bluuebunny/crossref_metadata_2025 huggingface dataset:
On standing gravity wave-depression cavity collapse and jetting
Authors: Krishna Raja D. , Das S. P. , Hopfinger E. J.
Published: March 2019

Parametrically forced gravity waves can give rise to high-velocity surface jets via the wave-depression cavity implosion. The present results have been obtained in circular cylindrical containers of 10 and 15 cm in diameter (Bond number of order $10^{3}$) in the large fluid depth limit. First, the phase diagrams of instability threshold and wave breaking conditions are determined for the working fluid used, here water with 1 % detergent added. The collapse of the wave-depression cavity is found to be self-similar. The exponent $\unicode[STIX]{x1D6FC}$ of the variation of the cavity radius $r_{m}$ with time $\unicode[STIX]{x1D70F}$, in the form $r_{m}/R\propto \unicode[STIX]{x1D70F}^{\unicode[STIX]{x1D6FC}}$, is close to 0.5, indicative of inertial collapse, followed by a viscous cut-off of $\unicode[STIX]{x1D6FC}\approx 1$. This supports a Froude number scaling of the surface jet velocity caused by cavity collapse. The dimensionless jet velocity scales with the cavity depth that is shown to be proportional to the last stable wave amplitude. It can be expressed by a power law or in terms of finite time singularity related to a singular wave amplitude that sets the transition from a non-pinching to pinch-off cavity collapse scenario. In terms of forcing amplitude, cavity collapse and jetting are found to occur in bands of events of non-pinching and pinching of a bubble at the cavity base. At large forcing amplitudes, incomplete cavity collapse and splashing can occur and, at even larger forcing amplitudes, wave growth is again stable up to the singular wave amplitude. When the cavity is formed, an impulse model shows the importance of the singular cavity diameter that determines the strength of the impulse.
Acoustic oscillations driven by boundary mass exchange
Authors: Offner Avshalom , Yang Rui , Felman Daniel , Elkayam Nimrod , Agnon Yehuda , Ramon Guy Z.
Published: March 2019

Thermoacoustic instability – self-sustained pressure oscillations triggered by temperature gradients – has become an increasingly studied topic in the context of energy conversion. Generally, the process relies on conductive heat transfer between a solid and the fluid in which the generated pressure oscillations are sustained. In the present study, the thermoacoustic theory is extended to include mass transfer; specifically, the working fluid is modified so as to incorporate a ‘reactive’ gas, able to exchange phase with a solid/liquid boundary through a sorption process (or through evaporation/condensation), such that most heat is transferred in the form of latent heat rather than through conduction. A set of differential equations is derived, accounting for phase-exchange heat and mass transfer, and de-coupled via a small-amplitude asymptotic expansion. These equations are solved and subsequently manipulated into the form of a wave equation, representing the small perturbation on the pressure field, and used to derive expressions for the time-averaged, second-order heat and mass fluxes. A stability analysis is performed on the wave equation, from which the marginal stability curve is calculated in terms of the temperature difference, $\unicode[STIX]{x0394}T_{onset}$, required for initiation of self-sustained oscillations. Calculated stability curves are compared with published experimental results, showing good agreement. Effects of gas mixture composition are studied, indicating that a lower heat capacity of the inert component, combined with a low boiling temperature and high latent heat of the reactive component substantially lower $\unicode[STIX]{x0394}T_{onset}$. Furthermore, an increase in the average mole fraction of the reactive gas, $C_{m}$ strongly affects onset conditions, leading to $\unicode[STIX]{x0394}T_{onset}\sim 5\,^{\circ }\text{C}$ at the highest value of $C_{m}$ achievable under atmospheric pressure. An analysis of the system limit cycle is performed for a wide range of parameters, indicating a systematic decrease in the temperature difference capable of sustaining the limit cycle, as well as a significant distortion of the acoustic wave form as the phase-exchange mechanism becomes dominant. These findings, combined, reveal the underlying mechanisms by which a phase-exchange engine may produce more acoustic power than its counterpart ‘classical’ thermoacoustic system, while its temperature difference is substantially lower.
A theoretical framework for investigating the context for creating employment success in information technology for individuals with autism
Authors: Annabi Hala , Locke Jill
Published: March 2019

There is limited research that addresses the inclusion of individuals with autism in the workforce. Autism employment in information technology (IT) is a new phenomenon and there is no established theory to draw from to investigate this phenomenon. In this paper, we review the existing literature on autism employment and present a theoretical framework to study information technology workplace readiness to equitably include individuals with autism. Our proposed framework extends Annabi and Lebovitz’s organizational interventions mitigating individual barriers theoretical framework to include Ajzen’s Theory of Planned Behavior constructs. The framework will contribute to advancing the knowledge and understanding of the needs of individuals with autism, the knowledge and attitudes of neurotypical information technology employees, and organization and employment characteristics. Ultimately, this work will lead to discoveries that broaden participation of individuals with autism in the information technology industry and beyond.
Dietary determinants of hepatic fat content and insulin resistance in overweight/obese children: a cross-sectional analysis of the Prevention of Diabetes in Kids (PREDIKID) study
Authors: Arenaza Lide , Medrano María , Oses Maddi , Huybrechts Inge , Díez Ignacio , Henriksson Hanna , Labayen Idoia
Published: March 2019

Paediatric non-alcoholic fatty liver disease has increased in parallel with childhood obesity. Dietary habits, particularly products rich in sugars, may influence both hepatic fat and insulin resistance (homeostatic model assessment for insulin resistance (HOMA-IR)). The aim of the study was to examine the association of the consumption of foods and food components, dairy desserts and substitutes (DDS), sugar-sweetened beverages (SSB), as well as total and added sugars, with hepatic fat and HOMA-IR. Dietary intake (two non-consecutive 24 h-recalls), hepatic fat (MRI) and HOMA-IR were assessed in 110 overweight/obese children (10·6 (sd 1·1) years old). Linear regression analyses were used to examine the association of dietary intake with hepatic fat and HOMA-IR adjusted for potential confounders (sex, age, energy intake, maternal educational level, total and abdominal adiposity and sugar intake). The results showed that there was a negative association between cereal intake and hepatic fat (β=–0·197, P<0·05). In contrast, both SSB consumption (β=0·217; P=0·028) and sugar in SSB (β=0·210, P=0·035), but not DDS or sugar in DDS or other dietary components, were positively associated with hepatic fat regardless of potential confounders including total sugar intake. In conclusion, cereal intake might decrease hepatic fat, whereas SSB consumption and its sugar content may increase the likelihood of having hepatic steatosis. Although these observations need to be confirmed using experimental evidence, these results suggest that healthy lifestyle intervention programs are needed to improve dietary habits as well as to increase the awareness of the detrimental effects of SSB consumption early in life.
Associations of calcium and dairy product intakes with all-cause, all-cancer, colorectal cancer and CHD mortality among older women in the Iowa Women’s Health Study
Authors: Um Caroline Y. , Prizment Anna , Hong Ching-Ping , Lazovich DeAnn , Bostick Roberd M.
Published: March 2019

Ca and dairy product intakes may be inversely associated with all-cause and cause-specific mortality, and non-Ca components of dairy products, such as insulin-like growth factor-1, may be independently associated with mortality. We investigated associations of Ca and dairy product intakes with all-cause, all-cancer, colorectal cancer (CRC) and CHD mortality among 35 221 55- to 69-year-old women in the prospective Iowa Women’s Health Study, who were cancer-free in 1986. We assessed diet using a Willett FFQ, and associations using multivariable Cox proportional hazards regression. We estimated residuals from linear regression models of dairy products with dietary Ca to investigate total and specific dairy products independent of their Ca content. Through 2012, 18 687 participants died, including 4665 from cancer (including 574 from CRC) and 3603 from CHD. For those in the highest relative to the lowest quintiles of intake, the multivariable-adjusted hazard ratios (HR) and 95 % CI for total Ca (dietary plus supplemental) were 0·88 (0·83, 0·93; P trend=0·001) for all-cause mortality, 0·91 (0·81, 1·02; P trend=0·34) for all-cancer mortality, 0·60 (0·43, 0·83; P trend=0·002) for CRC mortality and 0·73 (0·64, 0·83; P trend <0·0001) for CHD mortality. The corresponding HR for associations of whole milk, whole milk residuals, and low-/non-fat milk residuals with all-cause mortality were 1·20 (95 % CI 1·13, 1·27), 1·20 (95 % CI 1·13, 1·28) and 0·91 (95 % CI 0·86, 0·96), respectively. These results suggest that Ca may be associated with lower risk of all-cause, CRC and CHD mortality, and that non-Ca components of milk may be independently associated with mortality.
Dietary α-lactalbumin alters energy balance, gut microbiota composition and intestinal nutrient transporter expression in high-fat diet-fed mice
Authors: Boscaini Serena , Cabrera-Rubio Raul , Speakman John R. , Cotter Paul D. , Cryan John F. , Nilaweera Kanishka N.
Published: March 2019

Recently there has been a considerable rise in the frequency of metabolic diseases, such as obesity, due to changes in lifestyle and resultant imbalances between energy intake and expenditure. Whey proteins are considered as potentially important components of a dietary solution to the obesity problem. However, the roles of individual whey proteins in energy balance remain poorly understood. This study investigated the effects of a high-fat diet (HFD) containing α-lactalbumin (LAB), a specific whey protein, or the non-whey protein casein (CAS), on energy balance, nutrient transporters expression and enteric microbial populations. C57BL/6J mice (n 8) were given an HFD containing either 20 % CAS or LAB as protein sources or a low-fat diet containing CAS for 10 weeks. HFD-LAB-fed mice showed a significant increase in cumulative energy intake (P=0·043), without differences in body weight, energy expenditure, locomotor activity, RER or subcutaneous and epididymal white adipose tissue weight. HFD-LAB intake led to a decrease in the expression of glut2 in the ileum (P=0·05) and in the fatty acid transporter cd36 (P<0·001) in both ileum and jejunum. This suggests a reduction in absorption efficiency within the small intestine in the HFD-LAB group. DNA from faecal samples was used for 16S rRNA-based assessment of intestinal microbiota populations; the genera Lactobacillus, Parabacteroides and Bifidobacterium were present in significantly higher proportions in the HFD-LAB group. These data indicate a possible functional relationship between gut microbiota, intestinal nutrient transporters and energy balance, with no impact on weight gain.
Do policy instruments matter? Governments’ choice of policy mix and higher education performance in Western Europe
Authors: Capano Giliberto , Pritoni Andrea , Vicentini Giulia
Published: March 2019

Governments pursue their goals by adopting various mixes of policy instruments. This article proposes a specific operationalisation of these mixes and applies it to the analysis of reforms that many Western European governments have pursued, as they have adopted a similar policy design in their higher education systems (HESs) over the last 20 years. In fact, although these policies have similar templates, performance indicators exhibit remarkable variation between countries. Thus, by applying Qualitative Comparative Analysis to a large data set containing all changes in policy instruments undertaken in the last 20 years in 12 HESs in Western Europe, this article explores the possibility that differences in performance across national HESs could be associated –ceteris paribus– with different policy mixes. This article finds not only that the common template has been applied through very different national policy mixes but also that only a few instruments are regularly linked to good teaching performance, regardless of the other components of the actual policy mix.
ROBUST INFERENCE IN STRUCTURAL VECTOR AUTOREGRESSIONS WITH LONG-RUN RESTRICTIONS
Authors: Chevillon Guillaume , Mavroeidis Sophocles , Zhan Zhaoguo
Published: March 2019

Long-run restrictions are a very popular method for identifying structural vector autoregressions, but they suffer from weak identification when the data is very persistent, i.e., when the highest autoregressive roots are near unity. Near unit roots introduce additional nuisance parameters and make standard weak-instrument-robust methods of inference inapplicable. We develop a method of inference that is robust to both weak identification and strong persistence. The method is based on a combination of the Anderson-Rubin test with instruments derived by filtering potentially nonstationary variables to make them near stationary using the IVX instrumentation method of Magdalinos and Phillips (2009). We apply our method to obtain robust confidence bands on impulse responses in two leading applications in the literature.
Characterizing the social diversity of bilingualism using language entropy
Authors: Gullifer Jason W. , Titone Debra
Published: March 2019

Bilingual and multilingual individuals exhibit variation in everyday language experience. Studies on bilingualism account for individual differences with measures such as L2 age of acquisition, exposure, or language proficiency, but recent theoretical perspectives posit that the relative balance between the two or more languages throughout daily life (i.e.,interactional context) is a crucial determinant for language representation, access, and control. We propose an innovative measure to characterize this construct by usingentropyto estimate the social diversity of language use. Language entropy is computed from commonly-collected language history data and generalizes to multilingual communicative contexts. We show how language entropy relates to other indices of bilingual experience and that it predicts self-report L2 outcome measures over and above classic measures of language experience. Thus, we proffer language entropy as a means to characterize individual differences in bilingual (and multilingual) language experience related to the social diversity of language use.
A systematic review of food pantry-based interventions in the USA
Authors: An Ruopeng , Wang Junjie , Liu Junyi , Shen Jing , Loehmer Emily , McCaffrey Jennifer
Published: March 2019

Objective

Food pantries play a critical role in combating food insecurity. The objective of the present work was to systematically review and synthesize scientific evidence regarding the effectiveness of food pantry-based interventions in the USA.

Design

Keyword/reference search was conducted in PubMed, Web of Science, Scopus, Cochrane Library and CINAHL for peer-reviewed articles published until May 2018 that met the following criteria. Setting: food pantry and/or food bank in the USA; study design: randomized controlled trial (RCT) or pre–post study; outcomes: diet-related outcomes (e.g. nutrition knowledge, food choice, food security, diet quality); study subjects: food pantry/bank clients.

Results

Fourteen articles evaluating twelve distinct interventions identified from the keyword/reference search met the eligibility criteria and were included in the review. Five were RCT and the remaining seven were pre–post studies. All studies found that food pantry-based interventions were effective in improving participants’ diet-related outcomes. In particular, the nutrition education interventions and the client-choice intervention enhanced participants’ nutrition knowledge, cooking skills, food security status and fresh produce intake. The food display intervention helped pantry clients select healthier food items. The diabetes management intervention reduced participants’ glycaemic level.

Conclusions

Food pantry-based interventions were found to be effective in improving participants’ diet-related outcomes. Interventions were modest in scale and usually short in follow-up duration. Future studies are warranted to address the challenges of conducting interventions in food pantries, such as shortage in personnel and resources, to ensure intervention sustainability and long-term effectiveness.
Association between extrauterine growth restriction and changes of intestinal flora in Chinese preterm infants
Authors: Zhang J. , Dai Y. , Fan S. , Zhang K. , Shuai C. , Bian X. , Hui L. , Wu Z. , Zhang J. , Guo Z. , Deng F. , Guo M.
Published: March 2019

The aim of the study was to investigate any association between extrauterine growth restriction (EUGR) and intestinal flora of <30-week-old preterm infants. A total of 59 preterm infants were assigned to EUGR (n=23) and non-EUGR (n=36) groups. Intestinal bacteria were compared by using high-throughput sequencing of bacterial rRNA. The total abundance of bacteria in 344 genera (7568v.13,760;P<0.0001) and 456 species (10,032v.18,240;P<0.0001) was significantly decreased in the EUGR group compared with the non-EUGR group. After application of a multivariate logistic model and adjusting for potential confounding factors, as well as false-discovery rate corrections, we found four bacterial genera with higher and one bacterial genus with lower abundance in the EUGR group compared with the control group. In addition, the EUGR group showed significantly increased abundances of six species (Streptococcus parasanguinis,BacteriumRB5FF6, twoKlebsiellaspecies andMicrobacterium), but decreased frequencies of three species (oneAcinetobacterspecies,Endosymbiont_of_Sphenophorus_levand oneEnterobacter_species) compared with the non-EUGR group. Taken together, there were significant changes in the intestinal microflora of preterm infants with EUGR compared to preterm infants without EUGR.
The Functional Ability of MCI and Alzheimer’s Patients	Predicts Caregiver Burden
Authors: Lara-Ruiz Jose , Kauzor Kaitlyn , Gonzalez Katie , Nakhla Marina Z. , Banuelos Dayana , Woo Ellen , Apostolova Liana G. , Razani Jill
Published: March 2019

Abstract. Research shows that caregivers of dementia patients experience burden and psychological distress, but it is unclear whether or not caregivers of individuals with cognitive impairments that do not meet a diagnosis for dementia also experience similar burdens and psychological problems. Sixty patients and their caregivers participated in this study designed to examine caregiver burden. The patients completed activities-of-daily-living tasks and several neuropsychological tests assessing memory, abstract reasoning, and language. Caregivers completed self-report measures assessing caregiver burden and psychological distress. Results revealed that the caregivers of patients with mild Alzheimer’s disease (mAD) reported greater physical burden and feelings of missing out on life compared to individuals with mild cognitive impairment (MCI) caregivers. The mAD caregivers indicated greater depression and anxiety relative to MCI caregivers. Stepwise regression found that patient neuropsychological scores were worse predictors of caregiver burden than patients’ daily functioning. The conclusions of this study suggest that (1) caregivers of mAD are likely to experience more severe types of burden and psychological distress relative to caregivers of MCI patients, and that (2) patients’ daily functional abilities better predict caregivers’ burden and psychological distress than patients’ neuropsychological functioning. Study findings suggest that caregivers of those in the early stages of dementia, even in persons not yet meeting a diagnosis, experience psychological symptoms and burden, and that these caregivers’ experiences can be best predicted by the patients daily functional ability than by patients’ neuropsychological test scores.
The Formation of a Dry‐Belt in the North Side of Central Himalaya Mountains
Authors: Wang Yan , Yang Kun , Zhou Xu , Wang Binbin , Chen Deliang , Lu Hui , Lin Changgui , Zhang Fuqing
Published: March 2019

South Asian monsoon crosses the Himalayan Mountains (HMs) and brings moisture for precipitations in the South Tibetan Plateau. A distinct dry‐belt was found in the north of the central HM region, where there are the highest and steepest mountains in the world. Through in situ and remote‐sensing observations and convection‐permitting numerical experiments, the current study demonstrates that the formation of the dry‐belt is mainly due to the depletion of water vapor when the monsoonal flow climbs the steep south slope of the HMs. The foehn phenomenon is notable over the north slope of the HMs, but the hot and dry downslope flow does not significantly reduce the amount of the precipitation; instead, it can delay the peak of the diurnal precipitation in the north side of the HMs.
A Measurement‐Model Fusion Approach for Improved Wet Deposition Maps and Trends
Authors: Zhang Yuqiang , Foley Kristen M. , Schwede Donna B. , Bash Jesse O. , Pinto Joseph P. , Dennis Robin L.
Published: March 2019

Air quality models provide spatial fields of wet deposition (WD) and dry deposition that explicitly account for the transport and transformation of emissions from thousands of sources. However, many sources of uncertainty in the air quality model including errors in emissions and meteorological inputs (particularly precipitation) and incomplete descriptions of the chemical and physical processes governing deposition can lead to bias and error in the simulation of WD. We present an approach to bias correct Community Multiscale Air Quality model output over the contiguous United States using observation‐based gridded precipitation data generated by the Parameter‐elevation Regressions on Independent Slopes Model and WD observations at the National Atmospheric Deposition Program National Trends Network sites. A cross‐validation analysis shows that the adjusted annual accumulated WD for NO3−, NH4+, and SO42− from 2002 to 2012 has less bias and higher correlation with observed values than the base model output without adjustment. Temporal trends in observed WD are captured well by the adjusted model simulations across the entire contiguous United States. Consistent with previous trend analyses, WD NO3− and SO42− are shown to decrease during this period in the eastern half of the United States, particularly in the Northeast, while remaining nearly constant in the West. Trends in WD of NH4+ are more spatially and temporally heterogeneous, with some positive trends in the Great Plains and Central Valley of CA and slightly negative trends in the south.
Impact of Assimilating Himawari‐8‐Derived Layered Precipitable Water With Varying Cumulus and Microphysics Parameterization Schemes on the Simulation of Typhoon Hato
Authors: Lu Jiazheng , Feng Tao , Li Jun , Cai Zelin , Xu Xunjian , Li Li , Li Jinlong
Published: March 2019

Understanding moisture information ahead of tropical cyclone (TC) convection is very important for predicting TC track, intensity, and precipitation. The advanced Himawari imager onboard the Japanese Himawari‐8/‐9 satellite can provide high spatial and temporal resolution moisture information. Three‐layered precipitable water (LPW) with its three water vapor absorption infrared bands can be assimilated to generate better understanding and prediction of TC evolution. The impacts of LPW assimilation in the Weather Research and Forecasting model with nine combinations of physical parameterization schemes, including three cumulus parameterization (CP) and three microphysics parameterization (MP) schemes on TC prediction, have been comprehensively analyzed using Typhoon Hato as a case study. The results indicate that LPW assimilation reduces the average track error and speed up TC movement by better adjustment of the atmospheric circulation fields via changing the vertical structure of moisture and thermal profile. The track forecasts retain sensitivity to CP schemes after LPW assimilation. Also, LPW assimilation improves TC intensity prediction because the latent heat release process is accurately adjusted. It has been revealed that LPW assimilation can weaken the intensity sensitivity to MP schemes more than to CP schemes. Skill scores were used to evaluate precipitation forecasts after Hato's landfall. The results indicate that heavy precipitation forecasts are more sensitive to the choice of MP schemes. After LPW assimilation, the equitable threat scores among different results become similar and all forecast skills are increased. In addition, group statistic results with different initial time show the same conclusions.
Broadband Characteristics of Chaotic Pulse Trains Associated With Sequential Dart Leaders in a Rocket‐Triggered Lightning Flash
Authors: Pu Yunjiao , Qie Xiushu , Jiang Rubin , Sun Zhuling , Liu Mingyuan , Zhang Hongbo
Published: March 2019

Based on simultaneous measurements of fast E‐field change, very high frequency radiation and channel mapping, channel base current, and high‐speed video, the characteristics of chaotic pulse trains (CPTs) during propagation of dart leaders in a rocket‐triggered lightning were analyzed. The triggered lightning involved 16 subsequent leader‐return strokes traversing in the same grounding channel. At least five dart leaders showed significant CPT signals during its propagation, with much larger intensity than that in normal leader stage at broadband of low‐frequency–medium‐frequency, very high frequency, and visible light band. All CPTs occurred in the final stage of the leader development, within 150 μs prior to the return strokes. The leader velocity and the charge transfer are both related to the instantaneous intensity of CPT, but the relationship is not always solid when the two parameters are considered individually. Nevertheless, the large product of return stroke charge to 1 ms and the velocity of the leader (QV) could be a reliable proxy/indicator for CPT. All CPTs correspond to a larger local QV with a threshold higher than 1 × 107 C · m/s when CPT is determined as chaotic electric field pulses with magnitude larger than 3 std of the magnitude of E‐fluctuation waveform of the whole flash.
Linking the North American Dipole to the Pacific Meridional Mode
Authors: Ding Ruiqiang , Li Jianping , Tseng Yu‐heng , Sun Cheng , Li Yang , Xing Nan , Li Xiaofeng
Published: March 2019

The North American dipole (NAD) represents a meridional dipole of sea level pressure anomalies over the western tropical North Atlantic and northeastern North America. This study demonstrates that the NAD is intimately linked to the development of the Pacific meridional mode (PMM). In addition to the North Pacific Oscillation, the NAD provides another important remote forcing source to trigger the PMM. The NAD influences the PMM through both direct and indirect pathways. The direct effect is that the winter NAD influences the sea surface temperature (SST) and surface winds over the northeastern subtropical Pacific (NESP) through concurrent anticyclonic flow associated with the NAD, which tends to generate a weak initial warming over the NESP region during late winter and early spring. The indirect effect is that the NAD first induces SST cooling over the northern tropical Atlantic during spring, and the northern tropical Atlantic SST cooling then generates a low‐level anticyclonic flow anomaly over the NESP, which further strengthens the surface warming over the NESP, thereby causing the development of the PMM in the following months. The NAD can also exert an influence on the El Niño–Southern Oscillation through its effects on the PMM. In particular, El Niño episodes led by the combined NAD‐PMM events tend to take the form of the central Pacific El Niño, rather than the canonical eastern Pacific El Niño. We suggest that a better understanding of the NAD‐PMM‐El Niño–Southern Oscillation dynamic link could be useful for the prediction of different types of El Niño event.
Comparing Seawater Temperature Proxy Records for the Past 90 Myrs From the Shallow Shelf Record Bass River, New Jersey
Authors: de Bar M. W. , de Nooijer L. J. , Schouten S. , Ziegler M. , Sluijs A. , Reichart G.‐J.
Published: March 2019

We present a multiproxy (foraminifer Mg/Ca, δ18O, ∆47, and Sr/Ca, and biomarker TEX86H, MATmrs) low‐resolution paleotemperature record based on seven sets of high‐resolution time series from the late Cretaceous to Miocene from the Ocean Drilling Program Bass River site, New Jersey Shelf, North Atlantic. Along with insight into long‐term climate evolution, this allows testing for internal consistency between proxies. The bottom water temperatures (BWTs) reconstructed using benthic δ18O and Mg/Ca values show good agreement in recorded trends with the TEX86Hsea surface and shallow subsurface temperature record, and with the stacked global benthic oxygen isotope record. The Mg/Ca‐based BWTs are higher than the δ18O‐based BWTs, likely due to uncertainty in the assumptions associated with the Mg/Ca calibration to seawater Mg/Ca. Absolute δ18O‐based BWT reconstructions are supported by clumped isotope paleothermometry. The agreement in main trends of the independent paleotemperature proxies indicates that the underlying assumed mechanisms for the different proxy relations to temperature stayed largely intact back to at least 90 Ma. Consistent differences in absolute temperature values highlight, however, that a better understanding of the individual proxies is required in order to achieve accurate absolute temperature reconstructions
The Timing and Style of Oblique Deformation Within New Zealand's Kaikōura Ranges and Marlborough Fault System Based on Low‐Temperature Thermochronology
Authors: Collett C. M. , Duvall A. R. , Flowers R. M. , Tucker G. E. , Upton P.
Published: March 2019

The ~150‐km‐wide dextral Marlborough Fault System and adjacent Kaikōura Mountains accommodate oblique convergence between the Pacific and Australian plates at the NE end of the South Island, New Zealand. Low‐temperature thermochronology from this region places new limits on the timing and style of Marlborough faulting and mountain building. We sampled rocks for apatite and zircon (U‐Th/He) and apatite fission track dating from a range of elevations spanning ~2 km within the Kaikōura Ranges, which stand high above the active Marlborough dextral faults. The data reveal Miocene cooling localized to hanging wall rocks, first along the Clarence Fault in the Inland Kaikōura Range, then along the Jordan Thrust in the Seaward Kaikōura Range, followed by widespread, rapid cooling reflected in all samples across the study area starting at ~5 Ma. Our results suggest that topographic relief in this region predates the onset of dextral faulting and that portions of the Marlborough Faults were once thrust faults that coincided with the early development of the transpressive plate boundary. We relate Pliocene to present rapid exhumation across the field site, including at low‐elevation sample sites in Marlborough Fault foot walls, to seaward translation and overthrusting of crust atop the downgoing slab by dextral Marlborough Fault motion. Our results show that spatial and temporal patterns in exhumation reflect a complex and evolving deformation field in the Marlborough Fault System over the past ~25 million years of Kaikōura orogeny.
Extreme Rainfall Associated With Hurricane Maria Over Puerto Rico and Its Connections to Climate Variability and Change
Authors: Keellings David , Hernández Ayala José J.
Published: March 2019

Hurricane Maria was associated with record‐breaking rainfall over Puerto Rico and caused unprecedented flooding and landslides. Here we analyze the extreme rainfall produced by Hurricane Maria using 35 stations with daily precipitation data from 1956–2016. A covariate‐based extreme value analysis point process approach that accounts for natural climate variability and long‐term climate change influences on extreme rainfall is applied. Hurricane Maria produced the single largest maximum rainfall event since 1956 and had the highest total averaged precipitation of 129 storms that have impacted the island since 1956. Return periods for an event of Hurricane Maria's precipitation magnitude decreased in 48.6% of stations across Puerto Rico and at least halved when averaged across the island. Within the most affected areas it is likely that the probability of precipitation of Maria's magnitude has increased by a factor greater than 1 (best estimate 4.85) as a result of long‐term climate trends.
Vertical Structure of Terdiurnal Tides in the Antarctic MLT Region: 15‐Year Observation Over Syowa (69°S, 39°E)
Authors: Liu Huixin , Tsutsumi Masaki , Liu Hanli
Published: March 2019

The terdiurnal tide (TDT) in the Antarctic mesosphere and lower thermosphere region is poorly known. This study examines TDT using neutral wind observations at Syowa during years of 2004–2018. TDT is found to be a significant tidal component with distinct vertical structures and seasonal evolution. (1) It shows a prominent height‐dependent seasonal variation with phase reversal at 94 km. (2) The vertical wavelength in summer is ∼40 km shorter than in winter. These features differ largely from those in the Arctic, indicating hemispheric asymmetry. The phase structure reveals a dominant upward propagating mode in local summer but superposition of more than one mode in other seasons. A downward propagating mode above 94 km in winter suggests Joule heating/ion drag as additional tidal sources to lower atmosphere ones. These results provide new constrains and benchmarks for model simulations that seek to understand terdiurnal tidal forcing mechanisms in polar regions.
Correction to: RIP1 protects melanoma cells from apoptosis induced by BRAF/MEK inhibitors
Authors: Lei Fu Xi , Jin Lei , Liu Xiao Ying , Lai Fritz , Yan Xu Guang , Farrelly Margaret , Guo Su Tang , Zhao Xin Han , Zhang Xu Dong
Published: March 2019

Since publication of this paper, the authors have noticed that there were errors in Fig. 2A (the GAPDH of Mel-CV, Mel-CV.S, Mel-RMu and Mel-RMu.S), Fig. 2C (the GAPDH of Mel-CV.S and Mel-RMu.S), Fig. 3F (the GAPDH of Mel-CV.S and Mel-RMu.S), Fig. 3J(the GAPDH of Mel-RMu.S), Fig. 5C (the ERK1/2 of patient#3(post)), and Fig. 5F (the RIP1 of Mel-CV.S and Mel-RMu.S, the GAPDH of Mel-CV and Mel-RMu). As a result of the misfiling of the data during preparation of figures, incorrect images were inadvertently inserted in these figures. The correct figures are given below. The corrections do not alter the conclusions of the paper.
Sleep increases chromosome dynamics to enable reduction of accumulating DNA damage in single neurons
Authors: Zada D. , Bronshtein I. , Lerer-Goldshtein T. , Garini Y. , Appelbaum L.
Published: March 2019

Sleep is essential to all animals with a nervous system. Nevertheless, the core cellular function of sleep is unknown, and there is no conserved molecular marker to define sleep across phylogeny. Time-lapse imaging of chromosomal markers in single cells of live zebrafish revealed that sleep increases chromosome dynamics in individual neurons but not in two other cell types. Manipulation of sleep, chromosome dynamics, neuronal activity, and DNA double-strand breaks (DSBs) showed that chromosome dynamics are low and the number of DSBs accumulates during wakefulness. In turn, sleep increases chromosome dynamics, which are necessary to reduce the amount of DSBs. These results establish chromosome dynamics as a potential marker to define single sleeping cells, and propose that the restorative function of sleep is nuclear maintenance.
Sites of high local frustration in DNA origami
Authors: Kosinski Richard , Mukhortava Ann , Pfeifer Wolfgang , Candelli Andrea , Rauch Philipp , Saccà Barbara
Published: March 2019

The self-assembly of a DNA origami structure, although mostly feasible, represents indeed a rather complex folding problem. Entropy-driven folding and nucleation seeds formation may provide possible solutions; however, until now, a unified view of the energetic factors in play is missing. Here, by analyzing the self-assembly of origami domains with identical structure but different nucleobase composition, in function of variable design and experimental parameters, we identify the role played by sequence-dependent forces at the edges of the structure, where topological constraint is higher. Our data show that the degree of mechanical stress experienced by these regions during initial folding reshapes the energy landscape profile, defining the ratio between two possible global conformations. We thus propose a dynamic model of DNA origami assembly that relies on the capability of the system to escape high structural frustration at nucleation sites, eventually resulting in the emergence of a more favorable but previously hidden state.
A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae
Authors: Zhang Yueping , Wang Juan , Wang Zibai , Zhang Yiming , Shi Shuobo , Nielsen Jens , Liu Zihe
Published: March 2019

With rapid progress in DNA synthesis and sequencing, strain engineering starts to be the rate-limiting step in synthetic biology. Here, we report a gRNA-tRNA array for CRISPR-Cas9 (GTR-CRISPR) for multiplexed engineering of Saccharomyces cerevisiae. Using reported gRNAs shown to be effective, this system enables simultaneous disruption of 8 genes with 87% efficiency. We further report an accelerated Lightning GTR-CRISPR that avoids the cloning step in Escherichia coli by directly transforming the Golden Gate reaction mix to yeast. This approach enables disruption of 6 genes in 3 days with 60% efficiency using reported gRNAs and 23% using un-optimized gRNAs. Moreover, we applied the Lightning GTR-CRISPR to simplify yeast lipid networks, resulting in a 30-fold increase in free fatty acid production in 10 days using just two-round deletions of eight previously identified genes. The GTR-CRISPR should be an invaluable addition to the toolbox of synthetic biology and automation.
Analysis of human acetylation stoichiometry defines mechanistic constraints on protein regulation
Authors: Hansen Bogi Karbech , Gupta Rajat , Baldus Linda , Lyon David , Narita Takeo , Lammers Michael , Choudhary Chunaram , Weinert Brian T.
Published: March 2019

Lysine acetylation is a reversible posttranslational modification that occurs at thousands of sites on human proteins. However, the stoichiometry of acetylation remains poorly characterized, and is important for understanding acetylation-dependent mechanisms of protein regulation. Here we provide accurate, validated measurements of acetylation stoichiometry at 6829 sites on 2535 proteins in human cervical cancer (HeLa) cells. Most acetylation occurs at very low stoichiometry (median 0.02%), whereas high stoichiometry acetylation (>1%) occurs on nuclear proteins involved in gene transcription and on acetyltransferases. Analysis of acetylation copy numbers show that histones harbor the majority of acetylated lysine residues in human cells. Class I deacetylases target a greater proportion of high stoichiometry acetylation compared to SIRT1 and HDAC6. The acetyltransferases CBP and p300 catalyze a majority (65%) of high stoichiometry acetylation. This resource dataset provides valuable information for evaluating the impact of individual acetylation sites on protein function and for building accurate mechanistic models.
The use of technical replication for detection of low-level somatic mutations in next-generation sequencing
Authors: Kim Junho , Kim Dachan , Lim Jae Seok , Maeng Ju Heon , Son Hyeonju , Kang Hoon-Chul , Nam Hojung , Lee Jeong Ho , Kim Sangwoo
Published: March 2019

Accurate genome-wide detection of somatic mutations with low variant allele frequency (VAF, <1%) has proven difficult, for which generalized, scalable methods are lacking. Herein, we describe a new computational method, called RePlow, that we developed to detect low-VAF somatic mutations based on simple, library-level replicates for next-generation sequencing on any platform. Through joint analysis of replicates, RePlow is able to remove prevailing background errors in next-generation sequencing analysis, facilitating remarkable improvement in the detection accuracy for low-VAF somatic mutations (up to ~99% reduction in false positives). The method is validated in independent cancer panel and brain tissue sequencing data. Our study suggests a new paradigm with which to exploit an overwhelming abundance of sequencing data for accurate variant detection.
Spatiotemporal imaging of valence electron motion
Authors: Kübel M. , Dube Z. , Naumov A. Yu. , Villeneuve D. M. , Corkum P. B. , Staudte A.
Published: March 2019

Electron motion on the (sub-)femtosecond time scale constitutes the fastest response in many natural phenomena such as light-induced phase transitions and chemical reactions. Whereas static electron densities in single molecules can be imaged in real space using scanning tunnelling and atomic force microscopy, probing real-time electron motion inside molecules requires ultrafast laser pulses. Here, we demonstrate an all-optical approach to imaging an ultrafast valence electron wave packet in real time with a time-resolution of a few femtoseconds. We employ a pump-probe-deflect scheme that allows us to prepare an ultrafast wave packet via strong-field ionization and directly image the resulting charge oscillations in the residual ion. This approach extends and overcomes limitations in laser-induced orbital imaging and may enable the real-time imaging of electron dynamics following photoionization such as charge migration and charge transfer processes.
Anti-quenching NIR-II molecular fluorophores for in vivo high-contrast imaging and pH sensing
Authors: Wang Shangfeng , Fan Yong , Li Dandan , Sun Caixia , Lei Zuhai , Lu Lingfei , Wang Ting , Zhang Fan
Published: March 2019

The contrast and sensitivity of in vivo fluorescence imaging has been revolutionized by molecular fluorophores operating in the second near-infrared window (NIR-II; 1000-1700 nm), but an ongoing challenge is the solvatochromism-caused quenching in aqueous solution for the long-wavelength absorbing fluorophores. Herein, we develop a series of anti-quenching pentamethine cyanine fluorophores that significantly overcome the severe solvatochromism, thus affording stable absorption/emission beyond 1000 nm with up to ~ 44-fold enhanced brightness and superior photostability in aqueous solution. These advantages allow for deep optical penetration (8 mm) as well as high-contrast and highly-stable lymphatic imaging superior to clinical-approved indocyanine green. Additionally, these fluorophores exhibit pH-responsive fluorescence, allowing for noninvasive ratiometric fluorescence imaging and quantification of gastric pH in vivo. The results demonstrate reliable accuracy in tissue as deep as 4 mm, comparable to standard pH electrode method. This work unlocks the potential of anti-quenching pentamethine cyanines for NIR-II biological applications.
Island Ancestors and New World Biogeography: A Case Study from the Scorpions (Buthidae: Centruroidinae)
Authors: Esposito Lauren A. , Prendini Lorenzo
Published: March 2019

Scorpions are an excellent system for understanding biogeographical patterns. Most major scorpion lineages predate modern landforms, making them suitable for testing hypotheses of vicariance and dispersal. The Caribbean islands are endowed with a rich and largely endemic scorpion fauna, the origins of which have not been previously investigated with modern biogeographical methods. Three sets of hypotheses have been proposed to explain present patterns of diversity in the Caribbean: (1) connections via land bridges, (2) vicariance events, and (3) overwater dispersal from continents and among islands. The present study investigates the biogeographical diversification of the New World buthid scorpion subfamily Centruroidinae Kraus, 1955, a clade of seven genera and more than 110 species; infers the ancestral distributions of these scorpions; and tests the relative roles of vicariance and dispersal in the formation of their present distributions. A fossil-calibrated molecular phylogeny was estimated with a Bayesian criterion to infer the dates of diversification events from which ancestral distributions were reconstructed, and the relative likelihood of models of vicariance vs. dispersal, calculated. Although both the timing of diversification and the ancestral distributions were congruent with the GAARlandia land-bridge hypothesis, there was no significant difference between distance-dependent models with or without the land-bridge.HeteroctenusPocock, 1893, the Caribbean-endemic sister taxon ofCentruroidesMarx, 1890 provides evidence for a Caribbean ancestor, which subsequently colonized Central America and North America, and eventually re-colonized the Greater Antilles. This ‘reverse colonization’ event of a continent from an island demonstrates the importance of islands as a potential source of biodiversity.
Radiated and guided optical waves of a magnetic dipole-nanofiber system
Authors: Atakaramians Shaghik , Dong Feng Q. , Monro Tanya M. , Afshar V. Shahraam
Published: March 2019

Nanophotonics–photonic structures with subwavelength features–allow accessing high intensity and localized electromagnetic field and hence is an ideal platform for investigating and exploiting strong lightmatter interaction. In particular, such a strong light-matter interaction requires investigating the interaction of a magnetic dipole with the electromagnetic field– a less-explored topic, which has usually been ignored within the framework of electric dipole approximation. Motivated by recent advances in the emerging field of multipolar nanophotonics, here we develop an analytical model that provides a new insight into analyzing a magnetic dipole and a nanofiber. This method enables us to examine the effect of second term in the multipolar expansion of light-matter interaction, magnetic dipole approximation, with individual guided and radiation modes of the nanofiber. This is a critical key in developing nanophotonic integrated devices based on magnetic nature of light for super-imaging, biosensing, and optical computing.