bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geography and location are the primary drivers of office microbiome composition
Authors: Chase John H , Fouquier Jennifer , Zare Mahnaz , Sonderegger Derek L , Knight Rob , Kelley Scott , Siegel Jeffrey A , Caporaso J Gregory 
Published: January 2018

North Americans spend the majority of their time indoors where they are exposed to the microbiome of the built environment (BE) they inhabit. Despite the ubiquity of microbes in BEs, and their potential impacts on health and building materials, basic questions about the microbiology of these environments remain unanswered. We present a study on the impacts of geography, material type, human interaction, location in a room, seasonal variation, and indoor and microenvironmental parameters on bacterial communities in offices. Our data elucidates several important features of microbial communities in BEs. First, under normal office environmental conditions, bacterial communities do not differ based on surface material (e.g., ceiling tile or carpet), but do differ based on the location in a room (e.g., ceiling or floor), two features which are often conflated, but which we are able to separate here. We suspect that previous work showing differences in bacterial composition with surface material were likely detecting differences based on different usage patterns. Next, we find that offices have city-specific bacterial communities, such that we can accurately predict which city an office microbiome sample is derived from, but office-specific bacterial communities are less apparent. This differs from previous work which has suggested office-specific compositions of bacterial communities. We again suspect that the difference from prior work arises from different usage patterns. As has been previously shown, we observe that human skin contributes heavily to the composition of BE surfaces.
Our study highlights several points that should impact the design of future studies of the microbiology of the BEs. First, projects tracking changes to BE bacterial communities should focus sampling effort on surveying different locations in offices and in different cities, but not necessarily different materials or different offices in the same city. Next, disturbance due to repeat sampling, though detectable, is small compared to other variables, opening up a range of longitudinal study designs in the built environment. Next, studies requiring more samples than can be sequenced on a single sequencing run (which is increasingly common) must control for run effects by including some of the same samples on all sequencing runs as technical replicates. Finally, detailed tracking of indoor and material environment covariates is likely not essential for BE microbiome studies, as the normal range of indoor environmental conditions is likely not large enough to impact bacterial communities.
Why respiratory viruses or bacteria have the highest probability to be deposited in the respiratory tract in flu seasons
Authors: Ishmatov Aleksandr N 
Published: January 2018

Marc Lipsitch and Cécile Viboud (2009) (Lipsitch and Viboud, 2009): “Seasonal variation in the incidence of communicable diseases is among the oldest observations in population biology, dating back at least to ancient Greece, yet our understanding of the mechanisms underlying this phenomenon remains hazy at best.”
The latest researches show the infected people when breathing generate the infectious aerosols with particles below 1 µm. The airborne transmission of these particles is effective but the deposition of submicron particles in the respiratory tract (RT) has very low probability.
Here I investigated the processes in RT when breathing cold air and its role in the delivery of viruses and bacteria of submicron and ultrafine sizes in RT.
The original hypothesis of the highest probability of delivery and deposition of viruses or bacteria from inhaled air in the respiratory tract during flu seasons in different climatic conditions was investigated.
On the basis of estimation I have originally shown: Breathing cool air leads to the supersaturation of air in RT; the air supersaturation leads to the intensive condensational growth(CG) of inhaled viruses or bacteria in RT; CG leads to the intensive and dramatically growth of deposition rate of viruses or bacteria in RT.
Under normal conditions of inhaled air (T>20˚C; RH=60%) there is no transition in oversaturated condition in RT (CG is insignificant and probability of virus deposition on epithelium of RT is low – no more than 20%).
But with an increase in RH of inhaled air the oversaturation in RT occurs even at warm temperature of inhaled air. For inhaled air of T=20°C, RH>70% the local supersaturation in the airways occurs: the concentration of liquid water in the mixed air in RT (СLiq) is СLiq<2·4g/kg and for T=25°C; RH>90% СLiq<1·2g/kg.
The estimation also shown that for conditions of breathing cold air of T [-15..+15]˚C and Relatively Humidity (RH) of [30..60]% the supersaturation in the airways occurs: the concentration of liquid water in the mixed air in RT (СLiq) is [0·2..12·1]g/kg.
Under these conditions the growth of inhaled particles by condensation in RT is significant. It lead to the dramatically growth of deposition rate of the viruses and bacteria in RT (up to 97%).
These results correspond to influenza and seasonal respiratory infections in temperate and tropical climates and indicate the high probability of virus deposition on epithelium of RT.
It may be the key to ‘the age-old epidemiologic mystery of influenza seasonality in the different climatic conditions’.
Why respiratory viruses or bacteria have the highest probability to be deposited in the respiratory tract in flu seasons
Authors: Ishmatov Aleksandr N 
Published: January 2018

Objective:
In this study the main aspects of influenza transmission via fine and ultrafine bioaerosols were considered. Here, we aimed to estimate the impact of the different environment conditions on the deposition rate of the infectious bioaerosols in the respiratory tract (RT).

Background:

The latest researches show the infected people generate the fine and ultrafine infectious bioaerosols with submicron particles/droplets (size below 1 µm). The airborne transmission of these particles/droplets in the environment is effective. It is considered the deposition of submicron particles in RT has very low probability. But most studies examined the deposition of the particles in RT under normal environmental conditions and did not paid attention to the different environmental factors.

Methods:

We review the problems of epidemiology of respiratory infections and aspects of airborne transmission/spread of infectious agents. We contrast these approaches with known data from next area: inhalation toxicology, respiratory drug delivery and physics of heat and mass transfer in the airways.

Results:

On the basis of these analyses, we propose the next main concepts:
1 Breathing cool air leads to the supersaturation of air in RT;
2 the air supersaturation leads to the intensive condensational growth(CG) of inhaled viruses or bacteria in RT;
3 CG leads to the intensive and dramatically growth of deposition rate of viruses or bacteria in RT.

We have shown:

a) Under normal conditions of inhaled air (T>20˚C; Relatively Humidity, RH=60%) there is no transition in supersaturated condition in RT and CG is insignificant and probability of virus deposition on epithelium of RT is low – no more than 20%.
b) Breathing cool/cold air of T<+15˚C and RH of [30..60]% leads to the supersaturation in the airways and it can dramatically increase the deposition rate of inhaled bioaerosols in RT(up to 96%).
c) With an increase in RH of inhaled air the supersaturation in RT occurs even at warm temperature of inhaled air (for inhaled air of T<20°C and RH>70% ; T<25°C and RH>90%). It also indicates the high deposition rate of bioaerosols in RT.

Conclusion:

Under specific environmental conditions (when flu seasons) the processes of supersaturation in the RT can be observed. These results indicate the high probability of virus deposition on epithelium of RT and correspond to influenza and seasonal respiratory infections in temperate and tropical climates.
We believe the effect of supersaturation in the lungs can be the key to understanding of ‘the age-old epidemiologic mystery of influenza seasonality in the different climatic conditions.’
Identification of “on-off residues” in rat Cav1.2 α1C subunit channel using in silico analysis and docking simulation
Authors: Trezza Alfonso , Bernini Andrea , Spiga Ottavia 
Published: January 2018

Introduction
Voltage-dependent calcium channels (VSCC) is involved in important biological function as calcium ion transmembrane transport and cardiac contraction. VSCC is a multi-pass membrane protein, made up from α-1, α-2, β and δ subunits. α-1 subunit regulates the entry of ion calcium. Voltage-dependent L-type calcium channel subunit alpha-1C (Cav1.2 α1C subunit channel) is an isoform of VSCC, and is characterized from an high-voltage activation. Previous study have shown that class of molecules as benzothiazepines (Tikhonov D. et al, 2008), are able to block the alpha-1C subunit. Recent works have demonstrated that molecules belonged at the flavonoid class are able to inhibit or to raise channel activity (Saponara S. et al, 2011). In this work, we reported the sensing- residues that could play a key role in Cav1.2 α1C activity. Furthermore, we proposed a potential mechanism of action inside Cav1.2 α1C binding-site with differences between inhibitors and stimulants. Our work has clarifiedas the ligands operate on Cav1.2 α1C, this information could be useful in order to improve their usefulness.
Methods
The 3D structure of Cav1.2 α1C subunit channel was obtained on basis of previous work (Saponara S. et al, 2015). The structure of flavons were downloaded from Pubchem(Kim S. et al, 2015). Docking simulation was carried out through Autodock/Vina v.1.1.2 (O.Trott et al, 2010). PDBePISAwas used in order to evaluate buried surface area values (B.S.A). Protein-ligand interactions were obtained using protein–ligand interaction profiler (P.L.I.P)(Salentin S. et al, 2015). Pymol was used as molecular graphics system (The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.).
Results and discussion
I­­­­­n vitro analysis on rat Cav1.2 L-type channel of 20 flavonoids have shown stimulatory and inhibitory activities (Saponara S. et al, 2015).The 11 inhibitors and 8 stimulators derivatives are positioned in their corresponding binding-sites with peculiar sensing-residues interactions (shown in figure 1). Analyzing the network of interactions among the two classes of flavonoids we have observed hydrogen bonds, hydrophobic interactions and π–π stacking bonds characterizing their activities that could differently promote pore open/closed conformation and decreasing voltage-sensitive calcium channel activity (Tikhonov D. et al, 2009). Furthermore, on the basis of the selectivity filters model, we have evaluated B.S.A residues values present in the­­­ binding-sites, we have observed that B.S.A of some residues dramatically decrease, showing that these residues play a key role in the pore stabilization. The different mechanism of action of these molecules can be attributed to their chemical-physical proprieties as steric hindrance and different positions of hydroxyl groups.
Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies
Authors: Cabau Cédric , Escudié Frédéric , Djari Anis , Guiguen Yann , Bobe Julien , Klopp Christophe 
Published: January 2018

Background
De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved.
Results
We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1,3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts.
Conclusion
Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an ease to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available at http://www.sigenae.org/drap .
Angiosperm phylogeny poster (APP) – Flowering plant systematics
Authors: Cole Theodor C H , Hilger Hartmut H , Stevens Peter F 
Published: January 2018

The "Angiosperm Phylogeny Poster – Flowering Plant Systematics" is an educational tool presenting an overview of the evolutionary relationships among flowering plants according to APG IV and APweb as of 2016. The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher levels within the tree. The intuitive color-coding facilitates memorization and teaching.
Translations of the poster by internationally renown botanists are now available in 18 languages. Hyperlinks to APweb (Peter F. Stevens, Missouri Botanical Garden) are provided for the orders and higher ranks.
This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
Angiosperm phylogeny poster (APP) – Flowering plant systematics, 2017
Authors: Cole Theodor C H , Hilger Hartmut H , Stevens Peter F 
Published: January 2018

The "Angiosperm Phylogeny Poster – Flowering Plant Systematics" is an educational tool presenting an overview of the evolutionary relationships among flowering plants according to APG IV and APweb as of 2016. The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher levels within the tree. The intuitive color-coding facilitates memorization and teaching.
Translations of the poster by internationally renown botanists are now available in 18 languages. Hyperlinks to APweb (Peter F. Stevens, Missouri Botanical Garden) are provided for the orders and higher ranks.
This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
Angiosperm phylogeny poster (APP) – Flowering plant systematics, 2017
Authors: Cole Theodor C H , Hilger Hartmut H , Stevens Peter F 
Published: January 2018

The "Angiosperm Phylogeny Poster – Flowering Plant Systematics" is an educational tool presenting an overview of the evolutionary relationships among flowering plants according to APG IV and APweb as of 2016. The phylogenetic tree depicts the 64 orders and the majority of the 416 families, listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical, morphological, and phytochemical features for orders and higher levels within the tree. The intuitive color-coding facilitates memorization and teaching.
Translations of the poster by internationally renown botanists are now available in 20 languages. Hyperlinks to APweb (Peter F. Stevens, Missouri Botanical Garden) are provided for the orders and higher ranks.
This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
Bovine tuberculosis in cattle from 1986 to 2012 in and around badger-culled areas of the RBCT
Authors: Hendy David 
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of a trial where badgers were culled between 1998 and 2005. This trial, known as the Randomised Badger Culling Trial (RBCT), was performed across 100 km2 (nominal) zones in the West of England. The results were based on a model of new herd incidence data. It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence in surrounding areas.
This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates the data. The Animal and Plant Health Agency supplied this data in March 2016. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.
Whilst the proactive culls substantially and sustainably reduced cattle TB in treated areas, such culls did not significantly increase TB in the surrounding areas. In fact New Herd Incidents (NHI’s) between 2006 and 2012 dropped by 28%, 1% and 18% in the treated, outer 2km ring, and combined areas respectively. Based on the number of NHI’s prevented since 1998, a break-even cost for a badger removal exercise was calculated to be £8,454 per km2. This figure may be under-estimated because it takes no account of any NHI’s prevented after 2012.
The more limited reactive culls were found to have no significant impact. This applied to both the treated area and outer 2km ring.
The data also showed that the culls only reduced confirmed TB with no significant impact on unconfirmed TB. This was also found by the ISG when they reported results in 2007.
Arguments surrounding badger culling in the UK have been poorly based due to incomplete data. In view of this and media hype, it should be emphasised that after the first year of substantial culling across the study area, 9 years of data were needed to clearly see the full extent by which TB dropped in the RBCT. This has implications for the culls which started in South West England in 2013. If the current reporting delay of 20 months persists, it may be the autumn of 2023 at the earliest before the impact of these culls becomes clear. Also, if culls stop after year four in each zone, this risks benefits falling short of those achieved in the RBCT.
Randomised Badger Culling Trial: Impact based on more extensive data
Authors: Hendy David 
Published: January 2018

In 2007 the Independent Scientific Group (ISG) reported to the UK government the impact on bovine tuberculosis (TB) in cattle of a trial where badgers were culled between 1998 and 2005. This trial, known as the Randomised Badger Culling Trial (RBCT), was performed across 100 km2 (nominal) zones in the West of England. The results were based on a model of new herd incidence data. It was concluded that reactive culling generated overall detrimental effects, while proactive culling achieved very modest overall benefits at the cost of elevated incidence in surrounding areas.
This work looks at more extensive RBCT data to examine if these findings hold true. Instead of presenting the results of a model, this work directly illustrates the data. The Animal and Plant Health Agency supplied this data in March 2016. Such data covers a greater number of years (1986 to 2012) and includes the prevalence of herd restrictions as well as herd incidence.
Whilst the proactive culls substantially and sustainably reduced cattle TB in treated areas, such culls did not significantly increase TB in the surrounding areas. In fact New Herd Incidents (NHI’s) between 2006 and 2012 dropped by 28%, 1% and 18% in the treated, outer 2km ring, and combined areas respectively. Based on the number of NHI’s prevented since 1998, a break-even cost to complete a badger removal exercise was calculated to be £8,454 per km2. This figure may be under-estimated because it takes no account of any NHI’s prevented after 2012.
The more limited reactive culls were found to have no significant impact. This applied to both the treated area and outer 2km ring.
The data also showed that the culls only reduced confirmed TB with no significant impact on unconfirmed TB. This was also found by the ISG when they reported results in 2007.
Conclusions in the RBCT final report were made based on incomplete data so are poorly grounded. In addition to this, many mass media outlets are already adversely reporting the impact for culls which started in South West England in 2013. In the RBCT, after the first year of substantial culling, 9 years of data were needed to clearly see the full extent by which TB dropped when the data was not time-shifted. It is likely that the impact of the 2013 culls will not become clear until sometime between 2020 and 2025.
How does paw pad of Canine attenuate ground impacts: a micromechanical finite element study
Authors: Miao Huaibin , Fu Jun , Qian Zhihui , Ren Luquan , Ren Lei 
Published: January 2018

Background. Digitigraded mammals, e.g. dogs and cats, stand or walk on their digits or toes. Their paw pads beneath the digits or toes, rather than the entire sole of the foot, are in contact with the ground surface during locomotion. Digitigrades generally move more quickly and quietly than other animals. So far, little is known about the micro-scale structural characteristics of digitigrades' paw pads and its connection with the superior biomechanical functioning of their feet.
Methods. In this study, we investigated the micro-structure of the paw pad of German shepherd dog (GSD) using SEM and histological examination, and assessed the biomechanical functions of the micro-structured epidermis layer by using dynamic finite element (FE) simulations.
Results. We found that there exists a thick layer of stratified epithelium of a honeycomb like structure with conical protuberances (i.e. dermal papilla) embedded in each cell unit. Our FE simulation analyses revealed that this specially structured layer is capable of effectively attenuating the ground impact across a range of impact velocities. Moreover, this cushioning capacity becomes more pronounced with increased impact velocity. More importantly, this layer can also significantly reduce the mechanical stress transmitting to the soft dermal papillae and dermis by using an off-loading mechanism.
Discussion. This would provide more insights into the biomechanical functioning of the digitigrade's paw pads, and also facilitate the development of bio-inspired ground contacting components of robots and machines, and also the design of footwear and orthotics devices.