMPK signaling
Authors: Jin Ping , Jiang Jingwen , Xie Na , Zhou Li , Huang Zhao , Zhang Lu , Qin Siyuan , Fu Shuyue , Peng Liyuan , Gao Wei , Li Bowen , Lei Yunlong , Nice Edouard C. , Li Changlong , Shao Jichun , Xie Ke
Published: August 2019

Colorectal cancer (CRC) is one of the most frequently diagnosed cancers worldwide. Development of novel chemotherapeutics is still required to enable successful treatment and improve survival for CRC patients. Here, we found that osimertinib (OSI) exhibits potent anti-CRC effects by inducing apoptosis, independent of its selective inhibitory activity targeting the EGFR T790M mutation. Intriguingly, OSI treatment triggers autophagic flux in CRC cells. Inhibition of autophagy markedly augments OSI-induced apoptosis and growth inhibition in CRC cells, suggesting a protective role of autophagy in response to OSI treatment. Mechanistically, OSI upregulates the expression of monocarboxylate transporter 1 (MCT1) and subsequently activates LKB1/AMPK signaling, leading to autophagy induction in CRC cells. Notably, OSI significantly exaggerates the sensitivity of CRC cells to the first-line drugs 5-fluorouracil or oxaliplatin. Taken together, our study unravels a novel mechanism of OSI-mediated protective autophagy involving MCT1/LKB1/AMPK signaling, and suggests the use of OSI as a potential agent for clinical CRC treatment.
Long noncoding RNA ABHD11-AS1 functions as a competing endogenous RNA to regulate papillary thyroid cancer progression by miR-199a-5p/SLC1A5 axis
Authors: Zhuang Xi , Tong Houchao , Ding Yu , Wu Luyao , Cai Jingsheng , Si Yan , Zhang Hao , Shen Meiping
Published: August 2019

With the increasing incidence of papillary thyroid cancer (PTC), more attention has been paid to exploring the mechanism of PTC initiation and progression. In addition, ectopic expression of long noncoding RNAs (lncRNAs) is reported to play a pivotal role in multiple human cancers. Based on these findings, we examined lncRNA ABHD11 antisense RNA 1 (ABHD11-AS1) expression and its clinical significance, biological function and mechanism in PTC. First, we analyzed thyroid ABHD11-AS1 expression in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Then, qRT-PCR was applied to detect the expression in paired PTC tissues and adjacent normal tissues, as well as in PTC cell lines (TPC-1 and K-1) and a normal thyroid follicular epithelium cell line (Nthy-ori3-1). In addition, we validated the relationship between ABHD11-AS1 expression and clinicopathological features by the Pearson X2 test. The oncogenic role of ABHD11-AS1 and its regulation of miR-199a-5p in PTC were examined by biological assays. Finally, bioinformatics analysis and mechanism assays were used to elucidate the underlying mechanism. We found that ABHD11-AS1 was remarkably overexpressed in PTC, and high expression was related to tumor size, lymph node metastasis, extrathyroidal extension and advanced TNM stage. Moreover, ABHD11-AS1 enhanced the abilities of cell proliferation, migration, and invasion, inhibited apoptosis in vitro, promoted tumorigenesis in vivo via sponging miR-199a-5p and then induced SLC1A5 activation. In addition, rescue assays were performed to confirm the ABHD11-AS1/miR-199a-5p/SLC1A5 axis. Taken together, the data show that ABHD11-AS1 acts as a competing endogenous RNA (ceRNA) to exert malignant properties in PTC through the miR-199a-5p/SLC1A5 axis. Therefore, our study may shed light on PTC diagnosis and therapies.
A mechanism for increased sensitivity of acute myeloid leukemia to mitotoxic drugs
Authors: Panina Svetlana B. , Baran Natalia , Brasil da Costa Fabio H. , Konopleva Marina , Kirienko Natalia V.
Published: August 2019

Mitochondria play a central and multifunctional role in the progression of tumorigenesis. Although many recent studies have demonstrated correlations between mitochondrial function and genetic makeup or originating tissue, it remains unclear why some cancers are more susceptible to mitocans (anticancer drugs that target mitochondrial function to mediate part or all of their effect). Moreover, fundamental questions of efficacy and mechanism of action in various tumor types stubbornly remain. Here we demonstrate that cancer type is a significant predictor of tumor response to mitocan treatment, and that acute myeloid leukemias (AML) show an increased sensitivity to these drugs. We determined that AML cells display particular defects in mitochondrial metabolism that underlie their sensitivity to mitocan treatment. Furthermore, we demonstrated that combinatorial treatment with a mitocan (CCCP) and a glycolytic inhibitor (2-deoxyglucose) has substantial synergy in AML cells, including primary cells from patients with AML. Our results show that mitocans, either alone or in combination with a glycolytic inhibitor, display anti-leukemia effects in doses much lower than needed to induce toxicity against normal blood cells, indicating that mitochondria may be an effective and selective therapeutic target.
Net carbon emissions from African biosphere dominate pan-tropical atmospheric CO2 signal
Authors: Palmer Paul I. , Feng Liang , Baker David , Chevallier Frédéric , Bösch Hartmut , Somkuti Peter
Published: August 2019

Tropical ecosystems are large carbon stores that are vulnerable to climate change. The sparseness of ground-based measurements has precluded verification of these ecosystems being a net annual source (+ve) or sink (−ve) of atmospheric carbon. We show that two independent satellite data sets of atmospheric carbon dioxide (CO2), interpreted using independent models, are consistent with the land tropics being a net annual carbon emission of $$({\mathrm{median}}_{{\mathrm{minimum}}}^{{\mathrm{maximum}}})$$

(

median

minimum

maximum

)

$$1.03_{ - 0.20}^{ + 1.73}$$
1.0

3

-
0.20

+
1.73

and $$1.60_{ + 1.39}^{ + 2.11}$$
1.6

0

+
1.39

+
2.11

petagrams (PgC) in 2015 and 2016, respectively. These pan-tropical estimates reflect unexpectedly large net emissions from tropical Africa of $$1.48_{ + 0.80}^{ + 1.95}$$
1.4

8

+
0.80

+
1.95

PgC in 2015 and $$1.65_{ + 1.14}^{ + 2.42}$$
1.6

5

+
1.14

+
2.42

PgC in 2016. The largest carbon uptake is over the Congo basin, and the two loci of carbon emissions are over western Ethiopia and western tropical Africa, where there are large soil organic carbon stores and where there has been substantial land use change. These signals are present in the space-borne CO2 record from 2009 onwards.
RIG-I-like receptors direct inflammatory macrophage polarization against West Nile virus infection
Authors: Stone Amy E. L. , Green Richard , Wilkins Courtney , Hemann Emily A. , Gale Michael
Published: August 2019

RIG-I-Like Receptors (RLRs) RIG-I, MDA5, and LGP2, are vital pathogen recognition receptors in the defense against RNA viruses. West Nile Virus (WNV) infections continue to grow in the US. Here, we use a systems biology approach to define the contributions of each RLR in the innate immune response to WNV. Genome-wide RNAseq and bioinformatics analyses of macrophages from mice lacking either RLR reveal that the RLRs drive distinct immune gene activation and response polarization to mediate an M1/inflammatory signature while suppressing the M2/wound healing phenotype. While LGP2 functions to modulate inflammatory signaling, RIG-I and MDA5 together are essential for M1 macrophage polarization in vivo and the control of WNV infection through potential downstream control of ATF4 and SMAD4 to regulate target gene expression for cell polarization. These analyses reveal the RLR-driven signature of macrophage polarization, innate immune protection, and immune programming against WNV infection.
Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns
Authors: Keiper Sandra , Papasaikas Panagiotis , Will Cindy L. , Valcárcel Juan , Girard Cyrille , Lührmann Reinhard
Published: August 2019

Human pre-catalytic spliceosomes contain several proteins that associate transiently just prior to spliceosome activation and are absent in yeast, suggesting that this critical step is more complex in higher eukaryotes. We demonstrate via RNAi coupled with RNA-Seq that two of these human-specific proteins, Smu1 and RED, function both as alternative splicing regulators and as general splicing factors and are required predominantly for efficient splicing of short introns. In vitro splicing assays reveal that Smu1 and RED promote spliceosome activation, and are essential for this step when the distance between the pre-mRNA’s 5′ splice site (SS) and branch site (BS) is sufficiently short. This Smu1-RED requirement can be bypassed when the 5′ and 3′ regions of short introns are physically separated. Our observations suggest that Smu1 and RED relieve physical constraints arising from a short 5′SS-BS distance, thereby enabling spliceosomes to overcome structural challenges associated with the splicing of short introns.
Local orbital degeneracy lifting as a precursor to an orbital-selective Peierls transition
Authors: Bozin E. S. , Yin W. G. , Koch R. J. , Abeykoon M. , Hor Y. S. , Zheng H. , Lei H. C. , Petrovic C. , Mitchell J. F. , Billinge S. J. L.
Published: August 2019

Fundamental electronic principles underlying all transition metal compounds are the symmetry and filling of the d-electron orbitals and the influence of this filling on structural configurations and responses. Here we use a sensitive local structural technique, x-ray atomic pair distribution function analysis, to reveal the presence of fluctuating local-structural distortions at high temperature in one such compound, CuIr2S4. We show that this hitherto overlooked fluctuating symmetry-lowering is electronic in origin and will modify the energy-level spectrum and electronic and magnetic properties. The explanation is a local, fluctuating, orbital-degeneracy-lifted state. The natural extension of our result would be that this phenomenon is likely to be widespread amongst diverse classes of partially filled nominally degenerate d-electron systems, with potentially broad implications for our understanding of their properties.
GWAS for urinary sodium and potassium excretion highlights pathways shared with cardiovascular traits
Authors: Pazoki Raha , Evangelou Evangelos , Mosen-Ansorena David , Pinto Rui Climaco , Karaman Ibrahim , Blakeley Paul , Gill Dipender , Zuber Verena , Elliott Paul , Tzoulaki Ioanna , Dehghan Abbas
Published: August 2019

Urinary sodium and potassium excretion are associated with blood pressure (BP) and cardiovascular disease (CVD). The exact biological link between these traits is yet to be elucidated. Here, we identify 50 loci for sodium and 13 for potassium excretion in a large-scale genome-wide association study (GWAS) on urinary sodium and potassium excretion using data from 446,237 individuals of European descent from the UK Biobank study. We extensively interrogate the results using multiple analyses such as Mendelian randomization, functional assessment, co localization, genetic risk score, and pathway analyses. We identify a shared genetic component between urinary sodium and potassium expression and cardiovascular traits. Ingenuity pathway analysis shows that urinary sodium and potassium excretion loci are over-represented in behavioural response to stimuli. Our study highlights pathways that are shared between urinary sodium and potassium excretion and cardiovascular traits.
Mutations in topoisomerase IIβ result in a B cell immunodeficiency
Authors: Broderick Lori , Yost Shawn , Li Dong , McGeough Matthew D. , Booshehri Laela M. , Guaderrama Marisela , Brydges Susannah D. , Kucharova Karolina , Patel Niraj C. , Harr Margaret , Hakonarson Hakon , Zackai Elaine , Cowell Ian G. , Austin Caroline A. , Hügle Boris , Gebauer Corinna , Zhang Jianguo , Xu Xun , Wang Jian , Croker Ben A. , Frazer Kelly A. , Putnam Christopher D. , Hoffman Hal M.
Published: August 2019

B cell development is a highly regulated process involving multiple differentiation steps, yet many details regarding this pathway remain unknown. Sequencing of patients with B cell-restricted immunodeficiency reveals autosomal dominant mutations in TOP2B. TOP2B encodes a type II topoisomerase, an essential gene required to alleviate topological stress during DNA replication and gene transcription, with no previously known role in B cell development. We use Saccharomyces cerevisiae, and knockin and knockout murine models, to demonstrate that patient mutations in TOP2B have a dominant negative effect on enzyme function, resulting in defective proliferation, survival of B-2 cells, causing a block in B cell development, and impair humoral function in response to immunization.
Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection
Authors: Forde Brian M. , Roberts Leah W. , Phan Minh-Duy , Peters Kate M. , Fleming Brittany A. , Russell Colin W. , Lenherr Sara M. , Myers Jeremy B. , Barker Adam P. , Fisher Mark A. , Chong Teik-Min , Yin Wai-Fong , Chan Kok-Gan , Schembri Mark A. , Mulvey Matthew A. , Beatson Scott A.
Published: August 2019

Recurrent urinary tract infections (rUTIs) are extremely common, with ~ 25% of all women experiencing a recurrence within 1 year of their original infection. Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of rUTI. Here, we show the dynamics of an ST131 population over a 5-year period from one elderly woman with rUTI since the 1970s. Using whole genome sequencing, we identify an indigenous clonal lineage (P1A) linked to rUTI and persistence in the fecal flora, providing compelling evidence of an intestinal reservoir of rUTI. We also show that the P1A lineage possesses substantial plasmid diversity, resulting in the coexistence of antibiotic resistant and sensitive intestinal isolates despite frequent treatment. Our longitudinal study provides a unique comprehensive genomic analysis of a clonal lineage within a single individual and suggests a population-wide resistance mechanism enabling rapid adaptation to fluctuating antibiotic exposure.
Cellular internalization of bystander nanomaterial induced by TAT-nanoparticles and regulated by extracellular cysteine
Authors: Wei Yushuang , Tang Tang , Pang Hong-Bo
Published: August 2019

Entry into cells is necessary for many nanomaterial applications, and a common solution is to functionalize nanoparticles (NPs) with cell-penetrating ligands. Despite intensive studies on these functionalized NPs, little is known about their effect on cellular activities to engulf other cargo from the nearby environment. Here, we use NPs functionalized with TAT (transactivator of transcription) peptide (T-NPs) as an example to investigate their impact on cellular uptake of bystander cargo. We find that T-NP internalization enables cellular uptake of bystander NPs, but not common fluid markers, through a receptor-dependent macropinocytosis pathway. Moreover, the activity of this bystander uptake is stimulated by cysteine presence in the surrounding solution. The cargo selectivity and cysteine regulation are further demonstrated ex vivo and in vivo. These findings reveal another mechanism for NP entry into cells and open up an avenue of studying the interplay among endocytosis, amino acids, and nanomaterial delivery.
PlatformTM, a standards-based data custodianship platform for translational medicine research
Authors: Emam Ibrahim , Elyasigomari Vahid , Matthews Alex , Pavlidis Stelios , Rocca-Serra Philippe , Guitton Florian , Verbeeck Denny , Grainger Lucinda , Borgogni Erica , Del Giudice Giuseppe , Saqi Mansoor , Houston Paul , Guo Yike
Published: August 2019

Biomedical informatics has traditionally adopted a linear view of the informatics process (collect, store and analyse) in translational medicine (TM) studies; focusing primarily on the challenges in data integration and analysis. However, a data management challenge presents itself with the new lifecycle view of data emphasized by the recent calls for data re-use, long term data preservation, and data sharing. There is currently a lack of dedicated infrastructure focused on the ‘manageability’ of the data lifecycle in TM research between data collection and analysis. Current community efforts towards establishing a culture for open science prompt the creation of a data custodianship environment for management of TM data assets to support data reuse and reproducibility of research results. Here we present the development of a lifecycle-based methodology to create a metadata management framework based on community driven standards for standardisation, consolidation and integration of TM research data. Based on this framework, we also present the development of a new platform (PlatformTM) focused on managing the lifecycle for translational research data assets.
Glioblastoma multiforme restructures the topological connectivity of cerebrovascular networks
Authors: Hahn Artur , Bode Julia , Krüwel Thomas , Solecki Gergely , Heiland Sabine , Bendszus Martin , Tews Björn , Winkler Frank , Breckwoldt Michael O. , Kurz Felix T.
Published: August 2019

Glioblastoma multiforme alters healthy tissue vasculature by inducing angiogenesis and vascular remodeling. To fully comprehend the structural and functional properties of the resulting vascular network, it needs to be studied collectively by considering both geometric and topological properties. Utilizing Single Plane Illumination Microscopy (SPIM), the detailed capillary structure in entire healthy and tumor-bearing mouse brains could be resolved in three dimensions. At the scale of the smallest capillaries, the entire vascular systems of bulk U87- and GL261-glioblastoma xenografts, their respective cores, and healthy brain hemispheres were modeled as complex networks and quantified with fundamental topological measures. All individual vessel segments were further quantified geometrically and modular clusters were uncovered and characterized as meta-networks, facilitating an analysis of large-scale connectivity. An inclusive comparison of large tissue sections revealed that geometric properties of individual vessels were altered in glioblastoma in a relatively subtle way, with high intra- and inter-tumor heterogeneity, compared to the impact on the vessel connectivity. A network topology analysis revealed a clear decomposition of large modular structures and hierarchical network organization, while preserving most fundamental topological classifications, in both tumor models with distinct growth patterns. These results augment our understanding of cerebrovascular networks and offer a topological assessment of glioma-induced vascular remodeling. The findings may help understand the emergence of hypoxia and necrosis, and prove valuable for therapeutic interventions such as radiation or antiangiogenic therapy.
High-throughput metagenome analysis of the Sarcoptes scabiei internal microbiota and in-situ identification of intestinal Streptomyces sp.
Authors: Swe Pearl M. , Zakrzewski Martha , Waddell Rebecca , Sriprakash Kadaba S. , Fischer Katja
Published: August 2019

Multiple parasitic arthropods of medical importance depend on symbiotic bacteria. While the link between scabies and secondary bacterial infections causing post infective complications of Group A streptococcal and staphylococcal pyoderma is increasingly recognized, very little is known about the microbiota of Sarcoptes scabiei. Here we analyze adult female mite and egg metagenome datasets. The majority of adult mite bacterial reads matched with Enterobacteriaceae (phylum Proteobacteria), followed by Corynebacteriaceae (phylum Actinobacteria). Klebsiella was the most dominant genus (78%) and Corynebacterium constituted 9% of the assigned sequences. Scabies mite eggs had a more diverse microbial composition with sequences from Proteobacteria being the most dominant (75%), while Actinobacteria, Bacteroidetes and Firmicutes accounted for 23% of the egg microbiome sequences. DNA sequences of a potential endosymbiont, namely Streptomyces, were identified in the metagenome sequence data of both life stages. The presence of Streptomyces was confirmed by conventional PCR. Digital droplet PCR indicated higher Streptomyces numbers in adult mites compared to eggs. Streptomyces were localized histologically in the scabies mite gut and faecal pellets by Fluorescent In Situ Hybridization (FISH). Streptomyces may have essential symbiotic roles in the scabies parasite intestinal system requiring further investigation.
Synthesis of centimeter-size free-standing perovskite nanosheets from single-crystal lead bromide for optoelectronic devices
Authors: Zheng Jian-Yao , Manning Hugh G. , Zhang Yanhui , Wang Jing Jing , Purcell-Milton Finn , Pokle Anuj , Porter Stephen-Barry , Zhong Chuan , Li Jing , O’Reilly Meehan Rudi , Enright Ryan , Gun’ko Yurii K. , Nicolosi Valeria , Boland John J. , Sanvito Stefano , Donegan John F.
Published: August 2019

Considerable attention has been drawn to the lead halide perovskites (LHPs) because of their outstanding optoelectronic characteristics. LHP nanosheets (NSs) grown from single crystalline lead halide possess advantages in device applications as they provide the possibility for control over morphology, composition, and crystallinity. Here, free-standing lead bromide (PbBr2) single-crystalline NSs with sizes up to one centimeter are synthesized from solution. These NSs can be converted to LHP while maintaining the NS morphology. We demonstrate that these perovskite NSs can be processed directly for fabrication of photodetector and laser arrays on a large scale. This strategy will allow high-yield synthesis of large-size perovskite NSs for functional devices in an integrated photonics platform.
Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation
Authors: Júlio Aline Daniela Lopes , de Cássia Mourão Silva Ubiana , Medeiros Julliane Dutra , Morais Daniel Kumazawa , dos Santos Vera Lúcia
Published: August 2019

Metataxonomic approach was used to describe the bacterial community from a creosote-contaminated aquifer and to access the potential for in situ bioremediation of the polycyclic aromatic hydrocarbons (PAHs) by biostimulation. In general, the wells with higher PAH contamination had lower richness and diversity than others, using the Shannon and Simpson indices. By the principal coordinate analysis (PCoA) it was possible to observe the clustering of the bacterial community of most wells in response of the presence of PAH contamination. The significance analysis using edgeR package of the R program showed variation in the abundance of some Operational Taxonomic Units (OTUs) of contaminated wells compared to uncontaminated ones. Taxons enriched in the contaminated wells were correlated positively (p < 0.05) with the hydrocarbons, according to redundancy analysis (RDA). All these enriched taxa have been characterized as PAH degrading agents, such as the genus Comamonas, Geobacter, Hydrocarboniphaga, Anaerolinea and Desulfomonile. Additionally, it was possible to predict, with the PICRUSt program, a greater proportion of pathways and genes related to the degradation of PAHs in the wells with higher contamination levels. We conclude that the contaminants promoted the enrichment of several groups of degrading bacteria in the area, which strengthens the feasibility of applying biostimulation as an aquifer remediation strategy.
The role of surface air temperature over the east Asia on the early and late Indian Summer Monsoon Onset over Kerala
Authors: Choudhury Devanil , Nath Debashis , Wen Chen
Published: August 2019

This study investigates the physical mechanism for late Indian Summer Monsoon onset over Kerala (MOK). 14 early and 9 late onset years are selected based on the criteria when the onset is 5 days or more prior and after normal onset date (i.e 1st June according to India Meteorological Department) respectively. Then, we perform composite analyses of mean May monthly and daily evolution during early and late onset years to examine the differences in monsoon circulation features prior to the MOK. We find that advection of Surface Air Temperature (SAT) from the northern to the southern China and the eastern Tibetan Plateau (TP) plays an important role to modulate the MOK processes. In the late onset years, more low-level jet (LLJ) from the Bay of Bengal (BOB) divert towards the east Asia before the onset, which is due to an extension of the low sea level pressure and high SAT over the east Asia (eastern TP, east-central China). This strengthens the low-level convergence and upper level divergence over the eastern TP and southern China. As a result, a significant amount of moisture from the BOB is transported towards the eastern TP and southern China. Thereby, a comparatively weaker LLJ and deficit low-level moisture supply over the eastern BOB maintain the key roles in modulating the MOK processes.