bluuebunny/crossref_metadata_2025_split huggingface dataset:
Organic vegetables demand in urban area using a count outcome model: case study of Burkina Faso
Authors: Kini Janvier , Pouw Nicky , Gupta Joyeeta 
Published: September 2020

AbstractThis paper designs and tests a model for count outcomes to analyse the effective demand for organic vegetables in the city of Ouagadougou, Burkina Faso. From a ‘short value chain’ perspective, we show that the distance travelled by consumers to organic vegetable production sites primarily managed by women farmers’ associations, is a key determinant of organic food demand. Furthermore, the effect of the distance travelled on the demand is stronger for women than for men. In addition, consumers’ health awareness and the intended use of these vegetables are significant determinants of their demand. Moreover, social-relational factors affect the purchase decision both ways, including issues of trust and access to market information. Thus, this paper first introduces the socially subjective considerations of the demand for food in the close interaction between producers and consumers of organic food. Second, it contributes to filling the knowledge gap on the factors influencing consumer behaviour in purchasing organic food in urban production sites in developing countries.
Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests
Authors: Chen Cheng-Yu , Chen Chih-Kuan , Chen Yi-Ying , Fang Andrew , Shaw Grace Tzun-Wen , Hung Chih-Ming , Wang Daryi 
Published: September 2020

Abstract
Background
Knowledge is growing on how gut microbiota are established, but the effects of maternal symbiotic microbes throughout early microbial successions in birds remain elusive. In this study, we examined the contributions and transmission modes of maternal microbes into the neonatal microbiota of a passerine, the zebra finch (Taeniopygia guttata), based on fostering experiments.

Results
Using 16S rRNA amplicon sequencing, we found that zebra finch chicks raised by their biological or foster parents (the society finch Lonchura striata domestica) had gut microbial communities converging with those of the parents that reared them. Moreover, source-tracking models revealed high contribution of zebra finches’ oral cavity/crop microbiota to their chicks’ early gut microbiota, which were largely replaced by the parental gut microbiota at later stages. The results suggest that oral feeding only affects the early stage of hatchling gut microbial development.

Conclusions
Our study indicates that passerine chicks mainly acquire symbionts through indirect maternal transmission—passive environmental uptake from nests that were smeared with the intestinal and cloacal microbes of parents that raised them. Gut microbial diversity was low in hand-reared chicks, emphasizing the importance of parental care in shaping the gut microbiota. In addition, several probiotics were found in chicks fostered by society finches, which are excellent foster parents for other finches in bird farms and hosts of brood parasitism by zebra finches in aviaries; this finding implies that avian species that can transfer probiotics to chicks may become selectively preferred hosts of brood parasitism in nature.
Hill-based dissimilarity indices and null models for analysis of microbial community assembly
Authors: Modin Oskar , Liébana Raquel , Saheb-Alam Soroush , Wilén Britt-Marie , Suarez Carolina , Hermansson Malte , Persson Frank 
Published: September 2020

Abstract
Background
High-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.

Results
Using amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.

Conclusions
Hill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.
Genetic variants of the human host influencing the coronavirus-associated phenotypes (SARS, MERS and COVID-19): rapid systematic review and field synopsis
Authors: Di Maria Emilio , Latini Andrea , Borgiani Paola , Novelli Giuseppe 
Published: September 2020

AbstractThe COVID-19 pandemic has strengthened the interest in the biological mechanisms underlying the complex interplay between infectious agents and the human host. The spectrum of phenotypes associated with the SARS-CoV-2 infection, ranging from the absence of symptoms to severe systemic complications, raised the question as to what extent the variable response to coronaviruses (CoVs) is influenced by the variability of the hosts’ genetic background.To explore the current knowledge about this question, we designed a systematic review encompassing the scientific literature published from Jan. 2003 to June 2020, to include studies on the contemporary outbreaks caused by SARS-CoV-1, MERS-CoV and SARS-CoV-2 (namely SARS, MERS and COVID-19 diseases). Studies were eligible if human genetic variants were tested as predictors of clinical phenotypes.An ad hoc protocol for the rapid review process was designed according to the PRISMA paradigm and registered at the PROSPERO database (ID: CRD42020180860). The systematic workflow provided 32 articles eligible for data abstraction (28 on SARS, 1 on MERS, 3 on COVID-19) reporting data on 26 discovery cohorts. Most studies considered the definite clinical diagnosis as the primary outcome, variably coupled with other outcomes (severity was the most frequently analysed). Ten studies analysed HLA haplotypes (1 in patients with COVID-19) and did not provide consistent signals of association with disease-associated phenotypes. Out of 22 eligible articles that investigated candidate genes (2 as associated with COVID-19), the top-ranked genes in the number of studies were ACE2, CLEC4M (L-SIGN), MBL, MxA (n = 3), ACE, CD209, FCER2, OAS-1, TLR4, TNF-α (n = 2). Only variants in MBL and MxA were found as possibly implicated in CoV-associated phenotypes in at least two studies. The number of studies for each predictor was insufficient to conduct meta-analyses.Studies collecting large cohorts from different ancestries are needed to further elucidate the role of host genetic variants in determining the response to CoVs infection. Rigorous design and robust statistical methods are warranted.
Particle release from implantoplasty of dental implants and impact on cells
Authors: Barrak Fadi N. , Li Siwei , Muntane Albert M. , Jones Julian R. 
Published: September 2020

Abstract
Background
With increasing numbers of dental implants placed annually, complications such as peri-implantitis and the subsequent periprosthetic osteolysis are becoming a major concern. Implantoplasty, a commonly used treatment of peri-implantitis, aims to remove plaque from exposed implants and reduce future microbial adhesion and colonisation by mechanically modifying the implant surface topography, delaying re-infection/colonisation of the site. This in vitro study aims to investigate the release of particles from dental implants and their effects on human gingival fibroblasts (HGFs), following an in vitro mock implantoplasty procedure with a diamond burr.

Materials and methods
Commercially available implants made from grade 4 (commercially pure, CP) titanium (G4) and grade 5 Ti-6Al-4 V titanium (G5) alloy implants were investigated. Implant particle compositions were quantified by inductively coupled plasma optical emission spectrometer (ICP-OES) following acid digestion. HGFs were cultured in presence of implant particles, and viability was determined using a metabolic activity assay.

Results
Microparticles and nanoparticles were released from both G4 and G5 implants following the mock implantoplasty procedure. A small amount of vanadium ions were released from G5 particles following immersion in both simulated body fluid and cell culture medium, resulting in significantly reduced viability of HGFs after 10 days of culture.

Conclusion
There is a need for careful evaluation of the materials used in dental implants and the potential risks of the individual constituents of any alloy. The potential cytotoxicity of G5 titanium alloy particles should be considered when choosing a device for dental implants. Additionally, regardless of implant material, the implantoplasty procedure can release nanometre-sized particles, the full systemic effect of which is not fully understood. As such, authors do not recommend implantoplasty for the treatment of peri-implantitis.
Pharmacokinetics of anticoagulant edoxaban in overdose in a Japanese patient transported to hospital
Authors: Adachi Koichiro , Tuchiya Jumpei , Beppu Satoru , Nishiyama Kei , Shimizu Makiko , Yamazaki Hiroshi 
Published: September 2020

AbstractBackgroundThe anticoagulant edoxaban is used clinically at doses of 30–60 mg/day; however, we experienced a patient who had taken an overdose of edoxaban of 750 mg. We investigated the pharmacokinetics of edoxaban in this patient by using liquid chromatography–tandem spectrometry to estimate the follow-up period in emergency clinical practice with this medicine.Case presentationThe patient was a 57-year-old woman (body weight, 69 kg) who had taken a single oral dose of 750 mg of edoxaban in a suicide attempt. She was emergently admitted to Kyoto Medical Center. The patient’s edoxaban plasma concentrations during ambulance transport (8 h after oral administration) were ~ 4900 ng/ml, and the concentration gradually decreased to ~ 10 ng/mL and to detectable but unmeasurable levels of ~ 1.0 ng/mL at 60 h and 100 h, respectively. The linear range of the relationship between the dose and plasma concentration was assumed to have been exceeded during the first 8 h; however, the measured elimination rate of edoxaban was similar to that visualized curves predicted by a simplified physiologically based pharmacokinetic model previously established.ConclusionSimplified physiologically based pharmacokinetic models for creating visualized curves have proven to be useful not only during drug discovery or chemical risk assessment but also in cases of medical poisoning. We used a physiologically based pharmacokinetic model previously established for edoxaban to predict the pharmacokinetics in the current case. It is hoped that the results of this study, which encompass drug monitoring data in the patient and visualized pharmacokinetic prediction, will serve as an index when setting the treatment and follow-up period in cases of drug overdose for medicines such as edoxaban in emergency clinical practice.
An added boost in pyrogenic carbon when wildfire burns forest with high pre-fire mortality
Authors: Talucci Anna C. , Matosziuk Lauren M. , Hatten Jeff A. , Krawchuk Meg A. 
Published: September 2020

Abstract
Background
Wildfires produce pyrogenic carbon (PyC) through the incomplete combustion of organic matter, and its chemical characterization is critical to understanding carbon (C) budgets and ecosystem functions in forests. Across western North American forests, fires are burning through landscapes with substantial tree mortality from insect outbreaks, often referred to as short-interval disturbances. These short-interval disturbances often result in beetle-killed snags (snags that subsequently burn) that are heavily charred, while their fire-killed (alive at time of fire) counterparts are lightly charred. We investigated whether the chemical signature of PyC on heavily charred beetle-killed snags differs from lightly charred fire-killed snags.

Results
We evaluated differences in PyC chemical concentrations and condensation on beetle-killed (n = 3) and fire-killed snags (n = 3) with the benzene polycarboxylic acid (BPCA) molecular marker method. Beetle-killed snags exhibited over five times the grams of BPCA per kilogram of C, and over seven times the grams of BPCA per kilogram of material compared to fire-killed snags, indicating higher concentrations of PyC.

Conclusion
PyC concentrations were greater in samples from beetle-killed snags compared to fire-killed snags, pointing to an important compound effect from the interaction of beetle outbreak and wildfire in forest ecosystems. While this study was limited to a single fire event and sampling in individual trees, it provides insight into PyC on snags with different disturbance histories. The abundance of heavily charred snags from a fire burning through landscapes with high levels of existing mortality from drought, insect outbreaks, and previous wildfire events is becoming a more common legacy for contemporary western North American forests. Accordingly, the distinct wood-based PyC legacy could influence ecosystem functions: C sequestration, water purification, soil nutrient supply, and resources for wildlife.
Socio-demographic and lifestyle factors associated with understanding fast food consumption among adults in Cambodia
Authors: Samphors Sim , Chamroen Pall , S. Dewey Rebecca , Rachutorn Thiwakorn , Pisey Vong 
Published: September 2020

Background: Over the past decades, fast food has been rapidly gaining popularity and availability worldwide. Its consequential impact on human health is among the highest in terms of non-communicable diseases. Therefore, this study aimed to investigate the level of understanding of fast food consumption among adults in Phnom Penh, the capital city of Cambodia. Methods: A cross-sectional analytical study aimed to investigate the level of understanding of factors associated with fast food consumption, among adults in Phnom Penh. Multi-stage random sampling was used to select 749 respondents from 12 communes of five districts in Phnom Penh. A structured questionnaire was used to assess the level of understanding of fast food consumption, and associated factors. Data were analyzed using descriptive statistics, together with bivariate and multivariable logistic regression. Crude odds ratios (CORs) and adjusted odds ratios (AORs) with 95% confident intervals (CI) were calculated to show the strength of associations. Results: The understanding of factors associated with fast food consumption was poor in 52.07% (95% CI: 48.48-55.66), fair in 22.70% (95% CI: 19.69-25.70) and good in 25.23% (95% CI: 22.12-28.35) of those surveyed. After adjusting for other covariates, unsatisfactory levels of knowledge around fast food consumption were found to be significantly associated with not taking regular exercise (AOR = 1.53; 95% CI: 1.15-2.25; p<0.001) and sleeping less than eight hours per night (AOR = 1.64; 95% CI: 1.09-2.12; p=0.014). Conclusion: Health promotion and disease prevention should be conducted among at-risk populations in order to raise the level of understanding of factors around fast food consumption.
Benefits of Customer Loyalty in Markets with Endogenous Search Costs
Authors: Kuksov Dmitri , Zia Mohammad 
Published: September 2020

Managers have long appreciated having loyal customers, and academic research has explored the benefits of loyal consumers as coming from reduced price competition. This paper extends this research by considering how loyalty affects firms’ decisions to facilitate search for nonloyal consumers. We show that in equilibrium, the store with more loyal customers ends up having lower search costs even if facilitating search is costless. The intuition for this result is that nonloyal consumers expect higher prices at a store with a larger loyal segment, and therefore, this store has to set a lower search cost to counteract the negative effect of this expectation. Given this, it is optimal for the other store to set a higher search cost to avoid intensifying price competition. As a consequence, a larger loyal segment may lead to both higher prices and a higher market share among nonloyal customers. In other words, an advantage in customer loyalty leads to the store becoming the search hub of the nonloyal customers. This, in turn, implies that even a small advantage in customer loyalty may lead to a large increase in profits and may help explain why some managers place such a high value on earning customer loyalty. This paper was accepted by David Simchi-Levi, marketing.
800  Gbit/s transmission over 1  km single-mode fiber using a four-channel silicon photonic transmitter
Authors: Zhang Hongguang , Li Miaofeng , Zhang Yuguang , Zhang Di , Liao Qiwen , He Jian , Hu Shenglei , Zhang Bo , Wang Lei , Xiao Xi , Qi Nan , Yu Shaohua 
Published: September 2020

We demonstrate the optical transmission of an 800 Gbit/s (

4
×
200

Gbit
/
s

) pulse amplitude modulation-4 (PAM-4) signal and a 480 Gbit/s (

4
×
120

Gbit
/
s

) on–off-keying (OOK) signal by using a high-bandwidth (BW) silicon photonic (SiP) transmitter with the aid of digital signal processing (DSP). In this transmitter, a four-channel SiP modulator chip is co-packaged with a four-channel driver chip, with a measured 3 dB BW of 40 GHz. DSP is applied in both the transmitter and receiver sides for pre-/post-compensation and bit error rate (BER) calculation. Back-to-back (B2B) BERs of the PAM-4 signal and OOK signal are first measured for each channel of the transmitter with respect to a variety of data rates. Similar BER performance of four channels shows good uniformity of the transmitter between different channels. The BER penalty of the PAM-4 and OOK signals for 500 m and 1 km standard single-mode fiber (SSMF) transmission is then experimentally tested by using one channel of the transmitter. For a 200 Gbit/s PAM-4 signal, the BER is below the hard-decision forward error correction (HD-FEC) threshold for B2B and below the soft-decision FEC (SD-FEC) threshold after 1 km transmission. For a 120 Gbit/s OOK signal, the BER is below SD-FEC threshold for B2B. After 500 m and 1 km transmission, the data rate of the OOK signal shrinks to 119 Gbit/s and 118 Gbit/s with the SD-FEC threshold, respectively. Finally, the 800 Gbit/s PAM-4 signal with 1 km transmission is achieved with the BER of all four channels below the SD-FEC threshold.
“A Notion of the True System of the World”: Berkeley and his Use of Plato in Siris
Authors: Larsen Peter D. 
Published: September 2020

Abstract
This paper considers Berkeley’s use of Plato in Siris. Berkeley’s engagement with ancient thinkers in Siris has been a source of puzzlement for many readers. In this paper I focus on Siris § 266. In particular, I consider why Berkeley says of the Platonists that they “distinguished the primary qualities in bodies from the secondary” and why, given his own well-known misgivings about the distinction, he characterizes this as part of a “notion of the true system of the world.” I argue that in Siris Berkeley accepts a distinctive form of corpuscularianism, and that he thinks a distinction between primary and secondary qualities follows from this. I further argue that in § 266, and elsewhere in Siris, Berkeley engages in a careful reading of Plato’s Timaeus, which he uses to bolster his defense of the compatibility between corpuscularianism and his immaterialist idealism.
Compactness by Coarse-Graining in Long-Range Lattice Systems
Authors: Braides Andrea , Solci Margherita 
Published: September 2020

Abstract
We consider energies on a periodic set

ℒ

{\mathcal{L}}

of the form

∑

i
,
j

∈
ℒ

a

i
⁢
j

ε

⁢

|

u
i

-

u
j

|

{\sum_{i,j\in\mathcal{L}}a^{\varepsilon}_{ij}\lvert u_{i}-u_{j}\rvert}

, defined on spin functions

u
i

∈

{
0
,
1
}

{u_{i}\in\{0,1\}}

, and we suppose that the typical range of the interactions is

R
ε

{R_{\varepsilon}}

with

R
ε

→

+
∞

{R_{\varepsilon}\to+\infty}

, i.e., if

|

i
-
j

|

≤

R
ε

{\lvert i-j\rvert\leq R_{\varepsilon}}

, then

a

i
⁢
j

ε

≥
c
>
0

{a^{\varepsilon}_{ij}\geq c>0}

. In a discrete-to-continuum analysis, we prove that the overall behavior as

ε
→
0

{\varepsilon\to 0}

of such functionals is that of an interfacial energy. The proof is performed using a coarse-graining procedure which associates to scaled functions defined on

ε
⁢
ℒ

{\varepsilon\mathcal{L}}

with equibounded energy a family of sets with equibounded perimeter. This agrees with the case of equibounded

R
ε

{R_{\varepsilon}}

and can be seen as an extension of coerciveness result for short-range interactions, but is different from that of other long-range interaction energies, whose limit exits the class of surface energies. A computation of the limit energy is performed in the case

ℒ
=

ℤ
d

{\mathcal{L}=\mathbb{Z}^{d}}

.
On the Choice of Liability Rules
Authors: Kundu Rajendra P. , Pal Debabrata 
Published: September 2020

Abstract
Legal assignment of liabilities for losses arising out of interactions involving negative externalities usually depend on which of the interacting parties are negligent and which are not. It has been established in the literature that, if negligence is defined as failure to take some cost-justified precaution then there is no liability rule which can always lead to an efficient outcome. The objective of this paper is to try and understand if it is still possible to make pairwise comparisons between rules on the basis of efficiency and to use such a method to explain/evaluate choices from a given set of rules. We focus on a set of five of the most widely analyzed rules (no liability, strict liability, negligence, negligence with the defense of contributory negligence and strict liability with the defense of contributory negligence), and use a binary relation according to which a rule in the set is considered to be at least as efficient as another if and only if the set of applications for which it is inefficient is a subset of the set of applications for which the other one is inefficient. We show that, with respect to the above mentioned relation, pairwise comparisons between rules in this set fail. The paper, thus, demonstrates that an efficiency based explanation for any choice from these five rules is not consistent with the notion of negligence defined as failure to take some cost-justified precaution.