bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved scientific knowledge of methanogenesis and methanotrophy needed to slow climate change during the next 30 years
Authors: Davidson Eric A. , Semrau Jeremy D. , Nguyen Nguyen K. ,   On behalf of Steering Committee and participants of the ASM/AGU Colloquium: The Roles of Microbes in Mediating Methane Emissions
Published: September 2023

ABSTRACT
Owing to the high radiative forcing and short atmospheric residence time of methane, abatement of methane emissions offers a crucial opportunity for effective, rapid slowing of climate change. Here, we report on a colloquium jointly sponsored by the American Society for Microbiology and the American Geophysical Union, where 35 national and international experts from academia, the private sector, and government met to review understanding of the microbial processes of methanogenesis and methanotrophy. The colloquium addressed how advanced knowledge of the microbiology of methane production and consumption could inform waste management, including landfills and composts, and three areas of agricultural management: enteric emissions from ruminant livestock, manure management, and rice cultivation. Support for both basic and applied research in microbiology and its applications is urgently needed to accelerate the realization of the large potential for these near-term solutions to counteract climate change.
Genome sequence of
Enterococcus gallinarum
AH4, a milk oligosaccharide-degrading strain isolated from suckling rats
Authors: Yamamoto Yuji , Suzuki Yasunori , Tsukuda Reo , Asai Chikara , Ishizuka Masaki , Tsujikawa Yuji , Sakane Iwao , Osawa Ro , Mukai Takao 
Published: September 2023

ABSTRACT

We had previously isolated
Enterococcus gallinarum
AH4, a strain capable of degrading rat milk oligosaccharides. In this study, we determined the whole-genome sequence of AH4. This whole-genome information will expand our understanding of milk oligosaccharide-mediated symbioses between bacteria and host mammals.
Complete genome sequence of
Marinobacter shengliensis
D49 harboring
ectABC
genes for ectoine synthesis
Authors: Yasuda Shohei , Terada Akihiko 
Published: September 2023

ABSTRACT

A complete genome sequence of
Marinobacter shengliensis
D49 in the class
Gamma-proteobacteria
was isolated from activated sludge treati

ng landfill leachate. The genome encodes the functional genes for the biosynthesis of ectoine (
ectABC
), a compatible solute for cosmetics. Deciphering the genome helps pave the way for ectoine production by the isolate.
Diversity profiling of soil bacterial and fungal communities in the Ogasawara (Bonin) Islands, Japan
Authors: Shigyo Nobuhiko , Shichi Koji , Sugai Kyoko , Setsuko Suzuki 
Published: September 2023

ABSTRACT
Island biogeography research provides insight into microbial diversity patterns; however, little is known about the diversity and distribution of soil microbial communities on remote and poorly accessible islands. Here, we present amplicon sequencing data from bacterial and fungal communities in the surface soils of the Ogasawara (Bonin) Islands, Japan.
Complete genome sequence of Azrael100, a V cluster mycobacteriophage
Authors: Machowski Edith Erika , Ealand Christopher Shawn , Jacobs Olivia , Kana Bavesh Davandra 
Published: September 2023

ABSTRACT

Azrael100, a cluster V siphoviral mycobacteriophage, was isolated from a garden in Johannesburg, South Africa. It can infect and lyse
Mycobacterium smegmatis
mc
2
155. The double-stranded DNA genome contains 78,063 base pairs with a GC content of 56.9%, with 141 predicted open reading frames, 23 tRNAs, and one tmRNA.
Ecological inducers of the yeast filamentous growth pathway reveal environment-dependent roles for pathway components
Authors: Vandermeulen Matthew D. , Cullen Paul J. 
Published: September 2023

ABSTRACT

Signaling modules, such as mitogen-activated protein kinase (MAPK) pathways, are evolutionarily conserved drivers of cell differentiation and stress responses. In many fungal species including pathogens, MAPK pathways control filamentous growth, where cells differentiate into an elongated cell type. The convenient model budding yeast
Saccharomyces cerevisiae
undergoes filamentous growth by the filamentous growth (fMAPK) pathway; however, the inducers of the pathway remain unclear, perhaps because pathway activity has been mainly studied in laboratory conditions. To address this knowledge gap, an ecological framework was used, which uncovered new fMAPK pathway inducers, including pectin, a material found in plants, and the metabolic byproduct ethanol. We also show that induction by a known inducer of the pathway, the non-preferred carbon source galactose, required galactose metabolism and induced the pathway differently than glucose limitation or other non-preferred carbon sources. By exploring fMAPK pathway function in fruit, we found that induction of the pathway led to visible digestion of fruit rind through a known target,
PGU1
, which encodes a pectolytic enzyme. Combinations of inducers (galactose and ethanol) stimulated the pathway to near-maximal levels, which showed dispensability of several fMAPK pathway components (e.g., mucin sensor, p21-activated kinase), but not others (e.g., adaptor, MAPKKK) and required the Ras2-protein kinase A pathway. This included a difference between the transcription factor binding partners for the pathway, as Tec1p, but not Ste12p, was partly dispensable for fMAPK pathway activity. Thus, by exploring ecologically relevant stimuli, new modes of MAPK pathway signaling were uncovered, perhaps revealing how a pathway can respond differently to specific environments.

IMPORTANCE

Filamentous growth is a cell differentiation response and important aspect of fungal biology. In plant and animal fungal pathogens, filamentous growth contributes to virulence. One signaling pathway that regulates filamentous growth is an evolutionarily conserved MAPK pathway. The yeast
Saccharomyces cerevisiae
is a convenient model to study MAPK-dependent regulation of filamentous growth, although the inducers of the pathway are not clear. Here, we exposed yeast cells to ecologically relevant compounds (e.g., plant compounds), which identified new inducers of the MAPK pathway. In combination, the inducers activated the pathway to near-maximal levels but did not cause detrimental phenotypes associated with previously identified hyperactive alleles. This context allowed us to identify conditional bypass for multiple pathway components. Thus, near-maximal induction of a MAPK pathway by ecologically relevant inducers provides a powerful tool to assess cellular signaling during a fungal differentiation response.
Genetic diversity and characterization of rhinoviruses from Chinese clinical samples with a global perspective
Authors: Zhao Peng , Shao Nan , Dong Jie , Su Haoxiang , Sui Hongtao , Zhang Ting , Yang Fan 
Published: September 2023

ABSTRACT
Rhinovirus (RV) is a significant pathogen causing upper and lower respiratory diseases and is one of the most prevalent human respiratory viruses. However, research on the genetic diversity and evolutionary dynamics of RVs in China and worldwide remains limited. To address this knowledge gap, we utilized Chinese clinical RV samples as a starting point and detected and reported 22 types, including A9, B3, and C13, in China for the first time. Among these, A67, A76, and A106 were also detected and reported in Asia for the first time, characterizing their genetic diversity. We also identified A110 as a novel type of RVA and reported its distinctive characteristics in phylogeny, secondary structure, and capsid protein structure. Furthermore, by mining, refining, and annotating RV sequence data available worldwide, four previously unreported novel types, B107, C58, C59, and C60, were identified, and their genetic diversity was revealed. Furthermore, we observed variations in the guanine-cytosine (GC) content among different serotypes and clades. Also of note was that, based on a complete and refined VP1 data set, the evolutionary dynamics of RV were analyzed systematically and on a large scale for the first time.

IMPORTANCE
Based on clinical samples collected in China, we detected and reported 22 types for the first time in China, as well as three types for the first time in Asia, and reported their genetic characteristics and diversity. We identified a novel type of Rhinovirus (RV), A110, highlighting its unique genetic features. We annotated the genomic structure and serotype of all the existing RV sequences in the database, and four novel RV types were identified and their genetic diversity reported. Combined with the sequence annotation, we constructed a complete VP1 data set of RV and conducted the first large-scale evolutionary dynamics analysis of RV. Based on a high-quality data set, we conducted a comprehensive analysis of the guanine-cytosine (GC) content variations among serotypes of RVs. This study provides crucial theoretical support and valuable data for understanding RV’s genetic diversity and developing antiviral strategies.
Oceanic serpentinites: A potentially critical reservoir for deep nitrogen recycling
Authors: Li Kan , Yu Amber Jie , Barry Peter H. , Li Long 
Published: September 2023

Abstract
Serpentinized oceanic peridotites might be an important reservoir delivering volatile elements including nitrogen (N) into the mantle via subduction. To determine N sources and estimate the budget of alteration-added secondary N in the oceanic mantle peridotite reservoir, we examined oceanic serpentinites from four Ocean Drilling Program (ODP) sites in the Pacific and Atlantic Oceans. Our results showed that, despite large variation in serpentinization condition (high temperatures up to &gt;350 °C at Holes 895D, 1271B, and 920D; low temperatures &lt;150 °C at Hole 1274A), serpentinites from all sites displayed ubiquitous and similar magnitude of N enrichment (3.2–18.6 ppm) from sediments/seawater sources (δ15N = –3.3‰ to +4.4‰), and these values were significantly elevated relative to the low N concentration (0.04–2.0 ppm) and δ15N value (−5‰ ± 2‰) of the depleted mantle. Based on these data, the serpentinized oceanic mantle is estimated to contribute 0.4 ± 0.2–14.7 ± 6.9 × 109 mol N annually to global subduction zones. Although this flux is smaller than that of subducting sediments (57 × 109 mol·yr–1), comparison between oceanic serpentinites and meta-serpentinites from subduction zones suggests that N can be effectively retained in serpentinites during prograde metamorphism. This implies that the serpentinized slab mantle could be a critical reservoir to deliver N enriched in 15N to the mantle (at least 70 km depth) and potentially to the deepest portions of the mantle sampled by deep-rooted mantle plumes.
Trends and patterns of violence-related mortality in Nigeria: evidence from a 16-year analysis of secondary data
Authors: Ukoji Vitalis U , Ukoji Vitus N 
Published: September 2023

BackgroundNigeria is one of the most terrorised countries due to terrorist attacks and violent clashes. There have been many fatalities resulting from this violence, which started in the late 1960s and has significantly increased recently. Violence in Nigeria has been studied, but not about Nigeria’s mortality experience over time. This study described the patterns and trends of deaths related to violence in Nigeria over 16 years.MethodsSecondary data on lethal violence across Nigeria spanning from 2006 to 2021 were drawn from the Nigeria Watch database, an online database of lethal violence in Nigeria. Univariate analysis of the data was conducted to map the trends, patterns and sources of lethal violence across Nigeria.ResultsNigeria recorded no fewer than 169 033 violent deaths between 2006 and 2021, with 2014 reporting the highest number (22, 873) and Borno State being the most affected, followed by Lagos, Kaduna, Zamfara, Plateau, Delta, Benue, Rivers and Adamawa. The highest number of deaths (51, 425) was attributed to crime, followed by insurgency (50, 252) and road crashes (27, 645). Other significant causes of death were political issues (8, 324) and cattle grazing (5, 501).ConclusionViolence-related mortality is prevalent in Nigeria and significantly contributes to adult mortality. The government must develop strategies to identify, intervene in and end high-risk conflict situations to stop the growing contribution of violence to Nigeria’s mortality experience.
Weill-Marchesani syndrome: natural history and genotype-phenotype correlations from 18 news cases and review of literature
Authors: Marzin Pauline , Rondeau Sophie , Alessandri Jean-Luc , Dieterich Klaus , le Goff Carine , Mahaut Clémentine , Mercier Sandra , Michot Caroline , Moldovan Oana , Miolo Gianmaria , Rossi Massimiliano , Van-Gils Julien , Francannet Christine , Robert Matthieu P , Jaïs Jean-Philippe , Huber Céline , Cormier-Daire Valerie 
Published: September 2023

BackgroundWeill-Marchesani syndrome (WMS) belongs to the group of acromelic dysplasias, defined by short stature, brachydactyly and joint limitations. WMS is characterised by specific ophthalmological abnormalities, although cardiovascular defects have also been reported. Monoallelic variations inFBN1are associated with a dominant form of WMS, while biallelic variations inADAMTS10,ADAMTS17andLTBP2are responsible for a recessive form of WMS.ObjectiveNatural history description of WMS and genotype-phenotype correlation establishment.Materials and methodsRetrospective multicentre study and literature review. Inclusion criteria: clinical diagnosis of WMS with identified pathogenic variants.Results61 patients were included: 18 individuals from our cohort and 43 patients from literature. 21 had variants inADAMTS17, 19 inFBN1, 19 inADAMTS10and 2 inLTBP2. All individuals presented with eye anomalies, mainly spherophakia (42/61) and ectopia lentis (39/61). Short stature was present in 73% (from −2.2 to −5.5 SD), 10/61 individuals had valvulopathy. RegardingFBN1variants, patients with a variant located in transforming growth factor (TGF)-β-binding protein-like domain 5 (TB5) domain were significantly smaller than patients withFBN1variant outside TB5 domain (p=0.0040).ConclusionApart from the ophthalmological findings, which are mandatory for the diagnosis, the phenotype of WMS seems to be more variable than initially described, partially explained by genotype-phenotype correlation.
RecessiveMECRpathogenic variants cause an LHON-like optic neuropathy
Authors: Fiorini Claudio , Degiorgi Andrea , Cascavilla Maria Lucia , Tropeano Concetta Valentina , La Morgia Chiara , Battista Marco , Ormanbekova Danara , Palombo Flavia , Carbonelli Michele , Bandello Francesco , Carelli Valerio , Maresca Alessandra , Barboni Piero , Baruffini Enrico , Caporali Leonardo 
Published: September 2023

BackgroundLeber’s hereditary optic neuropathy (LHON) is a mitochondrial disorder characterised by complex I defect leading to sudden degeneration of retinal ganglion cells. Although typically associated with pathogenic variants in mitochondrial DNA, LHON was recently described in patients carrying biallelic variants in nuclear genesDNAJC30,NDUFS2andMCAT. MCAT is part of mitochondrial fatty acid synthesis (mtFAS), as also MECR, the mitochondrial trans-2-enoyl-CoA reductase.MECRmutations lead to a recessive childhood-onset syndromic disorder with dystonia, optic atrophy and basal ganglia abnormalities.MethodsWe studied through whole exome sequencing two sisters affected by sudden and painless visual loss at young age, with partial recovery and persistent central scotoma. We modelled the candidate variant in yeast and studied mitochondrial dysfunction in yeast and fibroblasts. We tested protein lipoylation and cell response to oxidative stress in yeast.ResultsBoth sisters carried a homozygous pathogenic variant inMECR(p.Arg258Trp). In yeast, the MECR-R258W mutant showed an impaired oxidative growth, 30% reduction in oxygen consumption rate and 80% decrease in protein levels, pointing to structure destabilisation. Fibroblasts confirmed the reduced amount of MECR protein, but failed to reproduce the OXPHOS defect. Respiratory complexes assembly was normal. Finally, the yeast mutant lacked lipoylation of key metabolic enzymes and was more sensitive to H2O2treatment. Lipoic Acid supplementation partially rescued the growth defect.ConclusionWe report the first family with homozygous MECR variant causing an LHON-like optic neuropathy, which pairs the recent MCAT findings, reinforcing the impairment of mtFAS as novel pathogenic mechanism in LHON.
Estimating the weight of consumed tobacco product waste in various Indian states: a novel method to assess the potential burden of tobacco product waste
Authors: Jain Yogesh Kumar , Bhardwaj Pankaj , Joshi Nitin Kumar , Singh Prashant Kumar , Lal Pranay , Kapoor Shivam , Gupta Manoj Kumar , Goel Akhil Dhanesh , Sharma Prem Prakash , Singh Shalini 
Published: September 2023

Introduction
The direct morbidity and mortality caused by tobacco are well documented, but such products also contribute to a range of environmental pollutants resulting from tobacco product waste. No previous studies have yet quantified tobacco product waste in a low-income and middle-income country (LMIC). This study estimates the potential annual waste generated due to consumption of smoked and smokeless tobacco products in India and its states.

Methodology
We systematically collected samples of smoked and smokeless tobacco products from 33 districts of 17 Indian states/union territories. Stratified weights of plastic, paper, foil and filter packaging components, and gross empty package weights were recorded. Prevalence of smoking and smokeless tobacco use at national and state-level estimates was derived from the Global Adult Tobacco Survey (2016–2017) to quantify waste potentially generated by tobacco products.

Results
We included 222 brands of tobacco products (70 cigarette, 94 bidi and 58 smokeless tobacco brands) in the final analysis. A total of 170 331 (±29 332) tonnes of waste was estimated to be generated annually, out of which 43.2% was plastic, 3.6% was foil and 0.8% was filter. Two-thirds of the overall waste was contributed by smokeless products alone. Maximum waste was generated in Uttar Pradesh (20.9%; 35 723.7±6151.6 tonnes), Maharashtra (8.9%; 15 116.84±2603.12 tonnes) and West Bengal (8.6%; 14 636.32±2520.37 tonnes).

Conclusion
This study provides first of its kind national-level evidence on the types (plastic, paper, foil and filter) and quantity of waste potentially generated by use of tobacco products in India. Similar studies from other LMICs can serve to raise consciousness about many negative environmental impacts of tobacco products and need for policies to address them.
Correction: numerical implementation and application of an internal state variable model to analyze the time-dependent behavior of mining excavations in rock salt
Authors: Aubertin Jonathan D. , Aubertin Michel , Jahanbakhshzadeh Abtin 
Published: September 2023

Résumé Le comportement géomécanique du sel gemme a été largement étudié au fil des ans. Les différentes études expérimentales ont permis d'identifier des caractéristiques distinctives associées à une réponse inélastique non-linéaire qui est fonction du temps et de l'historique de chargement. Ces caractéristiques doivent être reproduites par les équations constitutives utilisées pour analyser la réponse du sel gemme autour des ouvertures souterraines. Dans cet article, un modèle constitutif relativement simple est introduit dans le code numérique FLAC et appliqué pour analyser le comportement différé d'excavations dans des mines de sel. Le modèle unifié en fluage et plasticité comprend une variable d“état interne avec une loi d”évolution qui induit un écrouissage progressif jusqu'à ce qu“un état stationnaire soit atteint. Des analyses numériques sont effectuées avec le modèle ISV-SH pour évaluer les paramètres du matériau et simuler la réponse d”une ouverture circulaire et d'excavations minières rectangulaires créées séquentiellement. Les résultats sont présentés et comparés à ceux obtenus avec l“équation bien connue de la loi de puissance de Norton, couramment utilisée dans l”ingénierie des mines de sel. Les résultats des calculs, présentés en termes de l’évolution des contraintes, des déformations et de vitesses de déformation, illustrent certains des aspects clés du comportement du sel gemme et ils mettent en évidence l“influence majeure de la loi de comportement utilisée pour les analyses numériques. L”approche de simulation proposée ici constitue une alternative pratique et flexible aux outils de modélisation basés sur le fluage stationnaire, souvent utilisés pour l“analyse des ouvertures souterraines dans les opérations d”extraction de sel gemme.1 Ceci est une traduction fournie par l'auteur du résumé en anglais.
Column cyclic rank metric codes and linear complementary dual rank metric codes
Authors: de la Cruz Javier , Özbudak Ferruh 
Published: September 2023

We introduce and study column cyclic rank metric (CCRM) codes over finite fields. We present natural questions for the existence and characterization of CCRM codes. We completely solve these questions only in the first nontrivial case: The case of the minimum rank distance [Formula: see text] and the number of rows [Formula: see text]. We also consider linear complementary dual rank metric (LCDRM) codes both in the setting of CCRM codes and in the general setting of rank metric codes. We also ask the natural questions for the existence and characterization of CCRM codes in the subclass of LCDRM codes. We also completely solve these questions for this subclass of LCDRM codes only in the first nontrivial case that [Formula: see text] and [Formula: see text]. Moreover we extend a characterization of linear complementary dual (LCD) codes of Massey to arbitrary rank metric codes in the general setting.
On the existence of non-catastrophic p-encoders of (2,1) convolutional codes over ℤp2
Authors: Napp Diego , Pinto Raquel , Rocha Conceição 
Published: September 2023

In this work, we analyze the problem of catastrophicity of encoders of convolutional codes over the Laurent series with coefficients in [Formula: see text], [Formula: see text]. Kuijper and Pinto proved in [M. Kuijper and R. Pinto, On minimality of convolutional ring encoders, IEEE Trans. Autom. Control 55(11) (2009) 4890–4897] that, contrary to what happens for codes over [Formula: see text], where [Formula: see text] is a field, when dealing with [Formula: see text] there are convolutional codes that do not admit non-catastrophic encoders. Nevertheless it was conjectured that any catastrophic convolutional code admits another type of non-catastrophic encoder called [Formula: see text]-encoder. In this paper we solve this conjecture for a class of [Formula: see text] convolutional codes over [Formula: see text] and show that, in fact, these codes always admit a non-catastrophic p-encoder. We also describe a constructive procedure that allows us to obtain a non-catastrophic [Formula: see text]-encoder.