bluuebunny/crossref_metadata_2025_split huggingface dataset:
The three-cavity microstructures and mechanical properties of honeybee stingers
Authors: Miao Bo-Jun , Yang Qing-Sheng , Liu Li-Ya , Li Shuai-Wei 
Published: September 2020

Abstract
To investigate the microstructure-property relations of honeybee stingers, the cross-section microstructures were analyzed by scanning electron microscope (SEM) and the mechanical properties of honeybee stingers were tested by nanoindentation experiment in vivo in this paper. The Young’s modulus and hardness in the cross section of different segments of honeybee stingers were obtained. It is found that the honeybee stinger is of a hierarchical structure in cross section, which varies from the root to the tip and leads to quite different mechanical properties of the stingers. The natural optimized microstructure and excellent mechanical properties of the stingers effectively contribute to the biological function and self-protection performance of honeybees.
Design of a hybrid plasmonic waveguide device using a trench structure
Authors: Okamoto Hiroyuki , Kamada Shun , Haraguchi Masanobu , Okamoto Toshihiro 
Published: September 2020

Abstract
A hybrid plasmonic waveguide device was designed using a trench structure. This waveguide device was designed to improve the affinity of plasmonic devices with optical circuits by connecting them with traditional waveguide structures. The waveguide device consists of three structural segments, comprising two traditional waveguide sections for input and transmission and a hybrid plasmonic waveguide. The designed waveguide structure was evaluated using numerical analysis techniques such as the finite-difference time-domain method. The device's transmission property affects the interference between the guided light and the surface plasmon polaritons. Controlling the length of the hybrid waveguide device, which is composed of a traditional waveguide coated with a gold layer, allows the transmission intensity of the device to be controlled. The device's transmission characteristic can be controlled based on the relationship between the wavelength of the incident light and the length of the hybrid waveguide device. The device will transmit only specific incident light wavelengths because the length of the hybrid plasmonic waveguide remains constant. The characteristics of this device indicate potential for applications to nanoscale devices, optical integrated circuits and plasmonic sensors.
Personal Jurisdiction in Comparative Context
Authors: Dodson Scott 
Published: September 2020

Abstract
This Article places the recent evolution of U.S. personal jurisdiction in comparative context. Comparativism helps illuminate and explain both the modest convergences and the more pervasive divergences. On the convergences side, the Supreme Court’s acknowledgment of transnational litigation and express invocation of European approaches to personal jurisdiction have helped move general jurisdiction away from the exorbitant “doing business” jurisdiction that seemed previously to be settled U.S. law. But persistent divergences tell the more interesting story. The Court’s refusal to deviate from its commitment to transient jurisdiction, its recent narrowing of specific jurisdiction since 2011, its implicit rejection of pendent-party personal jurisdiction, and its adherence to a strong form of consent-based personal jurisdiction all reveal a stark contrast with other countries’ approaches to personal jurisdiction. That contrast is founded on deep and stubborn ties to American history, political structure, and litigation norms, all of which make broader convergence difficult, if not implausible. For these reasons, U.S. personal-jurisdiction doctrine is more likely to continue to develop on an independent track rather than hew to global trends. Some areas of parallelism might still occur, but substantial convergence is likely to remain elusive.
Preanalytical Sample Handling Conditions and Their Effects on the Human Serum Metabolome in Epidemiologic Studies
Authors: McClain Kathleen M , Moore Steven C , Sampson Joshua N , Henderson Theresa R , Gebauer Sarah K , Newman John W , Ross Sharon , Pedersen Theresa L , Baer David J , Zanetti Krista A 
Published: September 2020

Abstract
Many epidemiologic studies use metabolomics for discovery-based research. The degree to which sample handling may influence findings, however, is poorly understood. In 2016, serum samples from 13 volunteers from the US Department of Agriculture’s Beltsville Human Nutrition Research Center were subjected to different clotting (30 minutes/120 minutes) and refrigeration (0 minutes/24 hours) conditions, as well as different numbers (0/1/4) and temperatures (ice/refrigerator/room temperature) of thaws. The median absolute percent difference (APD) between metabolite levels and correlations between levels across conditions were estimated for 628 metabolites. The potential for handling artifacts to induce false-positive associations was estimated using variable hypothetical scenarios in which 1%–100% of case samples had different handling than control samples. All handling conditions influenced metabolite levels. Across metabolites, the median APD when extending clotting time was 9.08%. When increasing the number of thaws from 0 to 4, the median APD was 10.05% for ice and 5.54% for room temperature. Metabolite levels were correlated highly across conditions (all r’s ≥ 0.84), indicating that relative ranks were preserved. However, if handling varied even modestly by case status, our hypotheticals showed that results can be biased and can result in false-positive findings. Sample handling affects levels of metabolites, and special care should be taken to minimize effects. Shorter room-temperature thaws should be preferred over longer ice thaws, and handling should be meticulously matched by case status.
Laterality in foraging phalaropes promotes phenotypically assorted groups
Authors: Gutiérrez Jorge S , Soriano-Redondo Andrea 
Published: September 2020

Abstract
Asymmetry of the brain and behavior (lateralization) is widespread in the animal kingdom and could be particularly advantageous for gregarious organisms. Here, we investigate the possibility that lateralized behaviors affect the structure of foraging flocks. Phalaropes (Scolopacidae: Phalaropus) are highly aquatic shorebirds and the only vertebrates that spin on the water to feed, often in large flocks. There is anecdotal evidence that individuals spin in a single direction and that those spinning counter the majority are usually found at the periphery of a flock. Although such phenotypic segregation may reduce interference among socially foraging birds, its extent and underlying mechanism remain unexplored. Using over 900 spinning bouts from freely available video repositories, we find support for individual, but not population, lateralization of spinning in the three phalarope species. Although spinning direction was not determined by the position occupied within a flock (periphery vs. core), nearest neighbors were more likely to spin in the same direction; moreover, they were three times less likely to interfere with each other when aligning spinning direction. Our results indicate that a simple rule (keep foraging with similarly lateralized individuals) can generate self-organized interactions among flockmates, resulting in groups phenotypically assorted.
PyMod 3: a complete suite for structural bioinformatics in PyMOL
Authors: Janson Giacomo , Paiardini Alessandro 
Published: September 2020

Abstract

Summary
The PyMod project is designed to act as a fully integrated interface between the popular molecular graphics viewer PyMOL, and some of the most frequently used tools for structural bioinformatics, e.g. BLAST, HMMER, Clustal, MUSCLE, PSIPRED, DOPE and MODELLER. Here we report its latest release, PyMod 3, which has been completely renewed with a graphical interface written in PyQt, to make it compatible with the most recent PyMOL versions, and has been extended with a large set of new functionalities compared to its predecessor, i.e. PyMod 2. Starting from the amino acid sequence of a target protein, users can take advantage of PyMod 3 to carry out all the steps of the homology modeling process (i.e. template searching, target–template sequence alignment, model building and quality assessment). Additionally, the integrated tools in PyMod 3 may also be used alone, in order to extend PyMOL with a wide range of capabilities. Sequence similarity searches, multiple sequence/structure alignment building, phylogenetic trees and evolutionary conservation analyses, domain parsing, single/multiple chains and loop modeling can be performed in the PyMod 3/PyMOL environment.

Availability and implementation
A cross-platform PyMod 3 installer package for Windows, Linux and Mac OS X and a complete user guide with tutorials, are available at https://github.com/pymodproject/pymod

Supplementary information
Supplementary data are available at Bioinformatics online.
Can Existing Improvements of Water, Sanitation, and Hygiene (WASH) in Urban Slums Reduce the Burden of Typhoid Fever in These Settings?
Authors: Im Justin , Islam Md Taufiqul , Ahmmed Faisal , Kim Deok Ryun , Islam Khan Ashraful , Zaman Khalequ , Ali Mohammad , Marks Florian , Qadri Firdausi , Kim Jerome , Clemens John D 
Published: September 2020

Abstract

Background
Sustained investments in water, sanitation, and hygiene (WASH) have lagged in resource-poor settings; incremental WASH improvements may, nonetheless, prevent diseases such as typhoid in disease-endemic populations.

Methods
Using prospective data from a large cohort in urban Kolkata, India, we evaluated whether baseline WASH variables predicted typhoid risk in a training subpopulation (n = 28 470). We applied a machine learning algorithm to the training subset to create a composite, dichotomous (good, not good) WASH variable based on 4 variables, and evaluated sensitivity and specificity of this variable in a validation subset (n = 28 470). We evaluated in Cox regression models whether residents of “good” WASH households experienced a lower typhoid risk after controlling for potential confounders. We constructed virtual clusters (radius 50 m) surrounding each household to evaluate whether a prevalence of good WASH practices modified the typhoid risk in central household members.

Results
Good WASH practices were associated with protection in analyses of all households (hazard ratio [HR] = 0.57; 95% confidence interval [CI], .37–.90; P = .015). This protection was evident in persons ≥5 years old at baseline (HR = 0.47; 95% CI, .34–.93; P = .005) and was suggestive, though not statistically significant, in younger age groups (HR = 0.61; 95% CI, .27–1.38; P = .235). The level of surrounding household good WASH coverage was also associated with protection (HR = 0.988; 95% CI, .979–.996; P = .004, for each percent coverage increase). However, collinearity between household WASH and WASH coverage prevented an assessment of their independent predictive contributions.

Conclusions
In this typhoid-endemic setting, natural variation in household WASH was associated with typhoid risk. If replicated elsewhere, these findings suggest that WASH improvements may enhance typhoid control, short of major infrastructural investments.
Differences in biomarkers and molecular pathways according to age for patients with HFrEF
Authors: Ferreira João Pedro , Ouwerkerk Wouter , Santema Bernadet T , van Veldhuisen Dirk J , Lang Chim C , Ng Leong L , Anker Stefan D , Dickstein Kenneth , Metra Marco , Cleland John G F , Nilesh Samani J , Filippatos Gerasimos , Aboumsallem Joseph-Pierre , de Boer Rudolf A , Figarska Sylwia , Sama Iziah E , Voors Adriaan A , Zannad Faiez 
Published: September 2020

Abstract

Aims
Elderly patients with heart failure with reduced ejection fraction (HFrEF) have worse prognosis and less often receive guideline-recommended therapies. We aim to better understand the underlying pathophysiological processes associated with ageing in HFrEF potentially leading to targeted therapies in this vulnerable population.

Methods and results
From a panel of 363 cardiovascular biomarkers available in 1611 patients with HFrEF in the BIOSTAT-CHF index cohort and cross-validated in 823 patients in the BIOSTAT-CHF validation cohort, we tested which biomarkers were dysregulated in patients aged &gt;75 vs. &lt;65 years. Second, pathway overrepresentation analyses were performed to identify biological pathways linked to higher plasma concentrations of biomarkers in elderly vs. younger patients. After adjustment, multiple test correction [false discovery rate (FDR) 1%], and cross-validation, 27/363 biomarkers were associated with older age, 22 positively and 5 negatively. The biomarkers that were positively associated with older age were associated with tumour cell regulation, extra-cellular matrix organization, and inflammatory processes, whereas biomarkers negatively associated with older age were associated with pathways that may point to cell proliferation and tumourigenesis. Among the 27 biomarkers, WFDC2 (WAP four-disulphide core domain protein 2)—that broadly functions as a protease inhibitor—was associated with older age and had the strongest association with all outcomes. No protein-by-sex interaction was observed.

Conclusions
In elderly HFrEF patients, pathways associated with extra-cellular matrix organization, inflammatory processes, and tumour cell regulation were activated, while pathways associated with tumour proliferation functions were down-regulated. These findings may help in a better understanding of the ageing processes in HFrEF and identify potential therapeutic targets.
Co-expression of calcium and hERG potassium channels reduces the incidence of proarrhythmic events
Authors: Ballouz Sara , Mangala Melissa M , Perry Matthew D , Heitmann Stewart , Gillis Jesse A , Hill Adam P , Vandenberg Jamie I 
Published: September 2020

Abstract

Aims
Cardiac electrical activity is extraordinarily robust. However, when it goes wrong it can have fatal consequences. Electrical activity in the heart is controlled by the carefully orchestrated activity of more than a dozen different ion conductances. While there is considerable variability in cardiac ion channel expression levels between individuals, studies in rodents have indicated that there are modules of ion channels whose expression co-vary. The aim of this study was to investigate whether meta-analytic co-expression analysis of large-scale gene expression datasets could identify modules of co-expressed cardiac ion channel genes in human hearts that are of functional importance.

Methods and results
Meta-analysis of 3653 public human RNA-seq datasets identified a strong correlation between expression of CACNA1C (L-type calcium current, ICaL) and KCNH2 (rapid delayed rectifier K+ current, IKr), which was also observed in human adult heart tissue samples. In silico modelling suggested that co-expression of CACNA1C and KCNH2 would limit the variability in action potential duration seen with variations in expression of ion channel genes and reduce susceptibility to early afterdepolarizations, a surrogate marker for proarrhythmia. We also found that levels of KCNH2 and CACNA1C expression are correlated in human-induced pluripotent stem cell-derived cardiac myocytes and the levels of CACNA1C and KCNH2 expression were inversely correlated with the magnitude of changes in repolarization duration following inhibition of IKr.

Conclusion
Meta-analytic approaches of multiple independent human gene expression datasets can be used to identify gene modules that are important for regulating heart function. Specifically, we have verified that there is co-expression of CACNA1C and KCNH2 ion channel genes in human heart tissue, and in silico analyses suggest that CACNA1C–KCNH2 co-expression increases the robustness of cardiac electrical activity.
Crohn’s Disease: Is the Cold Chain Hypothesis Still Hot?
Authors: Hugot Jean-Pierre , Dumay Anne , Barreau Frédérick , Meinzer Ulrich 
Published: September 2020

Abstract
Crohn’s disease [CD] is an inflammatory bowel disease of unknown aetiology. During recent decades, significant technological advances led to development of -omic datasets allowing a detailed description of the disease. Unfortunately these have not, to date, resolved the question of the aetiology of CD. Thus, it may be necessary to [re]consider hypothesis-driven approaches to resolve the aetiology of CD. According to the cold chain hypothesis, the development of industrial and domestic refrigeration has led to frequent exposure of human populations to bacteria capable of growing in the cold. These bacteria, at low levels of exposure, particularly those of the genus Yersinia, are believed to be capable of inducing exacerbated inflammation of the intestine in genetically predisposed subjects. We discuss the consistency of this working hypothesis in light of recent data from epidemiological, clinical, pathological, microbiological, and molecular studies.
Trajectories of Late-Life Disability Vary by the Condition Leading to Death
Authors: Stolz Erwin , Gill Thomas M , Mayerl Hannes , Rásky Éva , Freidl Wolfgang 
Published: September 2020

Abstract

Background
Previous research suggested that there might be distinct patterns of functional decline in the last years of life depending on the condition leading to death, but the validity of these results and hence the explanatory value of the condition leading to death for late-life disability are uncertain.

Methods
A total of 636 decedents from a cohort of 754 community-living persons, 70+ years of age (Yale PEP Study) provided 33 700 monthly observations of self-/proxy-reported disability during the last 5 years of life. Nonlinear trajectories and short-term fluctuations of late-life disability by condition leading to death (cancer, organ failure, frailty, severe dementia, sudden death, other) were estimated with flexible mixed spline regression models.

Results
Disability trajectories at the end of life varied distinctively by the condition leading to death. Estimated disability trajectories among cancer deaths increased gradually up until about 6 months before death, after which a steep terminal decline set in. Among those with organ failure, frailty, and dementia, in contrast, disability was higher, increased more gradually, and there was no clear-cut terminal phase. Adding the condition leading to death to other known risk factors increased the amount of explained between-person variation in late-life disability from R2 = 0.35 to 0.49. Short-term fluctuations in disability were not specific for decedents with organ failure.

Conclusions
The condition leading to death is an important determinant of trajectories of late-life disability. These trajectories follow distinct patterns partially resembling a previously outlined theoretical typology.
Association Between the Multidimensional Prognostic Index and Mortality During 15 Years of Follow-up in the InCHIANTI Study
Authors: Pilotto Alberto , Veronese Nicola , Siri Giacomo , Bandinelli Stefania , Tanaka Toshiko , Cella Alberto , Ferrucci Luigi 
Published: September 2020

Abstract

Background
Multidimensional Prognostic Index (MPI) is recognized as a prognostic tool in hospitalized patients, but data on the value of MPI in community-dwelling older persons are limited. Using data from a representative cohort of community-dwelling persons, we tested the hypothesis that MPI explains mortality during 15 years of follow-up.

Methods
A standardized comprehensive geriatric assessment was used to calculate the MPI and to categorize participants in low-, moderate-, and high-risk classes. The results were reported as hazard ratios (HRs) and the accuracy was evaluated with the area under the curve (AUC), with 95% confidence intervals (CIs) and the C-index. We also reported the median survival time by standard age groups.

Results
All 1453 participants (mean age 68.9 years, women = 55.8%) enrolled in the InCHIANTI study at baseline were included. Compared to low-risk group, participants in moderate (HR = 2.10; 95% CI: 1.73–2.55) and high-risk MPI group (HR = 4.94; 95% CI: 3.91–6.24) had significantly higher mortality risk. The C-index of the model containing age, sex, and MPI was 82.1, indicating a very good accuracy of this model in explaining mortality. Additionally, the time-dependent AUC indicated that the accuracy of the model incorporating MPI to age and sex was excellent (&gt;85.0) during the whole follow-up period. Compared to participants in the low-risk MPI group across different age groups, those in moderate- and high-risk groups survived 2.9–7.0 years less and 4.3–8.9 years less, respectively.

Conclusions
In community-dwelling individuals, higher MPI values are associated with higher risk of all-cause mortality with a dose–response effect.
Upper-mantle discontinuities beneath Australia from transdimensional Bayesian inversions using multimode surface waves and receiver functions
Authors: Taira Toru , Yoshizawa Kazunori 
Published: September 2020

SUMMARYRadially anisotropic S-wave structures under the permanent seismic stations in Australia are reconstructed using multimode surface waves (SWs) and receiver functions (RFs) in a framework of the Bayesian inference. We have developed a fully nonlinear method of joint inversions incorporating P-RFs and multimode Rayleigh and Love waves, based on the transdimensional Hierarchical Bayesian formulation. The method allows us to estimate a probabilistic Earth model taking account of the complexity and uncertainty of Earth structure, by treating the model parameters and data errors as unknowns. The Parallel Tempering algorithm is employed for the effective parameter search based on the reversible-jump Markov Chain Monte Carlo method. The use of higher modes enables us to enhance the sensitivity to the depth below the continental asthenosphere. Synthetic experiments indicate the importance of higher mode SWs for the better recovery of radial anisotropy in the whole depth range of the upper mantle. The method is applied to five Global Seismographic Network stations in Australia. While the S-wave models in eastern Australia show shallow lithosphere–asthenosphere boundary (LAB) above 100 km depth, those in central and Western Australia exhibit both mid-lithosphere discontinuities (MLDs) and LAB. Also, seismic velocity jumps equivalent to the Lehmann discontinuity (L-D) are found in all seismic stations. The L-D under the Australian continents is found at around 200–300 km depth, depending on locations. Radial anisotropy in the depth range between LAB and L-D tends to show faster SH anomalies, which may indicate the effects of horizontal shear underneath the fast-moving Australian plate.
Monocyte-Independent and -Dependent Regulation of Regulatory T-Cell Development in Mycoplasma Infection
Authors: Takahashi Ryo , Shiohara Tetsuo , Mizukawa Yoshiko 
Published: September 2020

Abstract

Background
Although Mycoplasma pneumoniae (MP) infection has been implicated in the pathogenesis of allergic diseases, the mechanism of this trigger remains unknown. We explored the mechanism for how MP infection could tilt the balance between regulatory T cells (Tregs) and Th17 cells.

Methods
We analyzed the frequency, phenotype, and function of Tregs in patients at the different stages of MP and various virus infections over a period of more than 1 year. We examined the effect of monocytes to elucidate signals that can regulate the balance between Treg and Th17 cells.

Results
The functional activity of Tregs was profoundly impaired during the acute stage of MP as well as viral infections. Upon resolution, however, the Treg function remained impaired even 1 year after MP infection. In the resolution stage, the impaired Treg function was associated with an increase in interleukin (IL) 17A+ Tregs and Th17 cells. Development of Th17 cells was dependent on the “aberrant” proinflammatory monocytes (pMOs), characterized by potent ability to produce IL-6 in a Toll-like receptor 2–dependent manner.

Conclusions
Depending on the prevalence of the pMOs, Tregs and Th17 cells could mutually regulate the number and function of the other. The pMOs/IL-6 could be crucial therapeutic targets against MP-induced allergic diseases.