bluuebunny/crossref_metadata_2025 huggingface dataset:
Network development of the world’s high-speed railways
Authors: Tarkhov Sergey Anatolyevich
Published: December 2019

The first high-speed railway appeared in 1964 in Japan, which was the leader in this business up to its economic crisis in the 1990s. Certain European countries developed these railways in 1980-90s, and some other Asian states also joined this club. China commenced with the construction of its high-speed railways in the 2000s, transforming itself into the world’s new leader in the field. This article is dedicated to a geographical analysis of the network development of high-speed railways in the years 1964-2017. Graph theory methods (network analysis) are applied to compare processes of development.
Export activity patterns of border regions in Poland
Authors: Szejgiec-Kolenda Barbara
Published: December 2019

The study presents a brief review of Polish border regions’ participation in the global economy in 2013 based on export linkages at the local level (LAU 1). The paper offers an extended understanding of the export activity of intermediaries in foreign trade comparing to manufacturing companies. Results confirm the relatively greater importance of intermediaries activity in border areas, especially at the eastern border.
Topical Imiquimod and Subsequent Erythema Multiforme
Authors: Maxfield Luke , Gaston David , Peck Aurora , Hansen Katrina
Published: December 2019

Topical imiquimod is commonly used in the nonsurgical management of actinic keratosis and superficial basal cell carcinoma. Although adverse effects have been limited primarily to local irritation, another rare adverse reaction is erythema multiforme. We present a case of erythema multiforme involving the oral mucosa, trunk, and extremities that followed broad application of topical imiquimod for the management of suspected superficial basal cell skin cancers and actinic keratosis. The patient had used imiquimod previously without complication. Cessation of use and systemic corticosteroids resulted in prompt clearance.
Linnade (ümber)kirjutamise võimalustest / City (Re)writing Possibilities
Authors: Vaher Berk
Published: December 2019

.
The fast–slow continuum of longevity among yellow-bellied toad populations (Bombina variegata): intrinsic and extrinsic drivers of variation
Authors: Hantzschmann Alena Marcella , Gollmann Birgit , Gollmann Günter , Sinsch Ulrich
Published: December 2019

Yellow-bellied toad populations (Bombina variegata) show a wide fast–slow continuum of the life-history trait longevity ranging from 5 to 23 years. We investigated populations in Germany (n = 8) and Austria (n = 1) to determine their position within the continuum of longevity and the potential drivers of adult survival at the local and the continental scale. Intrinsic and extrinsic factors considered were local weather, nutritional state, allocation of ingested energy to somatic growth, pathogen prevalence, and geographical clines (latitude, altitude, and longitude). Capture-mark-recapture (CMR) monitoring and direct age assessment by skeletochronology allowed for reliable estimates of longevity and adult survival. Raw and corrected recapture rates as well as a probabilistic estimate of the lifespan of the eldest 1% adults of a cohort (CMR data) were used as surrogates for adult survival and thus longevity in a population. Additionally, survival rates were calculated from static life tables based on the age structure (skeletochronological data) of eight populations. Populations in Germany were short-lived with a maximum lifespan of annual cohorts varying from 5 to 8 years, whereas the population in Austria was long-lived with a cohort longevity of 13 to 23 years. We provide evidence that annual survival rates and longevity differ among years and between short- and long-lived populations, but there was no decrease of survival in older toads (i.e. absence of senescence). Variation of weather among years accounted for 90.7% of variance in annual survival rates of short-lived populations, whereas the sources of variation in the long-lived population remained unidentified. At the continental scale, longevity variation among B. variegata populations studied so far did not correspond to geographical clines or climate variation. Therefore, we propose that a population’s position within the fast–slow continuum integrates the response to local environmental stochasticity (extrinsic source of variation) and the efficiency of chemical antipredator protection determining the magnitude of longevity (intrinsic source of variation).
Significance of TP53 mutation in bladder cancer disease progression and drug selection
Authors: Wu Guang , Wang Fei , Li Kai , Li Shugen , Zhao Chunchun , Fan Caibin , Wang Jianqing
Published: December 2019

Background

The tumor protein p53 (TP53) mutant is one of the most frequent mutant genes in bladder cancer. In this study, we assessed the importance of the TP53 mutation in bladder cancer progression and drug selection, and identified potential pathways and core genes associated with the underlying mechanisms.

Methods

Gene expression data used in this study were downloaded from The Cancer Genome Atlas and cBioportal databases. Drug sensitivity data were obtained from the Genomics of Drug Sensitivity in Cancer. We did functional enrichment analysis by gene set enrichment analysis (GSEA) and the Database for Annotation, Visualization and Integrated Discovery (DAVID).

Results

We found the TP53 mutation in 50% of bladder cancer patients. Patients with the TP53 mutation were associated with a lower TP53 mRNA expression level, more advanced tumor stage and higher histologic grade. Three drugs, mitomycin-C, doxorubicin and gemcitabine, were especially more sensitive to bladder cancer with the TP53 mutation. As for the mechanisms, we identified 863 differentially expressed genes (DEGs). Functional enrichment analysis suggested that DEGs were primarily enriched in multiple metabolic progressions, chemical carcinogenesis and cancer related pathways. The protein–protein interaction network identified the top 10 hub genes. Our results have suggested the significance of TP53 mutation in disease progression and drug selection in bladder cancer, and identified multiple genes and pathways related in such program, offering novel basis for bladder cancer individualized treatment.
Análise e perspectivas do turismo no Brasil
Authors: Rabahy Wilson Abrahão
Published: December 2019

Este texto traz uma síntese da atividade turística no Brasil, apresentando e analisando estatísticas sob a perspectiva econômica. Para tanto, são reunidos dados das principais fontes oficiais disponíveis, bem como informações sobre o turismo produzidas pela Fundação Instituto de Pesquisas Econômicas (FIPE). Inicialmente são apresentadas análises sobre o mercado mundial de turismo. Em seguida, é discutida a realidade do turismo internacional receptivo do Brasil, incluindo relações entre renda, preços, taxa de câmbio e turismo. Três análises sobre o turismo no Brasil são destacadas: a importância do turismo doméstico, as oportunidades existentes no turismo receptivo internacional e os impactos do turismo na distribuição regional de renda. Por fim, o texto apresenta algumas recomendações para o turismo no Brasil.
Chemometrics Applied to Nuclear Magnetic Resonance Analysis
Authors: Beavis Guy , Rusilowicz Martin , Donarski James , Charlton Adrian , Wilson Julie
Published: December 2019

Nuclear magnetic resonance (NMR) spectroscopy provides information about the physical and chemical properties of atoms within a sample and has become an essential tool in metabolomics. Although less sensitive than mass spectrometry, NMR spectroscopy is highly reproducible and gives wider coverage in comparison to other techniques used for the analysis of complex mixtures. Recent advances in technology, advances in methodology, and increased computer power have increased the need to develop mathematical and statistical methods to analyze and interpret the complex datasets acquired. This has resulted in developments in the field of chemical informatics known aschemometrics. In contrast to targeted analyses, chemometric approaches do not initially attempt to identify particular metabolites. Instead, statistical techniques and pattern recognition methods are used to identify spectral features that show consistent trends or provide discrimination between classes. These features can provide a fingerprint for a metabolic state to be used, for example, for disease diagnostics, and individual features of interest can then be related to specific compounds and metabolic pathways using database searches.

NMR‐based chemometric methods are now used in a wide range of applications including clinical diagnostics, food science and traceability, process control, monitoring genetic modification, and predicting the side effects of pharmaceuticals and their environmental effects.
Fundamental Parameter Method inX‐Ray Fluorescence Analysis
Authors: Kawai Jun , Yamasaki Keita , Tanaka Ryohei
Published: December 2019

The fundamental parameter (FP) method for X‐ray fluorescence (XRF) analysis is explained using 18‐8 steel spectrum as an example. The accuracy and precision are discussed. Other related alpha parameter method and djmethod are compared. The FP method is a first‐principles calculation method of chemical element concentration from the measured XRF spectra using the FPs such as the X‐ray absorption coefficients, fluorescence yields, jump ratios, branching ratios, and the incident spectrum from the X‐ray tube. Based only on these physics parameters and the measured spectra, concentrations in the specimen can be obtained accurately in spite that the XRF spectra are heavily affected by the matrix effects, such as absorption and enhancement effects. The problems and future directions to the improvement of present FP method are also discussed.
Solid‐Phase Microextraction and Its Application to Natural Products and Biological Samples
Authors: Mottaleb M. Abdul , Meziani Mohammed J. , Islam M. Rafiq
Published: December 2019

Solid‐phase microextraction (SPME) is a simple, fast, and efficient sample preparation technique that eliminates the need for solvents and integrates sampling, isolation, and enrichment in one step. In SPME, the extraction is based on the partitioning of the analyte between the organic phase on the fused‐silica fiber or nanomaterials coated fiber and the matrix. Fibers or capillary tubes coated with an appropriate stationary phase are key players in the process. By controlling the polarity and thickness of the coating on fibers or tubes, sampling time, and other extraction parameters, an analyst can achieve very reliable, accurate, and highly quantifiable robust results at subfemtogram level, for gaseous to macromolecular target solutes, with a shorter analysis time compared to conventional extraction methods. This solvent‐free technique requires small samples, saves sample preparation time as well as solvent purchase and disposal costs. Moreover, it is environmental friendly and poses low health hazard risk to the laboratory associates. Today, SPME has been integrated to gas chromatography (GC), gas chromatography–mass spectrometry (GC–MS), high‐performance liquid chromatography (HPLC or LC), LC–MS, or capillary electrophoresis (CE) for analysis of complex mixtures of samples that include environmental, chemical, biochemical, biological, pharmaceuticals, clinical, biomedical, natural products, food abstracts, plant extracts, and organic compounds in media containing nanoparticles.
P
hycisphaeraceae
Authors: Fukunaga Yukiyo
Published: December 2019

Phy.ci.sphae.ra.ce'ae. N.L. fem. n.
Phycisphaera
, type genus of the family; aceae ending to denote a family; N.L. fem. pl. n.
Phycisphaeraceae
, the family of the genus
Phycisphaera
.

Planctomycetes / Phycisphaerae / Phycisphaerales / Phycisphaeraceae

The family
Phycisphaeraceae
is defined by phylogenetic analyses based on 16S rRNA gene sequences; the family contains the genera
Phycisphaera
and
Algisphaera
. All known species are Gram stain‐negative and show
binary fission
. Endospores are not observed. Motile. Aerobic and facultatively anaerobic. Oxidase‐negative, catalase‐positive. The major menaquinone is MK‐6. Known members of the family were isolated from a macroalgae in marine environment.

DNA G + C content (mol%)
: 63–73.

Type genus
:
Phycisphaera
Fukunaga, Kurahashi, Sakiyama, Ohuchi, Yokota and Harayama 2010, 2
VP
(Effective publication: Fukunaga, Kurahashi, Sakiyama, Ohuchi, Yokota and Harayama 2009, 273).
P
hycisphaera
Authors: Fukunaga Yukiyo , Ichikawa Natsuko
Published: December 2019

Phy.ci.spae'ra. Gr. neut. n.
phycos
, seaweed; L. fem. n.
sphaera
, a globe, sphere; N.L. fem. n.
Phycisphaera
, a spherical bacterium isolated from a seaweed.

Planctomycetes / Phycisphaerae / Phycisphaerales / Phycisphaeraceae / Phycisphaera

Members of the genus
Phycisphaera
are represented by Gram stain‐negative, motile, and spherical cells that are covered with pili. Weakly facultative anaerobes. Colonies are circular and pink pigmented. Reproduce by binary fission. Resistant to β‐lactam antibiotics. Chemoorganotrophs that grow well on complex organic media such as Marine Agar. Require seawater for growth. Neutrophilic and mesophilic. MK‐6 is the major menaquinone. The main fatty acids are C
16:0
, iso‐C
16:1
, and iso‐C
16:0
. Members of the phylum
Planctomycetes
, class
Phycisphaerae
, order
Phycisphaerales
, and family
Phycisphaeraceae
. Known habitats are marine environments.

DNA G + C content (mol%)
: 73 (HPLC).

Type species
:
Phycisphaera mikurensis
Fukunaga, Kurahashi, Sakiyama, Ohuchi, Yokota and Harayama 2010, 2
VP
(Effective publication: Fukunaga, Kurahashi, Sakiyama, Ohuchi, Yokota and Harayama 2009, 273).
Caenibacillus
Authors: Tsujimoto Yoshiyuki , Watanabe Kunihiko
Published: December 2019

Cae.ni.ba.cil'lus. L. neut. n.caenum,mud; L. masc. n.bacillus, a rod, and also a bacterial genus name (Bacillus); N.L. masc. n.Caenibacillus, aBacillus‐like organism that inhabits compost.

Firmicutes / Bacilli / Bacillales / Sporolactobacillaceae / Caenibacillus

Caenibacillusis a single species genus in the familySporolactobacillaceae. To date, it comprises one species,Caenibacillus caldisaponilyticus. Cells are Gram‐stain‐positive, aerobic, endospore‐forming, and rod‐shaped, occurring singly. Endospores are ellipsoidal, subterminal or terminal, and formed in swollen sporangia. The ranges of temperature, pH, and NaCl for the growth are 40–65°C, 4.8–8.1, and 0–1.5% (w/v), respectively. Catalase‐ and oxidase‐positive. The cell wall containsmeso‐diaminopimelic acid, alanine, glutamic acid, and galactose. The predominant polar lipids are phosphatidylglycerol, cardiolipin, and an unidentified phospholipid, and the major fatty acid is an anteiso‐C17:0. The menaquinone is MK‐7. Strain B157Twas isolated from acidulocompost at Oarai Aquarium in Japan.

DNA G + C content (mol%): 51.8 (genome).

Type species:Caenibacillus caldisaponilyticusTsujimoto, Saito, Furuya, Ishihara, Sahara, Kimura, Nishino, Tsuruoka, Shigeri and Watanabe 2016, 2689VP.
G
eothermomicrobium
Authors: Zhou En‐Min , Li Wen‐Jun
Published: December 2019

Ge.o.ther.mo.mi.cro'bi.um. Gr. fem. n.
ge
the earth; Gr. masc. adj.
thermos
hot; Gr. masc. adj.
mikros
small; Gr. masc. n.
bios
life; N.L. neut. n.
Geothermomicrobium
a microbe from hot earth.

Firmicutes / Bacilli / Bacillales / Thermoactinomycetaceae / Geothermomicrobium

The genus
Geothermomicrobium
is classified within the family
Thermoactinomycetaceae
, order
Bacillales
, and in the class
Bacilli
. Aerobic, Gram‐stain‐positive.
Thermotolerant
, growth at 30–60°C, with optimum at 50–55°C. The substrate mycelia are well developed, white to gray‐yellow, but the aerial mycelium is not produced.
Warty ornamented endospores produce singly along the substrate mycelium.
The menaquinone is
MK‐7
, the diagnostic diamino acid is

meso

‐diaminopimelic acid
, and the major cellular fatty acids are

iso‐C
14:0
, iso‐C
15:0

,

and iso‐C
16:0

. The major polar lipids are
diphosphatidylglycerol, phosphatidylmethylethanolamine, unidentified polar lipids, and unidentified phospholipids
. Currently, the genus consists of one species
Geothermomicrobium terrae
(the type species of the genus). The type strain of
Geothermomicrobium terrae
was isolated from geothermal soil. The phylogenetically nearest neighbor is the genus
Hazenella
.

DNA G + C content (mol%)
: 44–46 (HPLC).

Type species
:
Geothermomicrobium terrae
Zhou, Yu, Liu, Ming, Yin, Dong, et al. 2014, 3003
VP
.
B
rockia
Authors: Perevalova Anna A. , Chernyh Nikolay A. , Bonch‐Osmolovskaya Elizaveta A.
Published: December 2019

Broc'ki.a. N.L. fem. n.
Brockia
named in honor of the American microbiologist Thomas Dale Brock for his invaluable impact to our knowledge of thermophilic prokaryotes inhabiting volcanic environments.

Firmicutes / Clostridia / Thermoanaerobacterales / Brockiaceae / Brockia

Extremely thermophilic. Strictly anaerobic. Cells are spore‐forming rods with a Gram‐positive type of cell wall. Chemolithoautotrophic. Elemental sulfur, thiosulfate, or polysulfide are used as electron acceptors and molecular hydrogen or formate as electron donors. Growth at 46 –78°C and pH 5.5–8.5. The optimal growth (doubling time, 6.0 h) was at 60–65°C. The major fatty acid is C
16:0
. DNA G + C content is 63.4 mol% (genome). 16S rRNA gene sequence analysis places the genus in the family
Brockiaceae
. The most closely related strains are members of the genera
Ammonifex
and
Caldanaerobacter
. The genus currently accommodates the only one species
Brockia lithotrophica
. Known habitats are thermal hot springs.

DNA G + C content (mol%)
: 63.4 (genome).

Type species
:
Brockia lithotrophica
Perevalova et al. 2013, 482.
A
cutalibacter
Authors: Garzetti Debora , Jochum Lara , Stecher Bärbel
Published: December 2019

A.cu.ta.li.bac'ter. L. masc. adj.
acutalis
, tapered, pointed; N.L. masc. n.
bacter
, rod; N.L. masc. n.
Acutalibacter
, a rod‐shaped bacterium with tapered ends, pertaining to the cell morphology of the type strain of the type species.

Firmicutes / Clostridia / Clostridiales / Ruminococcaceae / Acutalibacter

Gram‐stain negative, strictly anaerobic, long rods with tapered ends. Cells occur singly. The genus
Acutalibacter
contains a single species, the type species
Acutalibacter muris
. The type species was isolated from the mouse gut and does not form colonies on solid medium. Motile cells have not been observed, but motility‐associated proteins are encoded in the genome. Cells do not lyse readily with standard lysis protocols and form endospores. The main cellular fatty acids are C
16:0
(22.1%), C
16:0
DMA (21.7%), iso‐C
15:0
(16.8%), anteiso‐C
15:0
(9.8%), and C
18:1
ω9
c
(12.2%). The diagnostic amino acid of the peptidoglycan type is
meso
‐diaminopimelic acid. Most related strains that are within family level distance (86.5%) based on 16S rRNA gene similarity were isolated from human feces or gut or the gastrointestinal tracts of animals. Some related strains were obtained from wastewater or other anaerobic sludge/soil habitats, indicating that these environments may also be a potential habitat for
Acutalibacter
species.

DNA G + C content (mol%)
: 54.6 (G + C count divided by total number of bases).

Type species
:
Acutalibacter muris
Lagkouvardos, Pukall, Abt, Foesel, Meier‐Kolthoff, Kumar et al. 2016b, 4299
VP
(Effective publication: Lagkouvardos, Pukall, Abt, Foesel, Meier‐Kolthoff, Kumar et al. 2016a, 10).
M
ageeibacillus
Authors: Austin Michele N. , Srinivasan Sujatha , Fredricks David N. , Hillier Sharon L.
Published: December 2019

Ma.gee.i.ba.cil'lus. N.L. n.
Mageea
named after Magee; L. masc. n.
bacillus
a rod; N.L. masc. n.
Mageeibacillus
a rod isolated at Magee‐Womens Research Institute.

Firmicutes / Clostridia / Clostridiales / Hungateiclostridiaceae / Mageeibacillus

Gram‐positive cell wall, obligately anaerobic, nonmotile, non‐spore‐forming rods with blunt or tapered ends. Cells occur in aggregates or small chains. Asaccharolytic, noncellulolytic, negative for catalase, oxidase, urease, esculin, and gelatin hydrolysis and lecithinase and lipase activity, and using amino acids as a primary source of carbon. Mesophilic with growth occurring between 35 and 42°C. Growth is supported by solid Brucella agar with 5% sheep's blood, hemin, and vitamin K. The major fatty acids are unbranched saturated and unsaturated forms. The G + C content is 44.2 mol% (genome analysis). Member of the class
Clostridia
, family
Hungateiclostridiaceae
. Known habitats are human skin, female genital tract, anus, bladder, male urethra, and ewe vagina.

DNA G + C content (mol%)
: 44.2 (genome analysis).

Type species
:
Mageeibacillus indolicus
Austin et al. 2015, VL172.
T
uricimonas
Authors: Jochum Lara , Garzetti Debora , Stecher Bärbel
Published: December 2019

Tu.ri.ci.mo'nas. L. neut. n.
Turicum
the Roman name for the city of Zurich; Gr. fem. n.
monas
a unit, a monad; N.L. fem. n.
Turicimonas
a unit of Turicum/Zurich; the type strain of the type species was isolated in the Swiss city Zurich.

Proteobacteria / Betaproteobacteria / Burkholderiales / Sutterellaceae / Turicimonas

Gram stain‐negative, rod shaped, and obligately anaerobic single, straight cells. The genus
Turicimonas
contains a single species, the type species
Turicimonas muris
, with the type strain
T. muris
YL45
T
. The type species was isolated from the cecum of a mouse, but close relatives are also found in the gut and feces of other mammals.
T. muris
YL45
T
is the only isolate of nonhuman origin within the family
Sutterellaceae
. The closest phylogenomic relative is
Parasutterella excrementihominis
. Colonies show slight α‐hemolysis on Columbia blood agar plates. The type strain of the type species is able to produce succinate.
T. muris
YL45
T
carries genes for dissimilatory nitrate reduction and ammonia assimilation; however, it is not reported to use either
in vitro
. While the taxonomy of the
Sutterellaceae
family is inconsistent,
Turicimonas
reproducibly forms a distinct genus‐level lineage within the family.

DNA G + C content (mol%)
: 44.1 (G + C count divided by total number of bases).

Type species
:
Turicimonas muris
Lagkouvardos, Pukall, Abt, Foesel, Meier‐Kolthoff, Kumar et al. 2017, 2
VP
(Effective publication: Lagkouvardos, Pukall, Abt, Foesel, Meier‐Kolthoff, Kumar et al. 2016, 14).
C
aedibacter
Authors: Salam Nimaichand , Qu Ping‐Hua , Li Wen‐Jun
Published: December 2019

Cae.di.bac'ter. L. fem. n.
caedes ‐is
act of killing; N.L. masc. n.
bacter
a rod; N.L. masc. n.
Caedibacter
the bacterium which kills.

Proteobacteria / Gammaproteobacteria / Thiotrichales / Fastidiosibacteraceae / Caedibacter

Gram‐negative, nonmotile. Obligate cytoplasmic endosymbionts of
Paramecium
spp. Presence of refractile inclusion (R) bodies confers killer traits upon their hosts. Cells containing R bodies are toxic to certain strains of paramecia (sensitive paramecia) and are usually larger than cells that do not contain R bodies. Culture outside the host organism has not been achieved or is exceedingly difficult.

DNA G + C content (mol%)
: 41–42 (genome);
DNA G + C content (mol%)
: 40–44 (HPLC).

Type species
:
Caedibacter taeniospiralis
(
ex
Preer et al. 1974) Preer and Preer 1982
VP
.
D
iaphorobacter
Authors: Vaz‐Moreira Ivone , Nunes Olga C. , Manaia Célia M.
Published: December 2019

Diaphorobacter
[Di.a.pho.ro.bac'ter. Gr. masc. adj.
diaphoros
different, profitable; N.L. masc. n.
bacter
rod; N.L. masc. n.
Diaphorobacter
distinguished and profitable rod, referring to usefulness in nitrogen removal].

Proteobacteria / Betaproteobacteria / Burkholderiales / Comamonadaceae / Diaphorobacter

Rods
, non‐spore‐forming, Gram‐stain‐negative. Motile with a single polar flagellum or nonmotile.
Aerobic or facultative aerobic
.
Mesophilic
with optimum growth conditions at a temperature around 28°C and pH 7. No special growth requirements. Catalase‐positive.

Cytochrome
c
oxidase test varies among species

.
Chemoorganotrophic
.
Denitrifying or nitrate reduction
.
No indole production or glucose fermentation
. Some members have the capacity to degrade poly(3‐hydroxybutyrate) (PHB) and poly(3‐hydroxybutyrate‐co‐3‐hydroxyvalerate) (PHBV). The major respiratory quinone is
ubiquinone 8
, and the major fatty acids are
C

16:0

, summed feature 3 (C

16:1

ω7
c
and/or iso‐C

15:0

2‐OH), and C

18:1

ω7
c

, and the predominant hydroxy fatty acid is
C

10:0

3‐OH
.

DNA G + C content (mol%)
: 62.9–66.8.

Type species
:
Diaphorobacter nitroreducens
Khan and Hiraishi 2002, VL92.
O
ryzisolibacter
Authors: Nunes Olga C. , Manaia Célia M. , Vaz‐Moreira Ivone
Published: December 2019

O.ry.zi.so.li.bac'ter. L. fem. n.
oryza
rice; L. neut. n.
solum
soil; N.L. masc. n.
bacter
rod; N.L. masc. n.
Oryzisolibacter
rod from rice crop bulk soil.

Proteobacteria / Betaproteobacteria / Burkholderiales / Comamonadaceae / Oryzisolibacter

Rods
1.9 ± 0.35‐μm long and 0.6 ± 0.04‐μm wide.
Motile
.
Gram‐negative
. Nonsporulating.
Facultative aerobe
. Nitrate is reduced to N
2
. Mesophilic, with the ability to grow between 15 and 37°C, pH 6–9, and at a NaCl concentration up to 4%.
Chemoorganotroph
, being able to assimilate glycerol, potassium gluconate, adipic acid, malic acid, and (trisodium) citrate. Catalase‐ and cytochrome
c
oxidase‐positive. The respiratory quinone is
ubiquinone 8
, and the major fatty acids are C
18:1
ω7
c
, C
16:0
, and the summed feature 3 (C
16:1
ω7
c
/iso‐C
15:0
2‐OH). The major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Isolated from rice paddy soil through an enrichment culture in the presence of propanil and 3,4‐dichloroaniline; the type strain of the type species
Oryzisolibacter propanilivorax
is able to degrade both compounds.

DNA G+C content (mol%)
: 69.4 (HPLC) or 69.2 (genome analysis).

Type species
:
Oryzisolibacter propanilivorax
Vaz‐Moreira et al. 2017
VP
.
H
ydromonas
Authors: Vaz‐Moreira Ivone , Nunes Olga C. , Manaia Célia M.
Published: December 2019

Hy.dro.mo'nas. Gr. neut. n.
hydor
water; L. fem. n.
monas
a unit, monad; N.L. fem. n.
Hydromonas
a unit (monad) from water.

Proteobacteria / Betaproteobacteria / Burkholderiales / Burkholderiaceae / Hydromonas

Rods with electron‐dense intracellular inclusions, non‐spore‐forming, Gram‐negative. Aerobic, mesophilic, with the ability to grow between 15 and 30°C, pH 6–8, and a concentration of NaCl of up to 1% and no special growth requirements. Chemoorganotroph with limited metabolic versatility, being able to assimilate
d
‐glucose,
d
‐mannitol, and
N
‐acetylglucosamine. Catalase‐ and cytochrome
c
oxidase‐positive. The respiratory quinone is ubiquinone 8, and the major fatty acids are C
16:1
ω7
c
and C
14:0
3‐OH. The major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. Isolated from freshwater.

DNA G + C content (mol%)
: 47 ± 1 (HPLC).

Type species
:
Hydromonas duriensis
Vaz‐Moreira et al. 2015
VP
.
T
epidiphilus
Authors: Manaia Célia M. , Vaz‐Moreira Ivone , Nunes Olga C.
Published: December 2019

Te.pi.di'phi.lus. L. masc. adj.
tepidus
lukewarm; Gr. masc. adj.
philos
friendly to; N.L. masc. n.
Tepidiphilus
liker of lukewarm conditions.

Proteobacteria / Hydrogenophilia / Hydrogenophilales / Hydrogenophilaceae / Tepidiphilus

Rods
with poly‐beta‐hydroxybutyrate granules, non‐spore forming,
Gram‐negative
with a
single polar flagellum
. Aerobic, able to grow anaerobically in the presence of nitrate.
Thermophilic
, with the ability to grow between 25°C and 61°C, with optimum at 50–55°C, pH 6–8 and no special growth requirements.
Chemo‐organotroph
. Organic acids and amino acids, but not sugars, can be used as single carbon sources. Catalase‐ and cytochrome c oxidase positive.
Ubiquinone 8
is the major respiratory quinone and the predominant fatty acids are
C

16:0

, cyclo‐C

17:0

, cyclo‐C

19:0

ω8
c
, C

18:1

ω6
c
/ω7
c
,

and
C

17:0

. Major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyl coline. Isolated from thermophilic digester, oil well or terrestrial hot spring.

DNA G + C content (mol%)
: 58.6–66.1 (HPLC method).

Type species
:
Tepidiphilus margaritifer
Manaia et al. 2003
VP
emend. Poddar et al. 2014.
N
atronobiforma
Authors: Sorokin Dimitry Y. , Oren Aharon , Elcheninov Alexander G. , Kublanov Ilya V.
Published: December 2019

Na.tro.no.bi.for'ma. Gr. neut. n.
natron
arbitrarily derived from Arabic n.
natrun
or
natron
soda; L. adv. num.
bis
twice; L. fem. n.
forma
form, shape; N.L. fem. n.
Natronobiforma
the dimorphic natronoarchaeon.

Euryarchaeota / Halobacteria / Natrialbales / Natrialbaceae / Natronobiforma

The genus
Natronobiforma
, classified within the family
Natrialbaceae
, order
Natrialbales
, in the class
Halobacteria
, currently consists of a single species,
Natronobiforma cellulositropha
. It is a moderately alkaliphilic, obligately aerobic, extreme halophile, forming pink colonies with large clearance zones on plates containing amorphous cellulose. The cells are pleomorphic flat motile rods or nonmotile coccoid cells. Multiple strains classified within this genus were isolated from alkaline hypersaline lakes in different locations. They grow optimally on insoluble native celluloses. Xylan, β‐mannan, cellobiose, and maltose can also be used as carbon and energy sources. Other organic compounds used by most members of the
Halobacteria
do not support growth.

DNA G + C content (mol%)
: 65.4–65.5 (genome sequences).

Type species
:

Natronobiforma cellulositropha

Sorokin et al. 2019, VL187.
Signalling Interactions in Flooding Tolerance
Authors: Mustroph Angelika , Steffens Bianka , Sasidharan Rashmi
Published: December 2019

Flooding is a frequently encountered abiotic stress that is extremely detrimental to plant growth and development, metabolism, function, and yield. Water severely restricts gas exchange impeding photosynthesis and respiration, and ultimately leads to an energy crisis that can prove fatal. Most land plants are extremely sensitive to prolonged waterlogging and submergence. However, some plant species are at home in frequently flooded environments. This is linked to a set of adaptive traits and metabolic adjustments that confer the ability to either avoid or cope with flooding‐induced oxygen deprivation. Here, we outline the current knowledge on these morphological, anatomical, and metabolic tolerance traits, and how they facilitate flooding survival. Furthermore, we elaborate on the molecular processes and signalling mechanisms that regulate some of these traits. A better understanding of these tolerance attributes is essential in the quest towards the generation of climate resilient crops in an era of global warming and increased food demand.
Exine and Aperture Patterns on the Pollen Surface: Their Formation and Roles in Plant Reproduction
Authors: Wang Rui , Dobritsa Anna A.
Published: December 2019

Pollen grains, the male gametophytes of seed plants, surround themselves with a complex pollen wall for protection from various environmental stresses. The deposition and assembly of exine, the outer layer of the pollen wall, lead to the formation of patterns on the pollen surface that are species specific, tremendously diverse, and often very beautiful. These patterns arise due to exine's assembly into various nano‐ and microstructures, and due to the absence of exine deposition at certain areas of the pollen surface. The areas that have reduced exine deposition, or lack it completely, are known as pollen apertures, and their patterns are also species specific and highly variable. Although the intricate patterns of exine and apertures have been drawing attention for centuries, it is still not clear how exactly they develop, what genes are involved in their formation, and what purpose they serve. Here, we review the current state of knowledge about the exine and aperture patterns, their perceived roles in plant reproduction, and the cellular and molecular mechanisms that guide their formation.
Novel mutation in optineurin causing aggressive ALS+/−frontotemporal dementia
Authors: Feng Shu‐Man , Che Chun‐Hui , Feng Shu‐Yan , Liu Chang‐Yun , Li Liu‐Yi , Li Yuan‐Xiao , Huang Hua‐Pin , Zou Zhang‐Yu
Published: December 2019

Objective

Mutations in optineurin (OPTN) have been identified in familial and sporadic amyotrophic lateral sclerosis (ALS). We screened a cohort of Chinese patients for mutations in optineurin. We also performed an extensive literatures review of all mutations in optineurin identified previously to detect genotype–phenotype associations.

Methods

All 16 exons of the OPTN gene in a cohort of 15 familial ALS indexes and 275 sporadic ALS patients of Chinese origin were sequenced by targeted next generation sequencing.

Results

Two known heterozygous missense mutations in the OPTN, c.1481T> G (p.L494W), and c.1546G> C (p.E516Q), as well as one novel heterozygous missense mutation c.1690G> C (p.D564H) were each detected in one sporadic ALS patient. The patient carrying the p.E516Q mutation developed clinical features of ALS‐frontotemporal dementia (FTD) and the patient carrying the p.D564H mutation showed a phenotype of ALS. They both had an aggressive course, with a survival of 18 and 14 months respectively. Literature review showed that the clinical phenotypes in OPTN mutated ALS were not homogeneous, although some individuals showed a relatively slow progression and a long duration, some mutations carriers developed an aggressive progression and a short survival.

Interpretation

OPTN mutations contribute to ALS in Chinese population and account for 0.8% of sporadic ALS patients and 1.5% of familial ALS in the pooled Chinese ALS cohorts. Mutations in optineurin can cause aggressive ALS+/−FTD.
Fatigue and Its Association With Social Participation, Functioning, and Quality of Life in Systemic Sclerosis
Authors: Murphy Susan L. , Kratz Anna L. , Whibley Daniel , Poole Janet L. , Khanna Dinesh
Published: December 2019

Objective

Fatigue is consistently ranked as one of the most problematic symptoms of systemic sclerosis (SSc), but the impact of fatigue on daily life is not well characterized. The purpose of this study was to examine the contribution of fatigue to deficits in social participation, functioning, and quality of life.

Methods

Baseline data from a sample undertaking a clinical trial were utilized (n = 267). Fatigue, pain interference, depressive symptoms, physical function, and social participation were assessed by measures from the Patient‐Reported Outcomes Measurement Information System. Hierarchical linear regressions were performed to determine the unique contribution of fatigue to social participation, physical function, and quality of life above and beyond the effects of demographic and clinical variables, pain interference, and depressive symptoms.

Results

The sample was predominantly female (91%), with an average age of 53.7 years, average disease duration of 9 years, and a mean fatigue T score of 58.7. Of all outcomes, fatigue was most strongly associated with deficits in social participation, explaining 48% of the variance beyond demographic and clinical factors, which is similar to the amount of variance contributed by pain interference and depressive symptoms combined (49%). Fatigue also accounted for significant amounts of variance in physical function and quality of life (R2 = 0.27 and 0.33, respectively) above and beyond the effects of demographic and clinical factors.

Conclusion

Fatigue is an important clinical problem in SSc and is strongly associated with decreased participation in social roles and activities. Rehabilitation interventions that focus on fatigue management may be necessary to maximize participation.
How Are Neighborhood Characteristics Associated With Mental and Physical Functioning Among Older Adults With Radiographic Knee Osteoarthritis?
Authors: Kowitt Sarah D. , Aiello Allison E. , Callahan Leigh F. , Fisher Edwin B. , Gottfredson Nisha C. , Jordan Joanne M. , Muessig Kathryn E.
Published: December 2019

Objective

To examine how neighborhood characteristics are associated with health outcomes among older adults with osteoarthritis.

Methods

In multilevel, cross‐sectional, and longitudinal analyses we examined whether 4 neighborhood characteristics were associated with depressive symptoms and reported knee impact scores, and whether the neighborhood characteristics interacted with race/ethnicity among older adults with radiographic knee osteoarthritis (n = 656 for cross‐sectional analyses and n = 434 for longitudinal analyses). The data came from the Johnston County Osteoarthritis Project, a prospective cohort study in North Carolina designed to examine risk factors for osteoarthritis.

Results

Although few longitudinal associations were found, cross‐sectional results suggested that greater perceived neighborhood social cohesion (B = –0.04, P < 0.001) and perceived neighborhood resources for physical activity and walking (B = –0.03, P < 0.001) were associated with fewer depressive symptoms, and that greater perceived neighborhood resources for physical activity and walking were associated with higher (better) knee impact scores (B = 0.48, P = 0.008). We also observed 2 significant interactions among neighborhood characteristics and race/ethnicity related to depressive symptoms (P < 0.01); for African American adults, greater perceived neighborhood resources for physical activity and walking were associated with fewer depressive symptoms (B = –0.03, P < 0.001), but for White adults, greater perceived neighborhood safety was associated with fewer depressive symptoms (B = –0.04, P = 0.003).

Conclusion

In a sample of older adults with radiographic knee osteoarthritis, neighborhood context mattered, but in nuanced ways. Interventions aiming to improve mental and physical functioning of older adults with knee osteoarthritis can look to this study as evidence for the importance of neighborhood characteristics.
Association of Low Muscle Density With Deteriorations in Muscle Strength and Physical Functioning in Rheumatoid Arthritis
Authors: Baker Joshua F. , Mostoufi-Moab Sogol , Long Jin , Taratuta Elena , Leonard Mary B. , Zemel Babette
Published: December 2019

Objective

Rheumatoid arthritis (RA) is associated with low muscle density due to the accumulation of intramuscular fat. The present study was undertaken to identify predictors of changes in muscle density and to determine whether low muscle density predicted changes in strength and physical function.

Methods

Patients with RA, ages 18–70 years, completed whole‐body dual‐energy x‐ray absorptiometry and peripheral quantitative computed tomography to quantify lean and fat mass indices and muscle density. Dynamometry was used to measure strength at the hand, knee, and lower leg. Disability and physical function were measured with the Health Assessment Questionnaire (HAQ) and the Short Physical Performance Battery (SPPB). Assessments were performed at baseline and at follow‐up. Regression analyses assessed associations between patient characteristics, muscle density, and deteriorations in strength and function.

Results

Muscle density was assessed at baseline in 107 patients with RA. Seventy‐nine of these patients (74%) returned for a follow‐up assessment at a median follow‐up time of 2.71 years (interquartile range 2.35–3.57). Factors associated with declines in muscle density included female sex, higher disease activity, smoking, and lower insulin‐like growth factor 1 (IGF‐1) levels. Greater muscle density Z score at baseline (per 1 SD) was associated with less worsening per year according to HAQ, SPPB, and 4‐meter walk time scores and a lower risk of a clinically important worsening in HAQ score (odds ratio [OR] 1.90 [95% confidence interval (95% CI) 1.06, 3.42]; P = 0.03) and walking speed (OR 2.87 [95% CI 1.05, 7.89]; P = 0.04).

Conclusion

Worsening of skeletal muscle density occurred in patients with higher disease activity, in smokers, and in those with lower IGF‐1. Low muscle density was associated with worsening of physical function. Interventions addressing reductions in muscle quality might prevent functional decline.
Substrate‐Free and Shapeless Planar Micro‐Supercapacitors
Authors: Das Pratteek , Shi Xiaoyu , Fu Qiang , Wu Zhong‐Shuai
Published: December 2019

Micro‐supercapacitors (MSCs), albeit powerful, are unable to broaden their potential applications primarily because they are not as flexible and morphable as electronics. To address this problem, a universal strategy to fabricate substrate‐free, ultrathin, shapeless planar‐MSCs with high‐performance tenability under serious deformation is put forward. These represent a new class of “all‐inside‐one” film supercapacitors, achieved by encapsulating two‐dimensional interdigital microelectrodes within chemically cross‐linked polyvinyl‐alcohol‐based hydrogel electrolyte containing graphene oxide (GO). GO nanosheets significantly improve ionic conductivity, enhance the capacitance, and boost robustness of hydrogel electrolyte. Consequently, the entire MSC, while being only 37 µm thick, can be crumpled and its shape can self‐adjust through fluid channel ten times smaller than its original size without any damage, demonstrating shapelessness. Using MXene as active material, high single‐cell areal capacitance of 40.8 mF cm−2 is achieved from microelectrodes as thin as 5 µm. Furthermore, to demonstrate wide applicability of this protocol, screen‐printed graphene‐based highly integrated MSCs connecting nine cells in series are fabricated to stably output a high voltage of 7.2 V while crumpling them from 0.11 to 0.01 cm−3, manifesting superior performance uniformity. This protocol allows the coexistence of high performance with incredible flexibility that may greatly diversify MSCs' applications.
Systematical Investigation of Ultrathin Doped Emissive Layer Structure: Achieving Highly Efficient and Long‐Lifetime Orange Organic Light‐Emitting Diodes
Authors: Zhao Yi , Wu Shiwei , Ling Zhitian , Chen Huimin , Yu Nanjie , Zhou Pengchao , Lian Hong , Lan Weixia , Liao Yingjie , Wei Bin , Wang Shuanglong
Published: December 2019

Phosphorescent organic light‐emitting diodes (PhOLEDs) with ultrathin emissive layer (UEML) structure have great potential in solid‐state lighting and display applications due to their relatively simple fabrication process. In this paper, the effect of doped UEML architecture on the performance of orange PhOLEDs is systematically investigated and highly efficient and long‐lifetime devices with the doped UEML structures are successfully constructed. Through strategic exciton management, the probability of exciton recombination is significantly enhanced, while simultaneously that of exciton annihilation is greatly suppressed, along with excellent charge balance. The resulting orange PhOLEDs based on tris[2‐(2‐pyridyl) imidazole] gallium(III):bis (2‐phenylbenzothiazolato) (acetylacetonate) iridium as emitter exhibit a maximum current efficiency of 60.8 cd A−1, power efficiency of 65.8 lm W−1, and external quantum efficiency of 23.4%, respectively. In addition, the doped UEML architecture greatly extends the device operational stability with a nearly fourfold lifetime improvement (time to reduce to 50% of the initial luminance at 2300 cd m−2) over the conventional phosphorescent device with doped bulk emitting layer. This should be the best results reported so far for orange PhOLEDs, indicating the use of doped UEML structure displays great potential value in designing highly efficient and long‐lifetime PhOLEDs.
2D Resistive Switching Based on Amorphous Zinc–Tin Oxide Schottky Diodes
Authors: Casa Branca Nuno , Deuermeier Jonas , Martins Jorge , Carlos Emanuel , Pereira Maria , Martins Rodrigo , Fortunato Elvira , Kiazadeh Asal
Published: December 2019

A room‐temperature‐processed resistive switching Schottky diode that can be operated in two distinct modes, depending solely on the choice of device initialization mode, is presented. Electroforming in the diode's reverse polarity leads to an abrupt filamentary switching with inherently long data retention at the expense of rectification. After this electroforming process, the devices may work in either a bipolar or unipolar manner with a resistance window of at least two orders of magnitude. Device initialization in the forward direction shows a smooth area‐dependent switching over two orders of magnitude, which conserves the current rectification and allows for analog control over the resistance states (dependence of device history and applied voltage stimuli). This secondary mechanism involves ion exchange or charge trapping at the Schottky interface without a contribution from the bulk (hence, it is termed 2D), which is reported for the first time for an amorphous oxide semiconductor switching matrix.
Dopant‐Free, Donor–Acceptor‐Type Polymeric Hole‐Transporting Materials for the Perovskite Solar Cells with Power Conversion Efficiencies over 20%
Authors: You Guofeng , Zhuang Qixin , Wang Lijun , Lin Xinyu , Zou Ding , Lin Zhenghuan , Zhen Hongyu , Zhuang Wenliu , Ling Qidan
Published: December 2019

The rich molecular design of electron donor (D)–acceptor (A) polymers offers many valuable clues to obtain high‐efficiency hole‐transporting materials (HTMs) for use in perovskite solar cells (PVSCs). The fused aromatic or heteroaromatic units can increase the conjugation of the polymer backbone to facilitate electron delocalization, which increases the rigidity of adjacent units to prevent rotational disorder and lower the reorganization energy, leading to improved carrier mobility and optimized film morphology. In this work, fused‐ring ladder‐type indacenodithiophene and indacenodithieno[3,2‐b]thiophene are used as D units, benzodithiophene‐4,8‐dione as the A unit, and thienothiophene as a π‐bridge to form the D–A polymers PBDTT and PBTTT, respectively. Both polymers exhibit favorable properties as HTMs including suitable energy levels, high hole mobility, and excellent film quality. Both dopant‐free HTMs endow n‐i‐p PVSCs with promising performance and stability. A maximum power conversion efficiency of 20.28% is achieved for PBDTT‐based devices, which is among the highest values reported to date.
Nature of FeSe2/N‐C Anode for High Performance Potassium Ion Hybrid Capacitor
Authors: Ge Junmin , Wang Bin , Wang Jue , Zhang Qingfeng , Lu Bingan
Published: December 2019

Potassium ion hybrid capacitors have great potential for large‐scale energy devices, because of the high power density and low cost. However, their practical applications are hindered by their low energy density, as well as electrolyte decomposition and collector corrosion at high potential in potassium bis(fluoro‐sulfonyl)imide‐based electrolyte. Therefore, anode materials with high capacity, a suitable voltage platform, and stability become a key factor. Here, N‐doping carbon‐coated FeSe2 clusters are demonstrated as the anode material for a hybrid capacitor, delivering a reversible capacity of 295 mAh g−1 at 100 mA g−1 over 100 cycles and a high rate capability of 158 mAh g−1 at 2000 mA g−1 over 2000 cycles. Meanwhile, through density functional theory calculations, in situ X‐ray diffraction, and ex situ transmission electron microscopy, the evolution of FeSe2 to Fe3Se4 for the electrochemical reaction mechanism is successfully revealed. The battery‐supercapacitor hybrid using commercial activated carbon as the cathode and FeSe2/N‐C as the anode is obtained. It delivers a high energy density of 230 Wh kg−1 and a power density of 920 W kg−1 (the energy density and power density are calculated based on the total mass of active materials in the anode and cathode).