bluuebunny/crossref_metadata_2025_split huggingface dataset:
Downregulated miR-383-5p contributes to the proliferation and migration of gastric cancer cells and is associated with poor prognosis
Authors: Wei Chao , Gao Jian-Jun 
Published: October 2019

Aim
The study aims to identify differentially expressed microRNAs (DEMs) in gastric cancer (GC) and explore the expression, prognosis and downstream regulation role of miR-383-5p in GC.

Methods
The GC miRNA-Seq and clinical information were downloaded from Firebrowse which stores integrated data sourced from The Cancer Genome Atlas database. The DEMs were identified with limma package in R software at the cut-off criteria of P < 0.05 and |log2 fold change| > 1.0 (|log2FC| > 1.0). The expression of miR-383-5p in GC cell lines and 54 paired GC tissues was measured by quantitative real-time polymerase chain reaction (qRT-PCR). The overall survival curve of miR-383-5p and the association between its expression and clinicopathological features were explored. Wound healing and cell counting kit-8 assays were performed to investigate the capacity of miR-383-5p in cell proliferation and migration. The downstream target genes were predicted by bioinformatics tools (miRDB, TargetScan and starBase). The consensus target genes were selected for gene functional enrichment analysis by FunRich v3.0 software. The luciferase reporter assay was performed to verify the potential targeting sites of miR-383-5p on lactate dehydrogenase A (LDHA).

Results
A total of 21 down-regulated miRNAs (including miR-383-5p) and 202 up-regulated miRNAs were identified by analyzing GC miRNA-Seq data. Survival analysis found that patients with low miR-383-5p expression had a shorter survival time (median survival time 21.1 months) than those with high expression (46.9 months). The results of qRT-PCR indicated that miR-383-5p was downregulated in GC cell lines and tissues, which was consistent with miRNA-Seq data. The expression of miR-383-5p was significantly associated with tumor size and differentiation grade. Besides, overexpression of miR-383-5p suppressed GC cells proliferation and migration. A total of 49 common target genes of miR-383-5p were obtained by bioinformatics tools and gene functional enrichment analysis showed that these predicted genes participated in PI3K, mTOR, c-MYC, TGF-beta receptor, VEGF/VEGFR and E-cadherin signaling pathways. The data showed that expression of miR-383-5p was negatively correlated with target LDHA (r = −0.203). Luciferase reporter assay suggested that LDHA was a target of miR-383-5p.

Conclusion
The present study concluded that miR-383-5p was downregulated and may act as a tumor suppressor in GC. Furthermore, its target genes were involved in important signaling pathways. It could be a prognostic biomarker and play a vital role in exploring the molecular mechanism of GC.
Fracture of the Humeral Bone as the First Clinical Presentation of Metastatic Papillary Thyroid Carcinoma in Ibadan
Authors: Ajani Mustapha Akanji , Awosusi Babatope Lanre , Fatunla Ebenezer O. , Adegoke Omolade O. , Salami Ayodeji A. 
Published: October 2019

Papillary thyroid carcinoma is the commonest type of thyroid cancer representing 75 to 85 per cent of all thyroid cancer cases. It is often well-differentiated, slow-growing, and localized, although it can metastasize. This is a case of a 49-year-old male who presented with a pathological fracture of the left humerus. A bone biopsy was done at the surgery which had a histological diagnosis of metastatic thyroid carcinoma. A total thyroidectomy was subsequently done and was histologically reported as a follicular variant of papillary thyroid carcinoma. The patient was clinically stable post-thyroidectomy and was discharged home on the 10th postoperative day and he is currently being followed-up in the surgical outpatient clinic. Pathological fracture as the initial clinical presentation is an unusual manifestation of metastatic thyroid carcinoma; therefore a high index of suspicion is needed to make this diagnosis. In any patient presenting with a pathologic fracture, the possibility of metastatic carcinoma from the thyroid gland should always be considered.
Vocational Education and Training Perception on Integration of Prisoners into the Society
Authors: Mbatha Clement Muinde , Kere Bonaventure W. , Ferej Ahmed , Kitainge Kisilu Mashtakh 
Published: October 2019

This study sought to evaluate Vocational Education and Training (VET) perception on integration of prisoners back into the society. The study was undertaken in Mombasa County with a primary focus drawn to Shimo La Tewa main prison and Shimo La Tewa Medium Security Prison. Questionnaire instruments were used for data collection. Different questionnaires were administered to different response groups. The groups included the prison administrators, the trainers, trainees and ex-prisoners. Sample selection method was majorly purposive for all groups except for the trainees who were selected randomly from a pool of those who undertook VET. The information was coded, cleaned and analyzed using the Predictive Analytical Software (PASW). Mixed methods such as qualitative and quantitative techniques were used as the data collected was both qualitative and quantitative. To facilitate the data collection that was qualitative in nature open ended questions were captured in the questionnaire. Both descriptive and inferential statistics were used to deduce meaningful information. Regression analysis was done to assess the perception on integration of prisoners into the society. The model was found to be statistically significant (and the degree of linear relationship while the total amount of variation explained by perception was significant. Other perceptions deduced to impact on integration back into the society, societal point of view on the released persons, the prison administration point of view on the role of VET for inmates in prison and finally, the perception of trainers based in remunerative impact of VET on them. The research recommends that an orientation programme on importance of VET be conducted for prisoners before they can make choices on the types of courses that they wish to undertake, civic education for the society should be done for it is an integral part in ensuring successful re-entry for the prisoners, policies to reduce discrimination against prisoner need to be formulated and enacted, there is need to enhance human resource capital in prisons and finally, material resources to facilitate implementation of VET need to conform with market requirements.
Sex Chromosome Turnovers in Evolution
Authors: Saunders Paul A 
Published: October 2019

Abstract

Animals and plants display a remarkable diversity in the way they determine sex. This implies that changes in the mode of sex determination occur over evolutionary time. Changes that involve a modification of the identity of sex chromosomes are called sex chromosome turnovers, and are caused by the spread of a mutant gene with sex‐determining properties or the translocation of the ancestral sex determiner to a new genomic location. Through both empirical and theoretical studies, the mysteries surrounding the proximate and ultimate mechanisms responsible for turnovers, and their consequences on sex chromosome evolution, are gradually being unravelled. Nevertheless, many questions surrounding these evolutionary transitions remain unanswered: Why do turnover rates vary across taxa? What are the driving evolutionary forces? Why do certain types of transitions seem more common than others?

Key Concepts

In many species with separate sexes, sex is determined genetically by a single gene, located on the sex chromosomes.

A sex chromosome turnover is a change in the identity of the sex chromosomes, resulting from a change in identity and/or location of the sex‐determining gene.

The study of sex chromosome turnovers in evolution has been driven mainly by theoretical work, but empirical studies are gradually catching up.

Different types of turnovers have been described, which have contrasting consequences for sex determination.

Rates of transitions vary dramatically across taxa: they are rare in some taxa and very frequent in others.

Many evolutionary mechanisms have been proposed as potential drivers of turnovers, but their relative implication and importance is still poorly understood.

Certain types of transitions seem more frequent than others, and some lineages experiencing frequent turnovers show nonrandom transitions.
Bizionia
Authors: Nedashkovskaya Olga I. , Kim Song‐Gun 
Published: October 2019

AbstractBi.zi.o'ni.a. N.L. fem. n.Bizionia, named in honor of the famous Italian naturalist Bartolomeo Bizio, for his important contribution to the development of microbiology.Bacteroidetes / Flavobacteriia / Flavobacteriales / Flavobacteriaceae / BizioniaThe genusBizionia,a member of the familyFlavobacteriaceae, was proposed by Nedashkovskaya et al. in 2005 to accommodate Gram‐negative, strictly aerobic, nonmotile by gliding, and oxidase‐positive bacteria. The close phylogenetic relatives of the genusBizioniaare members of the familyFlavobacteriaceaesuch asAquaticitalea, Arcticiflavibacter, Corallibacter, Formosa, Geojedonia, Ichthyenterobacterium, Lacinutrix, Olleya, Psychroserpens, andXanthomarinawith sequence similarity ranges of 93.6–96.5, 93.4–95.9, 93–94.8, 93.5–97.2, 93.1–96.1, 93.9–96.5, 92.3–96.4, 93.5–95.8, 91.9–95.5, and 94.2–96.5%, respectively. On marine agar, colonies of the majorityBizioniaspecies are circular, convex, smooth, yellow, with entire edges and golden yellow, orange, yellowish orange, or saffron pigmented. Growth occurs with 0–10% NaCl, at pH 5.5–9.0, and at −2–45°C. The optimal growth is observed with 1–3% NaCl, at pH 7.0–8.0, and at 20–30°C.Bizioniastrains cannot hydrolyze agar, chitin, carboxymethylcellulose, starch, and urea, and produce acid froml‐arabinose and maltose. The predominant cellular fatty acids of the known members of the genusBizioniaare iso‐C15:0, anteiso‐C15:0, iso‐C15:1G, and iso‐C16:03‐OH. The major respiratory quinone is MK‐6. The main polar lipid is phosphatidylethanolamine. At the time of writing, the genusBizioniacomprised 13 species with validly published names that were isolated from the different marine environments including seawater, sea‐ice brines, sediments, and animals. TheBizioniaspecies share 16S rRNA gene sequence similarities ranging from 93.9 to 99% to one another. The DNA–DNA relatedness between the type strains of theBizioniaspecies is 11–53%.DNA G + C content (mol%): 33–45 (Tm, and HPLC).Type species:Bizionia paragorgiaeNedashkovskaya, Kim, Lysenko, Frolova, Mikhailov and Bae 2005, 377VP.
D
esulfobotulus
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

Abstract

De.sul.fo.bo'tu.lus. L pref.
de
from; L. neut. n.
sulfur
sulfur; L. masc. n.
botulus
sausage; N.L. masc. n.
Desulfobotulus,
a sausage‐shaped sulfate reducer.

Desulfobacterota / Desulfobacteria / Desulfobacterales / Desulforegulaceae / Desulfobotulus

Vibrio‐shaped cells, 1.0–1.5 µm × 3–6.0 µm. Occur singly or in pairs. Sigmoid or spirilloid cells sometimes occur. Spore formation is not observed. Gram‐stain‐negative. Described species are motile. Strict anaerobe with a respiratory or fermentative type of metabolism. Chemoorganoheterotrophs, using fatty acids and pyruvate as electron donors and as carbon sources; growth substrates are incompletely oxidized to acetate. Sulfate and sulfite serve as terminal electron acceptors and are reduced to H
2
S. Growth in the absence of an external electron acceptor is only possible with pyruvate. Mesophilic, optimal temperature 32–34°C. Genus contains one neutrophilic and one haloalkaliphilic species. The haloalkaliphile can use thiosulfate as electron acceptor in addition to sulfate and sulfite. Anoxic medium, with sulfide as a reductant, is necessary for growth. Vitamins are not required. Cells contain cytochromes of the
b
‐ and
c
‐type. Storage granules of poly‐β‐hydroxyalkanoate occur.
Desulfobotulus
species are widespread in anoxic freshwater mud, but occur in brackish, marine or hypersaline sediments as well.

DNA G + C content (mol %)
: 50.8–53.5 (genome).

Type species
:
Desulfobotulus sapovorans
(Widdel 1981) Kuever, Rainey and Widdel 2009, 923
VP
(Effective publication: Kuever Rainey and Widdel 2005c, 971; basonym
Desulfovibrio sapovorans
Widdel 1981, 382).
D
esulfococcus
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

Abstract

De.sul.fo.coc'cus. L. pref.
de
from L. neut. n.
sulfur
sulfur; N.L. masc. n.
coccus
equivalent of Gr. masc. n.
kokkos
grain, berry; N.L. masc. n.
Desulfococcus
a berry shaped (spherical) sulfate‐reducer.

Desulfobacterota / Desulfobacteria / Desulfobacterales / Desulfococcaceae / Desulfococcus

Cells are spherical or lemon‐shaped, 1.4–2.3 µm in diameter. Occur singly or in pairs. Spore formation is not observed. Cells stain Gram‐negative and often contain granules of poly‐β‐hydroxybutyrate. The cells are nonmotile. Slime capsules may occur. Strict anaerobes with a respiratory and fermentative type of metabolism. Chemoorganoheterotrophic and nutritionally versatile. Many species use formate and higher monocarboxylic acids up to C
16
, lactate, pyruvate, and alcohols as electron donors and as carbon sources. Acetone and phenyl‐substituted organic acids may be utilized. These compounds are completely oxidized to CO
2
via the anaerobic C
1
pathway (carbon monoxide dehydrogenase or Wood–Ljungdahl pathway). Sulfate, sulfite, and thiosulfate (one species) serve as terminal electron acceptors and are reduced to H
2
S. In the absence of an external electron acceptor, slow growth occurs by fermentation of lactate or pyruvate to acetate and propionate. Mesophilic. The optimal temperature range for growth is 28–35°C. The optimal pH range for growth is 6.7–7.6. Growth occurs in simple, defined media containing a reductant (usually sulfide) and vitamins. Occur in anoxic mud of freshwater, brackish water, and marine habitats; also occur in the sludge of anaerobic sewage digesters.

DNA G + C content (mol%)
: 56.8–58.3 (genome).

Type species
:
Desulfococcus multivorans
Widdel 1981, 382 (Effective publication: Widdel 1980, 377).
D
esulfofrigus
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

Abstract

De.sul.fo.fri'gus. L. pref.
de
from; L. neut. n.
sulfur
sulfur; L. neut. n.
frigus
cold; N.L. neut. n.
Desulfofrigus
sulfate reducer living in the cold.

Desulfobacterota / Desulfobacteria / Desulfobacterales / Desulfolunaceae / Desulfofrigus

Cells are large, straight or slightly curved rods, 0.8–2.1 µm × 3.2–6.1 µm. Motile cells may be observed in old cultures. Cells stain Gram‐negative and do not form spores. Strict anaerobe with a respiratory and fermentative type of metabolism. Chemoorganoheterotrophs, using fatty acids, other carboxylic acids, amino acids, and alcohols as electron donors and also as carbon sources. Organic substrates oxidation varies between species, one species performs complete oxidation to CO
2
and another species performs incomplete oxidation to acetate. Sulfate serves as terminal electron acceptor and is reduced to sulfide. Ferric citrate may also serve as electron acceptor. The type strain can use thiosulfate and sulfite as electron acceptors; other electron acceptors are not used. Fermentative growth on pyruvate, malate, or other carbon substrates is possible. Sulfur and thiosulfate are not disproportionated. Obligate (only the type species) or facultatively psychrophilic. The temperature optimal for growth is 10–18°C, but growth still occurs at −1.8°C. The optimal pH for growth is between 7.0 and 7.5.
Desulfofrigus
species require NaCl and MgCl
2
, and optimal growth occurs at marine salt concentrations. Media containing a reductant are necessary for growth. Occur in permanently cold marine sediments.

DNA G + C content (mol%)
: 52.1–52.8 (LC).

Type species
:
Desulfofrigus oceanense
Knoblauch, Sahm and Jørgensen 1999, 1640
VP
D
esulfospira
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

Abstract

De.sul.fo.spi'ra. L. pref.
de
from; L. neut. n.
sulfur
sulfur; Gr. fem. n.
spira
a coil; N.L. fem. n.
Desulfospira
a sulfate‐reducing coil.

Desulfobacterota / Desulfobacteria / Desulfobacterales / Desulfobacteraceae / Desulfospira

Curved, often spirilloid cells 0.7–0.8 µm × 1–2 µm. Nonmotile. Gram‐stain‐negative. Endospores not formed. Anaerobic, having a respiratory type of metabolism. Fermentative growth does not occur. Catalase positive. Chemoorganoheterotrophic or chemoautotrophic, using a wide range of organic compounds as electron donors and also as carbon sources, for example, fatty acids, dicarboxylic acids, oxoacids, hydroxyacids, or compatible solutes; these compounds are completely oxidized to CO
2
via the anaerobic C
1
pathway (carbon monoxide dehydrogenase [CODH] or Wood–Ljungdahl pathway). The same pathway is used for autotrophic growth on H
2
plus CO
2
and formate. Sulfate, sulfite, thiosulfate, and sulfur serve as terminal electron acceptors and are reduced to H
2
S. The type strain grows well in sulfide‐free medium in the presence of high concentrations of amorphous iron Fe(III) hydroxide. Mesophilic. Neutrophilic. Na
+
and Mg
2+
are required for growth. The type strain requires biotin for growth. Isolated from iron‐rich, oxidized, marine surface sediment.

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

Type species
:
Desulfospira joergensenii
Finster, Liesack and Tindall 1997b, 1274 (Effective publication: Finster, Liesack and Tindall 1997a, 207).
Syntrophobacter
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

AbstractSyn.tro.pho.bac'ter. Gr. adj.syntogether with; Gr. n.trophosone who feeds; N.L. masc. n.bactersmall sfatt, rod; N.L. masc. n.Syntrophobacterrod which feeds together with (another species).Desulfobacterota / Syntrophobacteria / Syntrophobacterales / Syntrophobacteraceae / SyntrophobacterStraight rods with rounded ends, 0.6–1.0 µm × 1.0–4.5 µm, occur singly and in pairs. May form short chains and filamentous cells (up to 35 µm). Gram‐stain‐negative. Endospores not formed. Strictly anaerobic chemoorganoheterotroph. Mesophilic. Growth occurs at neutral pH (7.0) in low salinity media. Growth occurs by syntrophic metabolism and sulfate reduction. Propionate oxidation to acetate and CO2requires the presence of either a H2/formate‐utilizing organism (methanogen or sulfate reducer) or sulfate as the electron acceptor. Acetate and other fatty acids are not oxidized. Fermentative growth with pyruvate and fumarate. Other common bacterial substrates such as sugars and aromatic compounds are not used either in coculture with a H2/formate‐using organism or in pure culture with sulfate as the electron acceptor. The genus contains only one species, because three former species have been transferred to the new genusSyntrophobacterium. Mesophilic and neutrophilic. Habitat is sludge from anaerobic waste‐treatment facilities and biogas plants.DNA G + C content (mol%): not determined.Type species:Syntrophobacter woliniiBoone and Bryant 1984, 356VP(Effective publication: Boone and Bryant 1980, 631).
D
esulfobaculum
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

Abstract

De.sul.fo.ba'cu.lum. L. pref.
de
from; L. neut. n.
sulfur
sulfur; L. masc. n.
baculum
, a stick or rod; N.L. masc. n.
Desulfobaculum
a rod sulfate‐reducing bacterium.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfovibrionaceae / Desulfobaculum

Cells are short rods, 0.3–0.6 µm × 1.5–2.2 µm. Occur singly, in pairs. Spore formation is not observed. Stain Gram‐negative. Cells are motile by a single polar flagellum. Strictly anaerobic, having a respiratory and a fermentative type of metabolism. Chemoorganoheterotroph or chemolithoheterotroph. Simple organic compounds like lactate, pyruvate, succinate, fumarate, and malate are used as electron donors and carbon sources; organic compounds are most likely incompletely oxidized to acetate (although original description claim oxidation of acetate). H
2
can be used as electron donor in the presence of acetate as organic carbon source, allowing chemolithoheterotrophic growth. Sulfate and sulfite serve as terminal electron acceptors and are reduced to H
2
S. Thiosulfate and fumarate are used by one species. Sulfur and nitrate are not used. In the absence of an external electron acceptor, growth may occur by fermentation of pyruvate. Mesophilic, the optimum temperature range for growth is 35–40°C. Media containing a reductant are required for growth. Isolated from anoxic offshore mangrove sediments and solar saltern.

DNA G + C content (mol%)
: 62.0–64.5 (LC).

Type species
:
Desulfobaculum xiamenense
corrig. Zhao, Gao, Qin, Li and Ruan 2012, 1574
VP
.
P
seudodesulfovibrio
Authors: Galushko Alexander , Kuever Jan 
Published: October 2019

Abstract

Pseu.do.de.sul.fo.vi'bri.o. Gr. adj.
pseudes
false; N.L. masc. n.
Desulfovibrio
a bacterial genus; N.L. masc. n.
Pseudodesulfovibrio
like
Desulfovibrio
, referring to the close relationship to this genus.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfovibrionaceae / Pseudodesulfovibrio

Curved or occasionally straight rods, 0.4–1.0 µm × 1.7–6.0 µm. Occur singly or in pairs. Spore formation is absent. Stain Gram‐negative. Motile by means of single polar flagellum. Strictly anaerobic, having both a respiratory and a fermentative type of metabolism. Chemoorganoheterotrophs, using lactate, pyruvate, some species also fumarate, succinate, and malate as electron donors and carbon sources; organic compounds are incompletely oxidized to acetate. Some species can use alcohols, which are oxidized to their corresponding acids. H
2
can be used as electron donor in the presence of acetate as an organic carbon source (chemolithoheterotrophic growth) by most species. Formate can be used in the presence of acetate by most species. Sulfate serves as a terminal electron acceptor and is reduced to H
2
S. Sulfite and thiosulfate are used by most species. Other electron acceptors such as nitrate, fumarate, and dimethyl sulfoxide are used by few species. Growth may occur by fermentation of pyruvate, malate, or fumarate. Mesophilic, the optimum temperature range for growth is 25–40°C. All members require increased levels of NaCl. Some species are piezophilic. Media containing a reductant are required for growth; some species need vitamins. Cells contain
c
‐type cytochromes (such as
c
3
) and usually
b
‐type cytochromes. Most members of the genus
Pseudodesulfovibrio
contain desulfoviridin. Occur in anoxic marine and brackish water sediments, including deep‐sea sediments.

DNA G + C content (mol%)
:
49.9–65.2 (
T
m
, LC, genome).

Type species
:
Pseudodesulfovibrio indicus
Cao, Gayet, Zheng, Shao, Jebbar and Alain 2016a, 3910
VP
.