bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting Nash equilibria for microbial metabolic interactions
Authors: Cai Jingyi , Tan Tianwei , Chan Siu H J 
Published: November 2020

Abstract

Motivation
Microbial metabolic interactions impact ecosystems, human health and biotechnology profoundly. However, their determination remains elusive, invoking an urgent need for predictive models seamlessly integrating metabolism with evolutionary principles that shape community interactions.

Results
Inspired by the evolutionary game theory, we formulated a bi-level optimization framework termed NECom for which any feasible solutions are Nash equilibria of microbial community metabolic models with/without an outer-level (community) objective function. Distinct from discrete matrix games, NECom models the continuous interdependent strategy space of metabolic fluxes. We showed that NECom successfully predicted several classical games in the context of metabolic interactions that were falsely or incompletely predicted by existing methods, including prisoner’s dilemma, snowdrift and cooperation. The improved capability originates from the novel formulation to prevent ‘forced altruism’ hidden in previous static algorithms while allowing for sensing all potential metabolite exchanges to determine evolutionarily favorable interactions between members, a feature missing in dynamic methods. The results provided insights into why mutualism is favorable despite seemingly costly cross-feeding metabolites and demonstrated similarities and differences between games in the continuous metabolic flux space and matrix games. NECom was then applied to a reported algae-yeast co-culture system that shares typical cross-feeding features of lichen, a model system of mutualism. 488 growth conditions corresponding to 3221 experimental data points were simulated. Without training any parameters using the data, NECom is more predictive of species’ growth rates given uptake rates compared with flux balance analysis with an overall 63.5% and 81.7% reduction in root-mean-square error for the two species respectively.

Availability and implementation
Simulation code and data are available at https://github.com/Jingyi-Cai/NECom.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
On the validity of the planar wave approximation to compute synthetic seismograms of teleseismic body waves in a 3-D regional model
Authors: Monteiller Vadim , Beller Stephen , Plazolles Bastien , Chevrot Sébastien 
Published: November 2020

SUMMARYInjection methods are a very efficient means to compute synthetic seismograms of short-period teleseismic body waves in 3-D regional models. The principle is to inject an incident teleseismic wavefield inside a regional 3-D Cartesian spectral-element grid. We have developed an opern-source package that allows us to inject either an incident plane wave, computed with a frequency–wavenumber method, or the complete wavefield, computed in a spherically symmetric reference earth model with AxiSEM. The computations inside the regional spectral-element grid are performed with SPECFEM3D_Cartesian. We compare the efficiency and reliability of the two injection methods for teleseismic P waves, considering a wide range of epicentral distance and hypocentral depths. Our simulations demonstrate that in practice the effects of wave front and Earth curvature are negligible for moderate size regional domains (several hundreds of kilometres) and for periods larger than 2 s. The main differences observed in synthetic seismograms are related to secondary phases that have a different slowness from the one of the reference P phase.
Engineering CGTase to improve synthesis of alkyl glycosides
Authors: Ara Kazi Zubaida Gulshan , Linares-Pastén Javier A , Jönsson Jonas , Viloria-Cols Maria , Ulvenlund Stefan , Adlercreutz Patrick , Karlsson Eva Nordberg 
Published: November 2020

Abstract
Alkyl glycoside surfactants with elongated carbohydrate chains are useful in different applications due to their improved biocompatibility. Cyclodextrin glucanotransferases can catalyze the elongation process through the coupling reaction. However, due to the presence of a hydrophobic tail, the interaction between an alkyl glycoside acceptor and the active site residues is weaker than the interaction with maltooligosaccharides at the corresponding site. Here we report the mutations of F197, G263 and E266 near the acceptor subsites in the CGTase CspCGT13 from Carboxydocella sp. The results showed that substitutions of both F197 and G263 were important for the binding of acceptor substrate dodecyl maltoside during coupling reaction. The double mutant F197Y/G263A showed enhanced coupling activity and displayed a 2-fold increase of the primary coupling product using γ-cyclodextrin as donor when compared to wildtype CspCGT13. Disproportionation activity was also reduced, which was also the case for another double mutant (F197Y/E266A) that however not showed the corresponding increase in coupling. A triple mutant F197Y/G263A/E266A maintained the increase in primary coupling product (1.8-fold increase) using dodecyl maltoside as acceptor, but disproportionation was approximately at the same level as in the double mutants. In addition, hydrolysis of starch was slightly increased by the F197Y and G263A substitutions, indicating that interactions at both positions influenced the selectivity between glycosyl and alkyl moieties.
Community health worker models in South Africa: a qualitative study on policy implementation of the 2018/19 revised framework
Authors: Murphy Joshua P , Moolla Aneesa , Kgowedi Sharon , Mongwenyana Constance , Mngadi Sithabile , Ngcobo Nkosinathi , Miot Jacqui , Evans Denise , Pascoe Sophie 
Published: November 2020

Abstract
South Africa has a long history of community health workers (CHWs). It has been a journey that has required balancing constrained resources and competing priorities. CHWs form a bridge between communities and healthcare service provision within health facilities and act as the cornerstone of South Africa’s Ward-Based Primary Healthcare Outreach Teams. This study aimed to document the CHW policy implementation landscape across six provinces in South Africa and explore the reasons for local adaptation of CHW models and to identify potential barriers and facilitators to implementation of the revised framework to help guide and inform future planning. We conducted a qualitative study among a sample of Department of Health Managers at the National, Provincial and District level, healthcare providers, implementing partners [including non-governmental organizations (NGOs) who worked with CHWs] and CHWs themselves. Data were collected between April 2018 and December 2018. We conducted 65 in-depth interviews (IDIs) with healthcare providers, managers and experts familiar with CHW work and nine focus group discussions (FGDs) with 101 CHWs. We present (i) current models of CHW policy implementation across South Africa, (ii) facilitators, (iii) barriers to CHW programme implementation and (iv) respondents’ recommendations on how the CHW programme can be improved. We chronicled the differences in NGO involvement, the common facilitators of purpose and passion in the CHWs’ work and the multitude of barriers and resource limitations CHWs must work under. We found that models of implementation vary greatly and that adaptability is an important aspect of successful implementation under resource constraints. Our findings largely aligned to existing research but included an evaluation of districts/provinces that had not previously been explored together. CHWs continue to promote health and link their communities to healthcare facilities, in spite of lack of permanent employment, limited resources, such as uniforms, and low wages.
SARS-CoV-2–Specific Neutralizing Antibody Responses in Norwegian Health Care Workers After the First Wave of COVID-19 Pandemic: A Prospective Cohort Study
Authors: Trieu Mai-Chi , Bansal Amit , Madsen Anders , Zhou Fan , Sævik Marianne , Vahokoski Juha , Brokstad Karl Albert , Krammer Florian , Tøndel Camilla , Mohn Kristin G I , Blomberg Bjørn , Langeland Nina , Cox Rebecca J ,   Bergen COVID-19 Research Group, Kittang Bård , Linchausen Dagrunn Waag , Amdam Håkon , Onyango Therese Bredholt , Bredholt Geir , Ertesvåg Nina , Lartey Sarah , Sandnes Helene Heitmann , Grøvan Fredrik , Bartsch Hauke , Syre Heidi , Real Francisco , Berg Åse Garløv 
Published: November 2020

AbstractBackgroundDuring the coronavirus disease 2019 (COVID-19) pandemic, many countries experienced infection in health care workers (HCW) due to overburdened health care systems. Whether infected HCW acquire protective immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unclear.MethodsIn a Norwegian prospective cohort study, we enrolled 607 HCW before and after the first COVID-19 wave. Exposure history, COVID-19–like symptoms, and serum samples were collected. SARS-CoV-2–specific antibodies were characterized by spike-protein IgG/IgM/IgA enzyme-linked immunosorbent and live-virus neutralization assays.ResultsSpike-specific IgG/IgM/IgA antibodies increased after the first wave in HCW with, but not in HCW without, COVID-19 patient exposure. Thirty-two HCW (5.3%) had spike-specific antibodies (11 seroconverted with ≥4-fold increase, 21 were seropositive at baseline). Neutralizing antibodies were found in 11 HCW that seroconverted, of whom 4 (36.4%) were asymptomatic. Ninety-seven HCW were tested by reverse transcriptase polymerase chain reaction (RT-PCR) during follow-up; 8 were positive (7 seroconverted, 1 had undetectable antibodies).ConclusionsWe found increases in SARS-CoV-2 neutralizing antibodies in infected HCW, especially after COVID-19 patient exposure. Our data show a low number of SARS-CoV-2–seropositive HCW in a low-prevalence setting; however, the proportion of seropositivity was higher than RT-PCR positivity, highlighting the importance of antibody testing.
Rifabutin pharmacokinetics and safety among TB/HIV-coinfected children receiving lopinavir/ritonavir-containing second-line ART
Authors: Rawizza Holly E , Oladokun Regina , Ejeliogu Emeka , Oguche Stephen , Ogunbosi Babatunde O , Agbaji Oche , Odaibo Georgina , Imade Godwin , Olaleye David , Wiesner Lubbe , Darin Kristin M , Okonkwo Prosper , Kanki Phyllis J , Scarsi Kimberly K , McIlleron Helen M 
Published: November 2020

Abstract

Background
Treatment options are limited for TB/HIV-coinfected children who require PI-based ART. Rifabutin is the preferred rifamycin for adults on PIs, but the one study evaluating rifabutin with PIs among children was stopped early due to severe neutropenia.

Methods
We evaluated rifabutin safety and plasma pharmacokinetics among coinfected children 3–15 years of age receiving rifabutin 2.5 mg/kg daily with standard doses of lopinavir/ritonavir. The AUC0–24 at 2, 4 and 8 weeks after rifabutin initiation was described using intensive sampling and non-compartmental analysis. Clinical and laboratory toxicities were intensively monitored at 12 visits throughout the study.

Results
Among 15 children with median (IQR) age 13.1 (10.9–14.0) years and weight 25.5 (22.3–30.5) kg, the median (IQR) rifabutin AUC0–24 was 5.21 (4.38–6.60) μg·h/mL. Four participants had AUC0–24 below 3.8 μg·h/mL (a target for the population average exposure) at week 2 and all had AUC0–24 higher than 3.8 μg·h/mL at the 4 and 8 week visits. Of 506 laboratory evaluations during rifabutin, grade 3 and grade 4 abnormalities occurred in 16 (3%) and 2 (0.4%) instances, respectively, involving 9 (60%) children. Specifically, grade 3 (n = 4) and grade 4 (n = 1) neutropenia resolved without treatment interruption or clinical sequelae in all patients. One child died at week 4 of HIV-related complications.

Conclusions
In children, rifabutin 2.5 mg/kg daily achieved AUC0–24 comparable to adults and favourable HIV and TB treatment outcomes were observed. Severe neutropenia was relatively uncommon and improved with ongoing rifabutin therapy. These data support the use of rifabutin for TB/HIV-coinfected children who require lopinavir/ritonavir.
Too Much or Too Little Messaging? Situational Determinants of Guilt About Mobile Messaging
Authors: Halfmann Annabell , Meier Adrian , Reinecke Leonard 
Published: November 2020

Abstract
Mobile messaging has been associated with guilt. Guilt about too much messaging may result from self-control failures during goal conflicts. Conversely, guilt about too little messaging may result from violating the salient norm to be available. This research considers both boundary conditions of guilt about mobile communication—goal conflicts and availability norm salience—simultaneously for the first time. We conducted two preregistered experiments to investigate their interplay. Results from a vignette experiment, but not from a laboratory experiment, support the hypotheses that goal conflicts trigger guilt about using messengers and that guilt about not using messengers arises if the availability norm is salient. In both studies, using messengers elicited more guilt than not using messengers. The boundary conditions did not interact in influencing guilt. Overall, this research emphasizes the importance of self-control, norms, and usage contexts when studying effects of mobile media use on emotional well-being.
Differences in Bifenthrin and Fipronil Susceptibility Among Invasive Latrodectus spp. (Araneae: Theridiidae) and Nontarget Spiders in Japan
Authors: Hayasaka Daisuke , Numa Tomoki , Sawahata Takuo 
Published: November 2020

Abstract
Prompt responses to invasive Latrodectus spiders introduced unintentionally are needed worldwide due to their medical and ecological importance. Latrodectus species are chemically controlled using pyrethroid insecticides despite concerns about the ecological impacts of these compounds on biodiversity/ecosystems. Here, the relative sensitivities (acute toxicity: 48-h LC50) of Latrodectus hasseltii Thorell and Latrodectus geometricus C.L. Koch from Japan to the conventional neurotoxic insecticide bifenthrin (pyrethroid) and a new candidate insecticide, fipronil (phenylpyrazole), were examined. Acute residual toxicity tests of these compounds in two nontarget spiders (Parasteatoda tepidariorum C.L. Koch (Araneae: Theridiidae), Badumna insignis L. Koch (Araneae: Desidae)) were conducted for comparison. To test whether bifenthrin and fipronil toxicities differed among the four spiders, corresponding species sensitivity distributions (SSDs) were compared, and hazardous concentrations were determined. Sensitivity (especially in the nontarget species) was two to four orders of magnitude higher for bifenthrin than for fipronil. The SSD patterns of the two insecticides differed significantly, with the spider communities being more sensitive to bifenthrin than to fipronil. The lethal bifenthrin concentration for Latrodectus may reduce spider populations by over 70–90%. If L. hasseltii (established throughout Japan) is targeted for effective population suppression rather than L. geometricus (with a limited distribution range) using the specified insecticide concentration (LC50 value) for fipronil, less than 20% of spider communities will be impacted. Chemical operations aimed at the effective population management and subsequent eradication of invasive Latrodectus spiders while supporting local biodiversity conservation would benefit from considerations of fipronil dosages and target species sensitivities.
Prolonged growth during the food-restricted dry season in a small African mammal
Authors: Rimbach Rebecca , Pillay Neville , Schradin Carsten 
Published: November 2020

AbstractStudying how different environmental parameters, such as resource availability and ambient temperature, affect growth rates aids to understand the evolution of different growth strategies. Low levels of food availability restrict growth, and high ambient temperature can constrain growth via trade-offs between body temperature maintenance and heat produced during digestion. We studied growth of African striped mice (Rhabdomys pumilio), a small mammal living in a seasonally arid habitat. Striped mice are born during spring with high food availability and low ambient temperature, and typically enter the food-restricted dry season before reaching adulthood. We predicted low food availability and high ambient temperature would negatively affect growth. We therefore expected an extended period of slow growth during the long dry season. We repeatedly measured body length of 369 free-living individuals, examined how ambient temperature and food availability influenced growth rate, and seasonal changes in growth rate. In addition, we investigated whether mice (N = 27) born in summer (atypical breeding season) have slower growth rates than those born in spring. Growth rate increased with increasing food availability and decreased with increasing ambient temperature. Individuals born in summer grew slower than those born in spring. Sexes reached asymptotic body length at 258 days (females) and 285 days (males), which is an unusually long growth period compared with other small rodents. As most striped mice live for less than 1 year, this period encompasses the entire life for most individuals, but stops at old age, which could indicate senescence. Our results demonstrate a positive influence of food availability on growth, a relationship mediated by ambient temperature. We conclude that striped mice enter the food-restricted dry season before postnatal growth is terminated, and early exposure to harsh environmental conditions during the long dry season likely explains the prolonged growth period in striped mice.
Solar wind temperature–velocity relationship over the last five solar cycles and Forbush decreases associated with different types of interplanetary disturbance
Authors: Melkumyan A A , Belov A V , Abunina M A , Abunin A A , Eroshenko E A , Yanke V G , Oleneva V A 
Published: November 2020

ABSTRACT
The behaviour of the solar wind (SW) proton temperature and velocity and their relationship during Forbush decreases (FDs) associated with various types of solar source – coronal mass ejections (CMEs) and coronal holes (CHs) – have been studied. Analysis of cosmic ray variations, SW temperature, velocity, density, plasma beta, and magnetic field (from 1965–2019) is carried out using three databases: the OMNI database, Variations of Cosmic Rays database (IZMIRAN) and Forbush Effects & Interplanetary Disturbances database (IZMIRAN). Comparison of the observed SW temperature (T) and velocity (V) for the undisturbed SW allows us to derive a formula for the expected SW temperature (Texp, the temperature given by a T–V formula, if V is the observed SW speed). The results reveal a power-law T–V dependence with a steeper slope for low speeds (V &lt; 425 km s−1, exponent = 3.29 ± 0.02) and flatter slope for high speeds (V &gt; 425 km s−1, exponent = 2.25 ± 0.02). A study of changes in the T–V dependence over the last five solar cycles finds that this dependence varies with solar activity. The calculated temperature index KT = T/Texp can be used as an indicator of interplanetary and solar sources of FDs. It usually has abnormally large values in interaction regions of different-speed SW streams and abnormally low values inside magnetic clouds (MCs). The results obtained help us to identify the different kinds of interplanetary disturbance: interplanetary CMEs, sheaths, MCs, corotating interaction regions, high-speed streams from CHs, and mixed events.
New radial velocity observations of AH Her: evidence for material outside the tidal radius
Authors: Echevarría J , Hernández Santisteban J V , Segura Montero O , Ramírez S H , Ruelas-Mayorga A , Sánchez L J , Michel R , Costero R , González-Buitrago D H , Olivares J 
Published: November 2020

ABSTRACT
Spectroscopic observations of AH Herculis during a deep quiescent state are put forward. We found the object in a rare long minima, allowing us to derive accurately the semi-amplitudes: $K_1 =121 \pm \, 4$ km s−1 and K2 = 152 ± 2 km s−1 and its mass functions MWsin 3i = 0.30 ± 0.01 M⊙ and MRsin 3i = 0.24 ± 0.02 M⊙, while its binary separation is given by asin i = 1.39 ± 0.02 R⊙. The orbital period Porb = 0.25812 ± 0.00032 d was found from a power spectrum analysis of the radial velocities of the secondary star. These values are consistent with those determined by Horne, Wade & Szkody. Our observations indicate that K5 is the most likely spectral type of the secondary. We discuss why we favour the assumption that the donor in AH Her is a slightly evolved star, in which case we find that the best solution for the inclination yields i = 48° ± 2°. None the less, should the donor be a ZAMS star, we obtain that the inclination is between i = 43° and i = 44°. We also present Doppler tomography of H α and H β, and found that the emission in both lines is concentrated in a large asymmetric region at low velocities, but at an opposite position to the secondary star, outside the tidal radius and therefore at an unstable position. We also analyse the H α and H β line profiles, which show a single broad peak and compare it with the previous quiescent state study that shows a double-peaked profile, providing evidence for its transient nature.
The effect of impact parameter on tidal disruption events
Authors: Spaulding Alexandra , Chang Philip 
Published: November 2020

ABSTRACT
Stars that pass too close to a supermassive black hole are disrupted by the black hole’s tidal gravity. Some debris is ejected while the remainder accretes into the black hole. To better study the physics of these debris, we use the moving mesh code manga to follow the evolution of the star from its initial encounter to its complete destruction. By varying the impact parameter (β) of the star, we study the energy distribution of the remaining material and the fallback rate of the material into the black hole as a function of time. We show that the spread of energy in the debris and peak luminosity time (tpeak) are both directly related to the impact parameter. In particular, we find a β1/2 scaling for the energy spread for β = 2 − 10 that levels off at β ≳ 10. We discuss implication of this scaling for the rise time of the light curve and broadness of the luminosity peak for these lower β’s. These relationships provide a possible means of inferring the impact parameters for observed tidal disruption events.
3D spectroscopic analysis of helium-line white dwarfs
Authors: Cukanovaite Elena , Tremblay Pier-Emmanuel , Bergeron Pierre , Freytag Bernd , Ludwig Hans-Günter , Steffen Matthias 
Published: November 2020

ABSTRACT
In this paper, we present corrections to the spectroscopic parameters of DB and DBA white dwarfs with −10.0 ≤ log (H/He) ≤ −2.0, 7.5 ≤ log g ≤ 9.0, and $12\, 000$ ≲ Teff $\lesssim 34\, 000\,\mathrm{ K}$, based on 282 3D atmospheric models calculated with the co5bold radiation-hydrodynamics code. These corrections arise due to a better physical treatment of convective energy transport in 3D models when compared to the previously available 1D model atmospheres. By applying the corrections to an existing Sloan Digital Sky Survey (SDSS) sample of DB and DBA white dwarfs, we find significant corrections both for effective temperature and surface gravity. The 3D log g corrections are most significant for Teff ≲ 18 000 K, reaching up to −0.20 dex at log g = 8.0. However, in this low effective temperature range, the surface gravity determined from the spectroscopic technique can also be significantly affected by the treatment of the neutral van der Waals line broadening of helium and by non-ideal effects due to the perturbation of helium by neutral atoms. Thus, by removing uncertainties due to 1D convection, our work showcases the need for improved description of microphysics for DB and DBA model atmospheres. Overall, we find that our 3D spectroscopic parameters for the SDSS sample are generally in agreement with Gaia Data Release 2 absolute fluxes within 1σ–3σ for individual white dwarfs. By comparing our results to DA white dwarfs, we determine that the precision and accuracy of DB/DBA atmospheric models are similar. For ease of user application of the correction functions, we provide an example python code.