bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Clostridium difficile Infection in Al-Quwayiyah General Hospital, Riyadh, Kingdom of Saudi Arabia
Authors: Khater Enas Sh. , Faki Abd Alazim A. Al- 
Published: January 2021

Clostridium difficile infections (CDIs) is considered healthcare-associated infections which cause watery diarrhea to long stayed hospitalized patients and cause increased mortality rate.
Aim: Detection of the prevalence and risk factors of C. difficile in Al Quwayiyah General hospital, Riyadh, Kingdom of Saudi Arabia and compairing between GeneXpert® PCR assay and Quikchek complete-enzyme imunoassay QCC, (QCC-EIA) in detection of C. difficile infection and toxicity
Materials and Methods: A cross sectional and prospective study was performed for one year started from June 2019 to June 2020. The data collected include demographic, laboratory and clinical data. A total of 104 stool samples were collected from patients presented with diarrhea. GeneXpert® PCR assay and Quikchek complete-enzyme imunoassay QCC (QCC-EIA) were conducted to each stool sample.
Results: Only 15(14.4%) of the 104 studied patients had CDI while 89 (85.6%) were non CDI patients, 13 (86.7%) of the CDI patients were males and 2 (13.3%) were females with mean age for CDI cases 61 (±19.9), while non CDI cases involved 55(61.8%) were males and 34 (38.2%) were females with mean age for cases of non CDI, 60 (±18.7) years. Of the CDI and non CDI cases respectively 12 (80%) and 14(15.7%) had fever, 5 (27%) and 6 (6.7%) had vomitting and 7 (46.7%) and 12 (13.5%) of cases had abdominal pain. There was statistical significant difference between patients with fever while no statistical significant difference regarding vomitting and abdominal pain. There was statistical significant difference between patients with peptic ulcers, patients received proton pump inhibitors and patients received broad-spectrum antibiotics, while There was no statistical significant difference between cardiac disease, cerebrovascular disease, diabetes, pulmonary disease, hepatic disease and Renal disease. Gene expert PCR detected 15/104(14.4%) as positive CDI while QCC-EIA detected 21/104 (20.5%) as positive CDI. On comparison between gene expert PCR technique and QCC-EIA the sensitivity of QCC-EIA was 100%, while the specificity was 91%. The Positive Predictive Value was 74%, while the Negative Predictive Value was 100%.
Conclusion: The C. difficile infection prevalence rate in the hospital was 14.4%. There was statistical significant difference between patients with peptic ulcers, patients received proton pump inhibitors and patients received broad-spectrum antibiotics. The QCC-EIA can be used as a screening test for the detection of C. difficile toxin in stool samples but should be confirmed with a PCR assay or another confirmatory test Due to its decreased specificity.
Desulfuribacillia
class. nov.
Authors: Sorokin Dimitry Y. , Merkel Alexander Y. , Abin Christopher A. , Hollibaugh James T. 
Published: January 2021

Abstract

De.sul.fu.ri.ba.cil'li.a. N.L. pl. n.
Desulfuribacillia
the class of the type order
Desulfuribacillales
.

Firmicutes / Desulfuribacillia class. nov.

Class
Desulfuribacillia
forms a deep‐branching phylogenetic lineage at the base of the phylum
Firmicutes
and includes obligately anaerobic haloalkaliphilic bacteria with respiratory metabolism. It consists of a single order
Desulfuribacillales
, family
Desulfuribacillaceae,
and genus
Desulfuribacillus
.

Type order
:
Desulfuribacillales
.
Raineyaceae
Authors: Albuquerque Luciana , Egas Conceição 
Published: January 2021

Abstract

Rai.ney.a.ce'ae. N.L. fem. dim. n.
Raineya,
type genus of the family; suff. –
aceae,
ending denoting a family; N.L. fem. pl. n.
Raineyaceae
, the
Raineya
family.

Bacteroidetes / Cytophagia / Cytophagales / Raineyaceae

The family
Raineyaceae
is a member of the order
Cytophagales
. This family is monogeneric, presently embracing the genus
Raineya
composed of one validly published species named
Raineya orbicola
. Cells are rod‐shaped and are nonmotile. The organism stains Gram‐negative and endospores are not observed. The organism is slightly thermophilic and strictly aerobic. Grows in complex media with neutral pH. Carbohydrates and polyols are not utilized for growth. Some organic acids and amino acids are used as carbon and energy sources. The major respiratory quinone is menaquinone 7 (MK‐7). The polar lipid profile is composed of unidentified aminolipids, unidentified aminophospholipids, and additional unidentified lipids. The predominant fatty acids are iso‐branched and hydroxy fatty acids. Isolated from hydrothermal areas.

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

DNA G + C content (%)
: 37.6 (genome).

Type genus
:
Raineya
Albuquerque et al. 2018
VP
.
Rhodomicrobium
Authors: Imhoff Johannes F. 
Published: January 2021

AbstractRho.do.mi.cro' bi.um. Gr. neut. n.rhodonthe rose; Gr. masc. adj.microssmall; Gr. masc. n.bioslife; N.L. neut. n.Rhodomicrobiumred microbe.Proteobacteria / Alphaproteobacteria / Rhizobiales / Hyphomicrobiaceae / RhodomicrobiumMost characteristic forRhodomicrobiumspecies is the polar cell growth and the characteristic vegetative growth cycle which includes the formation of peritrichously flagellated swarmer cells and nonmotile “mother cells,” which form prosthecae from one to several times the length of the mother cell. Daughter cells originate as spherical buds at the end of the prosthecae and may undergo differentiation in various ways. They are Gram‐negative ovoid to elongate‐ovoid bacteria belonging to theAlphaproteobacteria. Internal photosynthetic membranes are of the lamellar type. Photosynthetic pigments are bacteriochlorophyllaand carotenoids of the spirilloxanthin series. The predominant cellular fatty acid is C18:1, which comprises more than 80% of the membrane‐bound fatty acids. Ubiquinone and rhodoquinone with 10 isoprene units are present, and the lipopolysaccharides are characterized by a glucosamine‐containing, phosphate‐free lipid A with amide‐bound C16:03 OH.DNA G + C content (mol%): 61.8–63.8.Type species:Rhodomicrobium vannieliiDuchow and Douglas 1949.
Phocoenobacter
Authors: Foster Geoffrey 
Published: January 2021

Abstract

Pho.coe.no.bac'ter. N.L. fem. n.
phocoena
derived from Gr. fem. n.
phokaina
porpoise; M.L. masc. n.
bacter
rod; M.L. masc. n.
Phocoenobacter
a rod from a porpoise.

Proteobacteria / Gammaproteobacteria / Pasteurellales / Pasteurellaceae / Phocoenobacter
Cells spherical, ovoid, or rod shaped, 0.2–0.5 × 0.5–1.0 μm. Occasional longer forms occur. Some cells demonstrate bipolar staining. Gram‐negative. Nonmotile. Facultative anaerobes. Optimum temperature for growth, 37°C. Do not require X or V factors for growth. No growth occurs on MacConkey agar. Catalase negative, oxidase positive. Nitrate is reduced to nitrite. Voges–Proskauer positive. Arginine dihydrolase, ornithine decarboxylase, lysine decarboxylase, urease, and indole are not produced. Acid produced from glucose. Isolated from a porpoise.

DNA G + C content (mol%)
: 41.5 (
T
m
).

Type species
:
Phocoenobacter uteri
Foster et al. 2000.
Kineothrix
Authors: Haas Kelly N. , Blanchard Jeffrey L. 
Published: January 2021

Abstract

Ki'ne.o.thrix. Gr. v.
kineo
to move; Gr. fem. n.
thrix, trichos
hair; N.L. fem. n.
Kineothrix
a moving hair.

Firmicutes / Clostridia / Clostridiales / Lachnospiraceae / Kineothrix

Kineothrix
is a genus in the phylum Firmicutes, Class Clostridia, Order Clostridiales, Family
Lachnospiraceae
. Currently, it contains only the representative species,
Kineothrix alysoides
. Though originally isolated from a forest‐soil seeded microcosm, close relatives are human gut associated, appearing in several gut microbiome sequencing surveys. It is broadly saccharolytic, including growth on many mucus‐associated sugars. The presence of typical nitrogen fixation genes and its ability to grow without added ammonium or urea suggest it may be capable of nitrogen fixation.
Kineothrix alysoides
grows optimally at pH 7 and 40° C. Colonies appear between 48 and 96 h and are convex, round, glossy, off‐white with entire margins. Older cultures develop undulating margins as the colonies spread across the agar. Cells are motile, due to a single polar flagellum. Cells are slender rods often occurring singly or in long chains. Individual cells are generally 0.5–0.6 μm in width by 3.3 to 6.7 μm in length, with chains regularly exceeding 30 μm. The dominant fatty acids are C
16:0
and C
14:0
.

DNA G + C content (mol%)
: 42.74% (genome).

Type species
:
Kineothrix alysoides
Haas and Blanchard 2017
VP
.
Thermodesulfomicrobium
gen. nov.
Authors: Galushko Alexander , Kuever Jan 
Published: January 2021

Abstract

Ther.mo.de.sul.fo.mi.cro'bi.um. Gr. fem. n.
thermê
, heat; L. pref.
de
, from; L. neut. n.
sulfur
, sulfur; N.L. pref.
desulfo‐
, desulfuricating (prefix used to characterize a dissimilatory sulfate‐reducing prokaryote); N.L. neut. n.
microbium
(from Gr. adj.
mikros
, small and Gr. n.
bios
, life), a microbe; N.L. neut. n.
Thermodesulfomicrobium
, thermophilic sulfate–reducing microbe.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfomicrobiaceae / Thermodesulfomicrobium gen. nov.

Rod‐shaped cells, 0.7 × 2–3 μm. Spore formation was not observed. Gram stain negative. Motile by means of a single polar flagellum. The genus currently accommodates a single, moderately thermophilic species
Thermodesulfomicrobium thermophilum
. Anaerobe with respiratory and fermentative types of metabolism. The only described species is a chemoorganoheterotroph using simple organic acids and alcohols as electron donors and carbon sources; these compounds are incompletely oxidized to acetate and are coupled to reduction of sulfate and other partially oxidized sulfur compounds to sulfide. Chemolithoautotrophic growth by sulfate reduction using H
2
and CO
2
as electron donor and carbon source, respectively. However, in contrast to many other autotrophic sulfate‐reducing bacteria, the genes for the Wood–Ljungdahl pathway are not present in the genome. The species can also grow by fermentation of pyruvate and fumarate. Cultivated in anoxic media with sulfide and cysteine as reductants. Vitamins are not required. Thermophilic with an optimal growth temperature of 55°C. Optimal pH for growth is 6.6. Desulfoviridin is absent and menaquinones are not known, a
c

3

– cytochrome is present. Sequence of 16S rRNA gene is most closely related to those of members of the genus
Desulfomicrobium
with a sequence identity of 92.5–94.0%. The only described species of genus was isolated from terrestrial hot spring in Paipa, Colombia. Representatives of the genus were detected by molecular techniques in some hot springs from various geographic locations and exploited hot petroleum reservoirs.

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

Type species
:
Thermodesulfomicrobium thermophilum
comb. nov. (basonym:
Desulfomicrobium thermophilum
Thevenieau et al. 2007, VL118).
Desulfocurvibacter
Authors: Galushko Alexander , Kuever Jan 
Published: January 2021

Abstract

De.sul.fo.cur.vi.bac'ter. L. pref.
de
, from; L. neut. n.
sulfur
, sulfur; N.L. pref.
desulfo‐
, desulfuricating (prefix used to characterize a dissimilatory sulfate‐reducing prokaryote); L. adj.
curvus
, curved; N.L. masc. n.
bacter
, rod; L. masc. adj.
Desulfocurvibacter
, a curved sulfate‐reducing rod.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfovibrionaceae / Desulfocurvibacter

Cells are vibrio to sigmoid shaped, 0.5 × 3.5–10.0 μm. Occur singly or in pairs. Spore formation is not observed. Stain Gram‐negative. Cells are motile by lophotrichous flagella or a single polar flagellum. Strictly anaerobic, having both respiratory and fermentative types of metabolism. Chemoorganoheterotrophs, using lactate, pyruvate, or ethanol as electron donors and carbon sources; organic compounds are incompletely oxidized to acetate. H
2
can serve as an electron donor in the presence of acetate or yeast extract as an organic carbon source (chemolithoheterotrophic growth). Formate can also be used with acetate or yeast extract. Sulfate, sulfite, and thiosulfate serve as terminal electron acceptors and are reduced to sulfide. Desulfoviridin is present. Sulfur slowly reduced, but might not support growth. Nitrate is not used as an electron acceptor. Does not require NaCl but tolerates up to 40 g/l. In the absence of an external electron acceptor, growth may occur by fermentation of pyruvate. Mesophilic, the optimum temperature for growth is 37°C. Neutrophilic, the optimum pH for growth is 7.0. Media containing a reductant are required for growth. Occur in anoxic freshwater, marine sediments, and soil.

DNA G + C content (mol%)
: 61.1–62.4 (LC, genome).

Type species:
Desulfocurvibacter africanus
Spring et al. 2019, VL188 (basonym:
Desulfovibrio africanus
Campbell et al. 1966
AL
).
Desulfohalovibrio
Authors: Galushko Alexander , Kuever Jan 
Published: January 2021

Abstract

De.sul.fo.ha.lo.vi'bri.o. L. pref.
de
, from; L. neut. n.
sulfur
, sulfur; N.L. pref.
desulfo
‐, desulfuricating (prefix used to characterize a dissimilatory sulfate‐reducing prokaryote); Gr. masc. n.
hals halos
, salt; L. v.
vibro
, to set in tremulous motion, move to and fro, vibrate; N.L. masc. n.
vibrio
, that which vibrates, and also a bacterial genus name of bacteria possessing a curved rod shape (
Vibrio
); N.L. masc. n.
Desulfohalovibrio
, a salt (‐loving) vibrio that reduces sulfur compounds.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfovibrionaceae / Desulfohalovibrio

Cells are curved to sigmoid‐shaped, 0.5–0.8 × 1.4– 5.0 μm. Occur singly or in pairs. Spore formation is not observed. Stain Gram‐negative. Cells are motile by a single polar flagellum. Strictly anaerobic, having both respiratory and fermentative types of metabolism. Chemoorganoheterotrophs, using lactate and pyruvate as electron donors and carbon sources; organic compounds are incompletely oxidized to acetate. Ethanol is used by one species and is oxidized to acetate. H
2
can serve as an electron donor in the presence of acetate as an organic carbon source (chemolithoheterotrophic growth). Formate is also used in the presence of acetate. Sulfate, sulfite, and thiosulfate serve as terminal electron acceptors and are reduced to sulfide. Desulfoviridin is present. Fumarate, nitrate, ferric iron are not used. In the absence of an external electron acceptor, growth may occur by fermentation of pyruvate. Mesophilic, the optimum temperature for growth is 37–43°C. Species are either neutrophilic with optimum pH of 7.5 or alkalitolerant with optimum of 9.0–9.4. All species require NaCl and a reductant for growth. One species requires yeast extract for growth. Cells contain desulfoviridin and cytochrome
c
3
. Major cellular fatty acids are anteiso‐C
15:0
, iso‐C
15:0
, and C
16:0
. The polar lipid composition is dominated by phosphatidylethanolamine, phosphatidylglycerol, and aminolipids. The major menaquinone is MK‐7. Occur in cyanobacterial mats of hypersaline lakes and corroding parts of heating plants, but might be more widespread in various habitats.

DNA G + C content (mol%)
: 64.5–65.5 (LC, genome).

Type species
:
Desulfohalovibrio reitneri
Spring et al. 2019, VL188.
“
Macrodesulfovibrio
” gen. nov.
Authors: Galushko Alexander , Kuever Jan 
Published: January 2021

Abstract

Ma.cro.de.sul.fo.vi'bri.o. Gr. masc. adj.
makros
, large; N.L. masc. n.
Desulfovibrio,
a bacterial genus; N.L. masc. n.
Macrodesulfovibrio
, a large
Desulfovibrio
.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfovibrionaceae /
Macrodesulfovibrio
gen. nov.

Cells are vibrio to rod shaped, 1.0–1.5 × 5.0–10.0 μm. Occur singly or in pairs. Spore formation is not observed. Stain Gram‐negative. Cells are motile by a single polar flagellum. Strictly anaerobic, having both respiratory and fermentative types of metabolism. Chemoorganoheterotrophic and chemolithoheterotrophic. Lactate and pyruvate serve as electron donors and carbon sources and are incompletely oxidized to acetate. H
2
can serve as an electron donor in the presence of acetate as an organic carbon source (chemolithoheterotrophic growth). Sulfate, sulfite, and thiosulfate serve as terminal electron acceptors and are reduced to H
2
S. Desulfoviridin is present. In the absence of an external electron acceptor, growth may occur by fermentation. Mesophilic, the optimum temperature range for growth is 35–37°C. Media containing cysteine as a reductant (all species) and as co‐substrate for growth (one species) and vitamins (one species) are required for growth. Occurs in anoxic freshwater, brackish water, and marine habitats.

DNA G + C content (mol%)
: 54.6–55.5 (
T
m
, LC).

Type species
:
“
Macrodesulfovibrio giganteus
”
comb. nov. (basonym:
Desulfovibrio giganteus
Esnault et al. 1988
AP
, VL26).
Oceanidesulfovibrio
gen. nov.
Authors: Galushko Alexander , Kuever Jan 
Published: January 2021

Abstract

O.ce.a.ni.de.sul.fo.vi'bri.o. L. masc. n.
oceanus
, ocean; N.L. masc. n.
Desulfovibrio,
a bacterial genus; N.L. masc. n.
Oceanidesulfovibrio
, a
Desulfovibrio
from the ocean.

Desulfobacterota / Desulfovibrionia / Desulfovibrionales / Desulfovibrionaceae /
Oceanidesulfovibrio
gen. nov.

Cells are vibrios or curved rods, 0.4–1.2 × 1.5–5.0 μm. Occur singly or in pairs. Spore formation is not observed. Stain Gram‐negative. Cells are motile by a single polar flagellum. Strictly anaerobic, having both respiratory and fermentative types of metabolism. Chemoorganoheterotrophs, using lactate, pyruvate, malate (some species), and fructose (some species) as electron donors and carbon sources; organic compounds are incompletely oxidized to acetate. Alcohols are oxidized by some species to their corresponding carboxylic acids. H
2
can serve as an electron donor in the presence of acetate as an organic carbon source (chemolithoheterotrophic growth). Formate is also used in the presence of acetate. Sulfate (all species), and often sulfite, thiosulfate, and sulfur serve as terminal electron acceptors and are reduced to H
2
S. Desulfoviridin is present. Fumarate is used by one species. In the absence of an external electron acceptor, growth may occur by fermentation of lactate, pyruvate, malate, or fumarate. Mesophilic, the optimum temperature for growth ranges from 15 to 50°C. Neutrophilic, with the growth pH range of 6.4–8.5. The genus contains three species transferred from the former genus
Desulfovibrio
. All species are moderately halophilic. Media containing a reductant are required for growth; some species also require vitamins. Occur in anoxic marine habitats.

DNA G + C content (mol%)
: 58.1–60.4 (LC).

Type species
:
Oceanidesulfovibrio gabonensis
comb. nov. (basonym:
Desulfovibrio gabonensis
Tardy‐Jacquenod et al. 1996
VP
).
Desulfuribacillus
Authors: Sorokin Dimitry Y. , Merkel Alexander Y. , Abin Christopher A. , Hollibaugh James T. 
Published: January 2021

Abstract

De.sul.fu.ri.ba.cil'lus L. pref.
de‐
, from; L. neut. n.
sulfur
, sulfur; N.L. masc. n.
bacillus
, a rod; N.L. masc. n.
Desulfuribacillus
, a sulfur‐reducing rod.

Firmicutes / Desulfuribacillia / Desulfuribacillales / Desulfuribacillaceae / Desulfuribacillus

The genus
Desulfuribacillus
was originally described as a deep unaffiliated lineage in the order
Bacillales
. However, according to more recent phylogenomic analyses, it can be assigned into a separate class‐level taxon. It includes obligately anaerobic, Gram‐positive, spore‐forming bacteria capable of anaerobic respiration of thiosulfate, sulfur, dimethyl sulfoxide (DMSO), arsenate, antimonate, nitrate, nitrite, selenate, and selenite. Members are low to moderately salt‐tolerant and alkaliphilic. They inhabit anaerobic sediments of soda lakes. The genus currently includes the type species
Desulfuribacillus alkaliarsenatis
and
Desulfuribacillus stibiiarsenatis
.

DNA G + C content (mol%)
: 37.5–38.2 (genomic).

Type species
:
Desulfuribacillus alkaliarsenatis
Sorokin et al. 2014, VL159.
Recent Advances in the Synthesis and Applications of α‐Ketothioesters
Authors: Naskar Sandip , Mal Kanchan , Maity Rajib , Das Indrajit 
Published: January 2021

Abstractα‐Ketothioesters have only recently received widespread attention as synthetic intermediates and an impressive growth has been realized for their utilization in synthetic and medicinal chemistry. Several elegant approaches such as oxidative thioesterification and radical coupling allow for their convenient synthesis from easily available starting materials, e. g., methyl ketones, alkenes, alkynes, and α‐hydroxyketones. Due to their multifaceted and diverse reactivities, several important reactions such as C(O)−S bond cleavage and S‐migration with various C‐, N‐, and O‐based nucleophiles, Ni‐catalyzed mono‐ and double‐decarbonylations, enantioselective carbonyl‐ene reaction, diastereoselective hetero Diels‐Alder reactions with olefins, and different types of cyclization reactions have been observed. They have also proven to be a valuable tool for the synthesis of heterocycles, pharmaceutically relevant anticancer drug, and natural product. However, in comparison to other 1,2‐dicarbonyl derivatives such as α‐ketooxoesters, α‐ketoamides, and α‐ketoaldehydes, they are much less appreciated as synthetic intermediates. This review summarizes the recent advancements achieved in the synthesis of α‐ketothioesters as well as their applications in the development of new reactions for the formation of C−C, C−N, and C−O bonds, including multiple bond‐forming processes.magnified image
Comparison of two different techniques in emergency surgery of colon diverticulitis: Hartmann's procedure and resection with primary anastomosis
Authors: Şentürk Mustafa , Çelik Abdulkadir , Çakır Murat , Yıldırım Mehmet Aykut , Belviranlı Mehmet Metin 
Published: January 2021

AbstractColon diverticula may require emergency or elective surgery depending on its complications. Our aim is to compare the Hartmann's procedure and resection with primary anastomosis in the patients with colon diverticulitis and to demonstrate the surgical approach of our clinic. Patients were evaluated retrospectively who were operated for colon diverticulitis between January 2010 and January 2020. The patients who underwent emergency surgery for left colon diverticulitis were divided into two groups as patients with primary anastomosis resection (group 1) and Hartmann's procedure (group 2) and the groups were compared. In the aspect of the development of complications there was no remarkable difference between the groups (P = .56). Postoperative early mortality rate was similar in two groups (P = .12). According to the Hinchey classification, 31.7% of the cases were stage I, 9.8% were stage II, 31.7% were stage III, and 26.8% were stage IV. There was not a distinction in morbidity and mortality rates between Hartmann's procedure and resection with primary anastomosis. The best surgical approach should be determined by considering the operation to be performed, the patient's preferences, clinical status, and the predicted results of the surgical treatment of perforated diverticulitis.