bluuebunny/crossref_metadata_2025 huggingface dataset:
Amphibians in an urban environment: a case study from a central European city (Wrocław, Poland)
Authors: Konowalik Agnieszka , Najbar Anna , Konowalik Kamil , Dylewski Łukasz , Frydlewicz Marzena , Kisiel Paweł , Starzecka Agata , Zaleśna Anna , Kolenda Krzysztof
Published: February 2020

In 2016, we studied the occurrence of amphibians in 231 selected ponds in the city of Wrocław (Lower Silesia, Poland) and confirmed the occurrence of 10 species: Bombina bombina, Bufo bufo, Bufotes viridis, Hyla arborea, Pelobates fuscus, Pelophylax esculentus complex, Rana arvalis, Rana temporaria, Lissotriton vulgaris and Triturus cristatus. Among all studied sites, the most common were P. esculentus complex (146 occupied sites, 63.2%) and B. bufo (119, 51.5%), while the rarest was P. fuscus (8, 3.5%). The number of species at a single site varied from 0 (28 sites, 12.1%) to 9 (1 site, 0.4%). Frequency and mean amphibian species richness reached 87.9% and 2.7 ± 1.9, respectively. The composition of amphibian species did not change in comparison to previous studies conducted in the years 1997–2009, but declining trends in five species (B. bombina, B. viridis, H. arborea, P. esculentus complex, P. fuscus) were observed (28 compared sites). The results revealed that the permanency of ponds, their occurrence in the vicinity of river valleys, and a high ratio of watercourse length and green area around ponds are positively correlated and have a significant influence on amphibian species richness within the city. Thus, these identified factors should be considered in the course of sustainable urban planning in order to avoid potential conflicts between nature conservation and urban development.
Peculiarities in the designations of hepatitis B virus genes, their products, and their antigenic specificities: a potential source of misunderstandings
Authors: Gerlich Wolfram H. , Glebe Dieter , Kramvis Anna , Magnius Lars O.
Published: February 2020

The nomenclature of the hepatitis B virus (HBV) genes and their products has developed stepwise, occasionally in an erratic way, creating many misunderstandings, especially among those who do not know the structure of HBV and its genome in detail. One of the most frequent misunderstandings, even presented in leading journals, is the designation of HBV “e”-antigen asenvelopeorearlyantigen. Another problem area are the so-called “pre” regions in the HBV genome present upstream of both the core and the surface genes of HBV, inadvertently suggesting that they may be a part of correspondingprecursorproteins. Misnomers and misclassifications are frequent in defining the subgenotypes and serological subtypes of HBV. Even the well-established terminology for HBV surface (HBs) or HBV core (HBc) antigen deviates from the conventional virological nomenclature for viral envelopes or capsid proteins/antigens, respectively. Another matter of undesirable variability between publications is the numbering of the nucleotides and the graphical representation of genomic maps. This editorial briefly explains how the nomenclature evolved, what it really means, and suggests how it could be adapted to today’s knowledge.
Spatial variability of organic matter degradability in tidal Elbe sediments
Authors: Zander Florian , Heimovaara Timo , Gebert Julia
Published: February 2020

Purpose

The microbial turnover of sediment organic matter (OM) in ports and waterways impacts water quality, sonic depth finding and presumably also rheological properties as well as greenhouse gas emissions, especially if organic carbon is released as methane. As a consequence, sediment management practices as a whole are affected. This study aimed to discern spatial OM degradability patterns in the Port of Hamburg and investigated correlations with standard analytical properties as a basis for future predictive modelling.

Materials and methods

Sediments in the Port of Hamburg were repeatedly sampled at nine locations along an east-west transect using a 1-m corer. In a stratified sampling approach, layers of suspended particulate matter (SPM), fluid mud (FM), pre-consolidated sediment (PS) and consolidated sediment (CS) were identified and individually analysed for long-term aerobic and anaerobic degradation of organic matter, DNA concentration, stable carbon isotope signature, density fractions and standard solids and pore water properties.

Results and discussion

The investigation area was characterised by a distinct gradient with a 10-fold higher OM degradability in upstream areas and lower degradability in downstream areas. Concomitantly, upstream locations showed higher DNA concentrations and more negative δ13C values. The share of bulk sediment in the heavy density fraction as well as the proportion and absolute amount of organic carbon were significantly larger at downstream locations. A depth and hence age-related gradient was found at individual locations, showing higher degradability of the upper, younger material, concomitant with higher DNA concentration, and lower OM turnover in the deeper, older and more consolidated material. Deeper layers were also characterised by higher concentrations of pore water ammonium, indicative of anaerobic nitrogen mineralisation.

Conclusions

Organic matter lability is inversely linked to its stabilisation in organo-mineral complexes. The observed degradability gradient is likely due to the different OM quality in relation to its origin. Downstream OM enters the system with the tidal flood current from the direction of the North Sea whereas upstream locations receive OM originating from the catchment, containing more autochthonous, plankton-derived and more easily degradable components. At individual sampling points, depth-related degradability gradients reflect an age gradient, with easily degradable material in top layers and increasing stabilisation of OM in organo-mineral compounds with depth.
Recommender System for Responsive Engagement of Senior Adults in Daily Activities
Authors: Kulev Igor , Valk Carlijn , Lu Yuan , Pu Pearl
Published: February 2020

Understanding and predicting how people change their behavior after an intervention from time series data is an important task for health recommender systems. This task is especially challenging when the time series data is frequently sampled. In this paper, we develop and propose a novel recommender system that aims to promote physical activeness in elderly people. The main novelty of our recommender system is that it learns how senior adults with different lifestyle change their activeness after a digital health intervention from minute-by-minute fitness data in an automated way. We trained the system and validated the recommendations using data from senior adults. We demonstrated that the low-level information contained in time series data is an important predictor of behavior change. The insights generated by our recommender system could help senior adults to engage more in daily activities.
Growth pattern can be used as a new characteristic to predict malignancy in breast cancer
Authors: Wang Bin , Zhu Lizhe , He Chenyang , Tai Minghui , Zhou Can , Ge Guanqun , Zhang Huimin , He Jianjun , Wang Ke
Published: February 2020

Background

To date, anatomic tumor length is a key criterion for cancer staging and can be used to evaluate the effectiveness of therapies. This article describes growth pattern that can be used as a new characteristic to represent disease burden and tumor features and predict lymphatic metastasis.

Methods

Patients with breast cancer were included in this 10-year (1999–2008) hospital-based multicenter retrospective study. The pathologic length/height ratio was used to illustrate the correlation between tumor features, behaviors and treatments in breast malignancies. The most appropriate ratio was chosen based on the comprehensive evaluation of p value and changing trend of each characteristic.

Results

The sample consisted of 4211 women diagnosed with breast cancer. Among them, 2037 patients with complete pathologic length, width and height information were included in the final analysis. There were 2.34 ± 4.77 metastatic lymph nodes for spheroid tumors and 3.21 ± 5.82 for ellipsoid tumors when the cutoff point was 2. In addition, the proportion of ellipsoidal tumors gradually increased from 54.36 to 56.67% in the upper outer quadrant (UOQ) and from 6.7 to 9.03% in the central region with an increase in the cutoff point. The proportion of ER + PR + ellipsoid tumors significantly decreased from 50.1 to 45.35% and that of ER–PR ellipsoid tumors significantly increased from 32.73 to 36.24% with an increase in the cutoff point. Additionally, the best length/weight ratio to distinguish spheroid and ellipsoid tumors was 2.

Conclusion

This study described for the first time how growth pattern is correlated with tumor malignancy and how it influences the selection of therapeutic strategies for patients.
The reverse Magnus effect in golf balls
Authors: Lyu Bin , Kensrud Jeffery , Smith Lloyd
Published: February 2020

The following considers the lift and drag response of three commercially available golf balls. The balls were projected with spin through still air in a laboratory setting to investigate a reverse Magnus effect, where balls move in the opposite direction of the expected lift force. The drag and lift coefficients were found by measuring ball position and speed at three points along its trajectory. Three ball types, with different dimple patterns, exhibited reverse Magnus behavior between 5 × 104 < Re < 7 × 104 and 750 < ω < 2250 rpm. The golf ball with circular dimples had the least severe reverse Magnus effect, CL = − 0.1, while the ball with hexagonal dimples had the greatest, CL = − 0.15. The magnitude of the reverse Magnus effect was related to the drag crisis of each ball model. As the slope of the drag crisis became steeper, the magnitude of the reverse Magnus effect increased.
The impact of major warming at 14.7 ka on environmental changes and activity of Final Palaeolithic hunters at a local scale (Orawa-Nowy Targ Basin, Western Carpathians, Poland
Authors: Lemanik Anna , Baca Mateusz , Wertz Krzysztof , Socha Paweł , Popović Danijela , Tomek Teresa , Lipecki Grzegorz , Kraszewska Anna , Miękina Barbara , Żeromska Aleksandra , Pereswiet-Soltan Andrea , Szyndlar Zbigniew , Cieśla Magda , Valde-Nowak Paweł , Mackiewicz Paweł , Nadachowski Adam
Published: February 2020

There is a widespread belief that the abrupt warming at 14.7 ka had a profound impact on the environment. However, the direct correlation between the global climatic event and changes in local environments is not obvious. We examined faunal succession in an intra-mountain basin of the Western Carpathians to assess the potential influence of the climatic change between Greenland Stadial-2a and Greenland Interstadial-1e on the local environment. We investigated three vertebrate assemblages (total number of identified specimens = 18,745; minimum number of individuals = 7515; 138 taxa) from Obłazowa Cave (western entrance) and a Rock overhang in Cisowa Rock, radiocarbon dated to the period before and after the global warming, between ca. 17.0 and 14.0 ka. Our data revealed that the major abrupt warming that occurred 14.7 ka had little impact on the local environment, which could suggest that ecosystems in Central Europe were resilient to the abrupt global climate changes. The increase in fauna population sizes and species diversities in local biotopes was gradual and began long before the temperature increase. This was supported by the analysis of ancient DNA of Microtus arvalis, which showed a gradual increase in effective population size after 19.0 ka. The results of palaeoclimatic reconstruction pointed out that the compared sites were characterized by similar climatic conditions. According to our calculations, the differences in the annual mean temperatures did not exceed 0.5 °C and mean annual thermal amplitude changed from 22.9 to 22.4 °C. The environmental changes before 14.7 ka had no impact on the activity of Final Palaeolithic hunters in the studied area.
Characterization of efficient networks in a generalized connections model with endogenous link strength
Authors: Olaizola Norma , Valenciano Federico
Published: February 2020

We consider a natural generalization of Jackson and Wolinsky’s (J Econ Theory 71:44–74, 1996) connections model where the quality or strength of a link depends on the amount invested in it and is determined by a non-decreasing function of that amount. The information that the nodes receive through the network is the revenue from investments in links. We prove that in this most general version of the connections model, the only possibly non-empty efficient networks, in the sense of maximizing the aggregate profit, are still the all-encompassing star and the complete network, with the sole and rare exception of a highly particular case where there is a draw between the all-encompassing star, the complete network and a whole range of a particular type of nested split graph structures intermediate between them.
The Impact of Parental Involvement Laws on the Abortion Rate of Minors
Authors: Joyce Theodore J. , Kaestner Robert , Ward Jason
Published: February 2020

In this article, we conduct a comprehensive analysis of the effect of parental involvement (PI) laws on the incidence of abortions to minors in the United States. We contribute to the extant literature in several ways. First, we explore differences in estimates of the effect of PI laws across time that may result from changes in contraception, the composition of pregnant minors, abortion access in nearby states, and differences in how these laws are enforced. We find that PI laws enacted before the mid-1990s are associated with a 15% to 20% reduction in abortions to minors, but PI laws enacted after this time are not associated with declines in abortions to minors. Second, we assess the role of out-of-state travel by minors and find that it is not a significant factor moderating the effect of PI laws. Third, we use a synthetic control approach to explore state-level heterogeneity in the effect of PI laws and find large differences in the effect of PI laws on abortions to minors by state that appear unrelated to the type of PI law or whether contiguous states have enacted PI laws. Finally, we show that estimates of the effect of PI laws using data from either the Centers for Disease Control or the Guttmacher Institute do not differ qualitatively once differences in the states and years available across these data are harmonized.
Enhancing Safety in the Polish High-Methane Coal Mines: an Overview
Authors: Szlązak Nikodem , Obracaj Dariusz , Swolkień Justyna
Published: February 2020

Polish coal mines are characterized by severe geological conditions and the co-occurrence of natural hazards. These hazards are associated with methane and dust emissions during mining processes which can provide methane, dust or methane-dust explosions. Besides, there are such natural hazards as gas and rock outbursts, rock bursts, spontaneous combustion of coal and environmental heat load. The mutual influences of various geological conditions, as well as the natural hazards, intensify the increase of the methane explosion hazard. The occurrence of methane explosions in the Polish mining industry between 2013 and 2108 are analyzed. Fatal accidents are compared with similar events in the global mining industry. The methods of preventing the explosion hazard as well as methane emission control in the Polish coal mining sector are presented. Methane hazard prevention should be adapted to levels and other natural hazards, especially those related to ventilation of underground mine. The methods of preventing methane emissions into mine excavations are often contrary to the means of preventing other ventilation-related hazards in the underground mine, e.g. the prevention of spontaneous combustion of coal in the goaf of longwall panel. Therefore, the design of longwall panels should be preceded by a detailed analysis of the results of both methane emission prediction and forecast of other ventilation-related hazards.
Effect of a Condom Cover on Vaginal Photoplethysmographic Responses
Authors: Sawatsky Megan L. , Lalumière Martin L.
Published: February 2020

Introduction

The vaginal photoplethysmograph (VPP) is a reusable intravaginal device often employed in sexual psychophysiology studies to assess changes in vaginal blood flow, an indicator of sexual arousal.

Aim

To test whether placing a disposable cover on the VPP probe impacts the acquired data. A condom cover would reduce risk of disease transmission and likely increase participant comfort but may negatively impact the VPP signal.

Method

The genital responses of 25 cisgender women (mean age = 21.3 years, standard deviation = 2.6) were assessed with VPP in a within-subjects design with 2 conditions—with and without a polyisoprene condom cover. Sexual responses were elicited by audiovisual film clips that varied in erotic intensity: nonsexual (nonsexual male-female interaction), low-intensity sexual (nude exercise), and high-intensity sexual (male-female intercourse). Women continuously rated their sexual arousal during stimulus presentations.

Main Outcome Measure

Change in vaginal pulse amplitude and also self-reported sexual arousal.

Results

The magnitude of sexual response to each stimulus category and the overall pattern of results were found to be highly similar in the cover-off and cover-on conditions. The high-intensity sexual stimulus category elicited a greater sexual response than all other categories. The low-intensity sexual category elicited a (small) genital response in only the cover-on condition, although we suspect this is a spurious finding. There was no difference in the average number of edited movement artifacts across conditions.

Clinical Implications

Potential benefits of encasing the VPP probe with a protective cover include enhanced participant safety and comfort, especially if assessing genital responses of high-risk or immunocompromised samples. The use of a cover complies with current guidelines for reprocessing semi-critical medical devices (eg, vaginal ultrasound probes) in many regions.

Strengths & Limitations

Although the idea of a VPP probe cover had been discussed among sexual psychophysiology researchers, this is the first study to empirically test whether a cover could jeopardize VPP data. Potential limitations include the use of a 10-Hz VPP sampling rate and a cover that was not tailored to the size of the VPP probe.

Conclusion

Placing a protective cover on the VPP probe did not appear to meaningfully impact sexual arousal or the VPP data. Based on these results and the potential advantages of a protective cover, researchers may wish to integrate the use a condom cover in their experiment protocols and clinical applications.
High-Frequency Pornography Use May Not Always Be Problematic
Authors: Bőthe Beáta , Tóth-Király István , Potenza Marc N. , Orosz Gábor , Demetrovics Zsolt
Published: February 2020

Background

Previously, variable-centered analytic approaches showed positive, weak-to-moderate associations between frequency of pornography use (FPU) and problematic pornography use (PPU). However, person-centered studies are sparse in the literature, and these could provide insight into whether there are individuals who use pornography frequently and do not experience problems or whether there are individuals with comparable high-frequency use who differ on reported experiencing of negative consequences.

Aim

The aims of the present study were (i) to identify profiles of pornography use based on FPU and PPU by applying a person-centered analytic approach and (ii) to examine whether the identified profiles could be distinguished based on theoretically relevant demographic and psychological constructs.

Methods

Latent profile analyses were conducted on 3 nonclinical samples recruited from general websites and a pornography site (study 1: N = 14,006; study 2: N = 483; study 3: N = 672).

Results

Results were consistent across all studies. 3 distinct pornography-use profiles emerged: nonproblematic low-frequency pornography use (68–73% of individuals), nonproblematic high-frequency pornography use (19–29% of individuals), and problematic high-frequency use (3–8% of individuals). Nonproblematic and problematic high-frequency-use groups showed differences in several constructs (ie, hypersexuality, depressive symptoms, boredom susceptibility, self-esteem, uncomfortable feelings regarding pornography, and basic psychological needs).

Clinical Translation

FPU should not be considered as a sufficient or reliable indicator of PPU because the number of people with nonproblematic high-frequency use was 3–6 times higher than that with problematic high-frequency use. These results suggest that individuals with PPU use pornography frequently; however, FPU may not always be problematic.

Strengths & Limitations

Self-report cross-sectional methods have possible biases that should be considered when interpreting findings (eg, underreporting or overreporting). However, the present research included 3 studies and involved large community samples and visitors of a pornography website. The present study is the first that empirically investigated pornography-use profiles with a wide range of correlates using both severity of PPU and FPU as profile indicators on specific and general samples.

Conclusion

The present study is a first step in the differentiated examination of pornography-use profiles, taking into consideration both PPU and FPU, and it provides a foundation for further clinical and large-scale studies. Different psychological mechanisms may underlie the development and maintenance of FPU with or without PPU, suggesting different treatment approaches. Therefore, the present results may guide clinical work when considering reasons for seeking treatment for PPU.
PRIMES REPRESENTED BY INCOMPLETE NORM FORMS
Authors: MAYNARD JAMES
Published: February 2020

Let

$K=\mathbb{Q}(\unicode[STIX]{x1D714})$

with

$\unicode[STIX]{x1D714}$

the root of a degree

$n$

monic irreducible polynomial

$f\in \mathbb{Z}[X]$

. We show that the degree

$n$

polynomial

$N(\sum _{i=1}^{n-k}x_{i}\unicode[STIX]{x1D714}^{i-1})$

in

$n-k$

variables takes the expected asymptotic number of prime values if

$n\geqslant 4k$

. In the special case

$K=\mathbb{Q}(\sqrt[n]{\unicode[STIX]{x1D703}})$

, we show that

$N(\sum _{i=1}^{n-k}x_{i}\sqrt[n]{\unicode[STIX]{x1D703}^{i-1}})$

takes infinitely many prime values, provided

$n\geqslant 22k/7$

.

Our proof relies on using suitable ‘Type I’ and ‘Type II’ estimates in Harman’s sieve, which are established in a similar overall manner to the previous work of Friedlander and Iwaniec on prime values of

$X^{2}+Y^{4}$

and of Heath-Brown on

$X^{3}+2Y^{3}$

. Our proof ultimately relies on employing explicit elementary estimates from the geometry of numbers and algebraic geometry to control the number of highly skewed lattices appearing in our final estimates.
Uprooting Narratives: Legacies of Colonialism in the Neoliberal University
Authors: Bowman Melanie , Rebolleda-Gómez María
Published: February 2020

Two intertwined stories evince the influence of colonialism on Western universities. The first story centers on a conflict about wild rice research between the Anishinaabe people and the University of Minnesota. Underlying this conflict is a genetic notion of biological identity that facilitates the commodification of wild rice. This notion of identity is inextricably linked to agricultural control and expansion. The second story addresses the foundation of Western universities on the goals of civilization and capitalist productivity. These norms persist even in diversity efforts through a focus on individualized notions of difference rather than socially contextualized and politically significant identities. The tendency to produce both knowledge and knowers as commodities results in the alienation, individuation, and abstraction of objects of research and researchers themselves. Decolonial change demands that we learn the specific histories of our universities and disciplines, break disciplinary boundaries, and contest commodification in knowledge production.
Association between symptoms of sleep apnea and problem behaviors in young adult twins and siblings
Authors: Madrid-Valero Juan J. , Barclay Nicola L. , Rowe Richard , Perach Rotem , Buysse Daniel J. , Ordoñana Juan R. , Eley Thalia C. , Gregory Alice M.
Published: February 2020

Background

Sleep apnea is one of the most common sleep disorders and it is related to multiple negative health consequences. Previous studies have shown that sleep apnea is influenced by genetic factors. However, studies have not investigated the genetic and environmental influences of symptoms of sleep apnea in young adults. Furthermore, the underpinnings of the relationship between apnea symptoms and internalizing/externalizing problems are unknown. The objectives of this study were to estimate the magnitude of: (1) genetic and environmental influences on self-reported apnea symptoms; (2) the relationship between self-reported apnea symptoms and internalizing/externalizing traits; (3) genetic and environmental influences on the associations between self-reported apnea symptoms, internalizing behaviors and externalizing behaviors.

Methods

In a twin/sibling study, univariate and multivariate models were fitted to estimate both individual variance and sources of covariance between symptoms of sleep apnea and internalizing/externalizing behaviors.

Results

Our results show that genetic influences account for 40% of the variance in sleep apnea symptoms. Moreover, there are modest associations between depression, anxiety and externalizing behaviors with apnea symptoms (ranging from r = 0.22–0.29). However, the origins of these associations differ. For example, whereas most of the covariation between symptoms of depression and sleep apnea can be explained by genes (95%), there was a larger role for the environment (53%) in the association between symptoms of anxiety and sleep apnea.

Conclusions

Genetic factors explain a significant proportion of variance in symptoms of apnea and most of the covariance with depression.
A cubical Squier’s theorem
Authors: Lucas Maxime
Published: February 2020

The homotopical Squier’s theorem relates rewriting properties of a presentation of a monoid with homotopical invariants of this monoid. This theorem has since been extended by Guiraud and Malbos, yielding a so-called polygraphic resolution of a monoid starting from a presentation with suitable rewriting properties. In this article, we argue that cubical categories are a more natural setting in which to express and possibly extend Guiraud and Malbos construction. As a proof-of-concept, we give a new proof of Squier’s homotopical theorem using cubical categories.
Capacity building and mentorship among pan-Canadian early career researchers in community-based primary health care
Authors: Nicholson Kathryn , Ganann Rebecca , Bookey-Bassett Sue , Garland Baird Lisa , Garnett Anna , Marshall Zack , Khan Anum Irfan , Pirrie Melissa , Sasseville Maxime , Ben Charif Ali , Poitras Marie-Ève , Kyoon-Achan Grace , Dionne Émilie , Hassani Kasra , Stewart Moira
Published: February 2020

Aim:

To describe activities and outcomes of a cross-team capacity building strategy that took place over a five-year funding period within the broader context of 12 community-based primary health care (CBPHC) teams.

Background:

In 2013, the Canadian Institutes of Health Research funded 12 CBPHC Teams (12-Teams) to conduct innovative cross-jurisdictional research to improve the delivery of high-quality CBPHC to Canadians. This signature initiative also aimed to enhance CBPHC research capacity among an interdisciplinary group of trainees, facilitated by a collaboration between a capacity building committee led by senior researchers and a trainee-led working group.

Methods:

After the committee and working group were established, capacity building activities were organized based on needs and interests identified by trainees of the CBPHC Teams. This paper presents a summary of the activities accomplished, as well as the outcomes reported through an online semistructured survey completed by the trainees toward the end of the five-year funding period. This survey was designed to capture the capacity building and mentorship activities that trainees either had experienced or would like to experience in the future. Descriptive and thematic analyses were conducted based on survey responses, and these findings were compared with the existing core competencies in the literature.

Findings:

Since 2013, nine webinars and three online workshops were hosted by trainees and senior researchers, respectively. Many of the CBPHC Teams provided exposure for trainees to innovative methods, CBPHC content, and showcased trainee research. A total of 27 trainees from 10 of the 12-Teams responded to the survey (41.5%). Trainees identified key areas of benefit from their involvement in this initiative: skills training, networking opportunities, and academic productivity. Trainees identified gaps in research and professional skill development, indicating areas for further improvement in capacity building programs, particularly for trainees to play a more active role in their education and preparation.
Fluorescence angiography compared to toe blood pressure in the	evaluation of severe limb ischemia
Authors: Seinturier Christophe , Blaise Sophie , Tiffet Théophile , Provencher Cynthia Brousseau , Cracowski Jean Luc , Pernod Gilles , Carpentier Patrick
Published: February 2020

Summary: Background: Severity of limb ischemia in peripheral arterial disease (PAD) patients is usually evaluated by clinical assessment and toe blood pressure (TBP) or transcutaneous oxygen pressures (TcPO 2). Indocyanin green angiography (IGA) is a promising tool generating a foot cartography of skin microvascular perfusion. However, there is no consensus about the fluorescence parameters that should be used to evaluate ischemia. The purpose of this cross-sectional evaluation and 3-month clinical follow-up was to determine the best fluorescence parameter for the evaluation of severe PAD, using TBP as reference. Patients and methods: IGA was realized in patients with clinical suspicion of CLI in addition to TBP and TcPO 2. Parameters from the time intensity fluorescence curve measured on the foot were compared with TBP (primary reference), and with TcPO2. Clinical outcomes (amputation, revascularization, death) were recorded at 3 months follow-up. Results: Thirty-four patients were included and IGA could be analysed in 29 of them. When all limbs were studied, no significant correlation was found between any of the measured fluorescence parameters (saturation time, ingress slope, amplitude, delay) and TBP pressure neither TCPO2. In the limbs with CLI, a significant correlation between the TBP and amplitude on the forefoot was found. According to the outcome, none of the fluorescence parameters showed a significant prognostic value in contrast to the significant results for TBP and TcPO2. Conclusions: In this study, quantitative analysis of IGA parameters did not show any prognostic value, nor was there any significant statistical association with well-established prognostic parameters such as TBP and TcPO 2 in patients with suspected CLI. A correlation was found between amplitude and TBP in patients with CLI. Topographical information such as perfusion heterogeneity was not evaluated and remains a valuable target to be investigated.
They Came From the Pacific: How Changing Arctic Currents Could Contribute to an Ecological Regime Shift in the Atlantic Ocean
Authors: Kelly S. J. , Popova E. , Aksenov Y. , Marsh R. , Yool A.
Published: February 2020

The Arctic Ocean is rapidly changing. With warming waters, receding sea ice, and changing circulation patterns, it has been hypothesized that previously closed ecological pathways between the Pacific and Atlantic Oceans will be opened as we move toward a seasonally ice‐free Arctic. The discovery of the Pacific diatom Neodenticula seminae in the Atlantic suggests that a tipping point may have already been reached and this “opening up” of the Arctic could already be underway. Here, we investigate how circulation connectivity between the Pacific and Atlantic Oceans has changed in recent decades, using a state‐of‐the‐art high‐resolution ocean model and a Lagrangian particle‐tracking method. We identify four main trans‐Arctic pathways and a fifth route that is sporadically available with a shorter connectivity timescale. We discuss potential explanations for the existence of this “shortcut” advective pathway, linking it to a shift in atmospheric and oceanic circulation regimes. Advective timescales associated with each route are quantified, and seasonal and interannual trends in the main four pathways are discussed, including an increase in Fram Strait outflow relative to the Canadian Archipelago. In conclusion, we note that while tipping points for ecological connectivity are species dependent, even the most direct routes require multiannual connectivity timescales.
Soil Organic Carbon Across Mexico and the Conterminous United States (1991–2010)
Authors: Guevara Mario , Arroyo Carlos , Brunsell Nathaniel , Cruz Carlos O. , Domke Grant , Equihua Julian , Etchevers Jorge , Hayes Daniel , Hengl Tomislav , Ibelles Alejandro , Johnson Kris , de Jong Ben , Libohova Zamir , Llamas Ricardo , Nave Lucas , Ornelas Jose L. , Paz Fernando , Ressl Rainer , Schwartz Anita , Victoria Arturo , Wills Skye , Vargas Rodrigo
Published: February 2020

Soil organic carbon (SOC) information is fundamental for improving global carbon cycle modeling efforts, but discrepancies exist from country‐to‐global scales. We predicted the spatial distribution of SOC stocks (topsoil; 0–30 cm) and quantified modeling uncertainty across Mexico and the conterminous United States (CONUS). We used a multisource SOC dataset (>10 000 pedons, between 1991 and 2010) coupled with a simulated annealing regression framework that accounts for variable selection. Our model explained ~50% of SOC spatial variability (across 250‐m grids). We analyzed model variance, and the residual variance of six conventional pedotransfer functions for estimating bulk density to calculate SOC stocks. Two independent datasets confirmed that the SOC stock for both countries represents between 46 and 47 Pg with a total modeling variance of ±12 Pg. We report a residual variance of 10.4 ±5.1 Pg of SOC stocks calculated from six pedotransfer functions for soil bulk density. When reducing training data to define decades with relatively higher density of observations (1991–2000 and 2001–2010, respectively), model variance for predicted SOC stocks ranged between 41 and 55 Pg. We found nearly 42% of SOC across Mexico in forests and 24% in croplands, whereas 31% was found in forests and 28% in croplands across CONUS. Grasslands and shrublands stored 29 and 35% of SOC across Mexico and CONUS, respectively. We predicted SOC stocks >30% below recent global estimates that do not account for uncertainty and are based on legacy data. Our results provide insights for interpretation of estimates based on SOC legacy data and benchmarks for improving regional‐to‐global monitoring efforts.
The UV Spectrum of the Lyman‐Birge‐Hopfield Band System of N2 Induced by Cascading from Electron Impact
Authors: Ajello Joseph M. , Evans J. Scott , Veibell Victoir , Malone Charles P. , Holsclaw Greg M. , Hoskins Alan C. , Lee Rena A. , McClintock William E. , Aryal Saurav , Eastes Richard W. , Schneider Nicholas
Published: February 2020

We have measured in the laboratory the far ultraviolet (FUV: 125.0–170.0 nm) cascade‐induced spectrum of the Lyman‐Birge‐Hopfield (LBH) band system (
) of N2 excited by 30–200 eV electrons. The cascading transition begins with two processes: radiative and collision‐induced electronic transitions (CIETs) involving two states (
and w1Δu → a1Πg), which are followed by a cascade induced transition
at the single‐scattering pressures employed here. Direct excitation to the a‐state produces a confined LBH spectral glow pattern around an electron beam. We have spatially resolved the electron‐induced glow pattern from an electron beam colliding with N2 at radial distances of 0–400 mm at three gas pressures. This imaging measurement is the first to isolate spectral measurements in the laboratory of single‐scattering electron‐impact‐induced fluorescence from two LBH emission processes: direct excitation, which is strongest in emission near the electron beam axis; and cascading‐induced, which is dominant far from the electron beam axis. The vibrational populations for vibrational levels from v′ = 0–2 of the a 1Πg state are enhanced by radiative cascade and CIETs, and the emission cross sections of the LBH band system for direct and cascading‐induced excitation are provided at 40, 50, 100, and 200 eV.
Photoswitching mechanism of a fluorescent protein revealed by time-resolved crystallography and transient absorption spectroscopy
Authors: Woodhouse Joyce , Nass Kovacs Gabriela , Coquelle Nicolas , Uriarte Lucas M. , Adam Virgile , Barends Thomas R. M. , Byrdin Martin , de la Mora Eugenio , Bruce Doak R. , Feliks Mikolaj , Field Martin , Fieschi Franck , Guillon Virginia , Jakobs Stefan , Joti Yasumasa , Macheboeuf Pauline , Motomura Koji , Nass Karol , Owada Shigeki , Roome Christopher M. , Ruckebusch Cyril , Schirò Giorgio , Shoeman Robert L. , Thepaut Michel , Togashi Tadashi , Tono Kensuke , Yabashi Makina , Cammarata Marco , Foucar Lutz , Bourgeois Dominique , Sliwa Michel , Colletier Jacques-Philippe , Schlichting Ilme , Weik Martin
Published: February 2020

Reversibly switchable fluorescent proteins (RSFPs) serve as markers in advanced fluorescence imaging. Photoswitching from a non-fluorescent off-state to a fluorescent on-state involves trans-to-cis chromophore isomerization and proton transfer. Whereas excited-state events on the ps timescale have been structurally characterized, conformational changes on slower timescales remain elusive. Here we describe the off-to-on photoswitching mechanism in the RSFP rsEGFP2 by using a combination of time-resolved serial crystallography at an X-ray free-electron laser and ns-resolved pump–probe UV-visible spectroscopy. Ten ns after photoexcitation, the crystal structure features a chromophore that isomerized from trans to cis but the surrounding pocket features conformational differences compared to the final on-state. Spectroscopy identifies the chromophore in this ground-state photo-intermediate as being protonated. Deprotonation then occurs on the μs timescale and correlates with a conformational change of the conserved neighbouring histidine. Together with a previous excited-state study, our data allow establishing a detailed mechanism of off-to-on photoswitching in rsEGFP2.
Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria
Authors: Garcia-Garcera Marc , Rocha Eduardo P. C.
Published: February 2020

We test the hypothesis that the frequency and cost of extracellular proteins produced by bacteria, which often depend on cooperative processes, vary with habitat structure and community diversity. The integration of the environmental distribution of bacteria (using 16S datasets) and their genomes shows that bacteria living in more structured habitats encode more extracellular proteins. In contrast, the effect of community diversity depends on protein function: it’s positive for proteins implicated in antagonistic interactions and negative for those involved in nutrient acquisition. Extracellular proteins are costly and endure stronger selective pressure for low cost and for low diffusivity in less structured habitats and in more diverse communities. Finally, Bacteria found in multiple types of habitats, including host-associated generalists, encode more extracellular proteins than niche-restricted bacteria. These results show that ecological variables, notably habitat structure and community diversity, shape the evolution of the repertoires of genes encoding extracellular proteins and thus affect the ability of bacteria to manipulate their environment.
Separability and geometry of object manifolds in deep neural networks
Authors: Cohen Uri , Chung SueYeon , Lee Daniel D. , Sompolinsky Haim
Published: February 2020

Stimuli are represented in the brain by the collective population responses of sensory neurons, and an object presented under varying conditions gives rise to a collection of neural population responses called an ‘object manifold’. Changes in the object representation along a hierarchical sensory system are associated with changes in the geometry of those manifolds, and recent theoretical progress connects this geometry with ‘classification capacity’, a quantitative measure of the ability to support object classification. Deep neural networks trained on object classification tasks are a natural testbed for the applicability of this relation. We show how classification capacity improves along the hierarchies of deep neural networks with different architectures. We demonstrate that changes in the geometry of the associated object manifolds underlie this improved capacity, and shed light on the functional roles different levels in the hierarchy play to achieve it, through orchestrated reduction of manifolds’ radius, dimensionality and inter-manifold correlations.
A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes
Authors: Beveridge Rebecca , Stadlmann Johannes , Penninger Josef M. , Mechtler Karl
Published: February 2020

Crosslinking-mass spectrometry (XL-MS) serves to identify interaction sites between proteins. Numerous search engines for crosslink identification exist, but lack of ground truth samples containing known crosslinks has precluded their systematic validation. Here we report on XL-MS data arising from measuring synthetic peptide libraries that provide the unique benefit of knowing which identified crosslinks are true and which are false. The data are analysed with the most frequently used search engines and the results filtered to an estimated false discovery rate of 5%. We find that the actual false crosslink identification rates range from 2.4 to 32%, depending on the analysis strategy employed. Furthermore, the use of MS-cleavable crosslinkers does not reduce the false discovery rate compared to non-cleavable crosslinkers. We anticipate that the datasets acquired during this research will further drive optimisation and development of XL-MS search engines, thereby advancing our understanding of vital biological interactions.
Fear of Killer Whales Drives Extreme Synchrony in Deep Diving Beaked Whales
Authors: Aguilar de Soto Natacha , Visser Fleur , Tyack Peter L. , Alcazar Jesús , Ruxton Graeme , Arranz Patricia , Madsen Peter T. , Johnson Mark
Published: February 2020

Fear of predation can induce profound changes in the behaviour and physiology of prey species even if predator encounters are infrequent. For echolocating toothed whales, the use of sound to forage exposes them to detection by eavesdropping predators, but while some species exploit social defences or produce cryptic acoustic signals, deep-diving beaked whales, well known for mass-strandings induced by navy sonar, seem enigmatically defenceless against their main predator, killer whales. Here we test the hypothesis that the stereotyped group diving and vocal behaviour of beaked whales has benefits for abatement of predation risk and thus could have been driven by fear of predation over evolutionary time. Biologging data from 14 Blainville’s and 12 Cuvier’s beaked whales show that group members have an extreme synchronicity, overlapping vocal foraging time by 98% despite hunting individually, thereby reducing group temporal availability for acoustic detection by killer whales to <25%. Groups also perform a coordinated silent ascent in an unpredictable direction, covering a mean of 1 km horizontal distance from their last vocal position. This tactic sacrifices 35% of foraging time but reduces by an order of magnitude the risk of interception by killer whales. These predator abatement behaviours have likely served beaked whales over millions of years, but may become maladaptive by playing a role in mass strandings induced by man-made predator-like sonar sounds.
Empathic responses to unknown others are modulated by shared behavioural traits
Authors: Anders Silke , Beck Christian , Domin Martin , Lotze Martin
Published: February 2020

How empathically people respond to a stranger’s pain or pleasure does not only depend on the situational context, individual traits and intentions, but also on interindividual factors. Here we ask whether empathic responses towards unknown others are modulated by behavioural similarity as a potential marker of genetic relatedness. Participants watched two supposed human players who were modelled as having a strong (player LP) or weak (player NLP) tendency to lead in social situations executing penalty shots in a virtual reality robot soccer game. As predicted, empathic response were modulated by shared behavioural traits: participants whose tendency to lead was more similar to player LP’s tendency to lead experienced more reward, and showed stronger neural activity in reward-related brain regions, when they saw player LP score a goal, and participants whose tendency to lead was more similar to player NLP’s tendency to lead showed stronger empathic responses when they saw player NLP score a goal. These findings highlight the potentially evolutionary grounded role of phenotypic similarity for neural processes underlying human social perception.
Formate dehydrogenase, ubiquinone, and cytochrome bd-I are required for peptidoglycan recognition protein-induced oxidative stress and killing in Escherichia coli
Authors: Kashyap Des R. , Kowalczyk Dominik A. , Shan Yue , Yang Chun-Kai , Gupta Dipika , Dziarski Roman
Published: February 2020

Mammalian Peptidoglycan Recognition Proteins (PGRPs) kill bacteria through induction of synergistic oxidative, thiol, and metal stress. PGRPs induce oxidative stress in bacteria through a block in the respiratory chain, which results in decreased respiration and incomplete reduction of oxygen (O2) to hydrogen peroxide (H2O2). In this study we identify the site of PGRP-induced generation of H2O2 in Escherichia coli. Tn-seq screening of E. coli Tn10 insertion library revealed that mutants in formate dehydrogenase (FDH) genes had the highest survival following PGRP treatment. Mutants lacking functional FDH-O had abolished PGRP-induced H2O2 production and the highest resistance to PGRP-induced killing, and formate enhanced PGRP-induced killing and H2O2 production in an FDH-dependent manner. Mutants in ubiquinone synthesis (but not menaquinone and demethylmenaquinone) and cytochrome bd-I (but not cytochromes bo3 and bd-II) also had completely abolished PGRP-induced H2O2 production and high resistance to PGRP-induced killing. Because electrons in the respiratory chain flow from dehydrogenases’ substrates through quinones and then cytochromes to O2, these results imply that the site of PGRP-induced incomplete reduction of O2 to H2O2 is downstream from dehydrogenases and ubiquinone at the level of cytochrome bd-I, which results in oxidative stress. These results reveal several essential steps in PGRP-induced bacterial killing.