bluuebunny/crossref_metadata_2025 huggingface dataset:
ON A CLASS OF NONLINEAR SCHRÖDINGER EQUATIONS ON FINITE GRAPHS
Authors: MAN SHOUDONG
Published: February 2020

Suppose that $G=(V,E)$ is a finite graph with the vertex set $V$ and the edge set $E$. Let $\unicode[STIX]{x1D6E5}$ be the usual graph Laplacian. Consider the nonlinear Schrödinger equation of the form $$\begin{eqnarray}-\unicode[STIX]{x1D6E5}u-\unicode[STIX]{x1D6FC}u=f(x,u),\quad u\in W^{1,2}(V),\end{eqnarray}$$ on the graph $G$, where $f(x,u):V\times \mathbb{R}\rightarrow \mathbb{R}$ is a nonlinear real-valued function and $\unicode[STIX]{x1D6FC}$ is a parameter. We prove an integral inequality on $G$ under the assumption that $G$ satisfies the curvature-dimension type inequality $CD(m,\unicode[STIX]{x1D709})$. Then by using the Poincaré–Sobolev inequality, the Trudinger–Moser inequality and the integral inequality on $G$, we prove that there is a nontrivial solution to the nonlinear Schrödinger equation if $\unicode[STIX]{x1D6FC}<2\unicode[STIX]{x1D706}_{1}^{2}/m(\unicode[STIX]{x1D706}_{1}-\unicode[STIX]{x1D709})$, where $\unicode[STIX]{x1D706}_{1}$ is the first positive eigenvalue of the graph Laplacian.
Tricarboxylic acid cycle dehydrogenases inhibition by naringenin: experimental and molecular modelling evidence
Authors: August Pauline Maciel , Grings Mateus , Grunwald Marcelo Sartori , Zanatta Geancarlo , Stone Vinícius , de Lemos Rodrigues Patricia Idalina , Stocher Daniela Pereira , Moreira José Cláudio Fonseca , Leipnitz Guilhian , Matté Cristiane
Published: February 2020

The study of polyphenols’ effects on health has been gaining attention lately. In addition to reacting with important enzymes, altering the cell metabolism, these substances can present either positive or negative metabolic alterations depending on their consumption levels. Naringenin, a citrus flavonoid, already presents diverse metabolic effects. The objective of this work was to evaluate the effect of maternal naringenin supplementation during pregnancy on the tricarboxylic acid cycle activity in offspring’s cerebellum. Adult female Wistar rats were divided into two groups: (1) vehicle (1 ml/kg by oral administration (p.o.)) or (2) naringenin (50 mg/kg p.o.). The offspring were euthanised at 7th day of life, and the cerebellum was dissected to analyse citrate synthase, isocitrate dehydrogenase (IDH), α-ketoglutarate dehydrogenase (α-KGDH) and malate dehydrogenase (MDH) activities. Molecular docking used SwissDock web server and FORECASTER Suite, and the proposed binding pose image was created on UCSF Chimera. Data were analysed by Student’s t test. Naringenin supplementation during pregnancy significantly inhibited IDH, α-KGDH and MDH activities in offspring’s cerebellum. A similar reduction was observed in vitro, using purified α-KGDH and MDH, subjected to pre-incubation with naringenin. Docking simulations demonstrated that naringenin possibly interacts with dehydrogenases in the substrate and cofactor binding sites, inhibiting their function. Naringenin administration during pregnancy may affect cerebellar development and must be evaluated with caution by pregnant women and their physicians.
Yogurt consumption and colorectal polyps
Authors: Rifkin Samara B. , Giardiello Francis M. , Zhu Xiangzhu , Hylind Linda M. , Ness Reid M. , Drewes Julia L. , Murff Harvey J. , Spence Emma H. , Smalley Walter E. , Gills Joell J. , Mullin Gerard E. , Kafonek David , La Luna Louis , Zheng Wei , Sears Cynthia L. , Shrubsole Martha J. ,   the Biofilm Study Consortium
Published: February 2020

Diet modifies the risk of colorectal cancer (CRC), and inconclusive evidence suggests that yogurt may protect against CRC. We analysed the data collected from two separate colonoscopy-based case–control studies. The Tennessee Colorectal Polyp Study (TCPS) and Johns Hopkins Biofilm Study included 5446 and 1061 participants, respectively, diagnosed with hyperplastic polyp (HP), sessile serrated polyp, adenomatous polyp (AP) or without any polyps. Multinomial logistic regression models were used to derive OR and 95 % CI to evaluate comparisons between cases and polyp-free controls and case–case comparisons between different polyp types. We evaluated the association between frequency of yogurt intake and probiotic use with the diagnosis of colorectal polyps. In the TCPS, daily yogurt intake v. no/rare intake was associated with decreased odds of HP (OR 0·54; 95 % CI 0·31, 0·95) and weekly yogurt intake was associated with decreased odds of AP among women (OR 0·73; 95 % CI 0·55, 0·98). In the Biofilm Study, both weekly yogurt intake and probiotic use were associated with a non-significant reduction in odds of overall AP (OR 0·75; 95 % CI 0·54, 1·04) and (OR 0·72; 95 % CI 0·49, 1·06) in comparison with no use, respectively. In summary, yogurt intake may be associated with decreased odds of HP and AP and probiotic use may be associated with decreased odds of AP. Further prospective studies are needed to verify these associations.
Effects of standard v. very long Roux limb Roux-en-Y gastric bypass on nutrient status: a 1-year follow-up report from the Dutch Common Channel Trial (DUCATI) Study
Authors: Leeman M. , Gadiot R. P. M. , Wijnand J. M. A. , Birnie E. , Apers J. A. , Biter L. U. , Dunkelgrun M.
Published: February 2020

Laparoscopic Roux-en-Y gastric bypass (RYGB) is considered the ‘gold standard’ for surgical treatment of morbid obesity. It is hypothesised that reducing the length of the common limb positively affects the magnitude and preservation of weight loss but may also impose a risk of malnutrition. The aim of this study was to compare patients’ nutrient and vitamin deficiencies in standard RYGB with a very long Roux limb RYGB (VLRL-RYGB). This study was part of the multicentre randomised controlled trial (Dutch Common Channel Trial), including 444 patients undergoing an RYGB or a VLRL-RYGB. Laboratory results, use of multivitamin supplements and reoperations were collected at baseline and 1 year postoperative. Primary outcome measure was nutrient deficiency after 1 year postoperative. Secondary outcome measure was the reoperation rate due to malabsorption. In total, 227 patients underwent RYGB and 196 patients underwent VLRL-RYGB. Most common deficiencies at 1 year postoperative were ferritin (17·2–18·2 %), Fe (23·4–35·6 %), K (7·4–15·2 %), vitamin B12 (9·0–9·9 %) and vitamin D (22·7–34·5 %). Patients undergoing VLRL-RYGB had slightly but significantly lower levels of Ca, Fe and vitamin D compared with those undergoing RYGB at 1 year postoperative, but significantly higher levels of folic acid and Na. Reoperation rates due to malabsorption were not significantly different between RYGB (2/227, 0·9 %) and VLRL-RYGB (7/196, 3·6 %) (P = 0·088). We concluded that patients undergoing VLRL-RYGB had significantly lower levels of Ca, Fe and vitamin D compared with those undergoing RYGB at 1 year postoperative, but higher levels of folic acid and Na. Reoperation rates did not differ. Close monitoring on nutrient deficiencies should be performed in patients undergoing VLRL-RYGB.
The wisdom of John Milbank: a critical appraisal of Milbank's sophiology
Authors: May Richard
Published: February 2020

Despite the theological controversy surrounding ‘Russian sophiology' amongst Orthodox theologians, John Milbank has claimed that it has proven to be one of the most daring theological breakthroughs within twentieth-century theology. He further considers it to be a fecund avenue of theological and philosophical reflection that has the potential to effectively communicate his central theological arguments in a new idiom. However, many of the positions which Milbank adopts within his sophiology prove to be controversial. This article offers a critical appraisal of Milbank's sophiology, drawing particular attention to several theological aporias it appears to generate and leave unresolved.
Early characteristics of bone deficits in children with Fontan palliation
Authors: Sarafoglou Kyriakie , Petryk Anna , Mishra Pooja E. , Polgreen Lynda E. , Panoskaltsis-Mortari Angela , Brown Roland , Marino Bradley S. , Gremmels David , Shepard Charles , Kelly Aaron S. , Miller Bradley S. , Rudser Kyle , McCracken Courtney , Kochilas Lazaros K.
Published: February 2020

Background:

This is a cross-sectional study aiming to understand the early characteristics and background of bone health impairment in clinically well children with Fontan circulation.

Methods:

We enrolled 10 clinically well children with Fontan palliation (operated >5 years before study entrance, Tanner stage ≤3, age 12.1 ± 1.77 years, 7 males) and 11 healthy controls (age 12.0 ± 1.45 years, 9 males) at two children’s hospitals. All patients underwent peripheral quantitative CT. For the Fontan group, we obtained clinical characteristics, NYHA class, cardiac index by MRI, dual x-ray absorptiometry, and biochemical studies. Linear regression was used to compare radius and tibia peripheral quantitative CT measures between Fontan patients and controls.

Results:

All Fontan patients were clinically well (NYHA class 1 or 2, cardiac index 4.85 ± 1.51 L/min/m2) and without significant comorbidities. Adjusted trabecular bone mineral density, cortical thickness, and bone strength index at the radius were significantly decreased in Fontan patients compared to controls with mean differences −30.13 mg/cm3 (p = 0.041), −0.31 mm (p = 0.043), and −6.65 mg2/mm4 (p = 0.036), respectively. No differences were found for tibial measures. In Fontan patients, the mean height-adjusted lumbar bone mineral density and total body less head z scores were −0.46 ± 1.1 and −0.63 ± 1.1, respectively, which are below the average, but within normal range for age and sex.

Conclusions:

In a clinically well Fontan cohort, we found significant bone deficits by peripheral quantitative CT in the radius but not the tibia, suggesting non-weight-bearing bones may be more vulnerable to the unique haemodynamics of the Fontan circulation.
Improved herbicide selectivity in tomato by safening action of benoxacor and fenclorim
Authors: Castro Edicarlos , Pucci Carolina , Duarte Stefano , Burgos Nilda Roma , Tseng Te Ming
Published: February 2020

Safeners have been widely used to reduce phytotoxicity to crops, thus serving as an alternative weed control strategy. Benoxacor and fenclorim safeners have the potential to protect plants from herbicide phytotoxicity by increasing glutathione S-transferase (GST) activity within the plant. The study aimed to evaluate the safening effect of benoxacor and fenclorim on tomato against selected herbicides applied POST. The experiment was conducted in a greenhouse in a completely randomized designed with four replications in a 9 × 3 factorial scheme, where Factor A consisted of eight herbicides including a nontreated control, and Factor B consisted of two safeners including a nontreated control. The herbicide treatments were sulfentrazone (0.220 kg ai ha−1), fomesafen (0.280 kg ai ha−1), flumioxazin (0.070 kg ai ha−1), linuron (1.200 kg ai ha−1), metribuzin (0.840 kg ai ha−1), pyroxasulfone (0.220 kg ai ha−1), and bicyclopyrone (0.040 kg ai ha−1). Safener treatments consisted of benoxacor (0.67 g L−1) and fenclorim (10 µM). Tomato seeds were immersed in safener solution before sowing and herbicides were applied when tomato plants were at the 3-leaf stage, or 25 days after sowing. Visible injury was scored at 3, 7, 14, and 21 d after application (DAA), and shoot biomass was recorded 21 DAA. Seed treatment with fenclorim reduced injury caused by imazamox and bicyclopyrone by 5.5 and 1.3 times, respectively, whereas benoxacor reduced the injury from bicyclopyrone 1.3 times. In addition, tomato plants pretreated with fenclorim showed a lesser reduction in biomass after application of imazamox, fomesafen, and metribuzin, whereas plants pretreated with benoxacor showed lesser biomass reduction after metribuzin application. Thus, the use of safeners promotes greater crop selectivity, allowing the application of herbicides with different mechanisms of action on the crop.
Impacts of Humidity Adjustment Through Radar Data Assimilation Using Cloud Analysis on the Analysis and Prediction of a Squall Line in Southern China
Authors: Pan Yujie , Wang Mingjun , Xue Ming
Published: February 2020

This study examines the impacts of humidity adjustment in a cloud analysis system on the analysis and forecast of a squall line that occurred in southeast China on 23–24 April 2007. Radial velocity data are assimilated using the ARPS three‐dimensional variational system while reflectivity data are assimilated by a cloud analysis system. Experiments with two different humidity adjustment schemes are performed, with the original and enhanced versions. Another experiment does not adjust moisture. Both schemes generally decrease the humidity in front of the convective line and increase the humidity within the convective and stratiform regions of squall line compared to no humidity adjustment, and the original scheme produces the higher humidity within precipitation regions, especially the stratiform region. Both schemes improve the forecast of squall line structure, including the leading convective line, a transition zone, and a trailing stratiform region. Among the three experiments, the enhanced scheme produces the highest precipitation forecast skill. The latent heating rates are also diagnosed to investigate the microphysical responses to the humidity adjustment. The cooling outside of the observed precipitation regions corresponding to the humidity reduction also acts to suppress spurious precipitation. Water vapor condensation into cloud water and cloud water evaporation generally dominate the latent heating/cooling below the freezing level. Compared to the enhanced scheme, the original scheme releases much more latent heat in the middle troposphere, causing more warming. This is linked to the higher cloud water condensation rate, due to the higher amount of moisture addition/adjustment by the original scheme.
Deriving Surface Ages on Mars Using Automated Crater Counting
Authors: Benedix G. K. , Lagain A. , Chai K. , Meka S. , Anderson S. , Norman C. , Bland P. A. , Paxman J. , Towner M. C. , Tan T.
Published: February 2020

Impact craters on solar system bodies are used to determine the relative ages of surfaces. The smaller the limiting primary crater size, the higher the spatial resolution in surface/resurfacing age dating. A manually counted database (Robbins & Hynek, 2012, https://doi.org/10.1029/2011JE003966) of >384,000 craters on Mars >1 km in diameter exists. But because crater size scales as a power law, the number of impact craters in the size range 10 m to 1 km is in the tens of millions, a number making precise analysis of local variations of age, over an entire surface, impossible to perform by manual counting. To decode this crater size population at a planetary scale, we developed an automated Crater Detection Algorithm based on the You Only Look Once v3 object detection system. The algorithm was trained by annotating images of the controlled Thermal Emission Imaging System daytime infrared data set. This training data set contains 7,048 craters that the algorithm used as a learning benchmark. The results were validated against the manually counted database as the ground truth data set. We applied our algorithm to the Thermal Emission Imaging System global mosaic between ±65° of latitude, returning a true positive detection rate of 91% and a diameter estimation error (~15%) consistent with typical manual count variation. Importantly, although a number of automated crater counting algorithms have been published, for the first time we demonstrate that automatic counting can be routinely used to derive robust surface ages.
Impact of Changes to the Atmospheric Soluble Iron Deposition Flux on Ocean Biogeochemical Cycles in the Anthropocene
Authors: Hamilton Douglas S. , Moore J. Keith , Arneth Almut , Bond Tami C. , Carslaw Ken S. , Hantson Stijn , Ito Akinori , Kaplan Jed O. , Lindsay Keith , Nieradzik Lars , Rathod Sagar D. , Scanza Rachel A. , Mahowald Natalie M.
Published: February 2020

Iron can be a growth‐limiting nutrient for phytoplankton, modifying rates of net primary production, nitrogen fixation, and carbon export ‐ highlighting the importance of new iron inputs from the atmosphere. The bioavailable iron fraction depends on the emission source and the dissolution during transport. The impacts of anthropogenic combustion and land use change on emissions from industrial, domestic, shipping, desert, and wildfire sources suggest that Northern Hemisphere soluble iron deposition has likely been enhanced between 2% and 68% over the Industrial Era. If policy and climate follow the intermediate Representative Concentration Pathway 4.5 trajectory, then results suggest that Southern Ocean (>30°S) soluble iron deposition would be enhanced between 63% and 95% by 2100. Marine net primary productivity and carbon export within the open ocean are most sensitive to changes in soluble iron deposition in the Southern Hemisphere; this is predominantly driven by fire rather than dust iron sources. Changes in iron deposition cause large perturbations to the marine nitrogen cycle, up to 70% increase in denitrification and 15% increase in nitrogen fixation, but only modestly impacts the carbon cycle and atmospheric CO2 concentrations (1–3 ppm). Regionally, primary productivity increases due to increased iron deposition are often compensated by offsetting decreases downstream corresponding to equivalent changes in the rate of phytoplankton macronutrient uptake, particularly in the equatorial Pacific. These effects are weaker in the Southern Ocean, suggesting that changes in iron deposition in this region dominates the global carbon cycle and climate response.
Rapid Shifts in Chemical and Isotopic Compositions of Sediment Pore Waters in the Amami Sankaku Basin in Response to Initial Arc Rifting in the Mid‐Oligocene
Authors: Zhang Zhaohui
Published: February 2020

Pore waters were recovered from the sediment cores drilled in the back‐arc Amami Sankaku Basin (ASB) during the International Ocean Discovery Program Expedition 351. The sediment sequence is composed of the recent mud and ooze from late Oligocene/early Miocene accumulated at 7 m/Ma and rapid deposition of thick volcaniclastic sequence at 50 m/Ma. Such variations are reflected in the evolutions of chemical and isotopic compositions of pore waters. Cl and Ca concentrations in pore waters increased rapidly with depth and became enriched in the deep portion. Before arc rifting, extremely high deposition rates of volcaniclastic gravity‐flow sediments from the nearby Kyushu‐Palau arc into the ASB resulted in strong alteration, removing Mg and Si from pore waters. Mg concentrations were initially almost zero but abruptly shifted to substantial increases after ~29.5 Ma, indicating extended rifting of the active volcanic axis from the ASB. The δ18O and δD values of pore waters also evolved from more depleted and wide range to more positive and narrow range as a response to reduced alteration and increasing influence of seawater. Concentrations of Si and Mn in pore waters rapidly increased since ~29.5 Ma but suddenly declined at ~17.5 Ma due to the cessation of input of volcaniclastic materials. Covariations of Ca and Mg in pore waters are very similar to those in the back‐arc West Philippine Basin but significantly different from those in the Izu‐Bonin fore‐arc basin. Variations in chemical and isotopic compositions of pore waters can assist the reconstruction of tectonic activities.
Elastic Strain Effects on Wave Scattering: Implications for Coda Wave Interferometry (CWI)
Authors: Azzola Jérôme , Schmittbuhl Jean , Zigone Dimitri , Lengliné Olivier , Masson Frédéric , Magnenet Vincent
Published: February 2020

Coda Wave Interferometry (CWI) is a highly sensitive monitoring technique built on the sensitivity of elastic coda waves to small changes in a diffusive medium. However, a clear connection between the physical processes involved in the evolution of the medium and the time changes observed by CWI has not been clearly described yet. Here, we quantify the impact of elastic deformation on CWI measurements at laboratory scales. We compare experimental results from wave scattering measurements during a uniaxial compression test to those of a numerical approach based on the combination of two codes (SPECFEM2D and Code_Aster), which allows us to model wave propagation in complex diffusive media during its elastic deformation. In both approaches, the reversible time delays measured between waveforms increase with the elastic deformation of the sample. From the numerical modeling, we gain insight to the relative contributions of different physical effects on the CWI measurement: local density changes from volumetric strain, the deformation of scatterers, and acoustoelastic effects. Our results suggest that acoustoelastics effects related to nonlinear elasticity are dominant.
Ocean Bottom Pressure Variability: Can It Be Reliably Modeled?
Authors: Androsov Alexey , Boebel Olaf , Schröter Jens , Danilov Sergey , Macrander Andreas , Ivanciu Ioana
Published: February 2020

Ocean bottom pressure (OBP) variability serves as a proxy of ocean mass variability, the knowledge of which is needed in geophysical applications. The question of how well it can be modeled by the present general ocean circulation models on time scales in excess of 1 day is addressed here by comparing the simulated OBP variability with the observed one. To this end, a new multiyear data set is used, obtained with an array of bottom pressure gauges deployed deeply along a transect across the Southern Ocean. We present a brief description of OBP data and show large‐scale correlations over several thousand kilometers at all time scales using daily and monthly averaged data. Annual and semiannual cycles are weak. Close to the Agulhas Retroflection, signals of up to 30 cm equivalent water height are detected. Further south, signals are mostly intermittent and noisy. It is shown that the models simulate consistent patterns of bottom pressure variability on monthly and longer scales except for areas with high mesoscale eddy activity, where high resolution is needed to capture the variability due to eddies. Furthermore, despite good agreement in the amplitude of variability, the in situ and simulated OBP show only modest correlation.
Secondary Gravity Waves Generated by Breaking Mountain Waves Over Europe
Authors: Heale C. J. , Bossert K. , Vadas S. L. , Hoffmann L. , Dörnbrack A. , Stober G. , Snively J. B. , Jacobi C.
Published: February 2020

A strong mountain wave, observed over Central Europe on 12 January 2016, is simulated in 2D under two fixed background wind conditions representing opposite tidal phases. The aim of the simulation is to investigate the breaking of the mountain wave and subsequent generation of nonprimary waves in the upper atmosphere. The model results show that the mountain wave first breaks as it approaches a mesospheric critical level creating turbulence on horizontal scales of 8–30 km. These turbulence scales couple directly to horizontal secondary waves scales, but those scales are prevented from reaching the thermosphere by the tidal winds, which act like a filter. Initial secondary waves that can reach the thermosphere range from 60 to 120 km in horizontal scale and are influenced by the scales of the horizontal and vertical forcing associated with wave breaking at mountain wave zonal phase width, and horizontal wavelength scales. Large‐scale nonprimary waves dominate over the whole duration of the simulation with horizontal scales of 107–300 km and periods of 11–22 minutes. The thermosphere winds heavily influence the time‐averaged spatial distribution of wave forcing in the thermosphere, which peaks at 150 km altitude and occurs both westward and eastward of the source in the 2 UT background simulation and primarily eastward of the source in the 7 UT background simulation. The forcing amplitude is
2
that of the primary mountain wave breaking and dissipation. This suggests that nonprimary waves play a significant role in gravity waves dynamics and improved understanding of the thermospheric winds is crucial to understanding their forcing distribution.
A Model for Turbulence Spectra in the Equilibrium Range of the Stable Atmospheric Boundary Layer
Authors: Cheng Yu , Li Qi , Argentini Stefania , Sayde Chadi , Gentine Pierre
Published: February 2020

Stratification can cause turbulence spectra to deviate from Kolmogorov's isotropic
power law scaling in the universal equilibrium range at high Reynolds numbers. However, a consensus has not been reached with regard to the exact shape of the spectra. Here we propose a shape of the turbulent kinetic energy and temperature spectra in horizontal wavenumber for the equilibrium range that consists of three regimes at small Froude number: the buoyancy subrange, a transition region, and the isotropic inertial subrange through dimensional analysis and substantial revision of previous theoretical approximation. These spectral regimes are confirmed by various observations in the atmospheric boundary layer. The representation of the transition region in direct numerical simulations will require large‐scale separation between the Dougherty‐Ozmidov scale and the Kolmogorov scale for strongly stratified turbulence at high Reynolds numbers, which is still challenging computationally. In addition, we suggest that the failure of Monin‐Obukhov similarity theory in the very stable atmospheric boundary layer is due to the fact that it does not consider the buoyancy scale that characterizes the transition region.
Impact of Flow Alteration and Temperature Variability on Hyporheic Exchange
Authors: Wu Liwen , Gomez‐Velez Jesus D. , Krause Stefan , Singh Tanu , Wörman Anders , Lewandowski Jörg
Published: February 2020

Coupled groundwater flow and heat transport within hyporheic zones extensively affect water, energy, and solute exchange with surrounding sediments. The local and cumulative implications of this tightly coupled process strongly depend on characteristics of drivers (i.e., discharge and temperature of the water column) and modulators (i.e., hydraulic and thermal properties of the sediment). With this in mind, we perform a systematic numerical analysis of hyporheic responses to understand how the temporal variability of river discharge and temperature affect flow and heat transport within hyporheic zones. We identify typical time series of river discharge and temperature from gauging stations along the headwater region of Mississippi River Basin, which are characterized by different degrees of flow alteration, to drive a physics‐based model of the hyporheic exchange process. Our modeling results indicate that coupled groundwater flow and heat transport significantly affects the dynamic response of hyporheic zones, resulting in substantial differences in exchange rates and characteristic time scales of hyporheic exchange processes. We also find that the hyporheic zone dampens river temperature fluctuations increasingly with higher frequency of temperature fluctuations. This dampening effect depends on the system transport time scale and characteristics of river discharge and temperature variability. Furthermore, our results reveal that the flow alteration reduces the potential of hyporheic zones to act as a temperature buffer and hinders denitrification within hyporheic zones. These results have significant implications for understanding the drivers of local variability in hyporheic exchange and the implications for the development of thermal refugia and ecosystem functioning in hyporheic zones.
Spin-preserving chiral photonic crystal mirror
Authors: Semnani Behrooz , Flannery Jeremy , Al Maruf Rubayet , Bajcsy Michal
Published: February 2020

Chirality refers to a geometric phenomenon in which objects are not superimposable on their mirror image. Structures made of nanoscale chiral elements can exhibit chiroptical effects, such as dichroism for left- and right-handed circularly polarized light, which makes these structures highly suitable for applications ranging from quantum information processing and quantum optics to circular dichroism spectroscopy and molecular recognition. At the same time, strong chiroptical effects have been challenging to achieve even in synthetic optical media, and chiroptical effects for light with normal incidence have been speculated to be prohibited in thin, lossless quasi-two-dimensional structures. Here, we report an experimental realization of a giant chiroptical effect in a thin monolithic photonic crystal mirror. Unlike conventional mirrors, our mirror selectively reflects only one spin state of light while preserving its handedness, with a near-unity level of circular dichroism. The operational principle of the photonic crystal mirror relies on guided-mode resonance (GMR) with a simultaneous excitation of leaky transverse electric (TE-like) and transverse magnetic (TM-like) Bloch modes in the photonic crystal slab. Such modes are not reliant on the suppression of radiative losses through long-range destructive interference, and even small areas of the photonic crystal exhibit robust circular dichroism. Despite its simplicity, the mirror strongly outperforms earlier reported structures and, contrary to a prevailing notion, demonstrates that near-unity reflectivity contrast for opposite helicities is achievable in a quasi-two-dimensional structure.
Loss of RE-1 silencing transcription factor accelerates exocrine damage from pancreatic injury
Authors: Bray Julie K. , Elgamal Ola A. , Jiang Jinmai , Wright Lais S. , Sutaria Dhruvitkumar S. , Badawi Mohamed , Borcyk Madeline G. , Liu Xiuli , Fredenburg Kristianna M. , Campbell-Thompson Martha L. , Schmittgen Thomas D.
Published: February 2020

Regulation of pancreas plasticity is critical for preventing injury and promoting regeneration upon tissue damage. The intricate process of pancreatic differentiation is governed by an orchestrated network of positive and negative transcription factors for appropriate gene expression. While the transcriptional repressor REST is well characterized as a silencer of neuronal genes in non-neuronal cells, the role of REST in regulating exocrine pancreas cell identity remains largely unexplored. Rest expression is increased upon injury in the mouse pancreas, such as induced acute and chronic pancreatitis and ductal adenocarcinoma. At the cellular level, Rest expression is lower in mature acinar cells compared with pancreas progenitor and ductal cells. To investigate the role of REST activity in pancreatic transdifferentiation and homeostasis, we developed a novel mouse model (Cre/RESTfl/fl) with conditional knockout (KO) of Rest expression within pancreas cells. The high Cre-mediated excision efficiency of Rest exon two KO caused decreased Rest expression and activity within the pancreas. Short-term organoid cultures of pancreatic acini to undergo acinar-to-ductal metaplasia (ADM) showed that loss of REST impedes induced ADM, while overexpression of REST increases ADM. Interestingly, REST ablation accelerated acute pancreatitis in mice treated with the cholecystokinin analog caerulein, as indicated by cellular morphology, elevated serum amylase levels and pancreatic edema. Furthermore, Cre/RESTfl/fl mice were more sensitive to acute pancreatitis injury and displayed augmented tissue damage and cellular lesions. These results suggest REST has a novel protective role against pancreatic tissue damage by acting as a regulator of exocrine cell identity.
ID1 confers cancer cell chemoresistance through STAT3/ATF6-mediated induction of autophagy
Authors: Meng Jiao , Liu Kaiyi , Shao Yang , Feng Xu , Ji Zhaodong , Chang Bin , Wang Yan , Xu Ling , Yang Gong
Published: February 2020

Chemoresistance is one of the major reasons leading to ovarian cancer high mortality and poor survival. Studies have shown that the alteration of cellular autophagy is associated with cancer cell chemoresistance. Here, we investigated whether the ovarian cancer chemoresistance is associated with the autophagy induced by the inhibitor of DNA binding 1 (ID1). By using gene overexpression or silencing, luciferase assay and human specimens, we show that ID1 induces high autophagy and confers cancer cell chemoresistance. The mechanistic study demonstrates that ID1 first activates the NF-κB signaling through facilitating the nuclear translocation of NF-κB p65, which strengthens the expression and secretion of IL-6 from cancer cells to subsequently activate the signal transducer and activator of transcription 3 (STAT3) through the protein phosphorylation at Y705. We further identified that STAT3 functions to promote the transcription of the activating transcription factor 6 (ATF6), which induces endoplasmic reticulum stress to promote cellular autophagy, granting cancer cell resistance to both cisplatin and paclitaxel treatment. Moreover, we found a significant correlation between the expression of ID1 and ATF6 in 1104 high grade serous ovarian cancer tissues, and that patients with the high expression of ID1 or ATF6 were resistant to platinum treatment and had the poor overall survival and progression-free survival. Thus, we have uncovered a mechanism in which ID1 confers cancer cell chemoresistance largely through the STAT3/ATF6-induced autophagy. The involved molecules, including ID1, STAT3, and ATF6, may have a potential to be targeted in combination with chemotherapeutic agents to improve ovarian cancer survival.
Rapid morphological divergence following a human-mediated introduction: the role of drift and directional selection
Authors: Sendell-Price Ashley T. , Ruegg Kristen C. , Clegg Sonya. M.
Published: February 2020

Theory predicts that when populations are established by few individuals, random founder effects can facilitate rapid phenotypic divergence even in the absence of selective processes. However, empirical evidence from historically documented colonisations suggest that, in most cases, drift alone is not sufficient to explain the rate of morphological divergence. Here, using the human-mediated introduction of the silvereye (Zosterops lateralis) to French Polynesia, which represents a potentially extreme example of population founding, we reassess the potential for morphological shifts to arise via drift alone. Despite only 80 years of separation from their New Zealand ancestors, French Polynesian silvereyes displayed significant changes in body and bill size and shape, most of which could be accounted for by drift, without the need to invoke selection. However, signatures of selection at genes previously identified as candidates for bill size and body shape differences in a range of bird species, also suggests a role for selective processes in driving morphological shifts within this population. Twenty-four SNPs in our RAD-Seq dataset were also found to be strongly associated with phenotypic variation. Hence, even under population founding extremes, when it is difficult to reject drift as the sole mechanism based on rate tests of phenotypic shifts, the additional role of divergent natural selection in novel environments can be revealed at the level of the genome.
Impact of two of the world's largest protected areas on longline fishery catch rates
Authors: Lynham John , Nikolaev Anton , Raynor Jennifer , Vilela Thaís , Villaseñor-Derbez Juan Carlos
Published: February 2020

Two of the largest protected areas on earth are U.S. National Monuments in the Pacific Ocean. Numerous claims have been made about the impacts of these protected areas on the fishing industry, but there has been no ex post empirical evaluation of their effects. We use administrative data documenting individual fishing events to evaluate the economic impact of the expansion of these two monuments on the Hawaii longline fishing fleet. Surprisingly, catch and catch-per-unit-effort are higher since the expansions began. To disentangle the causal effect of the expansions from confounding factors, we use unaffected control fisheries to perform a difference-in-differences analysis. We find that the monument expansions had little, if any, negative impacts on the fishing industry, corroborating ecological models that have predicted minimal impacts from closing large parts of the Pacific Ocean to fishing.
Migration, hotspots, and dispersal of HIV infection in Rakai, Uganda
Authors: Kate Grabowski Mary , Lessler Justin , Bazaale Jeremiah , Nabukalu Dorean , Nankinga Justine , Nantume Betty , Ssekasanvu Joseph , Reynolds Steven J. , Ssekubugu Robert , Nalugoda Fred , Kigozi Godfrey , Kagaayi Joseph , Santelli John S. , Kennedy Caitlin , Wawer Maria J. , Serwadda David , Chang Larry W. , Gray Ronald H.
Published: February 2020

HIV prevalence varies markedly throughout Africa, and it is often presumed areas of higher HIV prevalence (i.e., hotspots) serve as sources of infection to neighboring areas of lower prevalence. However, the small-scale geography of migration networks and movement of HIV-positive individuals between communities is poorly understood. Here, we use population-based data from ~22,000 persons of known HIV status to characterize migratory patterns and their relationship to HIV among 38 communities in Rakai, Uganda with HIV prevalence ranging from 9 to 43%. We find that migrants moving into hotspots had significantly higher HIV prevalence than migrants moving elsewhere, but out-migration from hotspots was geographically dispersed, contributing minimally to HIV burden in destination locations. Our results challenge the assumption that high prevalence hotspots are drivers of transmission in regional epidemics, instead suggesting that migrants with high HIV prevalence, particularly women, selectively migrate to these areas.
Author Correction: Genomic risk score offers predictive performance comparable to clinical risk factors for ischaemic stroke
Authors: Abraham Gad , Malik Rainer , Yonova-Doing Ekaterina , Salim Agus , Wang Tingting , Danesh John , Butterworth Adam S. , Howson Joanna M. M. , Inouye Michael , Dichgans Martin
Published: February 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Impaired mitophagy links mitochondrial disease to epithelial stress in methylmalonyl-CoA mutase deficiency
Authors: Luciani Alessandro , Schumann Anke , Berquez Marine , Chen Zhiyong , Nieri Daniela , Failli Mario , Debaix Huguette , Festa Beatrice Paola , Tokonami Natsuko , Raimondi Andrea , Cremonesi Alessio , Carrella Diego , Forny Patrick , Kölker Stefan , Diomedi Camassei Francesca , Diaz Francisca , Moraes Carlos T. , Di Bernardo Diego , Baumgartner Matthias R. , Devuyst Olivier
Published: February 2020

Deregulation of mitochondrial network in terminally differentiated cells contributes to a broad spectrum of disorders. Methylmalonic acidemia (MMA) is one of the most common inherited metabolic disorders, due to deficiency of the mitochondrial methylmalonyl-coenzyme A mutase (MMUT). HowMMUTdeficiency triggers cell damage remains unknown, preventing the development of disease–modifying therapies. Here we combine genetic and pharmacological approaches to demonstrate thatMMUTdeficiency induces metabolic and mitochondrial alterations that are exacerbated by anomalies in PINK1/Parkin–mediated mitophagy, causing the accumulation of dysfunctional mitochondria that trigger epithelial stress and ultimately cell damage. Using drug–disease network perturbation modelling, we predict targetable pathways, whose modulation repairs mitochondrial dysfunctions in patient–derived cells and alleviate phenotype changes inmmut–deficient zebrafish. These results suggest a link between primaryMMUTdeficiency, diseased mitochondria, mitophagy dysfunction and epithelial stress, and provide potential therapeutic perspectives for MMA.
Continuous-wave quantum dot photonic crystal lasers grown on on-axis Si (001)
Authors: Zhou Taojie , Tang Mingchu , Xiang Guohong , Xiang Boyuan , Hark Suikong , Martin Mickael , Baron Thierry , Pan Shujie , Park Jae-Seong , Liu Zizhuo , Chen Siming , Zhang Zhaoyu , Liu Huiyun
Published: February 2020

Semiconductor III–V photonic crystal (PC) laser is regarded as a promising ultra-compact light source with unique advantages of ultralow energy consumption and small footprint for the next generation of Si-based on-chip optical interconnects. However, the significant material dissimilarities between III-V materials and Si are the fundamental roadblock for conventional monolithic III-V-on-silicon integration technology. Here, we demonstrate ultrasmall III-V PC membrane lasers monolithically grown on CMOS-compatible on-axis Si (001) substrates by using III-V quantum dots. The optically pumped InAs/GaAs quantum-dot PC lasers exhibit single-mode operation with an ultra-low threshold of ~0.6 μW and a large spontaneous emission coupling efficiency up to 18% under continuous-wave condition at room temperature. This work establishes a new route to form the basis of future monolithic light sources for high-density optical interconnects in future large-scale silicon electronic and photonic integrated circuits.
A global assessment of the drivers of threatened terrestrial species richness
Authors: Howard Christine , Flather Curtis H. , Stephens Philip A.
Published: February 2020

High numbers of threatened species might be expected to occur where overall species richness is also high; however, this explains only a proportion of the global variation in threatened species richness. Understanding why many areas have more or fewer threatened species than would be expected given their species richness, and whether that is consistent across taxa, is essential for identifying global conservation priorities. Here, we show that, after controlling for species richness, environmental factors, such as temperature and insularity, are typically more important than human impacts for explaining spatial variation in global threatened species richness. Human impacts, nevertheless, have an important role, with relationships varying between vertebrate groups and zoogeographic regions. Understanding this variation provides a framework for establishing global conservation priorities, identifying those regions where species are inherently more vulnerable to the effects of threatening human processes, and forecasting how threatened species might be distributed in a changing world.
Genome of Tripterygium wilfordii and identification of cytochrome P450 involved in triptolide biosynthesis
Authors: Tu Lichan , Su Ping , Zhang Zhongren , Gao Linhui , Wang Jiadian , Hu Tianyuan , Zhou Jiawei , Zhang Yifeng , Zhao Yujun , Liu Yuan , Song Yadi , Tong Yuru , Lu Yun , Yang Jian , Xu Cao , Jia Meirong , Peters Reuben J. , Huang Luqi , Gao Wei
Published: February 2020

Triptolide is a trace natural product of Tripterygium wilfordii. It has antitumor activities, particularly against pancreatic cancer cells. Identification of genes and elucidation of the biosynthetic pathway leading to triptolide are the prerequisite for heterologous bioproduction. Here, we report a reference-grade genome of T. wilfordii with a contig N50 of 4.36 Mb. We show that copy numbers of triptolide biosynthetic pathway genes are impacted by a recent whole-genome triplication event. We further integrate genomic, transcriptomic, and metabolomic data to map a gene-to-metabolite network. This leads to the identification of a cytochrome P450 (CYP728B70) that can catalyze oxidation of a methyl to the acid moiety of dehydroabietic acid in triptolide biosynthesis. We think the genomic resource and the candidate genes reported here set the foundation to fully reveal triptolide biosynthetic pathway and consequently the heterologous bioproduction.
Tracing tumorigenesis in a solid tumor model at single-cell resolution
Authors: Praktiknjo Samantha D. , Obermayer Benedikt , Zhu Qionghua , Fang Liang , Liu Haiyue , Quinn Hazel , Stoeckius Marlon , Kocks Christine , Birchmeier Walter , Rajewsky Nikolaus
Published: February 2020

Characterizing the complex composition of solid tumors is fundamental for understanding tumor initiation, progression and metastasis. While patient-derived samples provide valuable insight, they are heterogeneous on multiple molecular levels, and often originate from advanced tumor stages. Here, we use single-cell transcriptome and epitope profiling together with pathway and lineage analyses to study tumorigenesis from a developmental perspective in a mouse model of salivary gland squamous cell carcinoma. We provide a comprehensive cell atlas and characterize tumor-specific cells. We find that these cells are connected along a reproducible developmental trajectory: initiated in basal cells exhibiting an epithelial-to-mesenchymal transition signature, tumorigenesis proceeds through Wnt-differential cancer stem cell-like subpopulations before differentiating into luminal-like cells. Our work provides unbiased insights into tumor-specific cellular identities in a whole tissue environment, and emphasizes the power of using defined genetic model systems.
Jouvence a small nucleolar RNA required in the gut extends lifespan in Drosophila
Authors: Soulé Stéphanie , Mellottée Lucille , Arab Abdelkrim , Chen Chongjian , Martin Jean-René
Published: February 2020

Longevity is influenced by genetic and environmental factors, but the underlying mechanisms remain elusive. Here, we functionally characterise a Drosophila small nucleolar RNA (snoRNA), named jouvence whose loss of function reduces lifespan. The genomic region of jouvence rescues the longevity in mutant, while its overexpression in wild-type increases lifespan. Jouvence is required in enterocytes. In mutant, the epithelium of the gut presents more hyperplasia, while the overexpression of jouvence prevents it. Molecularly, the mutant lack pseudouridylation on 18S and 28S-rRNA, a function rescued by targeted expression of jouvence in the gut. A transcriptomic analysis performed from the gut reveals that several genes are either up- or down-regulated, while restoring the mRNA level of two genes (ninaD or CG6296) rescue the longevity. Since snoRNAs are structurally and functionally well conserved throughout evolution, we identified putative jouvence orthologue in mammals including humans, suggesting that its function in longevity could be conserved.
Robust temporal pumping in a magneto-mechanical topological insulator
Authors: Grinberg Inbar Hotzen , Lin Mao , Harris Cameron , Benalcazar Wladimir A. , Peterson Christopher W. , Hughes Taylor L. , Bahl Gaurav
Published: February 2020

The transport of energy through 1-dimensional (1D) waveguiding channels can be affected by sub-wavelength disorder, resulting in undesirable localization and backscattering phenomena. However, quantized disorder-resilient transport is observable in the edge currents of 2-dimensional (2D) topological band insulators with broken time-reversal symmetry. Topological pumps are able to reduce this higher-dimensional topological insulator phenomena to lower dimensionality by utilizing a pumping parameter (either space or time) as an artificial dimension. Here we demonstrate a temporal topological pump that produces on-demand, robust transport of mechanical energy using a 1D magneto-mechanical metamaterial. We experimentally demonstrate that the system is uniquely resilient to defects occurring in both space and time. Our findings open a path towards exploration of higher-dimensional topological physics with time as a synthetic dimension.