bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thiothrix
Authors: Grabovich Margarita Yu. , Ravin Nikolai V. , Boden Rich 
Published: June 2023

AbstractThi'o.thrix. Gr. neut. n.theîon, brimstone, sulfur (Latin transliterationthium); Gr. fem. n.thrix, hair; N.L. fem. n.Thiothrix, sulfur hair.Proteobacteria / Gammaproteobacteria / Thiotrichales / Thiotrichaceae / ThiothrixGram‐stain‐negative, aerobic, and facultative anaerobic filamentous bacteria that can attach to surfaces. Distribution occurs with the help of gonidia. All species are capable of forming rosettes. Elemental sulfur is stored intracellularly. Nonmotile. Capable of chemolithoautotrophic and heterotrophic growth. Mixed metabolic modes are also observed, but it is not entirely clear if this is chemolithoheterotrophy or mixotrophy. Obligately respiratory metabolism. Molecular oxygen, nitrate, and thiosulfate can be used as terminal electron acceptors. CO2is fixed through the Calvin–Benson–Bassham cycle. Genomes encode all enzymes of the Krebs cycle, except for the canonical malate dehydrogenase (NAD+,mdh, EC 1.1.1.37) which is replaced by malate dehydrogenase (quinone,mqo, EC 1.1.5.4), which donates electrons to the quinone pool. Reduced sulfur compounds are oxidized to sulfate. Hydrogen sulfide is oxidized to elemental sulfur by bacterial sulfide:quinone reductase (Sqr, EC 1.8.5.4) and sulfide‐cytochromecreductase (flavocytochrome c, FccAB, EC 1.8.2.3) enzymes; sulfur then oxidized to (bi)sulfite by dissimilatory sulfite reductase (DsrAB, EC 1.8.99.5), and then to sulfate via the direct route by sulfite dehydrogenase (quinone, SoeABC, EC 1.8.5.6) and the indirect one via sulfate adenylyltransferase (Sat, EC 2.7.7.4) and adenylyl‐sulfate reductase (AprAB, EC 1.8.99.2). Thiosulfate is oxidized through a branched version of the Lu‐Kelly cycle (SoxABXYZ). Mesophilic. Dominant fatty acids are C16:1ω7, C16:0, and C18:1ω7. Known habitats are sulfidic springs and lakes, coastal seawater, sulfidic groundwaters, deep‐sea hydrothermal vents, activated sludge, sewage, and exoskeletons of someCrustacea.DNA G + C content (mol%):49.3–54.9 (genome sequence).Type species:Thiothrix niveaWinogradsky 1888AL(Beggiatoa niveaRabenhorst 1865).
Fournierella
Authors: Togo Amadou Hamidou , Million Matthieu , Raoult Didier 
Published: June 2023

Abstract

Four.nier.el'la
. N.L. fem. dim. n.
Fournierella
, named after the French clinical microbiologist Pierre‐Edouard Fournier for his contribution to the taxono‐genomic description of the bacteria.

Firmicutes / Clostridia / Clostridiales / Ruminococcaceae / Fournierella

Rods 0.5–2 μm. Non‐spore‐forming. Gram‐staining is negative. Nonmotile. Anaerobic and use carbohydrates as a source of energy. Growth occurs on 5 % sheep blood‐enriched Columbia agar. Optimal growth temperature, 37°C; optimal pH, 6–8.5. Catalase, oxidase, and urease are negative. Aesculin is hydrolyzed but not gelatin. The major fermentation product is acetic acid, but butyric acid, isobutyric acid, and propionic acid are also produced in small amounts. The predominant cellular fatty acids are the saturated acid C
16:0
and unsaturated acid C
18:1
n
9.

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

Type species
:
Fournierella massiliensis
Togo et al. 2017
VP
.
Caproiciproducens
Authors: Jeon Byoung Seung , Sang Byoung‐In 
Published: June 2023

Abstract

Ca.pro.i.ci.pro.du'cens. N.L. neut. n.
acidum caproicum
, caproic acid; L. pres. part.
producens
, producing; N.L. masc. n.
Caproiciproducens
, the bacteria producing caproic acid.

Firmicutes / Clostridia / Clostridiales / Ruminococcaceae / Caproiciproducens

Caproiciproducens
are Gram‐stain‐positive, non‐spore‐forming bacilli and strictly anaerobic bacteria.
Caproiciproducens
produce acids using carbohydrates such as glycerol,
l
‐arabinose,
l
‐ribose,
d
‐xylose,
l
‐galactose,
d
‐glucose,
d
‐fructose,
d
‐mannose, dulcitol,
glucosamine,
d
‐cellobiose, starch, glycogen,
d
‐tagatose
and
l
‐fucose.
Caproiciproducens
produces acetic acid, butyric acid, caproic acid, and H
2
and CO
2
. Especially,
Caproiciproducens
produces caproic acid mainly under the condition used carbohydrates like sugar alcohols. The major fatty acids of cellular membrane are C
16:0
DMA and C
16:0
aldehyde. Phylogenetically, the genus represents a distinct lineage in
Clostridium
Cluster IV.

DNA G + C content (mol%)
: 50.0 (
T
m
).

Type species
:
Caproiciproducens galactitolivorans
Kim et al. 2015
vp
.
Pseudogulbenkiania
Authors: Manaia Célia M. , Vaz‐Moreira Ivone , Nunes Olga C. 
Published: June 2023

Abstract

Pseu.do.gul.ben.ki.a'ni.a Gr. neut. adj.
pseudes
, false; N.L. fem. n.
Gulbenkiania
, a bacterial generic name; N.L. fem. n.
Pseudogulbenkiania
, false
Gulbenkiania
.

Proteobacteria / Betaproteobacteria / Neisseriales / Chromobacteriaceae / Pseudogulbenkiania

Rods
, non‐spore‐forming, Gram‐stain‐negative. Motile by a polar flagellum.
Aerobic
with chemo‐organotrophic respiratory metabolism.
Mesophilic
, growing between 15 and 42°C. React positively to cytochrome
c
oxidase and negatively to catalase tests. Sole carbon sources include sugars, organic acids, and amino acids. The DNA G + C content ranges between 63 and 66 mol%. Major fatty acids are C
16:1
ω7
c
and C
16:0
. Phylogenetically, belong to the family
Chromobacteriaceae
. The type species is
Pseudogulbenkiania subflava
and the genus includes also the species
Pseudogulbenkiania gefcensis. “Pseudogulbenkiania ferrooxidans”
is a nonvalidly published name.

DNA G + C content (mol%)
: 63.2–65.9 (HPLC) and 63.4 (WGS).

Type species
:
Pseudogulbenkiania subflava
, Lin et al. 2008
VP
.
Natronobacillus
Authors: Sorokin Dimitry Y. , Merkel Alexander Y. 
Published: June 2023

Abstract

Na.tro.no.ba.cil'lus N.L. neut. n.
natron
, soda, sodium carbonate (arbitrarily derived from the Arabic n.
natrun
or
natron
); N.L. pref.
natrono‐
, pertaining to soda; L. masc. n.
bacillus
, a small rod; N.L. masc. n.
Natronobacillus
, soda‐loving rod.

Firmicutes / Bacilli / Bacillales / Amphibacillaceae / Natronobacillus

The genus
Natronobacillus
is classified as a member of the family “
Amphibacillaceae
”, order
Bacillales
, class
Bacilli
, phylum
Firmicutes
. It includes high salt‐tolerant, obligately alkaliphilic, aerotolerant, fermentative, saccharolytic, spore‐forming anaerobes utilizing various carbohydrates as energy and carbon sources and capable of diazotrophic growth. The genus currently includes a single species
N. azotifigens
represented by multiple closely related isolates from soda soils and soda lake sediments.

DNA G
+
C content (mol%)
: 36.1–38.5 (
T
m
); 36.7 (whole genome sequence of the type strain).

Type species
:
Natronobacillus azotifigens
Sorokin et al. 2008b, VL125.
Halocatena
Authors: Kumar Pravin , Verma Ashish , Pal Yash , Krishnamurthi Srinivasan 
Published: June 2023

Abstract

Ha.lo.ca.te'na. Gr. masc. n.
hals
,
halos
salt; L. fem. n.
catena
, chain; N.L. fem. n.
Halocatena
, a salty chain.

Euryarchaeota / Halobacteria / Halobacteriales / Halobacteriaceae / Halocatena

The archaeal genus
Halocatena
(
Hct
.), belonging to the family
Halobacteriaceae
within the class
Halobacteria,
comprises only a single species that is extremely halophilic. The 16S rRNA gene and whole genome‐based phylogenetics revealed robust but distant relatedness with members of the genus
Halomarina
(
Hmr
). Cells are aerobic, Gram‐stain‐negative, pleomorphic in shape and size, have the ability to grow in absence of Mg
2+
ions, and remain intact in distilled water, unlike the majority of the family
Halobacteriaceae
. Acid production from most of the sugars is negative. Diethyl derivatives of phosphatidylglycerol (C20, C20, and C25, C20), phosphatidylglycerol phosphate methyl ester (C25, C20), sulfated glycosyl‐mannosyl‐glucosyl diether, two glycosyl‐mannosyl‐glucosyl diether lipids, and a glycolipid are the major polar lipid constituents.

DNA G + C content (mol%)
: 57.1 (genomic).

Type species
:
Halocatena pleomorpha
Verma et al. 2020
VP
.
Natranaerofaba
Authors: Sorokin Dimitry Y. , Merkel Alexander Y. 
Published: June 2023

Abstract

Natr.an.ae.ro.fa'ba. N.L. neut. n.
natron
, derived from Arabic
natrun
soda (sodium carbonate); Gr. pref.
an‐
, not; Gr. masc. n.
aêr
, air; L. fem. n.
faba
, bean; N.L. fem. n.
Natranaerofaba
, bean‐shaped soda loving anaerobe.

Firmicutes D / Natranaerobiia / Natranaerobiales / Natranaerofabaceae / Natranaerofaba

The genus
Natrabaerofaba
forms a deep‐branching lineage in the order
Natranaerobiales
, class
Natranaerobiia
. It includes obligately anaerobic bacteria utilizing CO and pyruvate during acetogenic growth and formate and lactate in the presence of thiosulfate, fumarate, or nitrate as electron acceptors. Nitrate is ammonified. They are extremely halophilic and obligately alkaliphilic, moderate thermophiles. The polar lipids are dominated by diethers, which is rare in bacteria. Currently includes a single species
Natranaerofaba carboxydovora
.

DNA G
+
C content (%)
: 35.3 (genome sequence).

Type species
:
Natranaerofaba carboxydovora
Sorokin et al. 2021, VL202.
Entomoplasmatales
Authors: Gasparich Gail E. , Brown Daniel R. 
Published: June 2023

Abstract

En.to.mo.plas.ma.ta'les. N.L. neut. n.
Entomoplasma
, type genus of the order; L. fem. pl. n. suff. ‐
ales
, ending to denote an order: N.L. fem. pl. n.
Entomoplasmatales
, the
Entomoplasma
order.

Tenericutes / Mollicutes / Entomoplasmatales

This order in the class
Mollicutes
has been assigned to a group of nonhelical and helical mollicutes that are regularly associated with arthropod or plant hosts. The description of organisms in the order is essentially the same as for the class. Two families are designated,
Entomoplasmataceae
for nonhelical mollicutes and
Spiroplasmataceae
for helical ones. The order consists of four major phylogenetic clades: the entomoplasmataceae clade, which consists of the genus
Entomoplasma,
and the Apis, Citri–Chrysopicola–Mirum, and Ixodetis clades of the genus
Spiroplasma
. All cells are chemo‐organotrophic, usually fermenting glucose through the phosphoenolpyruvate‐dependent sugar transferase system. Arginine may be hydrolyzed, but urea is not. Cells may require sterol for growth. Temperature optimum for growth is usually 30–32°C, with a few species able to grow at 37°C. Genome sizes range from 780 to 2220 kb by pulsed‐field gel electrophoresis (PFGE), with DNA G + C contents ranging from 25 to 34 mol%. Like members of the
Mycoplasmatales
, all organisms in this order are thought to utilize the UGA codon to encode tryptophan.

DNA G + C content (mol%)
: 25–34 (
T
m
, Bd).

Type genus
:
Entomoplasma
Tully 1993
VP
.
Kiritimatiellota emend
Authors: Spring Stefan 
Published: June 2023

Abstract

Ki.ri.ti.ma.ti.el.lo'ta. N.L. fem. dim. n.
Kiritimatiella
, type genus of the phylum; N.L. neut. pl. n. suff. ‐
ota
, ending to denote a phylum; N.L. neut. pl. n.
Kiritimatiellota
, the
Kiritimatiella
phylum.

Analysis of environmental 16S rRNA gene sequences suggests that members of this phylum prefer animal intestines and anoxic aquatic niches ranging in salinity from hypersaline to freshwater. These data further indicate that most members of the
Kiritimatiellota
are mesophilic and neutrophilic, being adapted to moderate habitats. Cells of cultivated strains divide by binary fission, do not form intracellular membranes, are spherical, nonmotile, and non‐spore‐forming. They have a cell wall of the Gram‐negative type that contains peptidoglycan and an outer membrane. Strains available in pure culture produce transparent exopolymers during growth. Based on the habitat preference, it can be concluded that most representatives are anaerobic bacteria with a fermentative and saccharolytic type of metabolism. In sequenced genomes of some representatives, extraordinarily high numbers of genes encoding putative glycoside hydrolases and sulfatases were detected, which may be necessary for the degradation of complex sulfated polysaccharides typically occurring in the animal intestine or marine environments (Spring et al., 2016; van Vliet et al., 2020). Cellular fatty acid patterns of axenic cultures were dominated by straight‐chain (C
18:0
) and
iso
‐branched fatty acids (
iso
‐C
12:0
,
iso
‐C
14:0
). The major polar lipids were identified as phosphatidylglycerol and diphosphatidylglycerol (cardiolipin). In some strains, respiratory lipoquinones (menaquinones MK‐6 – MK‐9) were detected. The genome sizes among described representatives of this phylum range from 2.9 to 8.6 Mb.

DNA G + C content (mol%)
: 53–63 (genome analyses).

Type genus
:
Kiritimatiella
Spring et al. 2016, VL174.
Extended Antibonding States and Phonon Localization Induce Ultralow Thermal Conductivity in Low Dimensional Metal Halide
Authors: Acharyya Paribesh , Pal Koushik , Ahad Abdul , Sarkar Debattam , Rana Kewal Singh , Dutta Moinak , Soni Ajay , Waghmare Umesh V. , Biswas Kanishka 
Published: June 2023

AbstractThermal conductivity, which measures the ease at which heat passes through a crystalline solid, is controlled by the nature of the chemical bonding and periodicity in the solid. This necessitates an in‐depth understanding of the crystal structure and chemical bonding to tailor materials with notable lattice thermal conductivity (κL). Herein, the nature of chemical bonding and its influence on the thermal transport properties (2–523 K) of all‐inorganic halide perovskite Cs3Bi2I9 are studied. The κL exhibits an ultralow value of ≈0.20 W m−1K−1 in 30–523 K temperature range. The antibonding states just below the Fermi level in the electronic structure arising from the interaction between bismuth 6s and iodine 5p orbitals, weakens the bond and causes soft elasticity in Cs3Bi2I9. First‐principles density functional theory (DFT) calculations reveal highly localized soft optical phonon modes originating from Cs‐rattling and dynamic double octahedral distortion of 0D [Bi2I9]3− in Cs3Bi2I9. These low energy nearly flat optical phonons strongly interact with transverse acoustic modes creating an ultrashort phonon lifetime of ≈1 ps. While the presence of extended antibonding states gives rise to soft anharmonic lattice; Cs rattling provides sharp localized optical phonon modes, which altogether result in strong lattice anharmonicity and ultralow κL.
Concurrent Terahertz Generation via Quantum Interference in a Quadratic Media
Authors: Peters Luke , Totero Gongora Juan Sebastian , Cecconi Vittorio , Olivieri Luana , Tunesi Jacob , Pasquazi Alessia , Peccianti Marco 
Published: June 2023

AbstractThe strive for efficiency in the generation of terahertz (THz) waves motivates intense research on novel field–matter interactions. Presently, THz generation via quadratic crystals remains the benchmark thanks to its simple and practical deployment. An interesting problem is whether new mechanisms can be exploited to elicit novel generation approaches and forms of control on the THz output in existing systems. THz generation via quantum interference (QI) leverages a third‐order nonlinear response under resonant absorption, and it has been recently explored to access surface generation in centrosymmetric systems. Its deployment in standard THz quadratic sources can potentially create a physical setting with the concurrence of two different mechanisms. Here, THz generation via QI in noncentrosymmetric crystals concurrent with phase‐matched quadratic generation in a bulk‐transmission setting is demonstrated. Beyond investigating a new physical setting, it is demonstrated that conversion efficiencies much larger than those typically associated with the medium become accessible for a typically adopted crystal, ZnTe. An inherent control on the relative amplitude and sign of the two generated THz components is also achieved. This approach provides disruptive boost and management of the optical‐to‐THz conversion performance of a well‐established technology, with significant ramifications in emerging spectroscopy and imaging applications.
Bioinspired In‐Sensor Reservoir Computing for Self‐Adaptive Visual Recognition with Two‐Dimensional Dual‐Mode Phototransistors
Authors: Jiang Nanjia , Tang Jian , Zhang Woyu , Li Yi , Li Na , Li Xiuzhen , Chen Xi , Fang Renrui , Guo Zeyu , Wang Fei , Wang Jun , Li Zhi , He Congli , Zhang Guangyu , Wang Zhongrui , Shang Dashan 
Published: June 2023

AbstractArtificial visual systems that dynamically process spatiotemporal optoelectronic signals under complex real‐life environments bear a wide spectrum of edge applications. Despite significant progress in optoelectronic sensors and neuromorphic computing algorithms, developing visual systems that can adapt to a broad illumination range while retaining high performance, high efficiency, and low training costs remains a challenge. Here, this work reports a bioinspired in‐sensor reservoir computing (RC) for self‐adaptive visual recognition. By leveraging voltage‐tunable photoresponses of the MoS2‐based phototransistor array, the RC system demonstrates both scotopic and photopic adaptation functions and maintains a recognition accuracy of 91%. The horizontal modulation (HM) block enables the reservoir to adapt automatically in real‐time under changing illumination conditions, yielding a 90.64% recognition accuracy (14.21% improvement over conventional RC systems). These results pave the way for the emergence of a reconfigurable in‐sensor RC system with broad applications and enhanced performance for an efficient artificial vision system at the edge.
Up‐ and Down‐Shifting Nanomaterials with Chiroptical Responses: Origin of their Chiroptical Activity and Applications
Authors: Francés‐Soriano Laura , Zaballos‐García Elena , Pérez‐Prieto Julia 
Published: June 2023

AbstractArtificial chiral nanoparticles exhibit unique optical and (photo)physical properties. They can be all‐inorganic or organic–inorganic materials that are usually confined to the nanoscale by anchoring organic ligands to their surface. The ligands can also possess distinctive optical and/or (photo)physical properties, thereby adding functionality to the whole nanosystem and constituting an organic–inorganic nanohybrid. Development of luminescent chiral nanoparticles and nanohybrids is pertinent to many applications, such as (bio)sensing, therapeutics, photocatalysis, and optoelectronics, among others. This review deals with different photoactive nanomaterials, displaying either up‐shifting emission (nanoparticles consisting of a photoactive or inert matrix doped with lanthanides, Ln3+, upconversion nanoparticles, UCNPs) or down‐shifting emission, such as coinage metal nanoclusters (e.g., gold nanoclusters, AuNCs) and lead halide perovskite nanoparticles (HP NPs), as well as very low emissive nanoparticles, such as plasmonic nanoparticles (such as gold nanoparticles, AuNPs). Special attention is paid to the origin of the chiroptical response of these materials, showing that it is varied and can be alike for some of them.
Porous Organic Polymers‐Based Single‐Atom Catalysts for Sustainable Energy‐Related Electrocatalysis
Authors: Li Haoyang , Pan Fuping , Qin Chen , Wang Ting , Chen Kai‐Jie 
Published: June 2023

AbstractSingle‐atom catalysts (SACs) have been emerging as attractive catalytic materials in electrocatalysis for sustainable energy storage and conversion. To realize the practical implementation of SACs, reliable support is highly imperative to stabilize atomically dispersed metals with strong metal–support interaction, tunable local electronic environment, and favorable electron/mass transport. Thanks to great designability and tunability of composition, structure, and morphology, porous organic polymers (POPs) have demonstrated grand promise as appropriate support platforms toward the design of SACs at the molecular level and the fabrication of SACs in a controlled manner. Herein, a comprehensive overview of recent advances toward the elucidation of general design principles, effective synthesis approaches, and fundamental catalytic mechanisms for boosting the development of high‐performance POPs‐based SACs in electrocatalytic transformations is provided. The authors first outline rationales for using POPs‐based supports to stabilize SACs and design principles for electrocatalysis, followed by discussing fabrication approaches of utilizing POPs and POPs‐derived nanocarbons to host single‐atom metals. Then, state‐of‐the‐art POPs‐based SACs and their applications in heterogeneous electrocatalysis (ORR, OER, HER, CO2RR, and NRR) are discussed, of which the focus is on revealing the structure–performance correlation and catalytic mechanisms. Finally, challenges and strategies associated with the rational design of high‐performance SACs are suggested.
Mechanisms of Cysteine‐Lysine Covalent Linkage—The Role of Reactive Oxygen Species and Competition with Disulfide Bonds**
Authors: Ye Jin , Bazzi Sophia , Fritz Tobias , Tittmann Kai , Mata Ricardo A. , Uranga Jon 
Published: June 2023

AbstractRecently, a new naturally occurring covalent linkage was characterised, involving a cysteine and a lysine, bridged through an oxygen atom. The latter was dubbed as the NOS bond, reflecting the individual atoms involved in this uncommon bond which finds little parallel in lab chemistry. It is found to form under oxidising conditions and is reversible upon addition of reducing agents. Further studies have identified the bond in crystal structures across a variety of systems and organisms, potentially playing an important role in regulation, cellular defense and replication. Not only that, double NOS bonds have been identified and even found to be competitive in relation to the formation of disulfide bonds. This raises several questions about how this exotic bond comes to be, what are the intermediates involved in its formation and how it competes with other pathways of sulfide oxidation. With this objective in mind, we revisited our first proposed mechanism for the reaction with model electronic structure calculations, adding information about the reactivity with alternative reactive oxygen species and other potential competing products of oxidation. We present a network with more than 30 reactions which provides one of the most encompassing pictures for cysteine oxidation pathways to date.
Photochemically Mediated Ring Expansion of Indoles and Pyrroles with Chlorodiazirines: Synthetic Methodology and Thermal Hazard Assessment
Authors: Joynson Ben W. , Cumming Graham R. , Ball Liam T. 
Published: June 2023

AbstractWe demonstrate that arylchlorodiazirines serve as photo‐activated halocarbene precursors for the selective one‐carbon ring expansion of N‐substituted pyrroles and indoles to the corresponding pyridinium and quinolinium salts. Preliminary investigations indicate that the same strategy also enables the conversion of N‐substituted pyrazoles to pyrimidinium salts. The N‐substituent of the substrate plays an essential role in: (1) increasing substrate scope by preventing product degradation, (2) enhancing yields by suppressing co‐product inhibition, and (3) activating the azinium products towards subsequent synthetic manipulations. This latter point is illustrated by subjecting the quinolinium salts to four complementary partial reductions, which provide concise access to ring‐expanded products with different degrees of increased C(sp3) character. Thermal analysis of the diazirines by differential scanning calorimetry (DSC) provides detailed insight into their energetic properties, and highlights the safety benefits of photolyzing—rather than thermolyzing—these reagents.