bluuebunny/crossref_metadata_2025 huggingface dataset:
The role of a creditor in the making of a debt crisis: the French government's financial support for Poland, between cold war interests and economic constraints, 1958-1981
Authors: Mourlon-Druol Emmanuel
Published: March 2020

In spite of considerable attention granted to sovereign debt failures, we still have limited knowledge of the incentives which induced creditors to lend at unsustainable levels. This article looks at the French government’s policy towards Poland from 1958, when economic cooperation between the two countries started, until Poland's announcement in 1981 that it could not service its debt. Export credit guarantees supported France's financial involvement, and this implied the government's strong influence on the decision to lend. This article brings out the tension between economic and political priorities in French policymaking during the cold war. Archival evidence reveals that as early as 1975 the French finance ministry warned that French risks were excessive; that Poland’s growing economic difficulties would render the country unable to repay its debts; and recommended limiting France's financial commitments. The French government, however, decided not only to carry on but also to increase lending, in order to support its political objective of using economic and financial means to relax East–West tensions. This article illustrates how creditors play a part in sovereign debt crises by voluntarily turning a blind eye to a country’s growing inability to repay its debts, and thus reinforce a vicious circle of indebtedness.
Prehospital Vital Signs Accurately Predict Initial Emergency Department Vital Signs
Authors: Trust Marc D. , Schellenberg Morgan , Biswas Subarna , Inaba Kenji , Cheng Vincent , Warriner Zachary , Love Bryan E. , Demetriades Demetrios
Published: March 2020

Introduction:

Prehospital vital signs are used to triage trauma patients to mobilize appropriate resources and personnel prior to patient arrival in the emergency department (ED). Due to inherent challenges in obtaining prehospital vital signs, concerns exist regarding their accuracy and ability to predict first ED vitals.

Hypothesis/Problem:

The objective of this study was to determine the correlation between prehospital and initial ED vitals among patients meeting criteria for highest levels of trauma team activation (TTA). The hypothesis was that in a medical system with short transport times, prehospital and first ED vital signs would correlate well.

Methods:

Patients meeting criteria for highest levels of TTA at a Level I trauma center (2008-2018) were included. Those with absent or missing prehospital vital signs were excluded. Demographics, injury data, and prehospital and first ED vital signs were abstracted. Prehospital and initial ED vital signs were compared using Bland-Altman intraclass correlation coefficients (ICC) with good agreement as >0.60; fair as 0.40-0.60; and poor as <0.40).

Results:

After exclusions, 15,320 patients were included. Mean age was 39 years (range 0-105) and 11,622 patients (76%) were male. Mechanism of injury was blunt in 79% (n = 12,041) and mortality was three percent (n = 513). Mean transport time was 21 minutes (range 0-1,439). Prehospital and first ED vital signs demonstrated good agreement for Glasgow Coma Scale (GCS) score (ICC 0.79; 95% CI, 0.77-0.79); fair agreement for heart rate (HR; ICC 0.59; 95% CI, 0.56-0.61) and systolic blood pressure (SBP; ICC 0.48; 95% CI, 0.46-0.49); and poor agreement for pulse pressure (PP; ICC 0.32; 95% CI, 0.30-0.33) and respiratory rate (RR; ICC 0.13; 95% CI, 0.11-0.15).

Conclusion:

Despite challenges in prehospital assessments, field GCS, SBP, and HR correlate well with first ED vital signs. The data show that these prehospital measurements accurately predict initial ED vitals in an urban setting with short transport times. The generalizability of these data to settings with longer transport times is unknown.
Emerging trends: Reviewing the reviewers (again)
Authors: Church Kenneth Ward
Published: March 2020

The ACL-2019 Business meeting ended with a discussion of reviewing. Conferences are experiencing a success catastrophe. They are becoming bigger and bigger, which is not only a sign of success but also a challenge (for reviewing and more). Various proposals for reducing submissions were discussed at the Business meeting. IMHO, the problem is not so much too many submissions, but rather, random reviewing. We cannot afford to do reviewing as badly as we do (because that leads to even more submissions). Negative feedback loops are effective. The reviewing process will improve over time if reviewers teach authors how to write better submissions, and authors teach reviewers how to write more constructive reviews. If you have received a not-ok (unhelpful/offensive) review, please help program committees improve by sharing your not-ok reviews on social media.
Metacognitive beliefs in depressed in-patients: adaptation and validation of the short version of the Metacognitions Questionnaire (MCQ-30) for French clinical and non-clinical samples
Authors: Baptista Axel , Soumet-Leman Charlotte , Visinet Arnauld , Jouvent Roland
Published: March 2020

Background:

The short form of the Metacognitions Questionnaire (MCQ-30) is a brief multi-dimensional measure which explores the metacognitive processes and beliefs about worry and cognition that are central to the vulnerability and maintenance of emotional disorders.

Aims:

The first aim of the study was to create and validate a French version of the MCQ-30 in a non-clinical and a clinical sample of depressed in-patients.

Method:

A French adaptation of the MCQ-30 was administered to a sample of 467 individuals from the general population and 73 hospitalized patients with major depressive disorder. Internal consistency was measured by Cronbach’s alpha reliability coefficients. Factor structure was assessed using a confirmatory factor analysis on the non-clinical group and a multi-trait–multi-method analysis on the psychiatric group. Criterion validity was explored by comparing the scores of the two samples. Measures of rumination, worry and depression were used to explore convergent validity.

Results:

Confirmatory factor analysis in the non-clinical sample indicated that the French version of the MCQ-30 has the same factor structure as the MCQ-30’s original five-factor solution. In the clinical sample, the multi-trait–multi-method analysis revealed discrepancies with the original factor structure, and the MCQ-30 and its subscales were less reliable. Our results provide evidence of a convergent validity. The MCQ-30 scores were also able to discriminate between psychiatric and non-clinical samples.

Conclusions:

Our results show that the French version of the MCQ-30 is a valid instrument for measuring metacognitive beliefs in non-clinical population. Further research is needed to support its use among depressed in-patients.
Climate impacts on nutrition and labor supply disentangled – an analysis for rural areas of Uganda
Authors: Antonelli Chiara , Coromaldi Manuela , Dasgupta Shouro , Emmerling Johannes , Shayegh Soheil
Published: March 2020

The entire agricultural supply chain, from crop production to food consumption, is expected to suffer significant damages from climate change. This paper empirically investigates the effects of warming on agricultural labor supply through variation in dietary intake in rural Uganda. We examine labor supply, food consumption, and overall social welfare under various climate change scenarios. First, we combine nationally representative longitudinal survey data with high-resolution climatic data using an instrumental variable approach. Controlling for calorie intake, our study shows that warming has a non-linear impact on agricultural labor supply, with the number of hours worked being optimized at an optimal temperature of 21.3°C. Using these econometric estimates to parametrize an overlapping generations model, we find that under RCP8.5, output per adult decreases by 20 per cent by the end of the century due to the combined effect of climate change on food consumption and labor supply.
Computational Designing of Sonic Morphologies
Authors: Worrall David
Published: March 2020

Much electroacoustic music composition and sound art, and the commentary that surrounds them, is locked into a materialist sound-object mindset in which the hierarchical organisation of sonic events, especially those developed through abstraction, are considered antithetical to sounds ‘being themselves’. This article argues that musical sounds are not just material objects, and that musical notations, on paper or in computer code, are not just symbolic abstractions, but instructions for embodied actions. When notation is employed computationally to control resonance and gestural actuators at multiple acoustic, psychoacoustic and conceptual levels of music form, vibrant sonic morphologies may emerge from the quantum-like boundaries between them. In order to achieve that result, it is necessary to replace our primary focus of compositional attention from the Digital Audio Workstation sound transformation tools currently in vogue, with those that support algorithmic thinking at all levels of compositional design.
Idiomatic Patterns and Aesthetic Influence in Computer Music Languages
Authors: McPherson Andrew , Tahıroğlu Koray
Published: March 2020

It is widely accepted that acoustic and digital musical instruments shape the cognitive processes of the performer on both embodied and conceptual levels, ultimately influencing the structure and aesthetics of the resulting performance. In this article we examine the ways in which computer music languages might similarly influence the aesthetic decisions of the digital music practitioner, even when those languages are designed for generality and theoretically capable of implementing any sound-producing process. We examine the basis for querying the non-neutrality of tools with a particular focus on the concept of idiomaticity: patterns of instruments or languages which are particularly easy or natural to execute in comparison to others. We then present correspondence with the developers of several major music programming languages and a survey of digital musical instrument creators examining the relationship between idiomatic patterns of the language and the characteristics of the resulting instruments and pieces. In an open-ended creative domain, asserting causal relationships is difficult and potentially inappropriate, but we find a complex interplay between language, instrument, piece and performance that suggests that the creator of the music programming language should be considered one party to a creative conversation that occurs each time a new instrument is designed.
Digital Musical Instruments as Probes: How computation changes the mode-of-being of musical instruments
Authors: Tahıroğlu Koray , Magnusson Thor , Parkinson Adam , Garrelfs Iris , Tanaka Atau
Published: March 2020

This article explores how computation opens up possibilities for new musical practices to emerge through technology design. Using the notion of thecultural probeas a lens, we consider the digital musical instrument as an experimental device that yields findings across the fields of music, sociology and acoustics. As part of an artistic-research methodology, the instrumental object as a probe is offered as a means for artists to answer questions that are often formulated outside semantic language. This article considers how computation plays an important role in the authors’ personal performance practices in different ways, which reflect the changed mode-of-being of new musical instruments and our individual and collective relations with them.
The North Indian Sarode and Questions Concerning Technology
Authors: Noone Matthew James
Published: March 2020

In three previous issues of OS (10/1, 2005, 13/3, 2008 and 19/2, 2014) a range of scholars explored non-Western instrumentation in electroacoustic music. These issues addressed concerns about sensitive cultural issues within electroacoustic music. This article builds upon this discussion through an examination of a number of electroacoustic composer-performers using non-Western instrumentation. This discussion will include the voices of ‘Western’ electroacoustic composers using non-Western instruments or sounds sources. It will also document some of the work of non-Western electroacoustic composers who incorporate traditional material or indigenous instruments in their music. Special attention will be given to the complexity of being in-between musical cultures through a critical engagement with theories relating to hybridity, orientalism and self-identity. In particular, this article will focus on my own practice of composing and performing electroacoustic music with the North Indian lute known as the sarode. It will discuss both cultural and artistic concerns about using the sarode outside the framework of Indian classical music and question whether Indian classical music can ever be ‘appropriately appropriated’ in an electroacoustic context. Two of my recent compositions will be explored and I will outline the development of my practice leading to the creation of a new ‘hybrid’ instrument especially for playing electroacoustic music.
“Just the Status Quo?”
Authors: Mitchell Michele
Published: March 2020

Abstract*

As much as recent scholarship, popular outlets, and even a documentary film have asserted that we find ourselves in another “Gilded Age” since the 1980s, such a conceit has its limits. Indeed, we should proceed with caution when it comes to embracing analogies that posit a “new” or “second” Gilded Age. We might instead profitably think about the late nineteenth and early twentieth centuries as being a period of high capitalism and our current moment as reflecting a particular, if not peculiar, phase of capitalism. And, as much as our understanding of gender and sexuality during the late nineteenth and early twentieth centuries might actually be hindered by separating “Gilded Age” and “Progressive Era,” considering gendered dynamics of our current moment—a moment that has been termed late-stage capitalism—deepens our analysis of the low-wage economy. When it comes to sexuality, we should be careful in drawing parallels between the Gilded Age and the present given that contemporary understandings of sexuality began to coalesce during the late nineteenth century. Still, debates about sex and sexuality certainly shaped the Gilded Age and they continue to inform our current moment in dynamic and even unprecedented ways. We might not find ourselves in another Gilded Age, but we should arguably build upon current interest in histories of capitalism as a means think about the significance of progressive social movements within capitalist societies.
Please, open the windows!
Authors: Ménard Claude
Published: March 2020

This comment concurs with Skarbek's paper that much more room should be made for qualitative evidence in economics. However, it raises questions about the modalities through which case studies could carry general lessons when it comes to broad institutional issues. It also suggests the need to extend the set of qualitative evidence beyond case studies and to complement them with formal approaches as well as with quantitative analysis. Persuading economists to open windows to alternative methods is at stake
Optimal delivery timing for dizygotic twins – the short- and long-term perspective
Authors: Imterat Majdi , Wainstock Tamar , Sheiner Eyal , Sergienko Ruslan , Landau Daniella , Walfisch Asnat
Published: March 2020

Major obstetrics and gynecology societies offer inconsistent recommendation regarding optimal delivery timing in uncomplicated dizygotic twins. We sought to investigate the impact of delivery timing within term gestation, in dizygotic twins, on the short- and long-term offspring morbidity. A prospectively analyzed cohort of dizygotic twin deliveries was conducted. All women delivered at a regional tertiary medical center, at term (≥37 0/7), between the years 1991 and 2014, were included. The primary exposure was delivery at 37 0/7–37 + 6/7 weeks, while delivery at ≥38 0/7 weeks’ gestation was considered the reference. Neonatal short- and long-term outcomes according to hospitalizations of offspring up to 18 years of age due to cardiac, respiratory, hematological, neurological, and infectious morbidity were compared. Kaplan–Meier survival curves were used to compare cumulative incidences per each major-system hospitalization. Cox regression models were used to estimate the adjusted hazard ratios, while adjusting for variables with clinical importance. During the study period, 612 dizygotic twin deliveries met the inclusion criteria. Of them, 200 (31.3%) occurred at 37–37 6/7 weeks, and 412 (68.7%) occurred at ≥38 0/7 weeks’ gestation. In the long-term analysis, rates of hospitalizations involving several major morbidity categories exhibited comparable rates in both groups. The Cox regression models did not demonstrate an independent association between gestational age within term and later major pediatric morbidity in offspring (total long-term morbidity: adjusted hazard ratio 1.33, 95% confidence interval 0.77–2.29). Dizygotic twin deliveries occurring at different gestational ages within term do not appear to significantly impact on major short- and long-term outcomes.
Applying Tipping Point Theory to Remote Sensing Science to Improve Early Warning Drought Signals for Food Security
Authors: Krishnamurthy R P. Krishna , Fisher Joshua B. , Schimel David S. , Kareiva Peter M.
Published: March 2020

Famines have long been associated with drought. With the severity of droughts growing in association with climate change, there is increasing pressure to do a better job predicting famines and delivering international aid to avert human suffering and civil instability. We examine recent advances in remote sensing technology, focusing on the latency, historical availability and spatial and temporal scales of the data these satellites provide. Because of their global coverage, seven variables derived from satellite observations emerge as especially pertinent to drought and famine: precipitation (TRMM/GPM), groundwater (GRACE/GRACE‐FO), snow (MODIS), soil moisture (SMOS, SMAP, Sentinel‐1), evapotranspiration (MODIS, ECOSTRESS), vegetation health (Landsat, AVHRR, MODIS, SPOT) and chlorophyll fluorescence (OCO‐2). We discuss tipping point theory as a possible framework for taking advantage of long time series of these satellite data where they exist in order to enhance the effectiveness of existing famine early warning systems.
Global Model for Depth‐Dependent Carbonyl Photochemical Production Rates in Seawater
Authors: Zhu Yuting , Kieber David J.
Published: March 2020

A photochemical model was used to quantify the global contribution of carbonyl photoproduction in the photodegradation of marine dissolved organic carbon (DOC). As model input, wavelength‐ and temperature‐dependent apparent quantum yields (AQYs) for the photochemical production of carbonyl compounds were determined in seawater collected from the Northwest Atlantic Ocean. These AQY data and published AQY data from the North Pacific were used with remotely sensed seawater optical properties and solar irradiance data in a global model to calculate depth‐resolved, mixed‐layer photochemical fluxes of acetaldehyde and glyoxal in seawater. Based on this model, the annual global surface mixed‐layer photochemical production is 89.7 ± 36 Tg year−1 for acetaldehyde and 20.0 ± 8.0 Tg year−1 for glyoxal. This work significantly improves our understanding of the impact of photochemistry on the cycling of DOC in the surface oceans. Low‐molecular‐weight carbonyl compounds represent the second largest carbon flux among all known carbon products that are produced during the photolysis of DOC. The annual photoproduction of carbonyl‐compound carbon is ~110 ± 23 Tg C year−1, comprising approximately 9.6% of the total carbon and 22% of the biologically labile carbon that are produced globally from the photolysis of marine DOC.
Nearly Magnitude‐Invariant Stress Drops in Simulated Crack‐Like Earthquake Sequences on Rate‐and‐State Faults with Thermal Pressurization of Pore Fluids
Authors: Perry Stephen M. , Lambert Valère , Lapusta Nadia
Published: March 2020

Stress drops, inferred to be magnitude‐invariant, are a key characteristic used to describe natural earthquakes. Theoretical studies and laboratory experiments indicate that enhanced dynamic weakening, such as thermal pressurization of pore fluids, may be present on natural faults. At first glance, magnitude invariance of stress drops and enhanced dynamic weakening seem incompatible since larger events may experience greater weakening and should thus have lower final stresses and higher stress drops. We hypothesize that enhanced dynamic weakening can be reconciled with magnitude‐invariant stress drops due to larger events having lower average prestress when compared to smaller events. We conduct numerical simulations of long‐term earthquake sequences in fault models with rate‐and‐state friction and thermal pressurization, and in the parameter regime that results mostly in crack‐like ruptures, we find that such models can explain both the observationally inferred stress drop invariance and increasing breakdown energy with event magnitude. Smaller events indeed have larger average initial stresses than medium‐sized events, and we find nearly constant stress drops for events spanning up to two orders of magnitude in average slip, comparable to approximately six orders of magnitude in seismic moment. Segment‐spanning events have more complex behavior, which depends on the properties of the arresting velocity‐strengthening region at the edges of the faults.
What Caused the Decline of Water Level of Yamzho Yumco During 1975–2012 in the Southern Tibetan Plateau?
Authors: Sang Yan‐Fang , Chen Deliang , Gong Tongliang
Published: March 2020

Variability of water balance in closed lakes in the Tibetan Plateau (TP) can be a useful indicator of climate change. While most of lakes over the TP have been expanding, especially in the inner TP, the Yamzho Yumco in the Southern TP faced a significant water level decline in 1975–2012. This study focused on attribution of the water level changes to various factors with the help of a physically based and a statistical model for the water balance of the lake, along with observed precipitation and lake surface evaporation data. Results showed that climatic conditions dominated the changes in water level until 1997, and human activity through the construction and operation of a hydropower station started to play a strong role after 1998. The lake level has gone up and down due to changes in precipitation‐generated recharge and evaporation over the study period. The water level decline in 1975–1997 was mainly due to low level of the recharge from precipitation and land runoff. However, the drastic decline of water level in 2006–2012 was far from the reach of the climatic conditions. It was indeed caused by the intensified influence of the building and operation of a nearby hydropower station. It was also found that the water level change during the whole period (1975–2012) followed the aridity index for the basin, especially before 1989. This provides an effective way to predict future changes of lake level, if reliable projections for future climate change and human activity are available.
Evaluating the Impact of Assimilating Aerosol Optical Depth Observations on Dust Forecasts Over North Africa and the East Atlantic Using Different Data Assimilation Methods
Authors: Choi Yonghan , Chen Shu‐Hua , Huang Chu‐Chun , Earl Kenneth , Chen Chih‐Ying , Schwartz Craig S. , Matsui Toshihisa
Published: March 2020

This study evaluates the impact of assimilating moderate resolution imaging spectroradiometer (MODIS) aerosol optical depth (AOD) data using different data assimilation (DA) methods on dust analyses and forecasts over North Africa and tropical North Atlantic. To do so, seven experiments are conducted using the Weather Research and Forecasting dust model and the Gridpoint Statistical Interpolation analysis system. Six of these experiments differ in whether or not AOD observations are assimilated and the DA method used, the latter of which includes the three‐dimensional variational (3D‐Var), ensemble square root filter (EnSRF), and hybrid methods. The seventh experiment, which allows us to assess the impact of assimilating deep blue AOD data, assimilates only dark target AOD data using the hybrid method. The assimilation of MODIS AOD data clearly improves AOD analyses and forecasts up to 48 hr in length. Results also show that assimilating deep blue data has a primarily positive effect on AOD analyses and forecasts over and downstream of the major North African source regions. Without assimilating deep blue data (assimilating dark target only), AOD assimilation only improves AOD forecasts for up to 30 hr. Of the three DA methods examined, the hybrid and EnSRF methods produce better AOD analyses and forecasts than the 3D‐Var method does. Despite the clear benefit of AOD assimilation for AOD analyses and forecasts, the lack of information regarding the vertical distribution of aerosols in AOD data means that AOD assimilation has very little positive effect on analyzed or forecasted vertical profiles of backscatter.
Geomagnetically Induced Currents and Harmonic Distortion: Storm‐Time Observations From New Zealand
Authors: Rodger Craig J. , Clilverd Mark A. , Mac Manus Daniel H. , Martin Ian , Dalzell Michael , Brundell James B. , Divett Tim , Thomson Neil R. , Petersen Tanja , Obana Yuki , Watson Neville R.
Published: March 2020

Large geomagnetic storms are a known space weather hazard to power transmission networks due to the effects of geomagnetically induced currents (GICs). However, research in this area has been hampered by a lack of GIC observations. Previous studies have noted that New Zealand is unusually fortunate in having a comparatively dense, high quality, set of GIC measurements, spanning >60 transformers in >20 substations. However, due to operational reasons these observations are clustered in the mid and lower South Island. In this paper we analyze space weather‐induced GIC impact patterns over the entire country by using a different set of sensors that monitor levels of harmonic distortion, with even and odd harmonics measured separately. GICs lead to half cycle transformer saturation and is one of the few ways in which even harmonics are produced in a well‐run power transmission network. We make use of harmonic distortion measurements at 377 circuit breakers made at 126 separate locations. Focusing on the intense geomagnetic storm activity during 6–9 September 2017, we show how the even harmonic distortion observations provide a useful new picture of GIC‐stressed transformers. These observations demonstrate how GIC effects can be monitored by using even harmonic distortion in locations where no GIC measurements are present (e.g., the most of the North Island). We understand that harmonic distortion measurements are fairly common in electrical networks and could provide a new tool for space weather researchers.
Discovery of New‐Structured Post‐Spinel MgFe2O4: Crystal Structure and High‐Pressure Phase Relations
Authors: Ishii Takayuki , Miyajima Nobuyoshi , Sinmyo Ryosuke , Kojitani Hiroshi , Mori Daisuke , Inaguma Yoshiyuki , Akaogi Masaki
Published: March 2020

Phase relations in MgFe2O4 at 20–27 GPa and 1,000–1,200 °C were investigated, and a novel post‐spinel phase of MgFe2O4 (space group, Pnma) was identified. This phase has a Z‐shape framework of edge‐sharing (Mg,Fe)O6 octahedra, with other Mg and Fe cations randomly occupying one tetrahedral and two octahedral sites in tunnel spaces within the framework. This structure is similar to Nax (Fe,Ti)xTi2‐xO4 phase (0.75 ≤ x ≤ 0.9) with (Fe,Ti)O6 Z‐shape framework and tricapped‐prism sites for Na. Compression data showed ~6% volume reduction at 16–20 GPa. The recovered phase may have transformed during decompression from the Nax (Fe,Ti)xTi2‐xO4‐type structure due to cations in the tunnel spaces shifting, probably because of cation‐size misfit. The novel phase may be found in impact craters and shocked meteorites and may serve as an indicator of shock P‐T conditions. Without crystal structure refinement, post‐spinel phases are likely to be misidentified due to similar crystallographic features.
Immune metabolism regulation of the germinal center response
Authors: Choi Seung-Chul , Morel Laurence
Published: March 2020

The humoral immune response requires germinal centers to produce high-affinity antigen-specific antibodies that counter pathogens. Numerous studies have provided a better understanding of how metabolic pathways regulate the development, activation and functions of immune cells. Germinal centers are transient, highly dynamic microanatomic structures that develop in lymphoid organs during a T-cell-dependent humoral immune response. Analysis of germinal centers provides an opportunity to understand how metabolic programs control the differentiation and function of highly specialized germinal center B cells and follicular helper CD4+ T cells. Targeting immunometabolism during the germinal center response may afford the possibility to improve vaccine design and to develop new therapies to alleviate autoimmunity. In this review, we discuss the major metabolic pathways that are used by germinal center B and T cells, as well as the plasma cells that they produce, all of which are influenced by the microenvironment of this unique structure of the adaptive immune system.
The CRISPR-Cas systems were selectively inactivated during evolution of Bacillus cereus group for adaptation to diverse environments
Authors: Zheng Ziqiang , Zhang Yulan , Liu Zhiyu , Dong Zhaoxia , Xie Chuanshuai , Bravo Alejandra , Soberón Mario , Mahillon Jacques , Sun Ming , Peng Donghai
Published: March 2020

CRISPR-Cas systems are considered as barriers to horizontal gene transfer (HGT). However, the influence of such systems on HGT within species is unclear. Also, little is known about the impact of CRISPR-Cas systems on bacterial evolution at the population level. Here, using Bacillus cereus sensu lato as model, we investigate the interplay between CRISPR-Cas systems and HGT at the population scale. We found that only a small fraction of the strains have CRISPR-Cas systems (13.9% of 1871), and most of such systems are defective based on their gene content analysis. Comparative genomic analysis revealed that the CRISPR-Cas systems are barriers to HGT within this group, since strains harboring active systems contain less mobile genetic elements (MGEs), have lower fraction of unique genes and also display limited environmental distributions than strains without active CRISPR-Cas systems. The introduction of a functional CRISPR-Cas system into a strain lacking the system resulted in reduced adaptability to various stresses and decreased pathogenicity of the transformant strain, indicating that B. cereus group strains could benefit from inactivating such systems. Our work provides a large-scale case to support that the CRISPR-Cas systems are barriers to HGT within species, and that in the B. cereus group the inactivation of CRISPR-Cas systems correlated with acquisition of MGEs that could result in better adaptation to diverse environments.
Longitudinal spatial dataset on travel times and distances by different travel modes in Helsinki Region
Authors: Tenkanen Henrikki , Toivonen Tuuli
Published: March 2020

Comparable data on spatial accessibility by different travel modes are frequently needed to understand how city regions function. Here, we present a spatial dataset called the Helsinki Region Travel Time Matrix that has been calculated for 2013, 2015 and 2018. This longitudinal dataset contains travel time and distance information between all 250 metres statistical grid cell centroids in the Capital Region of Helsinki, Finland. The dataset is multimodal and multitemporal by nature: all typical transport modes (walking, cycling, public transport, and private car) are included and calculated separately for the morning rush hour and midday for an average working day. We followed a so-called door-to-door principle, making the information between travel modes comparable. The analyses were based primarily on open data sources, and all the tools that were used to produce the data are openly available. The matrices form a time-series that can reveal the accessibility conditions within the city and allow comparisons of the changes in accessibility in the region, which support spatial planning and decision-making.
A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task
Authors: Chandravadia N. , Liang D. , Schjetnan A. G. P. , Carlson A. , Faraut M. , Chung J. M. , Reed C. M. , Dichter B. , Maoz U. , Kalia S. K. , Valiante T. A. , Mamelak A. N. , Rutishauser U.
Published: March 2020

A challenge for data sharing in systems neuroscience is the multitude of different data formats used. Neurodata Without Borders: Neurophysiology 2.0 (NWB:N) has emerged as a standardized data format for the storage of cellular-level data together with meta-data, stimulus information, and behavior. A key next step to facilitate NWB:N adoption is to provide easy to use processing pipelines to import/export data from/to NWB:N. Here, we present a NWB-formatted dataset of 1863 single neurons recorded from the medial temporal lobes of 59 human subjects undergoing intracranial monitoring while they performed a recognition memory task. We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. This combined data and code release is a case study for how to utilize NWB:N for human single-neuron recordings and enables easy re-use of this hard-to-obtain data for both teaching and research on the mechanisms of human memory.
Transcriptomic response to soybean meal-based diets as the first formulated feed in juvenile yellow perch (Perca flavescens)
Authors: Kemski Megan M. , Rappleye Chad A. , Dabrowski Konrad , Bruno Richard S. , Wick Macdonald
Published: March 2020

With increasing levels of fish meal (FM) protein in aquafeeds being replaced with soybean meal (SBM) protein, understanding the molecular mechanisms involved in response to alternative diets has become a critical concern. Thus, the goal of this study was to examine transcriptional differences in the intestine of juvenile yellow perch through RNA-sequencing (RNA-seq), after their initial introduction to a formulated diet with 75% SBM protein inclusion for 61 days, compared to those fed a traditional FM-based diet. Transcriptomic analysis revealed a concise set of differentially expressed genes in juveniles fed the SBM-based diet, the majority of which were intrinsic to the cholesterol biosynthesis pathway. Analysis of total body lipid and cholesterol levels were also investigated, with no between-treatment differences detected. Results of this study demonstrate that in response to SBM-based diets, yellow perch juveniles up-regulate the cholesterol biosynthesis pathway in order to maintain homeostasis. These findings suggest that the upregulation of the cholesterol biosynthesis pathway may negatively impact fish growth due to its large energy expenditure, and future studies are warranted.
Author Correction: Metagenomics of pigmented and cholesterol gallstones: the putative role of bacteria
Authors: Kose S. H. , Grice K. , Orsi W. D. , Ballal M. , Coolen M. J. L.
Published: March 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Bacterial chemotaxis towards polysaccharide pectin by pectin-binding protein
Authors: Konishi Hidenori , Hio Mamoru , Kobayashi Masahiro , Takase Ryuichi , Hashimoto Wataru
Published: March 2020

As opposed to typical bacteria exhibiting chemotaxis towards low-molecular-weight substances, such as amino acids and mono/oligosaccharides, gram-negative Sphingomonas sp. strain A1 shows chemotaxis towards alginate and pectin polysaccharides. To identify the mechanism of chemotaxis towards macromolecules, a genomic fragment was isolated from the wild-type strain A1 through complementation with the mutant strain A1-M5 lacking chemotaxis towards pectin. This fragment contained several genes including sph1118. Through whole-genome sequencing of strain A1-M5, sph1118 was found to harbour a mutation. In fact, sph1118 disruptant lost chemotaxis towards pectin, and this deficiency was recovered by complementation with wild-type sph1118. Interestingly, the gene disruptant also exhibited decreased pectin assimilation. Furthermore, the gene product SPH1118 was expressed in recombinant E. coli cells, purified and characterised. Differential scanning fluorimetry and UV absorption spectroscopy revealed that SPH1118 specifically binds to pectin with a dissociation constant of 8.5 μM. Using binding assay and primary structure analysis, SPH1118 was predicted to be a periplasmic pectin-binding protein associated with an ATP-binding cassette transporter. This is the first report on the identification and characterisation of a protein triggering chemotaxis towards the macromolecule pectin as well as its assimilation.
Divergent mammalian body size in a stable Eocene greenhouse climate
Authors: Ring Simon J. , Bocherens Hervé , Wings Oliver , Rabi Márton
Published: March 2020

A negative correlation between body size and the latitudinal temperature gradient is well established for extant terrestrial endotherms but less so in the fossil record. Here we analyze the middle Eocene site of Geiseltal (Germany), whose record is considered to span ca. 5 Myrs of gradual global cooling, and generate one of the most extensive mammalian Paleogene body size datasets outside North America. The δ18O and δ13C isotopic analysis of bioapatite reveals signatures indicative of a humid, subtropical forest with no apparent climatic change across Geiseltal. Yet, body mass of hippomorphs and tapiromorphs diverges rapidly from a respective median body size of 39 kg and 124 kg at the base of the succession to 26 kg and 223 kg at the top. We attribute the divergent body mass evolution to a disparity in lifestyle, in which both taxa maximize their body size-related selective advantages. Our results therefore support the view that intrinsic biotic processes are an important driver of body mass outside of abrupt climate events. Moreover, the taxonomy previously used to infer the duration of the Geiseltal biota is not reproducible, which precludes chronological correlation with Eocene marine temperature curves.
Periodic Fractal-Growth Branching to Nano-Structured Grating Aggregation in Phthalic Acid
Authors: Chen Tzu-Yu , Woo Eamor M. , Nagarajan Selvaraj
Published: March 2020

Small-molecule phthalic acid (PA), confined in micrometer thin films, was crystallized in the presence of strongly interacting tannic acid (TA) to investigate crystal assembly and correlation between banded patterns and branching structures. Several compositions of the mixture of ethanol/water solutions and evaporation temperatures were also manipulated to investigate the kinetic effects on the morphology of PA crystals. With increasing evaporation rate, the morphology of PA crystals systematically changes from circular-banded spherulites to highly ordered grating-banded patterns. A unique periodic fractal-branch pattern with contrasted birefringent bands exists at intermediate evaporation rate, and this unique grating architecture has never been found in other banded crystals. Crystal assembly of these three periodic morphologies was analyzed by utilizing atomic-force microscopy (AFM) and scanning electron microscopy (SEM) to reveal the mechanisms of formation of hierarchical structures of PA. The detailed growth mechanisms of the novel fractal-branching assembly into circular- or grating-banded patterns are analyzed in this work.
Food additives: distribution and co-occurrence in 126,000 food products of the French market
Authors: Chazelas Eloi , Deschasaux Mélanie , Srour Bernard , Kesse-Guyot Emmanuelle , Julia Chantal , Alles Benjamin , Druesne-Pecollo Nathalie , Galan Pilar , Hercberg Serge , Latino-Martel Paule , Esseddik Younes , Szabo Fabien , Slamich Pierre , Gigandet Stephane , Touvier Mathilde
Published: March 2020

Background. More than 330 food additives (e.g. artificial sweeteners, emulsifiers, dyes) are authorized in Europe, with a great variability of use across food products. Objective. The objective of this study was to investigate the distribution and co-occurrence of food additives in a large-scale database of foods and beverages available on the French market. Design. The open access crowdsourced Open Food Facts database (https://world.openfoodfacts.org/) was used to retrieve the composition of food and beverage products commonly marketed on the French market (n = 126,556), based on the ingredients list. Clustering of food additive variables was used in order to determine groups of additives frequently co-occurring in food products. The clusters were confirmed by network analysis, using theeLassomethod. Results. Fifty-three-point eight percent of food products contained at least 1 food additive and 11.3% at least 5. Food categories most likely to contain food additives (in more than 85% of food items) were artificially sweetened beverages, ice creams, industrial sandwiches, biscuits and cakes. The most frequently used food additives were citric acid, lecithins and modified starches (>10,000 products each). Some food additives with suspected health effects also pertained to the top 50: sodium nitrite, potassium nitrate, carrageenan, monosodium glutamate, sulfite ammonia caramel, acesulfame K, sucralose, (di/tri/poly) phosphates, mono- and diglycerides of fatty acids, potassium sorbate, cochineal, potassium metabisulphite, sodium alginate, and bixin (>800 food products each). We identified 6 clusters of food additives frequently co-occurring in food products. Conclusions. Food additives are widespread in industrial French products and some clusters of additives frequently co-occurring in food products were identified. These results pave the way to future etiological studies merging composition data to food consumption data to investigate their association with chronic disease risk, in particular potential ‘cocktail effects’.
Purification, Characterization and Mechanistic Evaluation of Angiotensin Converting Enzyme Inhibitory Peptides Derived from Zizyphus Jujuba Fruit
Authors: Memarpoor-Yazdi Mina , Zare-Zardini Hadi , Mogharrab Navid , Navapour Leila
Published: March 2020

The synthetic Angiotensin Converting Enzyme (ACE) inhibitors have side effects and hence demands for natural ACE inhibitors have been rising. The aim of this study is to purify and introduce natural ACE inhibitors extracted from Zizyphus jujuba fruits. Proteins from Zizyphus jujuba were lysed by trypsin, papain and their combination. Acquired peptides were purified and evaluated for ACE inhibitory activity. Peptide fractions with inhibitory activity were sequenced using tandem mass spectrometry. To elucidate the mode of peptide binding to ACE, homology modeling, molecular docking and molecular dynamics simulation were performed. Amino acid sequence of F2 and F4 peptides, which were the most active hydrolysates, were determined to be IER and IGK with the IC50 values of 0.060 and 0.072 mg/ml, respectively. Results obtained by computational analysis revealed that similar to the common ACE competitive inhibitors such as captopril, IER tripeptide binds to the enzyme active site, in vicinity of the zinc binding site, and occupies the S1 and S2’ subsites. Binding occurs through hydrogen bonding with Gln293, Lys522, His524, Tyr531 and also several hydrophobic interactions. Collectively, these findings indicate that IER tripeptide inhibits the rabbit ACE enzyme through a competitive mechanism of inhibition with IC50 values in the millimolar range.
Retraction Note: Oscillations of the baseline of solar magnetic field and solar irradiance on a millennial timescale
Authors: Zharkova V. V. , Shepherd S. J. , Zharkov S. I. , Popova E.
Published: March 2020

This article has been retracted.
In silico simulation of future hybrid performance to evaluate heterotic pool formation in a self-pollinating crop
Authors: Cowling Wallace A. , Gaynor R. Chris , Antolín Roberto , Gorjanc Gregor , Edwards Stefan M. , Powell Owen , Hickey John M.
Published: March 2020

Hybrid vigour has the potential to substantially increase the yield of self-pollinating crops such as wheat and rice, but future hybrid performance may depend on the initial strategy to form heterotic pools. We used in silico stochastic simulation of future hybrid performance in a self-pollinating crop to evaluate three strategies of forming heterotic pools in the founder population. The model included either 500, 2000 or 8000 quantitative trait nucleotides (QTN) across 10 chromosomes that contributed to a quantitative trait with population mean 100 and variance 10. The average degree of dominance at each QTN was either 0.2, 0.4 or 0.8 with variance 0.2. Three strategies for splitting the founder population into two heterotic pools were compared: (i) random split; (ii) split based on genetic distance according to principal component analysis of SNP genotypes; and (iii) optimized split based on F1 hybrid performance in a diallel cross among the founders. Future hybrid performance was stochastically simulated over 30 cycles of reciprocal recurrent selection based on true genetic values for additive and dominance effects. The three strategies of forming heterotic pools produced similar future hybrid performance, and superior future hybrids to a control population selected on inbred line performance when the number of quantitative trait nucleotides was ≥2000 and/or the average degree of dominance was ≥0.4.
Shoreline Erosion Assessment Modelling for Sohar Region: Measurements, Analysis, and Scenario
Authors: Abushandi E. , Abualkishik A.
Published: March 2020

The extended coastlines of Oman have been forced to change in the last few decades because of urbanization development or by natural disasters. Recently, Oman has suffered from a couple of tornados and cyclones, e.g. Cyclone Gonu on June 1, 2007, making the changes even much more dynamic. In order to protect the coastal regions infrastructure, an accurate estimation of shoreline erosion is required. This research paper presents an assessment of shoreline erosion magnitudes using field measurements coupled with Multiple Linear Regressions Models (MLR) to predict future changes. Inverse Distance Weighing and Kriging interpolation methods have been applied in order to visualize shoreline variations from gathered data prospective. The field measurements for the shoreline were taken at 19 different points, the space between the points in a range of 500–700 m approximately. The first field measurements were taken on 19th 20th 21st of June, 2016 while the second field measurements were taken on 14th 15th 16th of November 2016. Pearson correlation shows a strong relationship between the first and the second field trips with an average of 0.83. This significant relationship ensures the applicability of MLRs to project future changes on the shorelines. The results of the MLRs showed severe negative volumetric shoreline erosion with an average of 5.2 m/year with some exceptions at the catchment outlets.